Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Tumor_Sample_UUID Matched_Norm_Sample_UUID Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_Peaks DrugBank ref_context gc_content i_tumor_f t_ref_count t_alt_count SPEN 23013 broad.mit.edu 37 1 16259480 16259480 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr1:16259480delC uc001axk.1 + 11 6949 c.6745delC c.(6745-6747)CCCfs p.P2249fs SPEN_uc010obp.1_Frame_Shift_Del_p.P2208fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2249 RID.|Interaction with MSX2 (By similarity). interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) AGATCTGCAACCCCCCGCAGG 0.557 0.44 400 313 ARID1A 8289 broad.mit.edu 37 1 27100176 27100176 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr1:27100176delC uc001bmv.1 + 16 4345 c.3972delC c.(3970-3972)TACfs p.Y1324fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.Y1323fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.Y1324fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.Y941fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.Y170fs|ARID1A_uc009vsm.1_5'UTR|ARID1A_uc009vsn.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1324 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.Y1324fs*1(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CTAGCCGCTACCCCCCgcagc 0.517 0.35 112 60 SLC2A1 6513 broad.mit.edu 37 1 43396800 43396808 + In_Frame_Del DEL GAGCGTGGT - - rs80359831 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr1:43396800_43396808delGAGCGTGGT uc001cik.2 - 3 709_717 c.184_192delACCACGCTC c.(184-192)ACCACGCTCdel p.TTL62del NM_006516 NP_006507 P11166 GTR1_HUMAN solute carrier family 2 (facilitated glucose 62_64 Extracellular (Potential). carbohydrate metabolic process|energy reserve metabolic process|regulation of insulin secretion|water-soluble vitamin metabolic process integral to membrane|melanosome|membrane fraction|midbody D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity central_nervous_system(2)|pancreas(2)|ovary(1) 5 Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0122) Etomidate(DB00292) 0.000 0.35 428 232 TAL1 6886 broad.mit.edu 37 1 47685776 47685777 + Frame_Shift_Ins INS - T T 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr1:47685776_47685777insT uc001cqx.2 - 4 1188_1189 c.611_612insA c.(610-612)AACfs p.N204fs TAL1_uc009vyq.2_5'UTR|TAL1_uc001cqy.2_Frame_Shift_Ins_p.N204fs NM_003189 NP_003180 P17542 TAL1_HUMAN T-cell acute lymphocytic leukemia 1 204 Helix-loop-helix motif. basophil differentiation|cell fate commitment|cell proliferation|embryonic hemopoiesis|erythrocyte differentiation|megakaryocyte differentiation|positive regulation of cell division|positive regulation of chromatin assembly or disassembly|positive regulation of erythrocyte differentiation|positive regulation of mitotic cell cycle|positive regulation of protein complex assembly|positive regulation of transcription from RNA polymerase II promoter nuclear chromatin E-box binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity lung(1) 1 CAAAGGCCCCGTTCACATTCTG 0.559 0.44 343 274 JAK1 3716 broad.mit.edu 37 1 65339111 65339111 + Frame_Shift_Del DEL T - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr1:65339111delT uc001dbu.1 - 5 674 c.425delA c.(424-426)AAGfs p.K142fs JAK1_uc009wam.1_Frame_Shift_Del_p.K130fs|JAK1_uc001dbv.2_RNA NM_002227 NP_002218 P23458 JAK1_HUMAN janus kinase 1 142 FERM. interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway cytoskeleton|cytosol|endomembrane system|membrane|nucleus ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity p.K142fs*26(3) haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1) 61 BRCA - Breast invasive adenocarcinoma(111;0.0485) ATCTGGAATCTTTTTTTTCTC 0.478 0.43 547 419 HSP90B3P 343477 broad.mit.edu 37 1 92108916 92108916 + Frame_Shift_Del DEL A - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr1:92108916delA uc010osx.1 + 3 943 c.943delA c.(943-945)AAAfs p.K315fs NR_003130 SubName: Full=cDNA FLJ58812, highly similar to Endoplasmin (Heat shock protein 90kDa beta member 1); 0 ACGACTTCTGAAAAAGGGCTG 0.433 0.43 560 425 NOTCH2 4853 broad.mit.edu 37 1 120480570 120480571 + Frame_Shift_Ins INS - T T 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr1:120480570_120480571insT uc001eik.2 - 20 3502_3503 c.3246_3247insA c.(3244-3249)AAAGCAfs p.K1082fs NOTCH2_uc001eil.2_Frame_Shift_Ins_p.K1082fs NM_024408 NP_077719 Q04721 NOTC2_HUMAN notch 2 preproprotein 1082_1083 EGF-like 28.|Extracellular (Potential). anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1) 27 all_neural(166;0.153) all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809) Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133) TGGGACTCTGCTTTTTTCTGAA 0.485 0.39 933 597 NOTCH2 4853 broad.mit.edu 37 1 120497754 120497755 + Frame_Shift_Ins INS - G G rs141051853 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr1:120497754_120497755insG uc001eik.2 - 13 2383_2384 c.2127_2128insC c.(2125-2130)CCCGAGfs p.P709fs NOTCH2_uc001eil.2_Frame_Shift_Ins_p.P709fs|NOTCH2_uc001eim.3_Frame_Shift_Ins_p.P626fs NM_024408 NP_077719 Q04721 NOTC2_HUMAN notch 2 preproprotein 709_710 EGF-like 18; calcium-binding (Potential).|Extracellular (Potential). anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1) 27 all_neural(166;0.153) all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809) Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133) TGGGGTCCCTCGGGGCATATAC 0.530 0.37 502 298 MLLT11 10962 broad.mit.edu 37 1 151039752 151039752 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr1:151039752delC uc001ewq.2 + 2 937 c.52delC c.(52-54)CCCfs p.P18fs NM_006818 NP_006809 Q13015 AF1Q_HUMAN MLLT11 protein 18 positive regulation of apoptosis|positive regulation of mitochondrial depolarization|positive regulation of release of cytochrome c from mitochondria|positive regulation of transcription, DNA-dependent 0 Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211) CTGGAGGATGCCCATCCCAGA 0.507 0.27 631 232 DENND4B 9909 broad.mit.edu 37 1 153907278 153907279 + In_Frame_Ins INS - CTG CTG rs141373027 by1000genomes 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr1:153907278_153907279insCTG uc001fdd.1 - 18 3131_3132 c.2730_2731insCAG c.(2728-2733)insCAG p.910_911insQ uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910_911 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) GACACctgctcctgctgctgct 0.455 0.14 128 21 NLRP3 114548 broad.mit.edu 37 1 247597432 247597433 + Frame_Shift_Ins INS - T T 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr1:247597432_247597433insT uc001icr.2 + 7 2493_2494 c.2355_2356insT c.(2353-2358)GAGTGCfs p.E785fs NLRP3_uc001ics.2_Frame_Shift_Ins_p.E785fs|NLRP3_uc001icu.2_Frame_Shift_Ins_p.E785fs|NLRP3_uc001icw.2_Frame_Shift_Ins_p.E728fs|NLRP3_uc001icv.2_Frame_Shift_Ins_p.E728fs|NLRP3_uc010pyw.1_Intron NM_001079821 NP_001073289 Q96P20 NALP3_HUMAN NLR family, pyrin domain containing 3 isoform a 785_786 LRR 2. detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction cytoplasm ATP binding|peptidoglycan binding|protein binding lung(8)|skin(8)|ovary(7)|upper_aerodigestive_tract(1)|breast(1)|pancreas(1) 26 all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) all_cancers(173;0.0172) OV - Ovarian serous cystadenocarcinoma(106;0.0141) TCTCGCATGAGTGCTGCTTCGA 0.559 0.25 587 196 NRBP1 29959 broad.mit.edu 37 2 27658018 27658018 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr2:27658018delC uc002rko.2 + 8 1417 c.585delC c.(583-585)GACfs p.D195fs NRBP1_uc002rkq.2_Frame_Shift_Del_p.D195fs|NRBP1_uc002rkp.2_Frame_Shift_Del_p.D195fs|NRBP1_uc002rkr.2_5'Flank NM_013392 NP_037524 Q9UHY1 NRBP_HUMAN nuclear receptor binding protein 195 Protein kinase. ER to Golgi vesicle-mediated transport|gene expression|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor cell cortex|endomembrane system|lamellipodium|membrane|nucleoplasm ATP binding|protein homodimerization activity|protein kinase activity ovary(2)|lung(1) 3 Acute lymphoblastic leukemia(172;0.155) ACTCCTGTGACCCCCCCATCA 0.587 0.43 472 354 BIRC6 57448 broad.mit.edu 37 2 32820100 32820101 + Splice_Site INS - A A 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr2:32820100_32820101insA uc010ezu.2 + 68 13636 c.13502_splice c.e68-1 p.E4501_splice NM_016252 NP_057336 Q9NR09 BIRC6_HUMAN baculoviral IAP repeat-containing 6 anti-apoptosis|apoptosis intracellular acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1) 14 Acute lymphoblastic leukemia(172;0.155) ttaaataaCAGAAAAAAAACTG 0.243 0.33 139 68 TTN 7273 broad.mit.edu 37 2 179446352 179446352 + Frame_Shift_Del DEL T - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr2:179446352delT uc010zfg.1 - 265 59163 c.58939delA c.(58939-58941)ACCfs p.T19647fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.T13342fs|TTN_uc010zfi.1_Frame_Shift_Del_p.T13275fs|TTN_uc010zfj.1_Frame_Shift_Del_p.T13150fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 20574 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCAAAGCGGGTTTTCTGTAGA 0.473 0.45 730 592 HDAC4 9759 broad.mit.edu 37 2 240002823 240002823 + Frame_Shift_Del DEL G - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr2:240002823delG uc002vyk.3 - 22 3495 c.2703delC c.(2701-2703)CCCfs p.P901fs HDAC4_uc010fyy.2_Frame_Shift_Del_p.P858fs NM_006037 NP_006028 P56524 HDAC4_HUMAN histone deacetylase 4 901 Histone deacetylase. B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent histone deacetylase complex|transcriptional repressor complex activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding breast(3)|skin(2)|ovary(1) 6 all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159) Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04) CGTCTCCCATGGGGGGGTCCA 0.602 0.42 70 50 HDLBP 3069 broad.mit.edu 37 2 242170361 242170362 + Splice_Site INS - A A 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr2:242170361_242170362insA uc002waz.2 - 25 3517 c.3289_splice c.e25-1 p.P1097_splice HDLBP_uc002wba.2_Splice_Site_p.P1097_splice|HDLBP_uc002wbb.2_Splice_Site_p.P1049_splice NM_203346 NP_976221 Q00341 VIGLN_HUMAN high density lipoprotein binding protein cholesterol metabolic process|lipid transport cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane lipid binding|protein binding|RNA binding breast(3)|skin(1) 4 all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928) GTCCTGGGGCTAAAAAAGGAGA 0.505 0.38 339 212 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.46 7 6 FOXP1 27086 broad.mit.edu 37 3 71064782 71064782 + Frame_Shift_Del DEL G - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr3:71064782delG uc003dol.2 - 8 1215 c.892delC c.(892-894)CATfs p.H298fs FOXP1_uc003dom.2_Frame_Shift_Del_p.H222fs|FOXP1_uc003don.2_RNA|FOXP1_uc003doo.2_Frame_Shift_Del_p.H298fs|FOXP1_uc003dop.2_Frame_Shift_Del_p.H298fs|FOXP1_uc003doq.1_Frame_Shift_Del_p.H297fs|FOXP1_uc003doi.2_Frame_Shift_Del_p.H198fs|FOXP1_uc003doj.2_Frame_Shift_Del_p.H198fs|FOXP1_uc003dok.2_Frame_Shift_Del_p.H111fs|FOXP1_uc003dor.1_Frame_Shift_Del_p.H76fs NM_032682 NP_116071 Q9H334 FOXP1_HUMAN forkhead box P1 isoform 1 298 cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development cytoplasm|transcription factor complex chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding ovary(1)|lung(1) 2 Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209) BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05) GGATGGCTATGGGGGTGCTCC 0.433 0.38 521 325 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.46 60 51 IL1RAP 3556 broad.mit.edu 37 3 190345194 190345194 + Frame_Shift_Del DEL A - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr3:190345194delA uc003fsm.1 + 8 1064 c.858delA c.(856-858)GGAfs p.G286fs IL1RAP_uc003fsk.2_Frame_Shift_Del_p.G286fs|IL1RAP_uc003fsl.2_Frame_Shift_Del_p.G286fs|IL1RAP_uc010hzf.2_Frame_Shift_Del_p.G145fs|IL1RAP_uc010hzg.1_Frame_Shift_Del_p.G286fs|IL1RAP_uc003fsn.1_RNA|IL1RAP_uc003fso.1_Frame_Shift_Del_p.G286fs|IL1RAP_uc003fsp.1_RNA|IL1RAP_uc003fsq.2_Frame_Shift_Del_p.G286fs NM_002182 NP_002173 Q9NPH3 IL1AP_HUMAN interleukin 1 receptor accessory protein isoform 286 Extracellular (Potential).|Ig-like C2-type 3. inflammatory response|innate immune response|protein complex assembly extracellular region|integral to plasma membrane ovary(1) 1 all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21) Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06) GBM - Glioblastoma multiforme(93;0.00851) CCATTGATGGAAAAAAACCTG 0.388 0.43 280 211 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.44 70 56 NFKB1 4790 broad.mit.edu 37 4 103517351 103517351 + Frame_Shift_Del DEL A - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr4:103517351delA uc011ceq.1 + 14 1821 c.1354delA c.(1354-1356)AAAfs p.K452fs NFKB1_uc011cep.1_Frame_Shift_Del_p.K453fs|NFKB1_uc011cer.1_Frame_Shift_Del_p.K272fs NM_003998 NP_003989 P19838 NFKB1_HUMAN nuclear factor kappa-B, subunit 1 isoform 1 452 Interaction with CFLAR. anti-apoptosis|apoptosis|cellular response to mechanical stimulus|inflammatory response|innate immune response|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of calcidiol 1-monooxygenase activity|nerve growth factor receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter cytosol|I-kappaB/NF-kappaB complex|mitochondrion|nucleoplasm protein binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding ovary(2)|breast(2)|skin(1) 5 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;6.59e-08) Dexamethasone(DB01234)|Pranlukast(DB01411)|Thalidomide(DB01041) AAGTGATGACAAAAACACTGT 0.413 0.46 311 265 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 215 346 LIFR 3977 broad.mit.edu 37 5 38489248 38489248 + Frame_Shift_Del DEL A - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr5:38489248delA uc010ive.1 - 16 2599 c.2267delT c.(2266-2268)TTAfs p.L756fs LIFR_uc003jli.2_Frame_Shift_Del_p.L756fs NM_001127671 NP_001121143 P42702 LIFR_HUMAN leukemia inhibitory factor receptor precursor 756 Fibronectin type-III 6.|Extracellular (Potential). positive regulation of cell proliferation extracellular region|integral to plasma membrane ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity ovary(3)|large_intestine(1) 4 all_lung(31;0.00021) ATATCCTCTTAAAAAGCCTCT 0.363 0.45 461 378 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.49 82 79 CDK7 1022 broad.mit.edu 37 5 68568830 68568832 + In_Frame_Del DEL TTC - - rs139575116 byFrequency 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr5:68568830_68568832delTTC uc003jvs.3 + 10 1007_1009 c.826_828delTTC c.(826-828)TTCdel p.F276del CDK7_uc003jvt.3_In_Frame_Del_p.F235del|CDK7_uc003jvu.3_In_Frame_Del_p.F183del NM_001799 NP_001790 P50613 CDK7_HUMAN cyclin-dependent kinase 7 276 Protein kinase. androgen receptor signaling pathway|cell division|cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction holo TFIIH complex|mitochondrion androgen receptor binding|ATP binding|cyclin-dependent protein kinase activity|DNA-dependent ATPase activity|protein C-terminus binding|RNA polymerase II carboxy-terminal domain kinase activity|transcription coactivator activity lung(1) 1 Lung NSC(167;7.26e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198) OV - Ovarian serous cystadenocarcinoma(47;2.98e-56)|Epithelial(20;3.54e-52)|all cancers(19;9.11e-48)|Lung(70;0.0185) ACAAGGCTTATTCTTATTTAATC 0.350 0.43 649 491 NR2F1 7025 broad.mit.edu 37 5 92921101 92921102 + Frame_Shift_Ins INS - A A 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr5:92921101_92921102insA uc003kkj.2 + 1 2059_2060 c.372_373insA c.(370-375)GCCAACfs p.A124fs NM_005654 NP_005645 P10589 COT1_HUMAN nuclear receptor subfamily 2, group F, member 1 124_125 NR C4-type.|Nuclear receptor. negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor nucleoplasm ligand-regulated transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding urinary_tract(1)|ovary(1)|lung(1) 3 all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19) UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18) CATGCCGTGCCAACAGGAACTG 0.545 0.51 57 60 CHD1 1105 broad.mit.edu 37 5 98206409 98206409 + Frame_Shift_Del DEL T - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr5:98206409delT uc003knf.2 - 28 4108 c.3960delA c.(3958-3960)AAAfs p.K1320fs CHD1_uc010jbn.2_Frame_Shift_Del_p.K46fs NM_001270 NP_001261 O14646 CHD1_HUMAN chromodomain helicase DNA binding protein 1 1320 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117) COAD - Colon adenocarcinoma(37;0.0717) Epirubicin(DB00445) AAAGAGCTTCTTTTTTTGCAA 0.383 0.49 415 392 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.17 71 15 FANCE 2178 broad.mit.edu 37 6 35425715 35425715 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr6:35425715delC uc003oko.1 + 4 1108 c.923delC c.(922-924)GCCfs p.A308fs FANCE_uc010jvw.1_Frame_Shift_Del_p.A308fs NM_021922 NP_068741 Q9HB96 FANCE_HUMAN Fanconi anemia, complementation group E 308 Interaction with FANCC. DNA repair nucleoplasm protein binding ovary(1)|lung(1)|skin(1) 3 TTGGAGGATGCCCCCCCAGTT 0.542 0.41 174 123 SFRS3 6428 broad.mit.edu 37 6 36568939 36568941 + In_Frame_Del DEL AGG - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr6:36568939_36568941delAGG uc003omj.2 + 4 523_525 c.352_354delAGG c.(352-354)AGGdel p.R119del SFRS3_uc003omk.2_RNA NM_003017 NP_003008 P84103 SRSF3_HUMAN splicing factor, arginine/serine-rich 3 119 B-1.|2 X approximate repeats, basic.|Arg/Ser-rich (RS domain). mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription nucleoplasm nucleotide binding|protein binding|RNA binding 0 ATCTCCAAGAAGGAGAAGCTTCT 0.429 0.34 411 209 EPHA7 2045 broad.mit.edu 37 6 93969118 93969119 + Frame_Shift_Ins INS - T T 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr6:93969118_93969119insT uc003poe.2 - 10 2118_2119 c.1877_1878insA c.(1876-1878)AAGfs p.K626fs EPHA7_uc003pof.2_Frame_Shift_Ins_p.K621fs|EPHA7_uc011eac.1_Frame_Shift_Ins_p.K622fs NM_004440 NP_004431 Q15375 EPHA7_HUMAN ephrin receptor EphA7 precursor 626 Cytoplasmic (Potential). integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1) 28 all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142) BRCA - Breast invasive adenocarcinoma(108;0.0847) CATCTAGCTCCTTGGCGAATTG 0.431 0.31 314 144 EPHB6 2051 broad.mit.edu 37 7 142561447 142561448 + Frame_Shift_Ins INS - G G 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr7:142561447_142561448insG uc011kst.1 + 6 946_947 c.159_160insG c.(157-162)CCAGGGfs p.P53fs EPHB6_uc011ksu.1_Frame_Shift_Ins_p.P53fs|EPHB6_uc003wbs.2_Intron|EPHB6_uc003wbt.2_5'UTR|EPHB6_uc003wbu.2_Intron NM_004445 NP_004436 O15197 EPHB6_HUMAN ephrin receptor EphB6 precursor 53_54 Extracellular (Potential). extracellular region|integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1) 19 Melanoma(164;0.059) CCTACCCACCAGGGGGGGTGAG 0.574 0.33 20 10 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 4 32 KCNH2 3757 broad.mit.edu 37 7 150656686 150656686 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr7:150656686delC uc003wic.2 - 3 459 c.446delG c.(445-447)GGCfs p.G149fs KCNH2_uc011kux.1_Frame_Shift_Del_p.G53fs|KCNH2_uc003wie.2_Frame_Shift_Del_p.G149fs NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 149 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) GGTGGGGGGGCCCCGGTGGTT 0.582 0.37 127 75 WRN 7486 broad.mit.edu 37 8 30915971 30915971 + Frame_Shift_Del DEL A - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr8:30915971delA uc003xio.3 + 2 796 c.8delA c.(7-9)GAAfs p.E3fs NM_000553 NP_000544 Q14191 WRN_HUMAN Werner syndrome protein 3 Interaction with WRNIP1 (By similarity). base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance centrosome|nucleolus|nucleoplasm 3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1) 7 Breast(100;0.195) KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192) AAGATGAGTGAAAAAAAATTG 0.353 0.34 95 50 WRN 7486 broad.mit.edu 37 8 31001131 31001132 + Frame_Shift_Ins INS - A A 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr8:31001131_31001132insA uc003xio.3 + 28 4163_4164 c.3375_3376insA c.(3373-3378)TCTAAAfs p.S1125fs WRN_uc010lvk.2_Frame_Shift_Ins_p.S592fs NM_000553 NP_000544 Q14191 WRN_HUMAN Werner syndrome protein 1125_1126 base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance centrosome|nucleolus|nucleoplasm 3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1) 7 Breast(100;0.195) KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192) GTAACATTTCTAAAAAAAGGTA 0.292 0.27 555 210 VPS13B 157680 broad.mit.edu 37 8 100887781 100887781 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr8:100887781delC uc003yiv.2 + 62 12067 c.11956delC c.(11956-11958)CCCfs p.P3986fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.P3961fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 3986 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TGCAGAACCTCCCCCCTCCAC 0.468 0.43 290 218 HSF1 3297 broad.mit.edu 37 8 145535709 145535709 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr8:145535709delC uc003zbt.3 + 9 1091 c.921delC c.(919-921)AGCfs p.S307fs HSF1_uc003zbu.3_RNA NM_005526 NP_005517 Q00613 HSF1_HUMAN heat shock transcription factor 1 307 Regulatory domain. S->A: No phosphorylation. 5-fold derepression of transcriptional activity at control temperature; when associated with A-303. 1.5% increase in transcriptional activity on heat- treatment. 2.5-fold increase in transcriptional activity on heat treatment; when associated with A-303. cytoplasm protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055) 0.000 0.54 107 126 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.84 6 32 DAPK1 1612 broad.mit.edu 37 9 90321802 90321802 + Frame_Shift_Del DEL G - - rs56169226 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr9:90321802delG uc004apc.2 + 26 3954 c.3816delG c.(3814-3816)ATGfs p.M1272fs DAPK1_uc004apd.2_Frame_Shift_Del_p.M1272fs|DAPK1_uc011ltg.1_Frame_Shift_Del_p.M1206fs|DAPK1_uc011lth.1_Frame_Shift_Del_p.M1009fs|DAPK1_uc004apg.2_Frame_Shift_Del_p.M249fs NM_004938 NP_004929 P53355 DAPK1_HUMAN death-associated protein kinase 1 1272 apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade actin cytoskeleton|cytoplasm ATP binding|calmodulin binding|protein serine/threonine kinase activity ovary(1)|breast(1) 2 CCAACACCATGGGGGGGTACA 0.582 0.40 90 59 WNK2 65268 broad.mit.edu 37 9 96021418 96021419 + Frame_Shift_Ins INS - C C 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr9:96021418_96021419insC uc004ati.1 + 11 2588_2589 c.2588_2589insC c.(2587-2589)CACfs p.H863fs WNK2_uc011lud.1_Frame_Shift_Ins_p.H863fs|WNK2_uc004atj.2_Frame_Shift_Ins_p.H863fs|WNK2_uc004atk.2_Frame_Shift_Ins_p.H500fs|WNK2_uc010mrc.1_Frame_Shift_Ins_p.H811fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 863 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 AAGCTGCCCCACCCCCCTGGGG 0.698 0.32 82 39 NUP214 8021 broad.mit.edu 37 9 134007992 134007993 + Frame_Shift_Ins INS - A A 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr9:134007992_134007993insA uc004cag.2 + 6 784_785 c.673_674insA c.(673-675)GAAfs p.E225fs NUP214_uc004cah.2_Frame_Shift_Ins_p.E225fs|NUP214_uc004caf.1_Frame_Shift_Ins_p.E225fs NM_005085 NP_005076 P35658 NU214_HUMAN nucleoporin 214kDa 225 carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear pore|nucleoplasm protein binding breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1) 16 all_hematologic(7;0.0028) Myeloproliferative disorder(178;0.204) OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256) GACTTTGCAGGAAAAAAAAGTC 0.361 0.38 567 343 MAMDC4 158056 broad.mit.edu 37 9 139752132 139752133 + Frame_Shift_Ins INS - A A rs143805848 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr9:139752132_139752133insA uc004cjs.2 + 19 2398_2399 c.2348_2349insA c.(2347-2349)ACAfs p.T783fs MAMDC4_uc011mej.1_Frame_Shift_Ins_p.T120fs NM_206920 NP_996803 Q6UXC1 AEGP_HUMAN apical early endosomal glycoprotein precursor 862 MAM 5.|Extracellular (Potential). protein transport integral to membrane breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1) 7 all_cancers(76;0.0763)|all_epithelial(76;0.198) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171) GTGGTGGACACAAGCCCAGACG 0.678 0.41 47 33 MYST4 23522 broad.mit.edu 37 10 76781905 76781906 + In_Frame_Ins INS - GAA GAA rs138589645;rs111976843 by1000genomes 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr10:76781905_76781906insGAA uc001jwn.1 + 16 3781_3782 c.3288_3289insGAA c.(3286-3291)insGAA p.1104_1105insE MYST4_uc001jwm.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwo.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwp.1_In_Frame_Ins_p.921_922insE NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1104_1105 histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) aggaagaagaggaagaagaaga 0.203 0.26 388 139 FRAT1 10023 broad.mit.edu 37 10 99079640 99079640 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr10:99079640delC uc001knc.1 + 1 619 c.430delC c.(430-432)CCCfs p.P144fs NM_005479 NP_005470 Q92837 FRAT1_HUMAN GSK-3 binding protein FRAT1 144 Wnt receptor signaling pathway cytoplasm 0 Colorectal(252;0.0846) Epithelial(162;2.76e-09)|all cancers(201;1.57e-07) 0.000 0.23 409 124 CYP17A1 1586 broad.mit.edu 37 10 104594667 104594669 + In_Frame_Del DEL AGG - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr10:104594667_104594669delAGG uc001kwg.2 - 3 711_713 c.539_541delCCT c.(538-543)TCCTTG>TTG p.S180del NM_000102 NP_000093 P05093 CP17A_HUMAN cytochrome P450, family 17 180 androgen biosynthetic process|glucocorticoid biosynthetic process|sex differentiation|xenobiotic metabolic process endoplasmic reticulum membrane electron carrier activity|heme binding|oxygen binding|steroid 17-alpha-monooxygenase activity 0 Colorectal(252;0.122)|all_hematologic(284;0.152) Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215) NADH(DB00157)|Progesterone(DB00396) AAGCAGATCAAGGAGATGACATT 0.458 0.39 720 453 PIK3C2A 5286 broad.mit.edu 37 11 17190949 17190949 + Frame_Shift_Del DEL T - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr11:17190949delT uc001mmq.3 - 1 406 c.340delA c.(340-342)ACAfs p.T114fs PIK3C2A_uc009ygu.1_Intron|PIK3C2A_uc010rcw.1_Intron|PIK3C2A_uc001mmr.3_RNA|PIK3C2A_uc010rcx.1_Frame_Shift_Del_p.T114fs|PIK3C2A_uc009ygv.1_Frame_Shift_Del_p.T114fs NM_002645 NP_002636 O00443 P3C2A_HUMAN phosphoinositide-3-kinase, class 2 alpha 114 Interaction with clathrin. cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity lung(4)|central_nervous_system(4)|stomach(1)|ovary(1) 10 Phosphatidylserine(DB00144) AATACAGGTGTTTTTTTAGTC 0.408 0.47 720 627 MEN1 4221 broad.mit.edu 37 11 64572093 64572093 + Frame_Shift_Del DEL G - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr11:64572093delG uc001obj.2 - 10 1634 c.1561delC c.(1561-1563)CGGfs p.R521fs MAP4K2_uc001obh.2_5'Flank|MAP4K2_uc001obi.2_5'Flank|MAP4K2_uc010rnp.1_5'Flank|MEN1_uc001obk.2_Frame_Shift_Del_p.R521fs|MEN1_uc001obl.2_Frame_Shift_Del_p.R481fs|MEN1_uc001obm.2_Frame_Shift_Del_p.R516fs|MEN1_uc001obn.2_Frame_Shift_Del_p.R521fs|MEN1_uc001obo.2_Frame_Shift_Del_p.R521fs|MEN1_uc001obp.2_Frame_Shift_Del_p.R516fs|MEN1_uc001obq.2_Frame_Shift_Del_p.R521fs|MEN1_uc001obr.2_Frame_Shift_Del_p.R521fs NM_130800 NP_570712 O00255 MEN1_HUMAN menin isoform 1 521 DNA repair|histone lysine methylation|MAPKKK cascade|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of JNK cascade|negative regulation of osteoblast differentiation|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of telomerase activity|negative regulation of transcription from RNA polymerase II promoter|osteoblast development|positive regulation of protein binding|positive regulation of transforming growth factor beta receptor signaling pathway|response to gamma radiation|response to UV|transcription, DNA-dependent chromatin|cleavage furrow|cytosol|histone methyltransferase complex|nuclear matrix|soluble fraction double-stranded DNA binding|four-way junction DNA binding|protein binding, bridging|protein N-terminus binding|R-SMAD binding|transcription regulatory region DNA binding|Y-form DNA binding p.R516fs*15(1) parathyroid(105)|pancreas(64)|gastrointestinal_tract_(site_indeterminate)(15)|small_intestine(13)|lung(9)|pituitary(7)|NS(7)|adrenal_gland(5)|soft_tissue(4)|central_nervous_system(4)|thymus(2)|stomach(1)|retroperitoneum(1)|skin(1) 238 GGAGGCTTCCGGGGGGGTCCT 0.716 0.44 24 19 ANO1 55107 broad.mit.edu 37 11 69978156 69978158 + In_Frame_Del DEL TCT - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr11:69978156_69978158delTCT uc001opj.2 + 11 1534_1536 c.1229_1231delTCT c.(1228-1233)GTCTTC>GTC p.F412del ANO1_uc001opk.1_In_Frame_Del_p.F384del|ANO1_uc001opl.1_RNA|ANO1_uc010rqk.1_In_Frame_Del_p.F147del NM_018043 NP_060513 Q5XXA6 ANO1_HUMAN anoctamin 1, calcium activated chloride channel 412 Helical; (Potential). multicellular organismal development chloride channel complex|cytoplasm|plasma membrane intracellular calcium activated chloride channel activity ovary(1)|pancreas(1) 2 0.000 0.47 580 519 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 448 52 ARHGEF12 23365 broad.mit.edu 37 11 120351043 120351043 + Frame_Shift_Del DEL T - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr11:120351043delT uc001pxl.1 + 38 4148 c.4141delT c.(4141-4143)TTTfs p.F1381fs ARHGEF12_uc009zat.2_Frame_Shift_Del_p.F1362fs|ARHGEF12_uc009zau.1_Frame_Shift_Del_p.F1278fs NM_015313 NP_056128 Q9NZN5 ARHGC_HUMAN Rho guanine nucleotide exchange factor (GEF) 12 1381 apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|membrane G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity lung(2)|breast(2)|skin(2)|ovary(1) 7 Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231) TGGAGAGCACTTTTTTGATGC 0.453 0.45 634 511 DYRK4 8798 broad.mit.edu 37 12 4719362 4719362 + Frame_Shift_Del DEL A - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr12:4719362delA uc001qmx.2 + 11 1217 c.1057delA c.(1057-1059)AAAfs p.K353fs DYRK4_uc009zeh.1_Frame_Shift_Del_p.K468fs|DYRK4_uc001qmy.1_Frame_Shift_Del_p.K353fs|DYRK4_uc001qmz.1_Frame_Shift_Del_p.K67fs|DYRK4_uc001qna.1_5'UTR|DYRK4_uc010ser.1_5'UTR NM_003845 NP_003836 Q9NR20 DYRK4_HUMAN dual-specificity tyrosine-(Y)-phosphorylation 353 Protein kinase. Golgi apparatus ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(2)|skin(1) 3 Colorectal(7;0.103) CAACAGGGGGAAAAAAAGATA 0.398 0.29 473 197 CHD4 1108 broad.mit.edu 37 12 6691430 6691430 + Frame_Shift_Del DEL A - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr12:6691430delA uc001qpo.2 - 30 4552 c.4388delT c.(4387-4389)TTCfs p.F1463fs CHD4_uc001qpn.2_Frame_Shift_Del_p.F1456fs|CHD4_uc001qpp.2_Frame_Shift_Del_p.F1488fs|uc001qpq.1_Intron|SCARNA11_uc001qpr.1_5'Flank NM_001273 NP_001264 Q14839 CHD4_HUMAN chromodomain helicase DNA binding protein 4 1463 chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent microtubule organizing center|NuRD complex ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding central_nervous_system(2) 2 ATGCCGCATGAAAAGAGAGAC 0.478 0.75 3 9 ZNF384 171017 broad.mit.edu 37 12 6777181 6777186 + In_Frame_Del DEL GCCTGG - - rs140358670 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr12:6777181_6777186delGCCTGG uc010sfh.1 - 11 1636_1641 c.1428_1433delCCAGGC c.(1426-1434)GCCCAGGCT>GCT p.476_478AQA>A ZNF384_uc001qpz.2_In_Frame_Del_p.415_417AQA>A|ZNF384_uc001qqa.2_In_Frame_Del_p.415_417AQA>A|ZNF384_uc001qqb.2_In_Frame_Del_p.399_401AQA>A|ZNF384_uc001qqc.2_In_Frame_Del_p.415_417AQA>A|ZNF384_uc001qqd.2_In_Frame_Del_p.360_362AQA>A|ZNF384_uc001qqe.2_In_Frame_Del_p.399_401AQA>A NM_001135734 NP_001129206 Q8TF68 ZN384_HUMAN nuclear matrix transcription factor 4 isoform d 476_478 Ala-rich.|Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding EWSR1/ZNF384(4) haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1) 8 ttgagcttgagcctgggcctgggcca 0.146 0.19 307 71 PLEKHA5 54477 broad.mit.edu 37 12 19427544 19427545 + Frame_Shift_Ins INS - A A 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr12:19427544_19427545insA uc001reb.2 + 10 1008_1009 c.922_923insA c.(922-924)CAAfs p.Q308fs PLEKHA5_uc010sie.1_Frame_Shift_Ins_p.Q314fs|PLEKHA5_uc001rea.2_Frame_Shift_Ins_p.Q308fs|PLEKHA5_uc009zin.2_Frame_Shift_Ins_p.Q66fs|PLEKHA5_uc010sif.1_Frame_Shift_Ins_p.Q200fs|PLEKHA5_uc010sig.1_Frame_Shift_Ins_p.Q200fs|PLEKHA5_uc010sih.1_Frame_Shift_Ins_p.Q200fs|PLEKHA5_uc001rec.1_5'UTR NM_019012 NP_061885 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A 308 1-phosphatidylinositol binding|protein binding ovary(1)|kidney(1)|skin(1) 3 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) CCAAAACAATCAAAAAAACAAG 0.327 0.21 535 141 SCYL2 55681 broad.mit.edu 37 12 100676906 100676907 + Frame_Shift_Ins INS - A A rs34958515 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr12:100676906_100676907insA uc001thn.2 + 2 208_209 c.158_159insA c.(157-159)ACAfs p.T53fs SCYL2_uc009ztw.1_Intron|SCYL2_uc001thm.1_Frame_Shift_Ins_p.T53fs NM_017988 NP_060458 Q6P3W7 SCYL2_HUMAN SCY1-like 2 protein 53 Protein kinase. endosome to lysosome transport|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of clathrin-mediated endocytosis|positive regulation of receptor internalization clathrin-coated vesicle|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm ATP binding|protein kinase activity|receptor binding lung(3)|ovary(2)|skin(1) 6 TTTAATGGCACAAAAAAGTCAA 0.391 0.55 512 633 ATXN2 6311 broad.mit.edu 37 12 112036783 112036791 + In_Frame_Del DEL TGCTGCTGC - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr12:112036783_112036791delTGCTGCTGC uc001tsj.2 - 1 690_698 c.528_536delGCAGCAGCA c.(526-537)CAGCAGCAGCAA>CAA p.176_179QQQQ>Q ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_RNA|ATXN2_uc001tsm.1_5'Flank NM_002973 NP_002964 Q99700 ATX2_HUMAN ataxin 2 176_179 Poly-Gln. cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network protein C-terminus binding|RNA binding ovary(1)|breast(1) 2 ctgctgctgttgctgctgctgctgctgct 0.517 0.40 18 12 PXN 5829 broad.mit.edu 37 12 120653032 120653032 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr12:120653032delC uc001txt.2 - 8 1109 c.978delG c.(976-978)GGGfs p.G326fs PXN_uc001txu.2_Frame_Shift_Del_p.G138fs|PXN_uc001txv.2_Frame_Shift_Del_p.G207fs|PXN_uc001txx.2_Frame_Shift_Del_p.G159fs|PXN_uc001txy.2_Frame_Shift_Del_p.G292fs|PXN_uc001txz.2_RNA NM_001080855 NP_001074324 P49023 PAXI_HUMAN paxillin isoform 1 326 cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly cytoplasm|focal adhesion|lamellipodium|microtubule associated complex beta-catenin binding|vinculin binding|zinc ion binding ovary(1)|breast(1) 2 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) GCTTCGGGGGCCCCCCAGGGG 0.682 0.29 41 17 CAMKK2 10645 broad.mit.edu 37 12 121712245 121712246 + In_Frame_Ins INS - GCT GCT rs146079022 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr12:121712245_121712246insGCT uc001tzu.2 - 2 208_209 c.84_85insAGC c.(82-87)insAGC p.28_29insS CAMKK2_uc001tzt.2_In_Frame_Ins_p.28_29insS|CAMKK2_uc001tzv.2_In_Frame_Ins_p.28_29insS|CAMKK2_uc001tzw.2_In_Frame_Ins_p.28_29insS|CAMKK2_uc001tzx.2_In_Frame_Ins_p.28_29insS|CAMKK2_uc001tzy.2_In_Frame_Ins_p.28_29insS|CAMKK2_uc001uaa.1_In_Frame_Ins_p.28_29insS|CAMKK2_uc001uab.2_In_Frame_Ins_p.28_29insS|CAMKK2_uc001uac.2_In_Frame_Ins_p.28_29insS|CAMKK2_uc001uad.1_In_Frame_Ins_p.28_29insS NM_006549 NP_006540 Q96RR4 KKCC2_HUMAN calcium/calmodulin-dependent protein kinase 28_29 calcium-mediated signaling|MAPKKK cascade|positive regulation of transcription, DNA-dependent|protein autophosphorylation|regulation of protein kinase activity cytoplasm ATP binding|calcium ion binding|calmodulin binding|calmodulin-dependent protein kinase activity|protein tyrosine kinase activity lung(1)|large_intestine(1)|stomach(1) 3 all_neural(191;0.0684)|Medulloblastoma(191;0.0922) TTCTGGCTTTCGCTGCTGCTGC 0.649 0.17 132 27 ZMYM2 7750 broad.mit.edu 37 13 20611023 20611023 + Frame_Shift_Del DEL A - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr13:20611023delA uc001umr.2 + 13 2564 c.2266delA c.(2266-2268)AAAfs p.K756fs ZMYM2_uc001ums.2_Frame_Shift_Del_p.K756fs|ZMYM2_uc001umt.2_Frame_Shift_Del_p.K756fs|ZMYM2_uc010tco.1_RNA|ZMYM2_uc001umv.2_Frame_Shift_Del_p.K136fs|ZMYM2_uc001umw.2_Frame_Shift_Del_p.K209fs NM_003453 NP_003444 Q9UBW7 ZMYM2_HUMAN zinc finger protein 198 756 MYM-type 9. regulation of transcription, DNA-dependent|transcription, DNA-dependent PML body ubiquitin conjugating enzyme binding|zinc ion binding lung(3)|ovary(2)|prostate(1) 6 all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856) AGATTGCTGTAAAAAATTTCA 0.378 0.45 447 364 XPO4 64328 broad.mit.edu 37 13 21371026 21371027 + Frame_Shift_Ins INS - A A 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr13:21371026_21371027insA uc001unq.3 - 17 2528_2529 c.2492_2493insT c.(2491-2493)TTAfs p.L831fs NM_022459 NP_071904 Q9C0E2 XPO4_HUMAN exportin 4 831 protein transport cytoplasm|nucleus protein binding large_intestine(1)|ovary(1)|kidney(1) 3 all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244) all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548) GGAAGTCCATTAAAAAATTAAA 0.411 0.41 635 449 HSPH1 10808 broad.mit.edu 37 13 31714414 31714414 + Frame_Shift_Del DEL T - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr13:31714414delT uc001utj.2 - 14 2285 c.1887delA c.(1885-1887)AAAfs p.K629fs HSPH1_uc001utk.2_Frame_Shift_Del_p.K585fs|HSPH1_uc010aaw.2_Frame_Shift_Del_p.K588fs|HSPH1_uc001utl.2_Frame_Shift_Del_p.K631fs|HSPH1_uc010tds.1_Frame_Shift_Del_p.K553fs NM_006644 NP_006635 Q92598 HS105_HUMAN heat shock 105kD 629 positive regulation of MHC class I biosynthetic process|positive regulation of NK T cell activation|response to unfolded protein cytoplasm|extracellular region ATP binding 0 Lung SC(185;0.0257) all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125) CATTCCTTTCTTTTTCCAATT 0.343 0.44 19 15 BRCA2 675 broad.mit.edu 37 13 32954022 32954023 + Frame_Shift_Ins INS - A A rs67201695 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr13:32954022_32954023insA uc001uub.1 + 23 9316_9317 c.9089_9090insA c.(9088-9090)ACAfs p.T3030fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 3030 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) TTAGCAGCGACAAAAAAAACTC 0.312 0.36 305 173 ABCC4 10257 broad.mit.edu 37 13 95735432 95735432 + Frame_Shift_Del DEL A - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr13:95735432delA uc001vmd.3 - 21 2767 c.2648delT c.(2647-2649)TTGfs p.L883fs ABCC4_uc010afk.2_Frame_Shift_Del_p.L836fs NM_005845 NP_005836 O15439 MRP4_HUMAN ATP-binding cassette, sub-family C, member 4 883 ABC transmembrane type-1 2. platelet activation|platelet degranulation integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane 15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity central_nervous_system(3)|skin(1) 4 all_neural(89;0.0878)|Medulloblastoma(90;0.163) Cefazolin(DB01327) TGACGTTTCCAAAAAATATCG 0.443 0.49 388 380 TFDP1 7027 broad.mit.edu 37 13 114277558 114277559 + Frame_Shift_Ins INS - A A 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr13:114277558_114277559insA uc001vtw.2 + 4 355_356 c.143_144insA c.(142-144)CCAfs p.P48fs TFDP1_uc010tkd.1_5'UTR|TFDP1_uc010tke.1_5'UTR|TFDP1_uc001vty.3_Frame_Shift_Ins_p.P48fs|TFDP1_uc010agx.2_Frame_Shift_Ins_p.P48fs NM_007111 NP_009042 Q14186 TFDP1_HUMAN transcription factor Dp-1 48 cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|regulation of transcription from RNA polymerase II promoter transcription factor complex DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding lung(4)|ovary(2)|skin(1) 7 Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218) all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153) all cancers(43;0.0576) CAGCTCTTGCCAAAAACCTTTG 0.609 0.59 12 17 KTN1 3895 broad.mit.edu 37 14 56079187 56079187 + Frame_Shift_Del DEL A - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr14:56079187delA uc001xcb.2 + 3 723 c.421delA c.(421-423)AAAfs p.K141fs KTN1_uc001xce.2_Frame_Shift_Del_p.K141fs|KTN1_uc001xcc.2_Frame_Shift_Del_p.K141fs|KTN1_uc001xcd.2_Frame_Shift_Del_p.K141fs|KTN1_uc010trb.1_Frame_Shift_Del_p.K141fs|KTN1_uc001xcf.1_Frame_Shift_Del_p.K141fs NM_182926 NP_891556 Q86UP2 KTN1_HUMAN kinectin 1 isoform a 141 Lumenal (Potential). microtubule-based movement endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction breast(3)|ovary(2)|lung(1)|central_nervous_system(1) 7 GATTCCTGGCAAAAAAGTAGA 0.438 0.42 389 279 MARK3 4140 broad.mit.edu 37 14 103969537 103969538 + Frame_Shift_Ins INS - A A 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr14:103969537_103969538insA uc001ymz.3 + 18 2901_2902 c.2235_2236insA c.(2233-2238)TCCAAAfs p.S745fs MARK3_uc001ymx.3_Frame_Shift_Ins_p.S736fs|MARK3_uc001ymw.3_Frame_Shift_Ins_p.S721fs|MARK3_uc001yna.3_Frame_Shift_Ins_p.S705fs|MARK3_uc001ymy.3_Frame_Shift_Ins_p.S651fs|MARK3_uc010awp.2_Frame_Shift_Ins_p.S744fs|MARK3_uc010tyb.1_Frame_Shift_Ins_p.S540fs|MARK3_uc010awq.2_Frame_Shift_Ins_p.S318fs|MARK3_uc001ynd.2_Frame_Shift_Ins_p.S153fs NM_001128918 NP_001122390 P27448 MARK3_HUMAN MAP/microtubule affinity-regulating kinase 3 745_746 KA1. ATP binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|ovary(1)|stomach(1) 4 Melanoma(154;0.155) Epithelial(46;0.241) ATATTGCTTCCAAAATTGCCAA 0.401 0.53 14 16 TP53BP1 7158 broad.mit.edu 37 15 43730536 43730536 + Frame_Shift_Del DEL G - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr15:43730536delG uc001zrs.2 - 16 3310 c.3162delC c.(3160-3162)CCCfs p.P1054fs TP53BP1_uc010udp.1_Frame_Shift_Del_p.P1054fs|TP53BP1_uc001zrq.3_Frame_Shift_Del_p.P1059fs|TP53BP1_uc001zrr.3_Frame_Shift_Del_p.P1059fs|TP53BP1_uc010udq.1_Frame_Shift_Del_p.P1059fs NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 1054 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) TGGGTGTGGTGGGGGGATCCT 0.413 0.39 607 381 IL21R 50615 broad.mit.edu 37 16 27441412 27441413 + Frame_Shift_Ins INS - G G 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr16:27441412_27441413insG uc002doq.1 + 2 253_254 c.20_21insG c.(19-21)GCCfs p.A7fs IL21R_uc002dor.1_Frame_Shift_Ins_p.A7fs|IL21R_uc002dos.1_Frame_Shift_Ins_p.A7fs NM_181078 NP_851564 Q9HBE5 IL21R_HUMAN interleukin 21 receptor precursor 7 natural killer cell activation integral to membrane interleukin-21 receptor activity ovary(2)|lung(1)|breast(1) 4 GGCTGGGCCGCCCCCTTGCTCC 0.718 0.49 18 17 CBFB 865 broad.mit.edu 37 16 67070577 67070578 + Frame_Shift_Ins INS - T T 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr16:67070577_67070578insT uc002era.2 + 3 462_463 c.201_202insT c.(199-204)CAGTTTfs p.Q67fs CBFB_uc002erb.2_Frame_Shift_Ins_p.Q67fs|CBFB_uc010vja.1_Intron NM_001755 NP_001746 Q13951 PEBB_HUMAN core-binding factor, beta subunit isoform 2 67_68 transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity breast(2) 2 Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066) TGTCTCTCCAGTTTTTTCCGGC 0.446 0.42 363 268 TP53 7157 broad.mit.edu 37 17 7579471 7579471 + Frame_Shift_Del DEL G - - rs56275308 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr17:7579471delG uc002gim.2 - 4 410 c.216delC c.(214-216)CCCfs p.P72fs TP53_uc002gig.1_Frame_Shift_Del_p.P72fs|TP53_uc002gih.2_Frame_Shift_Del_p.P72fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.P72fs|TP53_uc010cni.1_Frame_Shift_Del_p.P72fs|TP53_uc002gij.2_Frame_Shift_Del_p.P72fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.P33fs|TP53_uc010cnk.1_Frame_Shift_Del_p.P87fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 72 Interaction with WWOX.|Interaction with HRMT1L2. P -> C (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> L (in a sporadic cancer; somatic mutation).|P -> H (in sporadic cancers; somatic mutation).|P -> G (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.R72fs*51(6)|p.G59fs*23(3)|p.R72C(2)|p.V73fs*76(2)|p.R72H(2)|p.V73fs*9(1)|p.R65fs*38(1)|p.E68fs*76(1)|p.V73fs*50(1)|p.D48fs*55(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.D57_A76del20(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.24 555 178 CHD3 1107 broad.mit.edu 37 17 7798765 7798765 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr17:7798765delC uc002gje.2 + 10 1762 c.1612delC c.(1612-1614)CCCfs p.P538fs CHD3_uc002gjd.2_Frame_Shift_Del_p.P597fs|CHD3_uc002gjf.2_Frame_Shift_Del_p.P538fs|CHD3_uc002gjg.1_Frame_Shift_Del_p.P366fs NM_001005273 NP_001005273 Q12873 CHD3_HUMAN chromodomain helicase DNA binding protein 3 538 Chromo 1. chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent microtubule organizing center|NuRD complex ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|zinc ion binding breast(1) 1 Prostate(122;0.202) AGATGTCCCACCCCCCCGTCC 0.577 0.61 7 11 MYH10 4628 broad.mit.edu 37 17 8415878 8415878 + Frame_Shift_Del DEL T - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr17:8415878delT uc002gll.2 - 22 2846 c.2750delA c.(2749-2751)AAGfs p.K917fs MYH10_uc002glm.2_Frame_Shift_Del_p.K948fs|MYH10_uc010cnx.2_Frame_Shift_Del_p.K926fs NM_005964 NP_005955 P35580 MYH10_HUMAN myosin, heavy polypeptide 10, non-muscle 917 Potential. actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape cell cortex|cleavage furrow|midbody|myosin complex|stress fiber actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity ovary(2) 2 TAATTCCTGCTTTTTAGCAGC 0.393 0.46 807 694 CSF3 1440 broad.mit.edu 37 17 38171995 38171995 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr17:38171995delC uc002htp.2 + 2 132 c.92delC c.(91-93)ACCfs p.T31fs CSF3_uc002hto.2_Frame_Shift_Del_p.T31fs|CSF3_uc002htq.2_Frame_Shift_Del_p.T27fs|CSF3_uc010wep.1_Frame_Shift_Del_p.T27fs NM_000759 NP_000750 P09919 CSF3_HUMAN colony stimulating factor 3 isoform a precursor 31 cytokine-mediated signaling pathway|granulocyte differentiation|immune response|positive regulation of cell proliferation extracellular space cytokine activity|enzyme binding|granulocyte colony-stimulating factor receptor binding|growth factor activity ovary(1) 1 Colorectal(19;0.000442) Myeloproliferative disorder(1115;0.0255) Filgrastim(DB00099)|Pegfilgrastim(DB00019) CAGGAAGCCACCCCCCTGGGC 0.642 0.44 62 49 MYST2 11143 broad.mit.edu 37 17 47869397 47869398 + Splice_Site INS - A A 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr17:47869397_47869398insA uc002ipm.2 + 2 289 c.163_splice c.e2+2 p.D55_splice MYST2_uc002ipl.1_Splice_Site_p.D55_splice|MYST2_uc010wma.1_Splice_Site_p.G55_splice|MYST2_uc010wmb.1_Splice_Site_p.D55_splice|MYST2_uc010wmc.1_Splice_Site_p.G55_splice|MYST2_uc010wmd.1_Splice_Site|MYST2_uc010wme.1_Splice_Site NM_007067 NP_008998 O95251 MYST2_HUMAN MYST histone acetyltransferase 2 DNA replication|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation histone acetyltransferase complex histone acetyltransferase activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1)|lung(1)|skin(1) 3 GTTCTCAAGGTAAAAAAACCTT 0.495 0.38 232 143 CARD14 79092 broad.mit.edu 37 17 78172264 78172264 + Frame_Shift_Del DEL G - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr17:78172264delG uc002jxw.1 + 13 1920 c.1725delG c.(1723-1725)CAGfs p.Q575fs CARD14_uc002jxt.1_RNA|CARD14_uc002jxv.2_Frame_Shift_Del_p.Q575fs|CARD14_uc010wud.1_RNA|CARD14_uc002jxx.2_Frame_Shift_Del_p.Q338fs NM_024110 NP_077015 Q9BXL6 CAR14_HUMAN caspase recruitment domain protein 14 isoform 1 575 PDZ. activation of NF-kappaB-inducing kinase activity|positive regulation of protein phosphorylation|regulation of apoptosis aggresome|cytoplasm|plasma membrane CARD domain binding ovary(4)|skin(1) 5 all_neural(118;0.0952) OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908) TGGCGTTCCAGGGGGATGCAT 0.687 0.47 24 21 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 47 145 AXL 558 broad.mit.edu 37 19 41727908 41727909 + Frame_Shift_Ins INS - C C 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr19:41727908_41727909insC uc010ehj.2 + 4 723_724 c.533_534insC c.(532-534)GTCfs p.V178fs CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Frame_Shift_Ins_p.V178fs|AXL_uc010ehk.2_Frame_Shift_Ins_p.V178fs NM_021913 NP_068713 P30530 UFO_HUMAN AXL receptor tyrosine kinase isoform 1 178 Ig-like C2-type 2.|Extracellular (Potential). integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1) 13 CAGGATGCTGTCCCCCTGGCCA 0.683 0.30 58 25 GSK3A 2931 broad.mit.edu 37 19 42741010 42741012 + In_Frame_Del DEL CTT - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr19:42741010_42741012delCTT uc002otb.1 - 3 672_674 c.553_555delAAG c.(553-555)AAGdel p.K186del GSK3A_uc002ota.1_In_Frame_Del_p.K104del|GSK3A_uc002otc.2_RNA NM_019884 NP_063937 P49840 GSK3A_HUMAN glycogen synthase kinase 3 alpha 186 Protein kinase. insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of insulin receptor signaling pathway|negative regulation of transferase activity|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process beta-catenin destruction complex|cytosol ATP binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|tau-protein kinase activity ovary(2)|lung(2) 4 Prostate(69;0.00682) GAGATCTCACCTTCTCGCCACTG 0.557 0.42 318 235 LMTK3 114783 broad.mit.edu 37 19 49001891 49001892 + Frame_Shift_Ins INS - C C 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr19:49001891_49001892insC uc002pjk.2 - 12 2521_2522 c.2521_2522insG c.(2521-2523)GCGfs p.A841fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.43 287 220 BAX 581 broad.mit.edu 37 19 49458971 49458972 + Frame_Shift_Del DEL GG - - rs141306106;rs36017265 byFrequency;byFrequency 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr19:49458971_49458972delGG uc002plk.2 + 3 183_184 c.114_115delGG c.(112-117)ATGGGGfs p.M38fs BAX_uc002plf.1_Frame_Shift_Del_p.M38fs|BAX_uc002plg.1_Frame_Shift_Del_p.M1fs|BAX_uc002plh.1_Intron|BAX_uc010xzx.1_RNA|BAX_uc002plj.2_Frame_Shift_Del_p.M38fs|BAX_uc002pll.2_Intron|BAX_uc002plm.2_Intron NM_138761 NP_620116 Q07812 BAX_HUMAN BCL2-associated X protein isoform alpha 38_39 activation of caspase activity by cytochrome c|activation of pro-apoptotic gene products|B cell apoptosis|cleavage of lamin|DNA fragmentation involved in apoptotic nuclear change|establishment or maintenance of transmembrane electrochemical gradient|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|induction of retinal programmed cell death|mitochondrial fragmentation involved in apoptosis|mitochondrial fusion|negative regulation of protein binding|negative regulation of survival gene product expression|nuclear fragmentation involved in apoptotic nuclear change|positive regulation of neuron apoptosis|protein homooligomerization|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|release of cytochrome c from mitochondria|release of matrix enzymes from mitochondria|response to toxin|transformed cell apoptosis cytosol|endoplasmic reticulum membrane|mitochondrial outer membrane|mitochondrial permeability transition pore complex|nucleus BH3 domain binding|channel activity|lipid binding|protein heterodimerization activity|protein homodimerization activity lung(1)|central_nervous_system(1)|skin(1) 3 all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261) OV - Ovarian serous cystadenocarcinoma(262;0.000159)|all cancers(93;0.00047)|GBM - Glioblastoma multiforme(486;0.018)|Epithelial(262;0.0279) CAGGGCGAATGGGGGGGGAGGC 0.594 0.42 54 39 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.43 13 10 BRSK1 84446 broad.mit.edu 37 19 55815035 55815036 + Frame_Shift_Ins INS - CC CC 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr19:55815035_55815036insCC uc002qkg.2 + 12 1404_1405 c.1127_1128insCC c.(1126-1128)GACfs p.D376fs BRSK1_uc002qkf.2_Frame_Shift_Ins_p.D392fs|BRSK1_uc002qkh.2_Frame_Shift_Ins_p.D71fs NM_032430 NP_115806 Q8TDC3 BRSK1_HUMAN BR serine/threonine kinase 1 376 establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV cell junction|cytoplasm|nucleus magnesium ion binding|protein serine/threonine kinase activity ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1) 6 Renal(1328;0.245) BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.0474) TGTCCCTCAGACCCCCCCCGGA 0.450 0.22 82 23 GNAS 2778 broad.mit.edu 37 20 57429216 57429217 + Frame_Shift_Ins INS - C C 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr20:57429216_57429217insC uc002xzw.2 + 1 1181_1182 c.896_897insC c.(895-897)AGCfs p.S299fs GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_RNA NM_080425 NP_536350 P63092 GNAS2_HUMAN GNAS complex locus XLas Error:Variant_position_missing_in_P63092_after_alignment activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1) 292 all_lung(29;0.0104) BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109) 0.000 0.45 305 253 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 415 78 COL18A1 80781 broad.mit.edu 37 21 46900038 46900038 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr21:46900038delC uc011afs.1 + 10 2632 c.2611delC c.(2611-2613)CCCfs p.P871fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.P456fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.P636fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 871 Triple-helical region 2 (COL2). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) gcctccagggcccccaggACC 0.498 0.53 8 9 COL18A1 80781 broad.mit.edu 37 21 46916425 46916425 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr21:46916425delC uc011afs.1 + 29 3786 c.3765delC c.(3763-3765)GGCfs p.G1255fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.G840fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.G1020fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1255 Triple-helical region 6 (COL6). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) GAATGCCCGGCCCCCCAGGAC 0.582 0.57 91 122 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.52 169 181 TNRC6B 23112 broad.mit.edu 37 22 40660740 40660740 + Frame_Shift_Del DEL G - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr22:40660740delG uc011aor.1 + 5 717 c.506delG c.(505-507)TGGfs p.W169fs TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Frame_Shift_Del_p.W169fs|TNRC6B_uc003ayo.2_5'UTR NM_001162501 NP_001155973 Q9UPQ9 TNR6B_HUMAN trinucleotide repeat containing 6B isoform 1 169 gene silencing by RNA|regulation of translation cytoplasmic mRNA processing body nucleotide binding|RNA binding 0 AATTCCACTTGGGGCTCGGGA 0.498 0.39 149 97 EP300 2033 broad.mit.edu 37 22 41574679 41574679 + Frame_Shift_Del DEL C - - 22RV1_PROSTATE NA 22RV1_PROSTATE NA g.chr22:41574679delC uc003azl.3 + 31 7359 c.6964delC c.(6964-6966)CCCfs p.P2322fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 2322 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 ACAGTCCCAGCCCCCCCACTC 0.612 0.44 197 157 HDAC6 10013 broad.mit.edu 37 X 48678572 48678572 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chrX:48678572delG uc011mmi.1 + 23 2342 c.2247delG c.(2245-2247)CTGfs p.L749fs HDAC6_uc004dks.1_Frame_Shift_Del_p.L749fs|HDAC6_uc010nig.1_Frame_Shift_Del_p.L597fs|HDAC6_uc004dkt.1_Frame_Shift_Del_p.L749fs|HDAC6_uc011mmk.1_Frame_Shift_Del_p.L730fs|HDAC6_uc004dkv.1_Frame_Shift_Del_p.L397fs|HDAC6_uc004dkw.1_Frame_Shift_Del_p.L397fs|HDAC6_uc004dkx.1_Frame_Shift_Del_p.L112fs NM_006044 NP_006035 Q9UBN7 HDAC6_HUMAN histone deacetylase 6 749 Histone deacetylase 2. aggresome assembly|cellular response to hydrogen peroxide|Hsp90 deacetylation|lysosome localization|macroautophagy|misfolded or incompletely synthesized protein catabolic process|negative regulation of proteolysis|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|polyubiquitinated misfolded protein transport|positive regulation of apoptosis|positive regulation of cellular chaperone-mediated protein complex assembly|positive regulation of epithelial cell migration|positive regulation of receptor biosynthetic process|positive regulation of signal transduction|regulation of androgen receptor signaling pathway|regulation of receptor activity|response to growth factor stimulus|response to toxin|transcription, DNA-dependent|tubulin deacetylation aggresome|caveola|cell leading edge|cytosol|histone deacetylase complex|microtubule associated complex|perinuclear region of cytoplasm actin binding|alpha-tubulin binding|beta-catenin binding|dynein complex binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|Hsp90 protein binding|microtubule binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|polyubiquitin binding|tau protein binding|tubulin deacetylase activity|zinc ion binding ovary(3)|upper_aerodigestive_tract(1) 4 Vorinostat(DB02546) GGGATCCGCTGGGGGGCTGCC 0.567 0.87 4 26 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 2313287_STOMACH NA 2313287_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 40 GPR112 139378 broad.mit.edu 37 X 135404968 135404968 + Frame_Shift_Del DEL T - - 2313287_STOMACH NA 2313287_STOMACH NA g.chrX:135404968delT uc004ezu.1 + 5 393 c.102delT c.(100-102)GATfs p.D34fs GPR112_uc010nsb.1_Intron NM_153834 NP_722576 Q8IZF6 GP112_HUMAN G-protein coupled receptor 112 34 Extracellular (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1) 12 Acute lymphoblastic leukemia(192;0.000127) AAAAGCTGGATTTTTTTGGAA 0.358 0.89 5 40 FLNA 2316 broad.mit.edu 37 X 153596328 153596328 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chrX:153596328delG uc004fkk.2 - 3 753 c.504delC c.(502-504)CCCfs p.P168fs FLNA_uc010nuu.1_Frame_Shift_Del_p.P168fs NM_001110556 NP_001104026 P21333 FLNA_HUMAN filamin A, alpha isoform 2 168 CH 2.|Actin-binding. actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering cell cortex|cytosol|extracellular region|nucleus|plasma membrane actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding breast(6) 6 all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176) GCCTCTGCTTGGGGGTCTGCT 0.647 0.90 1 9 TNFRSF4 7293 broad.mit.edu 37 1 1147441 1147441 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr1:1147441delG uc001ade.2 - 5 520 c.515delC c.(514-516)CCAfs p.P172fs TNFRSF4_uc001adf.2_Frame_Shift_Del_p.P176fs NM_003327 NP_003318 P43489 TNR4_HUMAN tumor necrosis factor receptor superfamily, 172 Extracellular (Potential). immune response|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|positive regulation of B cell proliferation|positive regulation of immunoglobulin secretion|T cell proliferation integral to plasma membrane tumor necrosis factor receptor activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199) 0.000 0.27 634 240 TP73 7161 broad.mit.edu 37 1 3644316 3644316 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr1:3644316delG uc001akp.2 + 8 1077 c.967delG c.(967-969)GGGfs p.G323fs TP73_uc001akq.2_Frame_Shift_Del_p.G323fs|TP73_uc010nzj.1_Frame_Shift_Del_p.G274fs|TP73_uc001akr.2_Frame_Shift_Del_p.G274fs|TP73_uc009vlk.1_Frame_Shift_Del_p.G274fs|TP73_uc001aks.2_Frame_Shift_Del_p.G274fs|TP73_uc010nzk.1_Frame_Shift_Del_p.G252fs|TP73_uc010nzl.1_5'UTR NM_005427 NP_005418 O15350 P73_HUMAN tumor protein p73 isoform a 323 cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mismatch repair|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of JUN kinase activity|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|protein tetramerization|response to gamma radiation|response to X-ray chromatin|cytosol|transcription factor complex chromatin binding|damaged DNA binding|double-stranded DNA binding|metal ion binding|p53 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|transcription repressor activity ovary(1)|lung(1) 2 all_cancers(77;0.0395)|Ovarian(185;0.0634)|Lung NSC(156;0.188)|all_lung(157;0.198) all_epithelial(116;7.42e-17)|all_lung(118;1.86e-06)|Lung NSC(185;0.000163)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.109)|Ovarian(437;0.127) Epithelial(90;5.57e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.87e-22)|GBM - Glioblastoma multiforme(42;5.72e-16)|Colorectal(212;2.22e-05)|COAD - Colon adenocarcinoma(227;8.48e-05)|Kidney(185;0.000539)|BRCA - Breast invasive adenocarcinoma(365;0.000868)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.00751)|Lung(427;0.226) CGCCAAGAACGGGGCCGCCAG 0.667 0.33 8 4 ARID1A 8289 broad.mit.edu 37 1 27106630 27106633 + Frame_Shift_Del DEL TGCC - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr1:27106630_27106633delTGCC uc001bmv.1 + 20 6614_6617 c.6241_6244delTGCC c.(6241-6246)TGCCTGfs p.C2081fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.C1864fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.C927fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.C409fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.C323fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 2081_2082 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CGAGAGCATTTGCCTGCCTGTCCT 0.598 0.42 48 35 TSSK3 81629 broad.mit.edu 37 1 32829722 32829722 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr1:32829722delG uc001bvf.2 + 2 1113 c.672delG c.(670-672)AAGfs p.K224fs uc001bve.1_5'Flank NM_052841 NP_443073 Q96PN8 TSSK3_HUMAN testis-specific serine kinase 3 224 Protein kinase. cell differentiation|multicellular organismal development|spermatogenesis ATP binding|magnesium ion binding|protein serine/threonine kinase activity stomach(1) 1 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.17)|Breast(348;0.212) AGCAGCAGAAGGGGGTGTCCT 0.562 0.42 62 45 SOX11 6664 broad.mit.edu 37 2 5833526 5833528 + In_Frame_Del DEL GAC - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr2:5833526_5833528delGAC uc002qyj.2 + 1 728_730 c.673_675delGAC c.(673-675)GACdel p.D233del NM_003108 NP_003099 P35716 SOX11_HUMAN SRY-box 11 233 Poly-Asp. cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis cytoplasm|nucleolus enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding central_nervous_system(3) 3 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) OV - Ovarian serous cystadenocarcinoma(76;0.132) 0.000 0.47 269 239 PAX8 7849 broad.mit.edu 37 2 113977718 113977718 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr2:113977718delG uc010yxt.1 - 11 1393 c.1227delC c.(1225-1227)CCCfs p.P409fs PAX8_uc010yxu.1_Frame_Shift_Del_p.P383fs|PAX8_uc010yxv.1_Frame_Shift_Del_p.P346fs|PAX8_uc002tjm.2_Frame_Shift_Del_p.P306fs|PAX8_uc002tjn.2_Frame_Shift_Del_p.P272fs NM_003466 NP_003457 Q06710 PAX8_HUMAN paired box 8 isoform PAX8A 409 branching involved in ureteric bud morphogenesis|cellular response to gonadotropin stimulus|central nervous system development|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|metanephric collecting duct development|metanephric comma-shaped body morphogenesis|metanephric distal convoluted tubule development|metanephric nephron tubule formation|metanephric S-shaped body morphogenesis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|otic vesicle development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric field specification|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of thyroid-stimulating hormone secretion|thyroid gland development|transcription, DNA-dependent nucleoplasm protein binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid-stimulating hormone receptor activity ovary(1)|lung(1) 2 0.000 0.26 794 276 GLI2 2736 broad.mit.edu 37 2 121726465 121726465 + Frame_Shift_Del DEL C - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr2:121726465delC uc010flp.2 + 5 849 c.819delC c.(817-819)TACfs p.Y273fs GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Intron|GLI2_uc002tmu.3_Intron|GLI2_uc002tmv.1_Frame_Shift_Del_p.R144fs|GLI2_uc010flo.1_Frame_Shift_Del_p.Y148fs|GLI2_uc002tmw.1_Frame_Shift_Del_p.Y273fs NM_005270 NP_005261 P10070 GLI2_HUMAN GLI-Kruppel family member GLI2 273 axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis nucleus|nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1) 13 Renal(3;0.0496) Prostate(154;0.0623) GCGGTTCCTACGGGCATCTGT 0.662 0.51 38 39 TTN 7273 broad.mit.edu 37 2 179498717 179498718 + Frame_Shift_Ins INS - T T 2313287_STOMACH NA 2313287_STOMACH NA g.chr2:179498717_179498718insT uc010zfg.1 - 180 35028_35029 c.34804_34805insA c.(34804-34806)ATGfs p.M11602fs TTN_uc010zfh.1_Frame_Shift_Ins_p.M5297fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.M5230fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.M5105fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 12529 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GACTACATGCATTTTTTCATGA 0.366 0.42 125 92 PMS1 5378 broad.mit.edu 37 2 190728930 190728930 + Frame_Shift_Del DEL A - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr2:190728930delA uc002urh.3 + 10 2847 c.2318delA c.(2317-2319)GAAfs p.E773fs PMS1_uc010zgb.1_Frame_Shift_Del_p.E712fs|PMS1_uc002urk.3_Frame_Shift_Del_p.E734fs|PMS1_uc002uri.3_Intron|PMS1_uc010zgc.1_Frame_Shift_Del_p.E597fs|PMS1_uc010zgd.1_Frame_Shift_Del_p.E597fs|PMS1_uc002urj.2_Intron|PMS1_uc010fry.1_Intron|PMS1_uc010frz.2_Intron|PMS1_uc002url.2_Intron|PMS1_uc002urm.2_Intron NM_000534 NP_000525 P54277 PMS1_HUMAN postmeiotic segregation 1 isoform a 773 mismatch repair|reciprocal meiotic recombination MutLalpha complex ATP binding|ATPase activity|mismatched DNA binding ovary(2)|kidney(1)|central_nervous_system(1) 4 OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751) GAGCCACTGGAAAAGCCAATT 0.303 0.48 50 47 ERBB4 2066 broad.mit.edu 37 2 212989590 212989591 + Frame_Shift_Ins INS - AG AG 2313287_STOMACH NA 2313287_STOMACH NA g.chr2:212989590_212989591insAG uc002veg.1 - 2 218_219 c.120_121insCT c.(118-123)TCTGACfs p.S40fs ERBB4_uc002veh.1_Frame_Shift_Ins_p.S40fs|ERBB4_uc010zji.1_Frame_Shift_Ins_p.S40fs|ERBB4_uc010zjj.1_Frame_Shift_Ins_p.S40fs|ERBB4_uc010fut.1_Frame_Shift_Ins_p.S40fs NM_005235 NP_005226 Q15303 ERBB4_HUMAN v-erb-a erythroblastic leukemia viral oncogene 40_41 Extracellular (Potential). cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway basolateral plasma membrane|cytoplasm|integral to membrane|nucleus ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 33 Renal(323;0.06)|Lung NSC(271;0.197) UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266) TGTTCCAGGTCAGAGAGAGAGC 0.450 0.33 154 77 SPEG 10290 broad.mit.edu 37 2 220348875 220348876 + Frame_Shift_Ins INS - C C 2313287_STOMACH NA 2313287_STOMACH NA g.chr2:220348875_220348876insC uc010fwg.2 + 30 6690_6691 c.6690_6691insC c.(6688-6693)CCACCCfs p.P2230fs NM_005876 NP_005867 Q15772 SPEG_HUMAN SPEG complex locus 2230_2231 Pro-rich. muscle organ development|negative regulation of cell proliferation nucleus ATP binding|protein serine/threonine kinase activity stomach(9)|ovary(4)|central_nervous_system(1) 14 Renal(207;0.0183) Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163) AGCCTGCACCACCCCCCCAGGC 0.678 0.37 19 11 IRS1 3667 broad.mit.edu 37 2 227660270 227660270 + Frame_Shift_Del DEL C - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr2:227660270delC uc002voh.3 - 1 3237 c.3185delG c.(3184-3186)GGCfs p.G1062fs NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 1062 fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) 0.000 0.48 601 561 IRS1 3667 broad.mit.edu 37 2 227661672 227661672 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr2:227661672delG uc002voh.3 - 1 1835 c.1783delC c.(1783-1785)CGGfs p.R595fs NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 595 fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) TGCCCCCCCCGACGCTCCAAG 0.687 0.35 17 9 ACVR2B 93 broad.mit.edu 37 3 38519754 38519754 + Frame_Shift_Del DEL C - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr3:38519754delC uc003cif.2 + 4 517 c.493delC c.(493-495)CCCfs p.P165fs ACVR2B_uc003cig.2_5'UTR NM_001106 NP_001097 Q13705 AVR2B_HUMAN activin A receptor, type IIB precursor 165 Cytoplasmic (Potential). activin receptor signaling pathway|anterior/posterior pattern formation|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|regulation of transcription, DNA-dependent cell surface|cytoplasm|integral to plasma membrane activin receptor activity|ATP binding|growth factor binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity lung(1) 1 Medulloblastoma(35;0.163) KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071) GCATCGCAAGCCCCCCTACGG 0.617 0.38 41 25 CAMKV 79012 broad.mit.edu 37 3 49897209 49897209 + Frame_Shift_Del DEL C - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr3:49897209delC uc003cxt.1 - 11 1241 c.1048delG c.(1048-1050)GCTfs p.A350fs CAMKV_uc011bcy.1_Frame_Shift_Del_p.A275fs|CAMKV_uc003cxv.1_Frame_Shift_Del_p.A322fs|CAMKV_uc003cxw.1_Frame_Shift_Del_p.A182fs|CAMKV_uc003cxx.1_Frame_Shift_Del_p.A182fs|CAMKV_uc003cxu.2_Frame_Shift_Del_p.A350fs|CAMKV_uc011bcz.1_Frame_Shift_Del_p.A313fs|CAMKV_uc011bda.1_Frame_Shift_Del_p.A307fs NM_024046 NP_076951 Q8NCB2 CAMKV_HUMAN CaM kinase-like vesicle-associated 350 Ala-rich. cytoplasmic vesicle membrane|plasma membrane ATP binding|protein serine/threonine kinase activity ovary(2)|lung(2)|large_intestine(2)|central_nervous_system(1) 7 BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621) 0.000 0.43 753 576 MYLK 4638 broad.mit.edu 37 3 123376260 123376260 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr3:123376260delG uc003ego.2 - 24 4283 c.4001delC c.(4000-4002)CCAfs p.P1334fs MYLK_uc010hrr.2_5'UTR|MYLK_uc011bjv.1_Frame_Shift_Del_p.P134fs|MYLK_uc011bjw.1_Frame_Shift_Del_p.P1334fs|MYLK_uc003egp.2_Frame_Shift_Del_p.P1265fs|MYLK_uc003egq.2_Frame_Shift_Del_p.P1334fs|MYLK_uc003egr.2_Frame_Shift_Del_p.P1265fs|MYLK_uc003egs.2_Frame_Shift_Del_p.P1158fs NM_053025 NP_444253 Q15746 MYLK_HUMAN myosin light chain kinase isoform 1 1334 Actin-binding (calcium/calmodulin- insensitive) (By similarity).|Fibronectin type-III. aorta smooth muscle tissue morphogenesis|muscle contraction cytosol actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity ovary(6)|skin(2)|stomach(1) 9 Lung NSC(201;0.0496) GBM - Glioblastoma multiforme(114;0.0736) TGTGCCAGCTGGGGGGTCTGG 0.527 0.49 38 37 TNIK 23043 broad.mit.edu 37 3 170781745 170781745 + Frame_Shift_Del DEL A - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr3:170781745delA uc003fhh.2 - 33 4353 c.4008delT c.(4006-4008)TTTfs p.F1336fs TNIK_uc003fhi.2_Frame_Shift_Del_p.F1281fs|TNIK_uc003fhj.2_Frame_Shift_Del_p.F1307fs|TNIK_uc003fhk.2_Frame_Shift_Del_p.F1328fs|TNIK_uc003fhl.2_Frame_Shift_Del_p.F1252fs|TNIK_uc003fhm.2_Frame_Shift_Del_p.F1273fs|TNIK_uc003fhn.2_Frame_Shift_Del_p.F1299fs|TNIK_uc003fho.2_Frame_Shift_Del_p.F1244fs|TNIK_uc003fhg.2_Frame_Shift_Del_p.F514fs NM_015028 NP_055843 Q9UKE5 TNIK_HUMAN TRAF2 and NCK interacting kinase isoform 1 1336 actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway cytoskeleton|nucleus|recycling endosome ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity ovary(4)|large_intestine(1) 5 all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122) LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14) GCACGGATGCAAAAAATACCT 0.403 0.52 53 58 PRKG2 5593 broad.mit.edu 37 4 82126093 82126094 + Frame_Shift_Ins INS - CT CT 2313287_STOMACH NA 2313287_STOMACH NA g.chr4:82126093_82126094insCT uc003hmh.2 - 1 122_123 c.108_109insAG c.(106-111)GAGTTGfs p.E36fs PRKG2_uc011cch.1_Frame_Shift_Ins_p.E36fs NM_006259 NP_006250 Q13237 KGP2_HUMAN protein kinase, cGMP-dependent, type II 36_37 platelet activation|signal transduction cytosol ATP binding|cGMP binding|cGMP-dependent protein kinase activity breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1) 7 TTCCTCCTCAACTCTCTCTCCA 0.530 0.40 205 139 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 2313287_STOMACH NA 2313287_STOMACH NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.50 13 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 2313287_STOMACH NA 2313287_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 76 87 MAML3 55534 broad.mit.edu 37 4 140810631 140810632 + In_Frame_Ins INS - GGT GGT 2313287_STOMACH NA 2313287_STOMACH NA g.chr4:140810631_140810632insGGT uc003ihz.1 - 3 2698_2699 c.1946_1947insACC c.(1945-1947)CCT>CCACCT p.649_649P>PP MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 649 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) GGAGCTGTGGAGGTGGCGgctg 0.416 0.29 40 16 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 2313287_STOMACH NA 2313287_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 28 50 MAST4 375449 broad.mit.edu 37 5 66460639 66460639 + Frame_Shift_Del DEL C - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr5:66460639delC uc003jut.1 + 28 5133 c.5065delC c.(5065-5067)CCCfs p.P1689fs MAST4_uc003juw.2_Frame_Shift_Del_p.P1617fs|MAST4_uc003jux.2_5'Flank NM_015183 NP_055998 O15021 MAST4_HUMAN microtubule associated serine/threonine kinase 1881 cytoplasm ATP binding|magnesium ion binding|protein serine/threonine kinase activity lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1) 13 Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245) Lung(70;0.011) TTGGTTCCTGCCCCCCAGCCG 0.547 0.33 8 4 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 2313287_STOMACH NA 2313287_STOMACH NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.27 322 122 ZNF608 57507 broad.mit.edu 37 5 123984684 123984684 + Frame_Shift_Del DEL C - - rs151227213 2313287_STOMACH NA 2313287_STOMACH NA g.chr5:123984684delC uc003ktq.1 - 4 1516 c.1393delG c.(1393-1395)GCCfs p.A465fs ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Frame_Shift_Del_p.A465fs|ZNF608_uc003ktt.1_Frame_Shift_Del_p.A465fs NM_020747 NP_065798 Q9ULD9 ZN608_HUMAN zinc finger protein 608 465 intracellular zinc ion binding skin(3)|ovary(2)|lung(1) 6 all_cancers(142;0.186)|Prostate(80;0.081) KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221) OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783) TTCCCATTGGCCCCCCCTCTG 0.627 0.41 19 13 FBN2 2201 broad.mit.edu 37 5 127713530 127713531 + Frame_Shift_Ins INS - T T 2313287_STOMACH NA 2313287_STOMACH NA g.chr5:127713530_127713531insT uc003kuu.2 - 13 2202_2203 c.1763_1764insA c.(1762-1764)AACfs p.N588fs FBN2_uc003kuv.2_Frame_Shift_Ins_p.N555fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 588 EGF-like 8; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) CGCATCGACCGTTTTTACAAAG 0.381 0.42 75 55 RAD50 10111 broad.mit.edu 37 5 131931451 131931452 + Frame_Shift_Ins INS - A A 2313287_STOMACH NA 2313287_STOMACH NA g.chr5:131931451_131931452insA uc003kxi.2 + 13 2543_2544 c.2156_2157insA c.(2155-2157)CTAfs p.L719fs RAD50_uc003kxh.2_Frame_Shift_Ins_p.L580fs NM_005732 NP_005723 Q92878 RAD50_HUMAN RAD50 homolog isoform 1 719 Zinc-hook.|Potential. DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding lung(2)|ovary(1)|skin(1) 4 all_cancers(142;0.0368)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GAATCAGAGCTAAAAAAAAAGG 0.416 0.31 36 16 CDC25C 995 broad.mit.edu 37 5 137627690 137627690 + Frame_Shift_Del DEL T - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr5:137627690delT uc003lcp.1 - 8 1002 c.731delA c.(730-732)AAGfs p.K244fs CDC25C_uc003lcq.1_Frame_Shift_Del_p.K171fs|CDC25C_uc003lcr.1_Frame_Shift_Del_p.K244fs|CDC25C_uc011cyp.1_Frame_Shift_Del_p.K261fs|CDC25C_uc003lcs.1_Frame_Shift_Del_p.K322fs NM_001790 NP_001781 P30307 MPIP3_HUMAN cell division cycle 25C isoform a 244 cell cycle checkpoint|cell division|cell proliferation|DNA replication|G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis|traversing start control point of mitotic cell cycle cytosol|nucleoplasm protein tyrosine phosphatase activity|WW domain binding lung(3) 3 KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592) AGAAAAATACTTTTTTTTAAC 0.388 0.51 120 124 DNAH8 1769 broad.mit.edu 37 6 38816440 38816440 + Frame_Shift_Del DEL A - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr6:38816440delA uc003ooe.1 + 35 5011 c.4411delA c.(4411-4413)AAAfs p.K1471fs NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 TGCTCCATTTAAAAAAAATAT 0.343 0.49 53 51 GLI3 2737 broad.mit.edu 37 7 42005573 42005573 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr7:42005573delG uc011kbh.1 - 15 3189 c.3098delC c.(3097-3099)CCGfs p.P1033fs GLI3_uc011kbg.1_Frame_Shift_Del_p.P974fs NM_000168 NP_000159 P10071 GLI3_HUMAN GLI-Kruppel family member GLI3 1033 negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis cilium|cytosol|nucleolus beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1) 19 GGCCATCGCCGGGGGGTTGCA 0.701 0.33 10 5 CDK14 5218 broad.mit.edu 37 7 90419931 90419933 + In_Frame_Del DEL GAA - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr7:90419931_90419933delGAA uc003uky.2 + 5 730_732 c.508_510delGAA c.(508-510)GAAdel p.E172del CDK14_uc003ukt.1_In_Frame_Del_p.E126del|CDK14_uc003ukv.1_In_Frame_Del_p.E126del|CDK14_uc003uku.1_In_Frame_Del_p.E126del|CDK14_uc003ukx.1_RNA|CDK14_uc003ukz.1_In_Frame_Del_p.E154del|CDK14_uc010les.1_In_Frame_Del_p.E126del|CDK14_uc011khl.1_In_Frame_Del_p.E43del NM_012395 NP_036527 O94921 CDK14_HUMAN PFTAIRE protein kinase 1 172 Protein kinase. cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane ATP binding|cyclin binding|cyclin-dependent protein kinase activity lung(3)|ovary(1) 4 CAGGCTGCAGGAAGAAGAAGGGA 0.389 0.38 223 136 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT 2313287_STOMACH NA 2313287_STOMACH NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.32 479 229 MLL3 58508 broad.mit.edu 37 7 151874012 151874013 + Frame_Shift_Ins INS - T T 2313287_STOMACH NA 2313287_STOMACH NA g.chr7:151874012_151874013insT uc003wla.2 - 38 8744_8745 c.8525_8526insA c.(8524-8526)AATfs p.N2842fs MLL3_uc003wkz.2_Frame_Shift_Ins_p.N1903fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.N351fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 2842 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TATTCTCATCATTTTTTTCAGT 0.381 0.37 188 110 MLL3 58508 broad.mit.edu 37 7 151874147 151874148 + Frame_Shift_Ins INS - T T 2313287_STOMACH NA 2313287_STOMACH NA g.chr7:151874147_151874148insT uc003wla.2 - 38 8609_8610 c.8390_8391insA c.(8389-8391)AAGfs p.K2797fs MLL3_uc003wkz.2_Frame_Shift_Ins_p.K1858fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.K306fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 2797 K -> R (in Ref. 1; AAK00583). intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding p.K2797fs*26(18) large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTTCTTGTTCCTTTTTTTTTGG 0.347 0.71 110 266 TNFRSF10D 8793 broad.mit.edu 37 8 22995737 22995738 + In_Frame_Ins INS - CCT CCT 2313287_STOMACH NA 2313287_STOMACH NA g.chr8:22995737_22995738insCCT uc003xcz.1 - 8 1082_1083 c.990_991insAGG c.(988-993)insAGG p.330_331insR NM_003840 NP_003831 Q9UBN6 TR10D_HUMAN tumor necrosis factor receptor superfamily, 330_331 Cytoplasmic (Potential). anti-apoptosis|apoptosis integral to membrane TRAIL binding|transmembrane receptor activity 0 Prostate(55;0.0421)|Breast(100;0.067) Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612) GGAACCAGCAGCCTCCTCCTCT 0.396 0.36 14 8 TRPS1 7227 broad.mit.edu 37 8 116616637 116616637 + Frame_Shift_Del DEL T - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr8:116616637delT uc003ynz.2 - 3 1979 c.1520delA c.(1519-1521)AAGfs p.K507fs TRPS1_uc011lhy.1_Frame_Shift_Del_p.K511fs|TRPS1_uc003yny.2_Frame_Shift_Del_p.K520fs|TRPS1_uc010mcy.2_Frame_Shift_Del_p.K507fs NM_014112 NP_054831 Q9UHF7 TRPS1_HUMAN zinc finger transcription factor TRPS1 507 negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) GAAGTCCTTCTTTTTAGCCCC 0.453 0.18 510 113 COL14A1 7373 broad.mit.edu 37 8 121379470 121379471 + Frame_Shift_Ins INS - C C 2313287_STOMACH NA 2313287_STOMACH NA g.chr8:121379470_121379471insC uc003yox.2 + 46 5403_5404 c.5138_5139insC c.(5137-5139)GGCfs p.G1713fs COL14A1_uc003yoz.2_Frame_Shift_Ins_p.G678fs NM_021110 NP_066933 Q05707 COEA1_HUMAN collagen, type XIV, alpha 1 precursor 1713 Triple-helical region 2 (COL1). cell-cell adhesion|collagen fibril organization collagen type XIV|extracellular space collagen binding|extracellular matrix structural constituent|protein binding, bridging ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1) 12 Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503) GGTCCAAGAGGCCCCCCTGGAC 0.371 0.17 106 22 ADCK5 203054 broad.mit.edu 37 8 145616369 145616369 + Frame_Shift_Del DEL C - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr8:145616369delC uc003zch.2 + 6 633 c.579delC c.(577-579)CTCfs p.L193fs ADCK5_uc003zcg.2_RNA|ADCK5_uc003zci.2_5'Flank NM_174922 NP_777582 Q3MIX3 ADCK5_HUMAN aarF domain containing kinase 5 193 Protein kinase. integral to membrane protein serine/threonine kinase activity stomach(1) 1 all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;8.96e-41)|Epithelial(56;4.08e-40)|all cancers(56;4.51e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055) TCCAGGCCCTCCCCCACGAGC 0.637 0.19 119 28 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency 2313287_STOMACH NA 2313287_STOMACH NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.13 811 116 OMD 4958 broad.mit.edu 37 9 95179830 95179830 + Frame_Shift_Del DEL A - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr9:95179830delA uc004asd.3 - 2 380 c.11delT c.(10-12)TTAfs p.L4fs CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron NM_005014 NP_005005 Q99983 OMD_HUMAN osteomodulin precursor 4 cell adhesion proteinaceous extracellular matrix ovary(2) 2 TATTGGACTTAAAAAACCCAT 0.328 0.13 47 7 CUBN 8029 broad.mit.edu 37 10 16967360 16967360 + Frame_Shift_Del DEL A - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr10:16967360delA uc001ioo.2 - 43 6578 c.6526delT c.(6526-6528)TGTfs p.C2176fs NM_001081 NP_001072 O60494 CUBN_HUMAN cubilin precursor 2176 CUB 15. cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1) 19 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) TGACTGCCACAAAAATGACCA 0.388 0.44 85 67 MASTL 84930 broad.mit.edu 37 10 27459056 27459056 + Frame_Shift_Del DEL A - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr10:27459056delA uc001itm.2 + 8 1807 c.1168delA c.(1168-1170)AAAfs p.K390fs MASTL_uc001itl.2_Frame_Shift_Del_p.K390fs|MASTL_uc009xkw.1_Frame_Shift_Del_p.K390fs|MASTL_uc009xkx.1_RNA NM_032844 NP_116233 Q96GX5 GWL_HUMAN microtubule associated serine/threonine 390 Protein kinase. cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus centrosome|cleavage furrow|nucleus ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity p.C392fs*17(1) stomach(1)|ovary(1)|lung(1) 3 AAACCTTGCTAAAAAATGCTT 0.418 0.37 36 21 ADAM12 8038 broad.mit.edu 37 10 127806699 127806699 + Frame_Shift_Del DEL T - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr10:127806699delT uc001ljk.2 - 6 933 c.520delA c.(520-522)AGCfs p.S174fs ADAM12_uc010qul.1_Frame_Shift_Del_p.S171fs|ADAM12_uc001ljm.2_Frame_Shift_Del_p.S174fs|ADAM12_uc001ljn.2_Frame_Shift_Del_p.S171fs|ADAM12_uc001ljl.3_Frame_Shift_Del_p.S171fs NM_003474 NP_003465 O43184 ADA12_HUMAN ADAM metallopeptidase domain 12 isoform 1 174 cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis extracellular region|integral to membrane|plasma membrane metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1) 9 all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22) COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216) CCCCGGACGCTTTTCAGCTTC 0.463 0.54 62 74 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 2313287_STOMACH NA 2313287_STOMACH NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.47 8 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 2313287_STOMACH NA 2313287_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 225 58 ZBTB16 7704 broad.mit.edu 37 11 114121272 114121272 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr11:114121272delG uc001pop.2 + 7 2281 c.2017delG c.(2017-2019)GTGfs p.V673fs ZBTB16_uc001poq.2_Frame_Shift_Del_p.V673fs NM_006006 NP_005997 Q05516 ZBT16_HUMAN promyelocytic leukemia zinc finger protein 673 apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent nuclear speck|PML body|transcriptional repressor complex protein homodimerization activity|zinc ion binding central_nervous_system(1)|skin(1) 2 all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438) BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018) CCTGTGCTATGTGTGAAGGGA 0.547 0.38 16 10 MLL 4297 broad.mit.edu 37 11 118342758 118342759 + Frame_Shift_Ins INS - G G 2313287_STOMACH NA 2313287_STOMACH NA g.chr11:118342758_118342759insG uc001pta.2 + 3 907_908 c.884_885insG c.(883-885)AAGfs p.K295fs MLL_uc001ptb.2_Frame_Shift_Ins_p.K295fs|MLL_uc001psz.1_Frame_Shift_Ins_p.K328fs|MLL_uc001ptd.1_Intron NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 295 apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) ATAGGAAGGAAGGGGGTACAAA 0.441 0.42 90 66 CBL 867 broad.mit.edu 37 11 119077179 119077179 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr11:119077179delG uc001pwe.2 + 1 190 c.52delG c.(52-54)GGGfs p.G18fs NM_005188 NP_005179 P22681 CBL_HUMAN Cas-Br-M (murine) ecotropic retroviral 18 epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis cytosol|nucleus calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1) 149 Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784) CAGCGGCTCCGGGGGCTCGGG 0.662 0.57 6 8 ERC1 23085 broad.mit.edu 37 12 1291166 1291166 + Frame_Shift_Del DEL A - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr12:1291166delA uc001qjb.2 + 10 2192 c.1951delA c.(1951-1953)AAAfs p.K651fs ERC1_uc001qiz.2_RNA|ERC1_uc001qjc.2_Frame_Shift_Del_p.K623fs|ERC1_uc001qja.2_RNA|ERC1_uc001qjd.2_RNA|ERC1_uc001qjf.2_Frame_Shift_Del_p.K651fs|ERC1_uc010sdv.1_Frame_Shift_Del_p.K399fs|ERC1_uc009zdp.2_Frame_Shift_Del_p.K291fs NM_178040 NP_829884 Q8IUD2 RB6I2_HUMAN RAB6-interacting protein 2 isoform epsilon 651 Potential. I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport Golgi membrane|IkappaB kinase complex|presynaptic membrane leucine zipper domain binding ovary(2)|lung(2)|breast(1) 5 all_epithelial(11;0.0698)|Ovarian(42;0.107) OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567) TGATAACTACAAAAAAGATCT 0.408 0.48 110 101 DYRK4 8798 broad.mit.edu 37 12 4719362 4719362 + Frame_Shift_Del DEL A - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr12:4719362delA uc001qmx.2 + 11 1217 c.1057delA c.(1057-1059)AAAfs p.K353fs DYRK4_uc009zeh.1_Frame_Shift_Del_p.K468fs|DYRK4_uc001qmy.1_Frame_Shift_Del_p.K353fs|DYRK4_uc001qmz.1_Frame_Shift_Del_p.K67fs|DYRK4_uc001qna.1_5'UTR|DYRK4_uc010ser.1_5'UTR NM_003845 NP_003836 Q9NR20 DYRK4_HUMAN dual-specificity tyrosine-(Y)-phosphorylation 353 Protein kinase. Golgi apparatus ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(2)|skin(1) 3 Colorectal(7;0.103) CAACAGGGGGAAAAAAAGATA 0.398 0.50 30 30 LRRK2 120892 broad.mit.edu 37 12 40702287 40702287 + Frame_Shift_Del DEL A - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr12:40702287delA uc001rmg.3 + 29 4099 c.3978delA c.(3976-3978)TTAfs p.L1326fs LRRK2_uc009zjw.2_Frame_Shift_Del_p.L164fs|LRRK2_uc001rmi.2_Frame_Shift_Del_p.L159fs NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 1326 activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) AACAGCGATTAAAAAAGGCTG 0.313 0.49 62 59 WNT1 7471 broad.mit.edu 37 12 49374348 49374348 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr12:49374348delG uc001rsu.2 + 3 698 c.500delG c.(499-501)TGGfs p.W167fs NM_005430 NP_005421 P04628 WNT1_HUMAN wingless-type MMTV integration site family, 167 brain segmentation|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|central nervous system morphogenesis|cerebellum formation|dermatome development|diencephalon development|embryonic axis specification|forebrain anterior/posterior pattern formation|fourth ventricle development|hemopoietic stem cell proliferation|hepatocyte differentiation|inner ear morphogenesis|mesoderm morphogenesis|midbrain development|midbrain-hindbrain boundary maturation during brain development|negative regulation of cell-cell adhesion|negative regulation of cell-substrate adhesion|negative regulation of DNA damage checkpoint|negative regulation of fat cell differentiation|neuron fate determination|positive regulation of fibroblast proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of lamellipodium assembly|positive regulation of Notch signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to wounding|signal transduction in response to DNA damage|Spemann organizer formation|T cell differentiation in thymus|Wnt receptor signaling pathway, calcium modulating pathway early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix cytokine activity|frizzled-2 binding|transcription regulatory region DNA binding kidney(1) 1 BRCA - Breast invasive adenocarcinoma(357;0.244) gACTGGCACTGGGGGGGCTGC 0.552 0.44 10 8 BTG1 694 broad.mit.edu 37 12 92537965 92537965 + Frame_Shift_Del DEL T - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr12:92537965delT uc001tby.3 - 2 769 c.407delA c.(406-408)AACfs p.N136fs BTG1_uc001tbv.1_5'Flank|BTG1_uc001tbw.1_5'Flank|BTG1_uc001tbx.1_5'Flank|BTG1_uc009zss.1_5'Flank|uc001tca.2_5'Flank NM_001731 NP_001722 P62324 BTG1_HUMAN B-cell translocation protein 1 136 cell migration|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of angiogenesis|positive regulation of endothelial cell differentiation|positive regulation of myoblast differentiation|regulation of apoptosis|regulation of transcription, DNA-dependent cytoplasm|nucleus kinase binding|transcription cofactor activity 0 Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09) GTTGGTGCTGTTTTGAGTGCT 0.488 0.46 109 91 MTUS2 23281 broad.mit.edu 37 13 29600993 29600993 + Frame_Shift_Del DEL C - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr13:29600993delC uc001usl.3 + 1 2246 c.2188delC c.(2188-2190)CCCfs p.P730fs NM_001033602 NP_001028774 Q5JR59 MTUS2_HUMAN hypothetical protein LOC23281 isoform a 720 Mediates interaction with MAPRE1. cytoplasm|microtubule microtubule binding|protein homodimerization activity 0 TGGAATCAAGCCCCCGGGACA 0.453 0.37 116 67 CSNK1A1L 122011 broad.mit.edu 37 13 37678703 37678704 + Frame_Shift_Ins INS - T T rs56252523 2313287_STOMACH NA 2313287_STOMACH NA g.chr13:37678703_37678704insT uc001uwm.1 - 1 1098_1099 c.690_691insA c.(688-693)AAACAAfs p.K230fs NM_145203 NP_660204 Q8N752 KC1AL_HUMAN casein kinase 1, alpha 1-like 230_231 Protein kinase. Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity large_intestine(1) 1 Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109) all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407) TCATATTTTTGTTTTTTTGTCA 0.426 0.45 138 111 FOXO1 2308 broad.mit.edu 37 13 41239933 41239933 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr13:41239933delG uc001uxl.3 - 1 802 c.417delC c.(415-417)CCCfs p.P139fs NM_002015 NP_002006 Q12778 FOXO1_HUMAN forkhead box O1 139 anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding PAX3/FOXO1(749)|PAX7/FOXO1(197) soft_tissue(946)|lung(1)|central_nervous_system(1) 948 Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194) all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815) 0.000 0.50 301 307 ERCC5 2073 broad.mit.edu 37 13 103524568 103524568 + Frame_Shift_Del DEL A - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr13:103524568delA uc001vpw.2 + 13 3142 c.2699delA c.(2698-2700)CAAfs p.Q900fs ERCC5_uc001vpu.1_Frame_Shift_Del_p.Q1354fs|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_Frame_Shift_Del_p.Q732fs NM_000123 NP_000114 P28715 ERCC5_HUMAN XPG-complementing protein 900 negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection nucleoplasm bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding ovary(4)|lung(1)|central_nervous_system(1)|skin(1) 7 all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211) CATGAAGCTCAAAAAAATCCA 0.373 0.44 43 34 NOVA1 4857 broad.mit.edu 37 14 27066542 27066542 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr14:27066542delG uc001wpy.2 - 1 419 c.101delC c.(100-102)CCTfs p.P34fs NOVA1_uc001wpz.2_Frame_Shift_Del_p.P34fs|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_Frame_Shift_Del_p.P34fs NM_002515 NP_002506 P51513 NOVA1_HUMAN neuro-oncological ventral antigen 1 isoform 1 34 Bipartite nuclear localization signal (Potential). locomotory behavior|RNA splicing|synaptic transmission nucleus RNA binding skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1) 5 GBM - Glioblastoma multiforme(265;0.0135) 0.000 0.40 903 599 BMP4 652 broad.mit.edu 37 14 54418949 54418950 + Splice_Site INS - G G 2313287_STOMACH NA 2313287_STOMACH NA g.chr14:54418949_54418950insG uc001xal.3 - 2 181 c.-6_splice c.e2-1 BMP4_uc010aoh.2_Splice_Site|BMP4_uc001xao.3_Splice_Site|BMP4_uc001xan.3_Splice_Site NM_130851 NP_570912 P12644 BMP4_HUMAN bone morphogenetic protein 4 preproprotein activation of MAPKK activity|blood vessel endothelial cell proliferation involved in sprouting angiogenesis|BMP signaling pathway involved in heart induction|BMP signaling pathway involved in nephric duct formation|branching involved in ureteric bud morphogenesis|bronchus development|bud dilation involved in lung branching|cardiac septum development|cartilage development|endocardial cushion development|epithelial cell proliferation involved in lung morphogenesis|intermediate mesodermal cell differentiation|lung alveolus development|lymphoid progenitor cell differentiation|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway|negative regulation of branching involved in ureteric bud morphogenesis|negative regulation of cell proliferation involved in heart morphogenesis|negative regulation of glomerular mesangial cell proliferation|negative regulation of glomerulus development|negative regulation of immature T cell proliferation in thymus|negative regulation of MAP kinase activity|negative regulation of metanephric comma-shaped body morphogenesis|negative regulation of metanephric S-shaped body morphogenesis|negative regulation of mitosis|negative regulation of myoblast differentiation|negative regulation of phosphorylation|negative regulation of striated muscle tissue development|negative regulation of thymocyte apoptosis|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of apoptosis|positive regulation of bone mineralization|positive regulation of cardiac muscle fiber development|positive regulation of cartilage development|positive regulation of collagen biosynthetic process|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of kidney development|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|protein localization to nucleus|pulmonary artery endothelial tube morphogenesis|secondary heart field specification|SMAD protein signal transduction|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway|steroid hormone mediated signaling pathway extracellular space|proteinaceous extracellular matrix BMP receptor binding|chemoattractant activity|cytokine activity|growth factor activity 0 ATGGTGTCTCTGGGGAGGGGGA 0.465 0.37 29 17 PRKCH 5583 broad.mit.edu 37 14 62014534 62014535 + Frame_Shift_Ins INS - T T 2313287_STOMACH NA 2313287_STOMACH NA g.chr14:62014534_62014535insT uc001xfn.2 + 13 2140_2141 c.1835_1836insT c.(1834-1836)CCTfs p.P612fs PRKCH_uc010tsa.1_Frame_Shift_Ins_p.P451fs|PRKCH_uc010tsb.1_Frame_Shift_Ins_p.P180fs|PRKCH_uc001xfo.2_RNA NM_006255 NP_006246 P24723 KPCL_HUMAN protein kinase C, eta 612 Protein kinase. intracellular signal transduction|platelet activation cytosol|plasma membrane ATP binding|enzyme binding|metal ion binding|protein kinase C activity ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1) 6 OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182) TTGAGACATCCTTTTTTTAAGG 0.520 0.40 148 98 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 2313287_STOMACH NA 2313287_STOMACH NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.71 4 10 MGA 23269 broad.mit.edu 37 15 42054008 42054008 + Frame_Shift_Del DEL A - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr15:42054008delA uc010ucy.1 + 21 7651 c.7470delA c.(7468-7470)CGAfs p.R2490fs MGA_uc010ucz.1_Frame_Shift_Del_p.R2281fs|MGA_uc010uda.1_Frame_Shift_Del_p.R1106fs NM_001164273 NP_001157745 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 1 2451 MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) TCCTGACTCGAAAACGGAATA 0.348 0.58 35 48 TP53BP1 7158 broad.mit.edu 37 15 43730536 43730536 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr15:43730536delG uc001zrs.2 - 16 3310 c.3162delC c.(3160-3162)CCCfs p.P1054fs TP53BP1_uc010udp.1_Frame_Shift_Del_p.P1054fs|TP53BP1_uc001zrq.3_Frame_Shift_Del_p.P1059fs|TP53BP1_uc001zrr.3_Frame_Shift_Del_p.P1059fs|TP53BP1_uc010udq.1_Frame_Shift_Del_p.P1059fs NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 1054 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) TGGGTGTGGTGGGGGGATCCT 0.413 0.40 111 74 TP53BP1 7158 broad.mit.edu 37 15 43748660 43748661 + Frame_Shift_Ins INS - T T 2313287_STOMACH NA 2313287_STOMACH NA g.chr15:43748660_43748661insT uc001zrs.2 - 12 2278_2279 c.2130_2131insA c.(2128-2133)AAAGAAfs p.K710fs TP53BP1_uc010udp.1_Frame_Shift_Ins_p.K710fs|TP53BP1_uc001zrq.3_Frame_Shift_Ins_p.K715fs|TP53BP1_uc001zrr.3_Frame_Shift_Ins_p.K715fs|TP53BP1_uc010udq.1_Frame_Shift_Ins_p.K715fs NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 710_711 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) TCTGAGCATTCTTTTTTTGGCA 0.401 0.37 97 56 TCF12 6938 broad.mit.edu 37 15 57565386 57565386 + Frame_Shift_Del DEL A - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr15:57565386delA uc002aec.2 + 18 2116 c.1832delA c.(1831-1833)GAAfs p.E611fs TCF12_uc010ugm.1_Frame_Shift_Del_p.E663fs|TCF12_uc010ugn.1_Frame_Shift_Del_p.E631fs|TCF12_uc002aea.2_Frame_Shift_Del_p.E635fs|TCF12_uc010bfs.2_Frame_Shift_Del_p.E32fs|TCF12_uc002aeb.2_Frame_Shift_Del_p.E635fs|TCF12_uc002aed.2_Frame_Shift_Del_p.E611fs|TCF12_uc002aee.2_Frame_Shift_Del_p.E441fs|TCF12_uc010bft.2_Frame_Shift_Del_p.E465fs|TCF12_uc010ugo.1_Frame_Shift_Del_p.E375fs|TCF12_uc010ugp.1_Frame_Shift_Del_p.E268fs|TCF12_uc010ugq.1_Frame_Shift_Del_p.E245fs|TCF12_uc010ugr.1_Frame_Shift_Del_p.E224fs NM_207038 NP_996921 Q99081 HTF4_HUMAN transcription factor 12 isoform b 611 Helix-loop-helix motif. immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity central_nervous_system(5)|ovary(2)|lung(1) 8 Colorectal(260;0.0907) all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239) TTGAAGAGTGAAAAACCCCAA 0.458 0.30 71 30 TLE3 7090 broad.mit.edu 37 15 70346913 70346913 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr15:70346913delG uc002asm.2 - 16 2818 c.1699delC c.(1699-1701)CGCfs p.R567fs TLE3_uc002ask.2_Frame_Shift_Del_p.R494fs|TLE3_uc002asl.2_Frame_Shift_Del_p.R567fs|TLE3_uc010ukd.1_Frame_Shift_Del_p.R557fs|TLE3_uc010bik.1_Frame_Shift_Del_p.R148fs|TLE3_uc010bil.1_Frame_Shift_Del_p.R564fs|TLE3_uc002asn.2_Frame_Shift_Del_p.R555fs|TLE3_uc002asp.2_Frame_Shift_Del_p.R559fs|TLE3_uc002aso.2_Frame_Shift_Del_p.R562fs NM_005078 NP_005069 Q04726 TLE3_HUMAN transducin-like enhancer protein 3 isoform a 567 WD 2. organ morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway nucleus protein binding|protein binding lung(2) 2 GCCTTGATGCGGGGCGTGGGC 0.652 0.64 5 9 GRIN2A 2903 broad.mit.edu 37 16 9857283 9857283 + Frame_Shift_Del DEL T - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr16:9857283delT uc002czo.3 - 13 4666 c.4118delA c.(4117-4119)GATfs p.D1373fs GRIN2A_uc010uym.1_Frame_Shift_Del_p.D1373fs|GRIN2A_uc010uyn.1_Frame_Shift_Del_p.M1102fs|GRIN2A_uc002czr.3_Frame_Shift_Del_p.M1259fs NM_001134407 NP_001127879 Q12879 NMDE1_HUMAN N-methyl-D-aspartate receptor subunit 2A isoform 1373 Cytoplasmic (Potential). response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1) 45 Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043) GCGTTGGTCATCCCTGTGGGA 0.552 0.48 87 79 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes 2313287_STOMACH NA 2313287_STOMACH NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.17 116 23 CDH1 999 broad.mit.edu 37 16 68771347 68771348 + In_Frame_Ins INS - GCT GCT 2313287_STOMACH NA 2313287_STOMACH NA g.chr16:68771347_68771348insGCT uc002ewg.1 + 1 153_154 c.29_30insGCT c.(28-30)GCG>GCGCTG p.15_16insL CDH1_uc010vlj.1_RNA|CDH1_uc010cfg.1_In_Frame_Ins_p.15_16insL NM_004360 NP_004351 P12830 CADH1_HUMAN cadherin 1, type 1 preproprotein 15_16 adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm cell adhesion molecule binding|gamma-catenin binding p.?(1)|p.L8fs*41(1) breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1) 243 all_neural(199;0.0189)|Ovarian(137;0.0563) Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261) 0.000 0.12 520 68 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C 2313287_STOMACH NA 2313287_STOMACH NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 4 30 RNF43 54894 broad.mit.edu 37 17 56435161 56435161 + Frame_Shift_Del DEL C - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr17:56435161delC uc002iwf.2 - 8 3932 c.1976delG c.(1975-1977)GGTfs p.G659fs RNF43_uc010wnv.1_Frame_Shift_Del_p.G618fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.G659fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.G659fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.G532fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 659 Pro-rich.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.34 339 176 AXIN2 8313 broad.mit.edu 37 17 63532585 63532585 + Frame_Shift_Del DEL C - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr17:63532585delC uc002jfi.2 - 8 2283 c.1994delG c.(1993-1995)GGCfs p.G665fs AXIN2_uc002jfh.2_Frame_Shift_Del_p.G600fs NM_004655 NP_004646 Q9Y2T1 AXIN2_HUMAN axin 2 665 cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding central_nervous_system(1)|skin(1) 2 CCCGCTGTTGCCCCCCCACAG 0.657 0.33 8 4 ROCK1 6093 broad.mit.edu 37 18 18549135 18549136 + Frame_Shift_Ins INS - T T 2313287_STOMACH NA 2313287_STOMACH NA g.chr18:18549135_18549136insT uc002kte.2 - 24 3795_3796 c.2854_2855insA c.(2854-2856)ATTfs p.I952fs NM_005406 NP_005397 Q13464 ROCK1_HUMAN Rho-associated, coiled-coil containing protein 952 Glu-rich. actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction centriole|cytosol|Golgi membrane ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity lung(2)|breast(2)|central_nervous_system(1) 5 Melanoma(1;0.165) TAATATTTCAATATCTTTGGTT 0.337 0.41 97 68 STK11 6794 broad.mit.edu 37 19 1221314 1221314 + Frame_Shift_Del DEL C - - rs67873004 2313287_STOMACH NA 2313287_STOMACH NA g.chr19:1221314delC uc002lrl.1 + 6 1952 c.837delC c.(835-837)GGCfs p.G279fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 279 Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.P281fs*6(2)|p.?(2)|p.Y246fs*3(1)|p.G279F(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) GCGACTGTGGCCCCCCGCTCT 0.607 0.96 1 25 SMARCA4 6597 broad.mit.edu 37 19 11132635 11132635 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr19:11132635delG uc002mqf.3 + 19 3135 c.2851delG c.(2851-2853)GGGfs p.G951fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.G951fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.G951fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.G951fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.G951fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.G951fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.G951fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.G951fs|SMARCA4_uc010dxt.1_Frame_Shift_Del_p.G171fs|SMARCA4_uc002mqh.3_Frame_Shift_Del_p.G74fs|SMARCA4_uc002mqi.1_Frame_Shift_Del_p.G154fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 951 chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) 0.000 0.48 720 678 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 2313287_STOMACH NA 2313287_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.31 18 8 CD79A 973 broad.mit.edu 37 19 42383610 42383610 + Frame_Shift_Del DEL C - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr19:42383610delC uc002orv.2 + 3 570 c.385delC c.(385-387)CCCfs p.P129fs CD79A_uc002oru.2_Frame_Shift_Del_p.P91fs NM_001783 NP_001774 P11912 CD79A_HUMAN CD79A antigen isoform 1 precursor 129 Extracellular (Potential). B cell differentiation|B cell proliferation|B cell receptor signaling pathway B cell receptor complex|external side of plasma membrane|integral to membrane|membrane raft|multivesicular body transmembrane receptor activity ovary(2)|pancreas(1) 3 0.000 0.41 398 271 CIC 23152 broad.mit.edu 37 19 42794441 42794441 + Frame_Shift_Del DEL C - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr19:42794441delC uc002otf.1 + 10 1561 c.1521delC c.(1519-1521)CGCfs p.R507fs NM_015125 NP_055940 Q96RK0 CIC_HUMAN capicua homolog 507 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1) 11 Prostate(69;0.00682) 0.000 0.47 882 784 LMTK3 114783 broad.mit.edu 37 19 49001892 49001892 + Frame_Shift_Del DEL C - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr19:49001892delC uc002pjk.2 - 12 2521 c.2521delG c.(2521-2523)GCGfs p.A841fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.54 305 361 LMTK3 114783 broad.mit.edu 37 19 49002150 49002151 + Frame_Shift_Ins INS - G G 2313287_STOMACH NA 2313287_STOMACH NA g.chr19:49002150_49002151insG uc002pjk.2 - 12 2262_2263 c.2262_2263insC c.(2260-2265)CCCGCCfs p.P754fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.34 298 151 BRSK1 84446 broad.mit.edu 37 19 55823335 55823335 + Frame_Shift_Del DEL C - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr19:55823335delC uc002qkg.2 + 19 2513 c.2236delC c.(2236-2238)CCCfs p.P746fs BRSK1_uc002qkf.2_Frame_Shift_Del_p.P762fs|BRSK1_uc002qkh.2_Frame_Shift_Del_p.P441fs NM_032430 NP_115806 Q8TDC3 BRSK1_HUMAN BR serine/threonine kinase 1 746 establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV cell junction|cytoplasm|nucleus magnesium ion binding|protein serine/threonine kinase activity ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1) 6 Renal(1328;0.245) BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.0474) 0.000 0.36 584 325 JAG1 182 broad.mit.edu 37 20 10632855 10632856 + Frame_Shift_Ins INS - C C 2313287_STOMACH NA 2313287_STOMACH NA g.chr20:10632855_10632856insC uc002wnw.2 - 7 1445_1446 c.929_930insG c.(928-930)GGAfs p.G310fs JAG1_uc010gcd.1_5'Flank NM_000214 NP_000205 P78504 JAG1_HUMAN jagged 1 precursor 310 EGF-like 3.|Extracellular (Potential). angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation extracellular region|integral to plasma membrane calcium ion binding|growth factor activity|Notch binding|structural molecule activity lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1) 9 TGCTACAAGTTCCCCCGTTGAG 0.495 0.46 59 50 E2F1 1869 broad.mit.edu 37 20 32264549 32264549 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr20:32264549delG uc002wzu.3 - 7 1443 c.1303delC c.(1303-1305)CTGfs p.L435fs NECAB3_uc002wzm.3_5'Flank|NECAB3_uc002wzn.3_5'Flank|NECAB3_uc002wzo.3_5'Flank|NECAB3_uc002wzp.3_5'Flank|NECAB3_uc002wzq.3_5'Flank|NECAB3_uc002wzr.3_5'Flank|NECAB3_uc010geo.2_5'Flank NM_005225 NP_005216 Q01094 E2F1_HUMAN E2F transcription factor 1 435 Transactivation. apoptosis|cell proliferation|G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|mRNA stabilization|negative regulation of transcription involved in G1/S phase of mitotic cell cycle|positive regulation of fibroblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle mitochondrion|Rb-E2F complex sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription factor binding 0 0.000 0.26 557 198 TP53RK 112858 broad.mit.edu 37 20 45315440 45315440 + Frame_Shift_Del DEL T - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr20:45315440delT uc002xsk.2 - 2 937 c.714delA c.(712-714)AAAfs p.K238fs SLC13A3_uc002xsg.1_5'Flank|SLC13A3_uc010gho.1_5'Flank|TP53RK_uc002xsj.2_3'UTR NM_033550 NP_291028 Q96S44 PRPK_HUMAN p53-related protein kinase 238 Protein kinase. lipopolysaccharide biosynthetic process membrane|nucleus ATP binding|p53 binding|protein serine/threonine kinase activity|protein tyrosine kinase activity 0 Myeloproliferative disorder(115;0.0122) CTTCATCTAATTTTTTTAGCA 0.448 0.42 227 164 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 2313287_STOMACH NA 2313287_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 53 459 MCM3AP 8888 broad.mit.edu 37 21 47663397 47663397 + Frame_Shift_Del DEL G - - 2313287_STOMACH NA 2313287_STOMACH NA g.chr21:47663397delG uc002zir.1 - 24 5314 c.5278delC c.(5278-5280)CGGfs p.R1760fs MCM3APAS_uc002zim.2_Intron|MCM3APAS_uc002zin.2_Intron|MCM3AP_uc002zio.1_Frame_Shift_Del_p.R255fs|MCM3AP_uc002zip.1_Frame_Shift_Del_p.R501fs|MCM3AP_uc002ziq.1_Frame_Shift_Del_p.R687fs|MCM3APAS_uc002zis.1_Intron NM_003906 NP_003897 O60318 MCM3A_HUMAN minichromosome maintenance complex component 3 1760 DNA replication|protein import into nucleus cytosol|nucleus DNA binding|nucleotide binding large_intestine(2)|lung(1)|ovary(1)|skin(1) 5 Breast(49;0.112) ACAGGAAGCCGGGGGGGCGTC 0.527 0.44 48 37 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 2313287_STOMACH NA 2313287_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 77 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.39 25 16 SDHB 6390 broad.mit.edu 37 1 17345435 17345435 + Frame_Shift_Del DEL C - - 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr1:17345435delC uc001bae.2 - 8 935 c.784delG c.(784-786)GCTfs p.A262fs NM_003000 NP_002991 P21912 DHSB_HUMAN succinate dehydrogenase complex, subunit B, iron 262 respiratory electron transport chain|transport|tricarboxylic acid cycle mitochondrial respiratory chain complex II 2 iron, 2 sulfur cluster binding|3 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|protein binding|succinate dehydrogenase (ubiquinone) activity|ubiquinone binding breast(1) 1 Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0049)|COAD - Colon adenocarcinoma(227;1.18e-05)|BRCA - Breast invasive adenocarcinoma(304;2.41e-05)|Kidney(64;0.000188)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19) Succinic acid(DB00139) TCTGCAATAGCTTTCCCTGGA 0.373 0.45 51 41 YSK4 80122 broad.mit.edu 37 2 135743731 135743734 + Frame_Shift_Del DEL GTAA - - 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr2:135743731_135743734delGTAA uc002tue.1 - 7 2739_2742 c.2708_2711delTTAC c.(2707-2712)CTTACAfs p.L903fs YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Frame_Shift_Del_p.L790fs|YSK4_uc010zbg.1_Intron|YSK4_uc002tuh.3_Frame_Shift_Del_p.L631fs|YSK4_uc002tui.3_Frame_Shift_Del_p.L920fs NM_025052 NP_079328 Q56UN5 YSK4_HUMAN Yeast Sps1/Ste20-related kinase 4 isoform 1 903_904 ATP binding|protein serine/threonine kinase activity stomach(2)|urinary_tract(1)|ovary(1)|breast(1) 5 BRCA - Breast invasive adenocarcinoma(221;0.112) AGAGAAATTTGTAAGTGTTTTAGA 0.328 0.26 75 26 BMP2K 55589 broad.mit.edu 37 4 79792082 79792083 + In_Frame_Ins INS - CAG CAG rs5859654;rs35071794 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr4:79792082_79792083insCAG uc003hlk.2 + 11 1543_1544 c.1377_1378insCAG c.(1375-1380)insCAG p.486_487insQ BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Ins_p.486_487insQ|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486_487 Gln/His-rich. nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 GTCATCCTCACcagcagcagca 0.262 0.11 59 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 7 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.26 54 19 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.79 16 59 CSF1R 1436 broad.mit.edu 37 5 149433732 149433758 + In_Frame_Del DEL CTGCTGCTGCTGCCGCTGCCACCGCTT - - rs147476583;rs140118369;rs41287092 byFrequency 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr5:149433732_149433758delCTGCTGCTGCTGCCGCTGCCACCGCTT uc003lrl.2 - 21 2988_3014 c.2793_2819delAAGCGGTGGCAGCGGCAGCAGCAGCAG c.(2791-2820)AGAAGCGGTGGCAGCGGCAGCAGCAGCAGT>AGT p.RSGGSGSSS931del CSF1R_uc011dcd.1_In_Frame_Del_p.KRWQRQQQQ493del|CSF1R_uc010jhc.2_RNA|CSF1R_uc003lrm.2_In_Frame_Del_p.RSGGSGSSS931del NM_005211 NP_005202 P07333 CSF1R_HUMAN colony stimulating factor 1 receptor precursor 931_939 Cytoplasmic (Potential). cell proliferation|multicellular organismal development|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane|receptor complex ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity haematopoietic_and_lymphoid_tissue(38)|lung(6)|central_nervous_system(3)|liver(3)|breast(2)|endometrium(1)|ovary(1) 54 KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147) Imatinib(DB00619)|Sunitinib(DB01268) CTCCAGCTCActgctgctgctgccgctgccaccgcttctgctgctgc 0.485 0.11 70 9 BAT3 7917 broad.mit.edu 37 6 31612922 31612923 + Frame_Shift_Ins INS - G G 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr6:31612922_31612923insG uc003nvg.3 - 10 1501_1502 c.1187_1188insC c.(1186-1188)CCAfs p.P396fs BAT3_uc003nvf.3_Frame_Shift_Ins_p.P390fs|BAT3_uc003nvh.3_Frame_Shift_Ins_p.P390fs|BAT3_uc003nvi.3_Frame_Shift_Ins_p.P390fs|BAT3_uc011dnw.1_Frame_Shift_Ins_p.P390fs|BAT3_uc011dnx.1_Frame_Shift_Ins_p.P390fs|BAT3_uc003nvj.1_Frame_Shift_Ins_p.P390fs NM_004639 NP_004630 P46379 BAG6_HUMAN HLA-B associated transcript-3 isoform a 396 Pro-rich.|4 X 29 AA approximate repeats. apoptosis in response to endoplasmic reticulum stress|brain development|cell differentiation|chromatin modification|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|embryo development|internal peptidyl-lysine acetylation|kidney development|lung development|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|protein stabilization|spermatogenesis|synaptonemal complex assembly|tail-anchored membrane protein insertion into ER membrane|transport|ubiquitin-dependent protein catabolic process BAT3 complex|nucleus polyubiquitin binding|proteasome binding|ribosome binding 0 CATTGGGAGTTGGGGGGGGCCG 0.579 0.33 12 6 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.85 2 11 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.91 2 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 130 18 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 50 454 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.33 29 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 32 191 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 5 43 LZTR1 8216 broad.mit.edu 37 22 21346079 21346079 + Frame_Shift_Del DEL C - - 253J_URINARY_TRACT NA 253J_URINARY_TRACT NA g.chr22:21346079delC uc002zto.2 + 9 1057 c.954delC c.(952-954)TTCfs p.F318fs LZTR1_uc002ztn.2_Frame_Shift_Del_p.F277fs|LZTR1_uc011ahy.1_Frame_Shift_Del_p.F299fs|LZTR1_uc010gsr.1_Frame_Shift_Del_p.F189fs NM_006767 NP_006758 Q8N653 LZTR1_HUMAN leucine-zipper-like transcription regulator 1 318 Kelch 5. anatomical structure morphogenesis sequence-specific DNA binding transcription factor activity ovary(2)|lung(2) 4 all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195) ACGTGGACTTCCAGACCTGGG 0.637 0.92 4 45 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 3 36 DENND4B 9909 broad.mit.edu 37 1 153907279 153907281 + In_Frame_Del DEL CTG - - 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr1:153907279_153907281delCTG uc001fdd.1 - 18 3129_3131 c.2728_2730delCAG c.(2728-2730)CAGdel p.Q910del uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) ACACctgctcctgctgctgctgc 0.463 0.16 38 7 PMS1 5378 broad.mit.edu 37 2 190660531 190660535 + Frame_Shift_Del DEL AACGG - - 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr2:190660531_190660535delAACGG uc002urh.3 + 3 698_702 c.169_173delAACGG c.(169-174)AACGGGfs p.N57fs PMS1_uc010zga.1_Frame_Shift_Del_p.N57fs|PMS1_uc010zgb.1_Intron|PMS1_uc002urk.3_Frame_Shift_Del_p.N57fs|PMS1_uc002uri.3_Frame_Shift_Del_p.N57fs|PMS1_uc010zgc.1_Translation_Start_Site|PMS1_uc010zgd.1_Intron|PMS1_uc002urj.2_RNA|PMS1_uc010fry.1_Frame_Shift_Del_p.N57fs|PMS1_uc010frz.2_Frame_Shift_Del_p.N57fs|PMS1_uc010zfz.1_Frame_Shift_Del_p.N57fs NM_000534 NP_000525 P54277 PMS1_HUMAN postmeiotic segregation 1 isoform a 57_58 mismatch repair|reciprocal meiotic recombination MutLalpha complex ATP binding|ATPase activity|mismatched DNA binding ovary(2)|kidney(1)|central_nervous_system(1) 4 OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751) GGTGCGAGATAACGGGGAGGGTATC 0.327 0.48 44 40 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.52 15 16 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.50 12 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.39 111 72 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.45 44 36 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.31 24 11 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.17 228 48 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 60 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.23 774 236 PTEN 5728 broad.mit.edu 37 10 89653865 89653866 + Frame_Shift_Ins INS - G G 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr10:89653865_89653866insG uc001kfb.2 + 3 1194_1195 c.163_164insG c.(163-165)AGGfs p.R55fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 55 Phosphatase tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.?(4)|p.R55fs*1(4)|p.R55_F56ins15(3)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.R55R(1)|p.R55S(1)|p.R55fs*2(1)|p.R55G(1)|p.V54fs*29(1)|p.R55_L70>S(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) TGATGTAGTAAGGTAAGAATGC 0.292 0.90 9 78 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 808 175 RB1 5925 broad.mit.edu 37 13 48941711 48941712 + Frame_Shift_Del DEL AA - - 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr13:48941711_48941712delAA uc001vcb.2 + 10 1187_1188 c.1021_1022delAA c.(1021-1023)AAAfs p.K341fs RB1_uc010act.1_Frame_Shift_Del_p.K42fs NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 341 androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.?(6)|p.D340fs*5(1) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) GGATCATGATAAAACTCTTCAG 0.282 0.95 1 18 MAPK6 5597 broad.mit.edu 37 15 52350860 52350860 + Frame_Shift_Del DEL T - - 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr15:52350860delT uc002abp.2 + 4 1525 c.731delT c.(730-732)ATTfs p.I244fs NM_002748 NP_002739 Q16659 MK06_HUMAN mitogen-activated protein kinase 6 244 Protein kinase. cell cycle ATP binding|MAP kinase activity lung(3)|ovary(1) 4 all cancers(107;0.0028) ATGCAGCTGATTTTAGAATCT 0.358 0.20 156 38 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 7 89 MAST3 23031 broad.mit.edu 37 19 18235444 18235451 + Splice_Site DEL GCCCCTAG - - 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr19:18235444_18235451delGCCCCTAG uc002nhz.3 + 10 859 c.859_splice c.e10-1 p.E287_splice NM_015016 NP_055831 O60307 MAST3_HUMAN microtubule associated serine/threonine kinase ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity large_intestine(2)|ovary(2)|stomach(1) 5 GCCCTCCTGTGCCCCTAGGAGTTTGACC 0.341 0.39 23 15 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.15 73 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 93 528 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 11 119 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 0.000 0.17 360 73 MN1 4330 broad.mit.edu 37 22 28194924 28194925 + In_Frame_Ins INS - TGT TGT 42MGBA_CENTRAL_NERVOUS_SYSTEM NA 42MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr22:28194924_28194925insTGT uc003adj.2 - 1 2562_2563 c.1607_1608insACA c.(1606-1608)CAG>CAACAG p.536_536Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 536 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 0.000 0.14 466 75 SHROOM4 57477 broad.mit.edu 37 X 50350728 50350729 + In_Frame_Ins INS - TCC TCC rs143151534 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chrX:50350728_50350729insTCC uc004dpe.2 - 6 3439_3440 c.3413_3414insGGA c.(3412-3414)GAA>GAGGAA p.1138_1138E>EE SHROOM4_uc004dpd.3_RNA NM_020717 NP_065768 Q9ULL8 SHRM4_HUMAN shroom family member 4 1138 Glu-rich. actin filament organization|brain development|cell morphogenesis|cognition apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus actin filament binding upper_aerodigestive_tract(1) 1 Ovarian(276;0.236) cttcttcttcttcctcctcctc 0.223 0.77 3 10 HEPH 9843 broad.mit.edu 37 X 65393494 65393495 + Frame_Shift_Ins INS - C C 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chrX:65393494_65393495insC uc011moz.1 + 4 545_546 c.485_486insC c.(484-486)GGCfs p.G162fs HEPH_uc004dwn.2_Frame_Shift_Ins_p.G162fs|HEPH_uc004dwo.2_5'UTR|HEPH_uc010nkr.2_Frame_Shift_Ins_p.G162fs|HEPH_uc011mpa.1_Frame_Shift_Ins_p.G162fs NM_138737 NP_620074 Q9BQS7 HEPH_HUMAN hephaestin isoform a 159 Extracellular (Potential).|Plastocyanin-like 1. cellular iron ion homeostasis|copper ion transport|transmembrane transport integral to membrane|plasma membrane copper ion binding|oxidoreductase activity lung(5)|ovary(4) 9 CCCCCGGGGGGCAGCCATATCT 0.535 0.19 225 52 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 5 114 ELF4 2000 broad.mit.edu 37 X 129201226 129201226 + Frame_Shift_Del DEL G - - 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chrX:129201226delG uc004evd.3 - 9 1847 c.1462delC c.(1462-1464)CAAfs p.Q488fs ELF4_uc004eve.3_Frame_Shift_Del_p.Q488fs NM_001421 NP_001412 Q99607 ELF4_HUMAN E74-like factor 4 488 natural killer cell proliferation|NK T cell proliferation|positive regulation of transcription from RNA polymerase II promoter PML body protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity ovary(1) 1 GCCAGAAGTTGGGGGAGGCCA 0.657 0.58 5 7 TTN 7273 broad.mit.edu 37 2 179615116 179615119 + Frame_Shift_Del DEL GAAA - - 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr2:179615116_179615119delGAAA uc002unb.2 - 46 12232_12235 c.12008_12011delTTTC c.(12007-12012)CTTTCAfs p.L4003fs TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron NM_133379 NP_596870 Q8WZ42 TITIN_HUMAN titin isoform novex-3 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) ATGAACAGATGAAAGAGTTAATAT 0.328 0.30 259 109 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.28 34 13 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 287 67 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.14 100 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 208 230 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 59 104 GRK6 2870 broad.mit.edu 37 5 176861029 176861029 + Frame_Shift_Del DEL G - - 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr5:176861029delG uc011dfz.1 + 9 1013 c.853delG c.(853-855)GAAfs p.E285fs GRK6_uc003mgp.2_Frame_Shift_Del_p.E285fs|GRK6_uc003mgq.2_Frame_Shift_Del_p.E285fs|GRK6_uc003mgs.1_Frame_Shift_Del_p.E255fs NM_002082 NP_002073 P43250 GRK6_HUMAN G protein-coupled receptor kinase 6 isoform B 285 Protein kinase. regulation of G-protein coupled receptor protein signaling pathway membrane ATP binding|G-protein coupled receptor kinase activity|signal transducer activity large_intestine(1)|stomach(1)|breast(1) 3 all_cancers(89;1.15e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152) all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) TGGCTTCCCCGAAGCGCGGGC 0.662 0.48 185 169 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.49 122 117 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.22 216 62 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 2 20 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.37 412 242 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.74 9 25 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 5 52 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.17 101 21 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 84 479 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 5637_URINARY_TRACT NA 5637_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 29 450 AR 367 broad.mit.edu 37 X 66941758 66941758 + Frame_Shift_Del DEL C - - 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chrX:66941758delC uc004dwu.1 + 6 3517 c.2402delC c.(2401-2403)ACCfs p.T801fs AR_uc004dwv.1_Frame_Shift_Del_p.T269fs NM_000044 NP_000035 P10275 ANDR_HUMAN androgen receptor isoform 1 800 Ligand-binding.|Interaction with MYST2. cell death|cell growth|cell proliferation|cell-cell signaling|negative regulation of apoptosis|negative regulation of integrin biosynthetic process|positive regulation of cell proliferation|positive regulation of integrin biosynthetic process|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|regulation of establishment of protein localization in plasma membrane|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transport cytoplasm|nuclear chromatin|nucleoplasm androgen binding|androgen receptor activity|beta-catenin binding|enzyme binding|ligand-regulated transcription factor activity|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding ovary(3)|lung(2)|breast(2)|central_nervous_system(1) 8 all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102) all_lung(315;1.3e-11) Bicalutamide(DB01128)|Cyproterone(DB04839)|Dromostanolone(DB00858)|Finasteride(DB01216)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Nandrolone(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Testosterone(DB00624) CTCCAAATCACCCCCCAGGAA 0.527 1.00 0 21 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.74 10 29 MSH6 2956 broad.mit.edu 37 2 48028293 48028293 + Frame_Shift_Del DEL G - - 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr2:48028293delG uc002rwd.3 + 4 3323 c.3171delG c.(3169-3171)TTGfs p.L1057fs MSH6_uc002rwc.2_Frame_Shift_Del_p.L1057fs|MSH6_uc010fbj.2_Frame_Shift_Del_p.L755fs|MSH6_uc010yoi.1_Frame_Shift_Del_p.L927fs|MSH6_uc010yoj.1_Frame_Shift_Del_p.L755fs NM_000179 NP_000170 P52701 MSH6_HUMAN mutS homolog 6 1057 determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes MutSalpha complex ATP binding|DNA-dependent ATPase activity|protein binding large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1) 168 Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) TCGCAGTGTTGGGTAAGACTT 0.398 0.33 42 21 STRADB 55437 broad.mit.edu 37 2 202339422 202339423 + Frame_Shift_Ins INS - AT AT 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr2:202339422_202339423insAT uc002uyd.3 + 6 733_734 c.368_369insAT c.(367-369)TGGfs p.W123fs NM_018571 NP_061041 Q9C0K7 STRAB_HUMAN STE20-related kinase adaptor beta 123 Protein kinase. activation of protein kinase activity|cell cycle arrest|insulin receptor signaling pathway|protein export from nucleus|regulation of fatty acid oxidation cytosol|nucleus ATP binding|protein binding|protein kinase activity skin(2)|stomach(1)|lung(1) 4 ACAACTTATTGGACAGTTTTCA 0.356 0.45 78 63 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 29 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.76 25 78 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.81 5 22 CHD1 1105 broad.mit.edu 37 5 98206408 98206409 + Frame_Shift_Ins INS - T T 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr5:98206408_98206409insT uc003knf.2 - 28 4108_4109 c.3960_3961insA c.(3958-3963)AAAGAAfs p.K1320fs CHD1_uc010jbn.2_Frame_Shift_Ins_p.K46fs NM_001270 NP_001261 O14646 CHD1_HUMAN chromodomain helicase DNA binding protein 1 1320_1321 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117) COAD - Colon adenocarcinoma(37;0.0717) Epirubicin(DB00445) GAAAGAGCTTCTTTTTTTGCAA 0.381 0.48 56 51 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.60 4 6 CDC5L 988 broad.mit.edu 37 6 44360566 44360569 + Splice_Site DEL GTAA - - 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr6:44360566_44360569delGTAA uc003oxl.2 + 3 570 c.311_splice c.e3+1 p.L104_splice NM_001253 NP_001244 Q99459 CDC5L_HUMAN CDC5-like cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus DNA binding|RNA binding lung(3)|ovary(1)|kidney(1)|skin(1) 6 all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208) Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536) AATTTCTTCTGTAAGTGAGTCTTC 0.382 0.36 28 16 PHIP 55023 broad.mit.edu 37 6 79664660 79664662 + In_Frame_Del DEL TCT - - 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr6:79664660_79664662delTCT uc003pir.2 - 35 4148_4150 c.3922_3924delAGA c.(3922-3924)AGAdel p.R1308del PHIP_uc003piq.2_In_Frame_Del_p.R332del|PHIP_uc011dyp.1_In_Frame_Del_p.R1307del|PHIP_uc003pio.3_In_Frame_Del_p.R194del NM_017934 NP_060404 Q8WWQ0 PHIP_HUMAN pleckstrin homology domain interacting protein 1308 insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis nucleus insulin receptor binding large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1) 6 all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219) BRCA - Breast invasive adenocarcinoma(397;0.231) TATTACGTAATCTTCTTCTAGGC 0.315 0.29 44 18 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.88 3 21 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 1 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 296 143 STYK1 55359 broad.mit.edu 37 12 10782198 10782198 + Frame_Shift_Del DEL T - - 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr12:10782198delT uc001qys.2 - 6 1048 c.527delA c.(526-528)AACfs p.N176fs NM_018423 NP_060893 Q6J9G0 STYK1_HUMAN serine/threonine/tyrosine kinase 1 176 Protein kinase. integral to membrane|plasma membrane ATP binding|non-membrane spanning protein tyrosine kinase activity central_nervous_system(3)|ovary(2)|lung(2)|breast(1) 8 CTGCACCAGGTTTTTGTGTTT 0.522 0.14 179 30 GUCY2C 2984 broad.mit.edu 37 12 14796510 14796510 + Frame_Shift_Del DEL T - - 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr12:14796510delT uc001rcd.2 - 17 2065 c.1928delA c.(1927-1929)AAGfs p.K643fs NM_004963 NP_004954 P25092 GUC2C_HUMAN guanylate cyclase 2C precursor 643 Cytoplasmic (Potential).|Protein kinase. intracellular signal transduction|receptor guanylyl cyclase signaling pathway integral to membrane ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity ovary(4)|skin(2) 6 TTACAGACCCTTTTTTGGAGG 0.388 0.30 80 34 APAF1 317 broad.mit.edu 37 12 99056326 99056327 + Frame_Shift_Del DEL GT - - 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr12:99056326_99056327delGT uc001tfz.2 + 6 1380_1381 c.803_804delGT c.(802-804)AGTfs p.S268fs APAF1_uc001tfy.2_Frame_Shift_Del_p.S257fs|APAF1_uc001tga.2_Frame_Shift_Del_p.S257fs|APAF1_uc001tgb.2_Frame_Shift_Del_p.S268fs|APAF1_uc001tgc.2_Frame_Shift_Del_p.S268fs NM_181861 NP_863651 O14727 APAF_HUMAN apoptotic peptidase activating factor 1 isoform 268 NB-ARC. activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development cytosol|Golgi apparatus|nucleus ATP binding|caspase activator activity|protein binding ovary(2)|lung(1) 3 Adenosine triphosphate(DB00171) AGAGACAAGAGTGTTACAGATT 0.317 0.34 72 37 C15orf2 23742 broad.mit.edu 37 15 24921926 24921927 + Frame_Shift_Ins INS - GA GA 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr15:24921926_24921927insGA uc001ywo.2 + 1 1386_1387 c.912_913insGA c.(910-915)GATGAGfs p.D304fs NM_018958 NP_061831 Q9NZP6 CO002_HUMAN hypothetical protein LOC23742 304_305 Pro-rich. cell differentiation|multicellular organismal development|spermatogenesis ovary(2)|large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1) 8 all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086) all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229) GGATGCCTGATGAGAAGCCTTT 0.574 0.33 76 37 EIF2AK4 440275 broad.mit.edu 37 15 40282507 40282508 + Frame_Shift_Ins INS - T T rs35250897 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr15:40282507_40282508insT uc001zkm.1 + 16 2610_2611 c.2560_2561insT c.(2560-2562)ATTfs p.I854fs EIF2AK4_uc010bbj.1_Frame_Shift_Ins_p.I555fs|EIF2AK4_uc001zkn.1_5'Flank NM_001013703 NP_001013725 Q9P2K8 E2AK4_HUMAN eukaryotic translation initiation factor 2 alpha 854 Protein kinase 2. translation cytosolic ribosome aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity lung(2)|stomach(1)|skin(1) 4 all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119) GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616) GCCTGTCAACATTTTTTTGGAT 0.356 0.37 69 41 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.13 55 8 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 87 1002 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.18 75 17 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.29 42 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 285 918 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 639V_URINARY_TRACT NA 639V_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 5 47 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 5 39 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.58 15 21 TPRXL 348825 broad.mit.edu 37 3 14106310 14106311 + In_Frame_Ins INS - CCAGCACCAGCAGTC CCAGCACCAGCAGTC 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr3:14106310_14106311insCCAGCACCAGCAGTC uc011avd.1 + 3 1089_1090 c.634_635insCCAGCACCAGCAGTC c.(634-636)TCC>TCCAGCACCAGCAGTCCC p.217_218insSTSSP TPRXL_uc003byh.1_In_Frame_Ins_p.217_218insSTSSP|TPRXL_uc003byg.2_In_Frame_Ins_p.217_218insSTSSP NR_002223 RecName: Full=Putative protein TPRXL; 0 cagcagcagctccagcaccagc 0.213 0.35 15 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 103 148 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 11 32 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.63 34 58 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.80 2 8 NUP153 9972 broad.mit.edu 37 6 17633077 17633078 + Splice_Site INS - AA AA rs36027788;rs147103527 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr6:17633077_17633078insAA uc003ncd.1 - 17 2665 c.2465_splice c.e17-1 p.G822_splice NUP153_uc011dje.1_Splice_Site_p.G853_splice|NUP153_uc010jpl.1_Splice_Site_p.G780_splice NM_005124 NP_005115 P49790 NU153_HUMAN nucleoporin 153kDa carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm DNA binding|protein binding|transporter activity|zinc ion binding lung(4)|ovary(2)|breast(2)|skin(1) 9 Breast(50;0.0259)|Ovarian(93;0.0584) all_hematologic(90;0.125) all cancers(50;0.0981)|Epithelial(50;0.112) CTGAACTTCCTAAAAAAAAAAA 0.406 0.16 43 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 1 10 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.88 7 52 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 54 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.55 99 119 CSPG4 1464 broad.mit.edu 37 15 75968009 75968026 + In_Frame_Del DEL ATGGCCTGGCCTGGCTCC - - 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr15:75968009_75968026delATGGCCTGGCCTGGCTCC uc002baw.2 - 10 6927_6944 c.6834_6851delGGAGCCAGGCCAGGCCAT c.(6832-6852)GTGGAGCCAGGCCAGGCCATC>GTC p.EPGQAI2279del NM_001897 NP_001888 Q6UVK1 CSPG4_HUMAN chondroitin sulfate proteoglycan 4 precursor 2279_2284 Cytoplasmic (Potential). angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane protein kinase binding|signal transducer activity ovary(2)|pancreas(1) 3 TGTGAGCGGGATGGCCTGGCCTGGCTCCACCTTGCGAA 0.647 0.12 510 67 CDH3 1001 broad.mit.edu 37 16 68679613 68679614 + Frame_Shift_Ins INS - A A 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr16:68679613_68679614insA uc002ewf.2 + 2 1252_1253 c.120_121insA c.(118-123)GCGGGAfs p.A40fs CDH3_uc010vli.1_Intron NM_001793 NP_001784 P22223 CADH3_HUMAN cadherin 3, type 1 preproprotein 40_41 adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception integral to membrane calcium ion binding p.?(1) ovary(3)|breast(1)|skin(1) 5 Ovarian(137;0.0564) OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384) 0.000 1.00 0 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.69 66 149 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.28 52 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.61 194 300 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 647V_URINARY_TRACT NA 647V_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 9 75 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.04 -1 28 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.19 164 38 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 10 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 107 434 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 3 47 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.15 96 17 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 769P_KIDNEY NA 769P_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 31 DUSP7 1849 broad.mit.edu 37 3 52088062 52088062 + Frame_Shift_Del DEL G - - 769P_KIDNEY NA 769P_KIDNEY NA g.chr3:52088062delG uc003dct.2 - 2 925 c.846delC c.(844-846)CCCfs p.P282fs DUSP7_uc010hma.2_Frame_Shift_Del_p.P282fs NM_001947 NP_001938 Q16829 DUS7_HUMAN dual specificity phosphatase 7 282 inactivation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm MAP kinase tyrosine/serine/threonine phosphatase activity|protein binding|protein tyrosine phosphatase activity ovary(1) 1 BRCA - Breast invasive adenocarcinoma(193;5.14e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716) CGAAGGCGTTGGGTAGGTTGG 0.577 0.82 2 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 769P_KIDNEY NA 769P_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.34 58 30 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 769P_KIDNEY NA 769P_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 33 20 WRN 7486 broad.mit.edu 37 8 30925776 30925777 + Frame_Shift_Ins INS - G G 769P_KIDNEY NA 769P_KIDNEY NA g.chr8:30925776_30925777insG uc003xio.3 + 7 1445_1446 c.657_658insG c.(655-660)GCTGGTfs p.A219fs NM_000553 NP_000544 Q14191 WRN_HUMAN Werner syndrome protein 219_220 Interaction with WRNIP1 (By similarity).|3'-5' exonuclease. base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance centrosome|nucleolus|nucleoplasm 3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1) 7 Breast(100;0.195) KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192) TTTTATAGGCTGGTTTTATTAT 0.277 0.23 58 17 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 769P_KIDNEY NA 769P_KIDNEY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.37 58 34 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 769P_KIDNEY NA 769P_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 10 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency 769P_KIDNEY NA 769P_KIDNEY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.41 561 392 NUMA1 4926 broad.mit.edu 37 11 71724001 71724015 + In_Frame_Del DEL CTTGGCACCCTCATA - - 769P_KIDNEY NA 769P_KIDNEY NA g.chr11:71724001_71724015delCTTGGCACCCTCATA uc001orl.1 - 15 4706_4720 c.4534_4548delTATGAGGGTGCCAAG c.(4534-4548)TATGAGGGTGCCAAGdel p.YEGAK1512del NUMA1_uc009ysw.1_In_Frame_Del_p.YEGAK1075del|NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_In_Frame_Del_p.YEGAK1512del|NUMA1_uc001orn.2_In_Frame_Del_p.YEGAK1075del|NUMA1_uc009ysx.1_In_Frame_Del_p.YEGAK1512del|NUMA1_uc001oro.1_In_Frame_Del_p.YEGAK1512del NM_006185 NP_006176 Q14980 NUMA1_HUMAN nuclear mitotic apparatus protein 1 1512_1516 Potential. G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole protein binding|structural molecule activity ovary(3)|lung(2)|skin(2)|central_nervous_system(1) 8 GGACCTTGACCTTGGCACCCTCATACTTGGCAGTC 0.595 0.31 100 44 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 769P_KIDNEY NA 769P_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 60 16 FANCM 57697 broad.mit.edu 37 14 45646019 45646019 + Frame_Shift_Del DEL A - - 769P_KIDNEY NA 769P_KIDNEY NA g.chr14:45646019delA uc001wwd.3 + 14 4161 c.4062delA c.(4060-4062)AGAfs p.R1354fs FANCM_uc010anf.2_Frame_Shift_Del_p.R1328fs|FANCM_uc001wwe.3_Frame_Shift_Del_p.R890fs|FANCM_uc010ang.2_Frame_Shift_Del_p.R568fs NM_020937 NP_065988 Q8IYD8 FANCM_HUMAN Fanconi anemia, complementation group M 1354 DNA repair Fanconi anaemia nuclear complex ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding ovary(3)|lung(2)|breast(2) 7 CTAAGATAAGAAAGGAAATAC 0.303 0.94 4 66 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C 769P_KIDNEY NA 769P_KIDNEY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 8 92 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 769P_KIDNEY NA 769P_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.27 41 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 769P_KIDNEY NA 769P_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 119 388 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 769P_KIDNEY NA 769P_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 44 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes 769P_KIDNEY NA 769P_KIDNEY NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.24 51 16 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 786O_KIDNEY NA 786O_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.99 1 110 CYP1B1 1545 broad.mit.edu 37 2 38298287 38298288 + Frame_Shift_Ins INS - GGTGGCATGA GGTGGCATGA rs72466463;rs72549377 786O_KIDNEY NA 786O_KIDNEY NA g.chr2:38298287_38298288insGGTGGCATGA uc002rqo.2 - 4 1612_1613 c.1209_1210insTCATGCCACC c.(1207-1212)ACCACTfs p.T403fs NM_000104 NP_000095 Q16678 CP1B1_HUMAN cytochrome P450, family 1, subfamily B, 403_404 visual perception|xenobiotic metabolic process endoplasmic reticulum membrane|microsome aromatase activity|electron carrier activity|heme binding|oxygen binding|protein binding ovary(1)|central_nervous_system(1) 2 all_hematologic(82;0.21) Estrone(DB00655) GTGTTGGCAGTGGTGGCATGAG 0.530 0.16 158 31 VHL 7428 broad.mit.edu 37 3 10183841 10183841 + Frame_Shift_Del DEL G - - 786O_KIDNEY NA 786O_KIDNEY NA g.chr3:10183841delG uc003bvc.2 + 1 523 c.310delG c.(310-312)GGCfs p.G104fs VHL_uc003bvd.2_Frame_Shift_Del_p.G104fs NM_000551 NP_000542 P40337 VHL_HUMAN von Hippel-Lindau tumor suppressor isoform 1 104 Involved in binding to CCT complex. G -> A (in cerebellar hemangioblastoma). anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus protein binding|transcription factor binding p.G104fs*55(6)|p.G104fs*23(2)|p.P103fs*27(1)|p.G104fs*22(1)|p.P102fs*27(1)|p.T100_G106>S(1)|p.Y98fs*27(1) kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1) 1346 Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569) 0.000 0.89 80 659 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 786O_KIDNEY NA 786O_KIDNEY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.50 69 69 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 786O_KIDNEY NA 786O_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 189 233 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 786O_KIDNEY NA 786O_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 21 56 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 786O_KIDNEY NA 786O_KIDNEY NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.21 46 12 AKAP9 10142 broad.mit.edu 37 7 91631094 91631095 + Frame_Shift_Del DEL AT - - 786O_KIDNEY NA 786O_KIDNEY NA g.chr7:91631094_91631095delAT uc003ulg.2 + 8 2088_2089 c.1863_1864delAT c.(1861-1866)GAATTAfs p.E621fs AKAP9_uc003ule.2_Frame_Shift_Del_p.E633fs|AKAP9_uc003ulf.2_Frame_Shift_Del_p.E621fs|AKAP9_uc003uli.2_Frame_Shift_Del_p.E246fs NM_005751 NP_005742 Q99996 AKAP9_HUMAN A-kinase anchor protein 9 isoform 2 633_634 Glu-rich.|Potential. G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport centrosome|cytosol|Golgi apparatus receptor binding breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1) 26 all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) AAGAAGCTGAATTAGAGAGGCT 0.327 0.53 126 140 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes 786O_KIDNEY NA 786O_KIDNEY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 26 PAXIP1 22976 broad.mit.edu 37 7 154760644 154760644 + Frame_Shift_Del DEL G - - 786O_KIDNEY NA 786O_KIDNEY NA g.chr7:154760644delG uc003wlp.2 - 7 1310 c.1267delC c.(1267-1269)CAGfs p.Q423fs PAXIP1_uc003wlq.1_Frame_Shift_Del_p.Q389fs|PAXIP1_uc011kvs.1_Frame_Shift_Del_p.Q387fs|PAXIP1_uc003wlr.1_Frame_Shift_Del_p.Q332fs NM_007349 NP_031375 Q6ZW49 PAXI1_HUMAN PAX interacting protein 1 423 Gln-rich. DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent histone methyltransferase complex|nuclear matrix lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_neural(206;0.119) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.0296) UCEC - Uterine corpus endometrioid carcinoma (81;0.178) TGCATTATCTGCTGGGGCTGA 0.318 0.80 57 226 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 786O_KIDNEY NA 786O_KIDNEY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.23 263 80 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 786O_KIDNEY NA 786O_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 56 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 786O_KIDNEY NA 786O_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 321 78 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes 786O_KIDNEY NA 786O_KIDNEY NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.33 196 96 IRS2 8660 broad.mit.edu 37 13 110436296 110436297 + In_Frame_Ins INS - CGG CGG rs34412495 786O_KIDNEY NA 786O_KIDNEY NA g.chr13:110436296_110436297insCGG uc001vqv.2 - 1 2618_2619 c.2104_2105insCCG c.(2104-2106)GTG>GCCGTG p.701_702insA NM_003749 NP_003740 Q9Y4H2 IRS2_HUMAN insulin receptor substrate 2 701_702 fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus cytosol|plasma membrane insulin receptor binding|signal transducer activity large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|skin(1)|ovary(1)|kidney(1) 8 all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155) Breast(118;0.159) all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147) 0.000 0.41 557 385 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - 786O_KIDNEY NA 786O_KIDNEY NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 0.83 4 19 ATP8B1 5205 broad.mit.edu 37 18 55365040 55365040 + Frame_Shift_Del DEL T - - 786O_KIDNEY NA 786O_KIDNEY NA g.chr18:55365040delT uc002lgw.2 - 6 614 c.614delA c.(613-615)AATfs p.N205fs uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 205 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) 0.000 0.12 51 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 786O_KIDNEY NA 786O_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.67 193 387 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 786O_KIDNEY NA 786O_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 22 413 SHROOM4 57477 broad.mit.edu 37 X 50350728 50350729 + In_Frame_Ins INS - TCC TCC rs143151534 8305C_THYROID NA 8305C_THYROID NA g.chrX:50350728_50350729insTCC uc004dpe.2 - 6 3439_3440 c.3413_3414insGGA c.(3412-3414)GAA>GAGGAA p.1138_1138E>EE SHROOM4_uc004dpd.3_RNA NM_020717 NP_065768 Q9ULL8 SHRM4_HUMAN shroom family member 4 1138 Glu-rich. actin filament organization|brain development|cell morphogenesis|cognition apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus actin filament binding upper_aerodigestive_tract(1) 1 Ovarian(276;0.236) cttcttcttcttcctcctcctc 0.223 0.50 6 6 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 8305C_THYROID NA 8305C_THYROID NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 3 44 UBXN11 91544 broad.mit.edu 37 1 26608874 26608885 + In_Frame_Del DEL GGGGCCGGGACC - - rs140364749;rs1134581;rs1134580 by1000genomes 8305C_THYROID NA 8305C_THYROID NA g.chr1:26608874_26608885delGGGGCCGGGACC uc001blw.2 - 16 1741_1752 c.1468_1479delGGTCCCGGCCCC c.(1468-1479)GGTCCCGGCCCCdel p.GPGP490del UBXN11_uc001blz.1_In_Frame_Del_p.GPGP457del|UBXN11_uc001blv.2_In_Frame_Del_p.GPGP452del|UBXN11_uc001bly.2_In_Frame_Del_p.GPGP370del|UBXN11_uc001blx.2_In_Frame_Del_p.GPGP248del|UBXN11_uc001bma.2_In_Frame_Del_p.GPGP457del|UBXN11_uc001bmb.1_In_Frame_Del_p.GPGP490del NM_183008 NP_892120 Q5T124 UBX11_HUMAN socius isoform 2 490_493 Pro-rich.|3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|1. Missing.|Missing. cytoplasm|cytoskeleton ovary(1) 1 gaccgggactggggccgggaccgggaccggga 0.292 0.56 14 18 PDE4DIP 9659 broad.mit.edu 37 1 144918891 144918892 + Frame_Shift_Del DEL TG - - rs148279833 8305C_THYROID NA 8305C_THYROID NA g.chr1:144918891_144918892delTG uc001elw.3 - 10 1585_1586 c.1294_1295delCA c.(1294-1296)CAGfs p.Q432fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.Q498fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.Q432fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.Q432fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.Q595fs|PDE4DIP_uc001eme.1_5'UTR|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.Q219fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 432 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) GTTTTGTTCCTGGGTTCGAATC 0.441 0.34 214 111 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - 8305C_THYROID NA 8305C_THYROID NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.15 296 52 MUC1 4582 broad.mit.edu 37 1 155162068 155162069 + Frame_Shift_Ins INS - T T rs139437006 8305C_THYROID NA 8305C_THYROID NA g.chr1:155162068_155162069insT uc010pft.1 - 2 130_131 c.64_65insA c.(64-66)ACGfs p.T22fs RAG1AP1_uc010pey.1_Intron|MUC1_uc001fhy.2_5'Flank|MUC1_uc001fhz.2_5'Flank|MUC1_uc010pfb.1_5'UTR|MUC1_uc010pfc.1_RNA|MUC1_uc009wph.2_5'UTR|MUC1_uc010pfd.1_5'UTR|MUC1_uc010pfe.1_RNA|MUC1_uc010pff.1_Frame_Shift_Ins_p.L70fs|MUC1_uc009wpi.2_5'UTR|MUC1_uc010pfg.1_RNA|MUC1_uc010pfh.1_Frame_Shift_Ins_p.L70fs|MUC1_uc010pfi.1_Frame_Shift_Ins_p.L70fs|MUC1_uc010pfj.1_Frame_Shift_Ins_p.L70fs|MUC1_uc010pfk.1_RNA|MUC1_uc010pfl.1_RNA|MUC1_uc001fin.2_Frame_Shift_Ins_p.T31fs|MUC1_uc009wpk.2_Intron|MUC1_uc001fip.2_5'UTR|MUC1_uc009wqg.2_5'UTR|MUC1_uc009wpo.2_Intron|MUC1_uc009wps.2_Frame_Shift_Ins_p.T31fs|MUC1_uc009wpt.2_Frame_Shift_Ins_p.T31fs|MUC1_uc001fic.2_Frame_Shift_Ins_p.T22fs|MUC1_uc009wpu.2_RNA|MUC1_uc009wpq.2_Intron|MUC1_uc009wpv.2_5'UTR|MUC1_uc001fim.2_Frame_Shift_Ins_p.T22fs|MUC1_uc001fib.2_5'UTR|MUC1_uc009wpw.2_Frame_Shift_Ins_p.T31fs|MUC1_uc001fie.2_Frame_Shift_Ins_p.T22fs|MUC1_uc009wpr.2_Intron|MUC1_uc001fig.2_Frame_Shift_Ins_p.T31fs|MUC1_uc001fif.2_Frame_Shift_Ins_p.T22fs|MUC1_uc009wpx.2_Frame_Shift_Ins_p.T31fs|MUC1_uc001fid.2_Frame_Shift_Ins_p.T22fs|MUC1_uc009wpj.2_RNA|MUC1_uc001fij.2_Frame_Shift_Ins_p.T31fs|MUC1_uc009wpy.2_RNA|MUC1_uc010pfm.1_5'UTR|MUC1_uc001fiq.2_5'UTR|MUC1_uc009wpz.2_Frame_Shift_Ins_p.T31fs|MUC1_uc010pfn.1_Frame_Shift_Ins_p.T22fs|MUC1_uc009wqa.2_5'UTR|MUC1_uc010pfo.1_5'UTR|MUC1_uc010pfp.1_5'UTR|MUC1_uc001fii.2_RNA|MUC1_uc001fih.2_RNA|MUC1_uc001fia.2_Frame_Shift_Ins_p.T22fs|MUC1_uc009wqc.2_5'UTR|MUC1_uc009wqd.2_5'UTR|MUC1_uc009wqb.2_5'UTR|MUC1_uc010pfq.1_5'UTR|MUC1_uc010pfr.1_Frame_Shift_Ins_p.T31fs|MUC1_uc001fit.2_5'UTR|MUC1_uc009wqe.2_Frame_Shift_Ins_p.T31fs|MUC1_uc001fil.2_Frame_Shift_Ins_p.T22fs|MUC1_uc009wpm.2_Frame_Shift_Ins_p.T22fs|MUC1_uc009wpp.2_Frame_Shift_Ins_p.T22fs|MUC1_uc010pfs.1_RNA|MUC1_uc001fik.2_Frame_Shift_Ins_p.T22fs|MUC1_uc001fio.2_Frame_Shift_Ins_p.T22fs|MUC1_uc009wqf.2_5'UTR|MUC1_uc009wpl.2_Frame_Shift_Ins_p.T31fs|MUC1_uc009wpn.2_Frame_Shift_Ins_p.T31fs|MUC1_uc001fis.1_Frame_Shift_Ins_p.T22fs|uc009wqh.2_5'Flank|MUC1_uc001fiv.1_Frame_Shift_Ins_p.T31fs|MUC1_uc001fiw.1_Frame_Shift_Ins_p.T22fs|MIR92B_hsa-mir-92b|MI0003560_5'Flank P15941 MUC1_HUMAN SubName: Full=MUC1 isoform M13; 22 apical plasma membrane|cell surface|cytoplasm|extracellular region|integral to plasma membrane|nucleus protein binding large_intestine(1)|pancreas(1)|breast(1)|skin(1) 4 all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) ACCAGAACCCGTAACAACTGTT 0.455 0.32 17 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 8305C_THYROID NA 8305C_THYROID NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.31 96 43 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 8305C_THYROID NA 8305C_THYROID NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.39 36 23 MET 4233 broad.mit.edu 37 7 116371717 116371741 + Splice_Site DEL TCCAGACACTTCTGAGAAATTCATC - - rs45441497;rs67495248 8305C_THYROID NA 8305C_THYROID NA g.chr7:116371717_116371741delTCCAGACACTTCTGAGAAATTCATC uc003vij.2 + 3 1388 c.1201_splice c.e3-1 p.T401_splice MET_uc010lkh.2_Splice_Site_p.T401_splice|MET_uc011knc.1_Splice_Site_p.T401_splice|MET_uc011knd.1_Splice_Site_p.T401_splice|MET_uc011kne.1_Splice_Site_p.T401_splice|MET_uc011knf.1_Splice_Site_p.T401_splice|MET_uc011kng.1_Splice_Site_p.T401_splice|MET_uc011knh.1_Splice_Site_p.T401_splice|MET_uc011kni.1_Splice_Site_p.T401_splice|MET_uc011knj.1_Splice_Site|MET_uc010lkg.2_Splice_Site_p.T401_splice|MET_uc011kna.1_Splice_Site_p.T401_splice|MET_uc011knb.1_Splice_Site_p.T401_splice NM_000245 NP_000236 P08581 MET_HUMAN met proto-oncogene isoform b precursor axon guidance|cell proliferation basal plasma membrane|integral to plasma membrane ATP binding|hepatocyte growth factor receptor activity|protein binding upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1) 159 all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125) Ovarian(593;0.133) GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512) CATATTTTATTCCAGACACTTCTGAGAAATTCATCAGGCTGTGAA 0.333 0.25 41 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 8305C_THYROID NA 8305C_THYROID NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 8305C_THYROID NA 8305C_THYROID NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 213 59 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C 8305C_THYROID NA 8305C_THYROID NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 20 132 MPRIP 23164 broad.mit.edu 37 17 17039562 17039567 + In_Frame_Del DEL CAGCAG - - rs148686165;rs113250356 8305C_THYROID NA 8305C_THYROID NA g.chr17:17039562_17039567delCAGCAG uc002gqu.1 + 6 590_595 c.534_539delCAGCAG c.(532-540)ACCAGCAGC>ACC p.SS187del MPRIP_uc002gqv.1_In_Frame_Del_p.SS187del|MPRIP_uc002gqw.1_5'UTR NM_201274 NP_958431 Q6WCQ1 MPRIP_HUMAN myosin phosphatase-Rho interacting protein 187_188 Ser-rich.|Interaction with F-actin (By similarity). Missing (in Ref. 2; BAD89507 and 6; AAH09982). cytoplasm|cytoskeleton actin binding 0 TGGCTGTTACcagcagcagcagcagc 0.490 0.40 6 4 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 8305C_THYROID NA 8305C_THYROID NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.34 63 33 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes 8305C_THYROID NA 8305C_THYROID NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.36 7 4 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 8305C_THYROID NA 8305C_THYROID NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.18 110 24 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 8305C_THYROID NA 8305C_THYROID NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 115 388 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 8305C_THYROID NA 8305C_THYROID NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 112 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - 8505C_THYROID NA 8505C_THYROID NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.56 89 115 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 8505C_THYROID NA 8505C_THYROID NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.36 14 8 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A 8505C_THYROID NA 8505C_THYROID NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.26 54 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 8505C_THYROID NA 8505C_THYROID NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.49 47 45 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 8505C_THYROID NA 8505C_THYROID NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 26 16 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 8505C_THYROID NA 8505C_THYROID NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.41 191 131 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes 8505C_THYROID NA 8505C_THYROID NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 1 9 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 8505C_THYROID NA 8505C_THYROID NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.42 28 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 8505C_THYROID NA 8505C_THYROID NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency 8505C_THYROID NA 8505C_THYROID NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.63 211 355 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 8505C_THYROID NA 8505C_THYROID NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.70 8 19 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 8505C_THYROID NA 8505C_THYROID NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 344 109 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C 8505C_THYROID NA 8505C_THYROID NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 5 66 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 8505C_THYROID NA 8505C_THYROID NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 94 544 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 8505C_THYROID NA 8505C_THYROID NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.86 5 32 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.55 17 21 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 19 ULK4 54986 broad.mit.edu 37 3 41977368 41977368 + Frame_Shift_Del DEL A - - 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr3:41977368delA uc003ckv.3 - 4 504 c.303delT c.(301-303)TTTfs p.F101fs ULK4_uc003ckw.2_Frame_Shift_Del_p.F101fs|ULK4_uc003ckx.1_Frame_Shift_Del_p.F101fs NM_017886 NP_060356 Q96C45 ULK4_HUMAN unc-51-like kinase 4 101 Protein kinase. ATP binding|protein serine/threonine kinase activity 0 KIRC - Kidney renal clear cell carcinoma(284;0.214) GGTCAATTCCAAATTCTCTCA 0.358 0.90 3 28 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 231 55 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.43 21 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.38 96 60 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.30 101 43 APC 324 broad.mit.edu 37 5 112177642 112177643 + In_Frame_Ins INS - GCT GCT 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr5:112177642_112177643insGCT uc010jby.2 + 16 6731_6732 c.6351_6352insGCT c.(6349-6354)insGCT p.2122_2123insA APC_uc011cvt.1_In_Frame_Ins_p.2104_2105insA|APC_uc003kpz.3_In_Frame_Ins_p.2122_2123insA|APC_uc003kpy.3_In_Frame_Ins_p.2122_2123insA|APC_uc010jbz.2_In_Frame_Ins_p.1839_1840insA|APC_uc010jca.2_In_Frame_Ins_p.1422_1423insA NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 2122_2123 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.A2122_C2123insA(1)|p.?(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GTTTACATCAAGCTGCTGCTGC 0.406 0.33 150 74 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 1 9 SGK223 157285 broad.mit.edu 37 8 8197043 8197043 + Frame_Shift_Del DEL G - - rs56187292 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr8:8197043delG uc003wsh.3 - 3 2265 c.2265delC c.(2263-2265)ACCfs p.T755fs NM_001080826 NP_001074295 Q86YV5 SG223_HUMAN pragmin 755 ATP binding|non-membrane spanning protein tyrosine kinase activity p.T757T(1)|p.T755T(1) 0 CCGTGGAGCCGGTGGTGAAGC 0.532 1.00 0 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 93 21 SIK2 23235 broad.mit.edu 37 11 111571666 111571667 + Frame_Shift_Ins INS - G G 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr11:111571666_111571667insG uc001plt.2 + 5 653_654 c.535_536insG c.(535-537)AGCfs p.S179fs NM_015191 NP_056006 Q9H0K1 SIK2_HUMAN SNF1-like kinase 2 179 Protein kinase. intracellular protein kinase cascade|regulation of insulin receptor signaling pathway Golgi apparatus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|skin(1) 3 ATGGTGTGGCAGCCCCCCTTAT 0.431 0.19 78 18 MAP3K12 7786 broad.mit.edu 37 12 53880801 53880802 + Frame_Shift_Del DEL AA - - 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr12:53880801_53880802delAA uc001sdm.1 - 3 373_374 c.275_276delTT c.(274-276)TTTfs p.F92fs MAP3K12_uc001sdn.1_Frame_Shift_Del_p.F125fs NM_006301 NP_006292 Q12852 M3K12_HUMAN mitogen-activated protein kinase kinase kinase 92 histone phosphorylation|JNK cascade|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation cytosol|membrane fraction|plasma membrane ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding lung(2)|ovary(1)|breast(1)|skin(1) 5 GCAGGCAGCCAAAGAGGCCCTC 0.619 0.29 17 7 ZMYM5 9205 broad.mit.edu 37 13 20425560 20425560 + Frame_Shift_Del DEL G - - 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr13:20425560delG uc010tcn.1 - 4 786 c.521delC c.(520-522)CCTfs p.P174fs ZMYM5_uc001umm.1_5'UTR|ZMYM5_uc001umn.2_Frame_Shift_Del_p.P174fs|ZMYM5_uc001umo.2_Frame_Shift_Del_p.P174fs NM_001142684 NP_001136156 Q9UJ78 ZMYM5_HUMAN zinc finger protein 237 isoform 3 174 nucleus zinc ion binding 0 all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431) CATTCTACCAGGGTTAAAAGG 0.398 0.16 500 96 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 9 25 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.29 192 79 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.65 222 413 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 8MGBA_CENTRAL_NERVOUS_SYSTEM NA 8MGBA_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.99 1 74 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 A101D_SKIN NA A101D_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 47 FMO4 2329 broad.mit.edu 37 1 171301990 171301990 + Frame_Shift_Del DEL A - - A101D_SKIN NA A101D_SKIN NA g.chr1:171301990delA uc001gho.2 + 7 987 c.770delA c.(769-771)GAAfs p.E257fs NM_002022 NP_002013 P31512 FMO4_HUMAN flavin containing monooxygenase 4 257 xenobiotic metabolic process integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding kidney(2)|skin(1) 3 all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181) TGGATTCAAGAAAGGAAGTTG 0.299 0.56 67 87 TTN 7273 broad.mit.edu 37 2 179438935 179438944 + Frame_Shift_Del DEL TTGGCCTTCA - - A101D_SKIN NA A101D_SKIN NA g.chr2:179438935_179438944delTTGGCCTTCA uc010zfg.1 - 275 64435_64444 c.64211_64220delTGAAGGCCAA c.(64210-64221)CTGAAGGCCAACfs p.L21404fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.L15099fs|TTN_uc010zfi.1_Frame_Shift_Del_p.L15032fs|TTN_uc010zfj.1_Frame_Shift_Del_p.L14907fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 22331_22334 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GTTGCTGAAGTTGGCCTTCAGCCACCGTCC 0.433 0.32 79 37 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 A101D_SKIN NA A101D_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 18 13 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A A101D_SKIN NA A101D_SKIN NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 77 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 A101D_SKIN NA A101D_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 47 70 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 A101D_SKIN NA A101D_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 10 23 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes A101D_SKIN NA A101D_SKIN NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.50 5 5 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes A101D_SKIN NA A101D_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.87 3 20 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - A101D_SKIN NA A101D_SKIN NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.69 4 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 A101D_SKIN NA A101D_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039791 + In_Frame_Del DEL CAGCAGCAGCAGCAG - - rs113070757;rs62639301;rs139102413;rs145170448;rs147609454;rs142219087 byFrequency;byFrequency;byFrequency;byFrequency;byFrequency A101D_SKIN NA A101D_SKIN NA g.chr9:2039777_2039791delCAGCAGCAGCAGCAG uc003zhc.2 + 4 766_780 c.667_681delCAGCAGCAGCAGCAG c.(667-681)CAGCAGCAGCAGCAGdel p.QQQQQ233del SMARCA2_uc003zhd.2_In_Frame_Del_p.QQQQQ233del|SMARCA2_uc010mha.2_In_Frame_Del_p.QQQQQ224del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 233_237 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagcagcagcagcagc 0.270 0.46 15 13 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - A101D_SKIN NA A101D_SKIN NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.98 1 61 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 A101D_SKIN NA A101D_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 228 87 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes A101D_SKIN NA A101D_SKIN NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.27 63 23 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 A101D_SKIN NA A101D_SKIN NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.76 8 26 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C A101D_SKIN NA A101D_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 47 337 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 A101D_SKIN NA A101D_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.31 52 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 A101D_SKIN NA A101D_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 199 542 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 A101D_SKIN NA A101D_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 9 211 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.99 1 73 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.30 16 7 IL17RD 54756 broad.mit.edu 37 3 57136602 57136603 + Frame_Shift_Ins INS - C C A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr3:57136602_57136603insC uc003dil.2 - 10 972_973 c.883_884insG c.(883-885)GCCfs p.A295fs IL17RD_uc003dik.2_Frame_Shift_Ins_p.A271fs|IL17RD_uc010hna.2_Frame_Shift_Ins_p.A151fs|IL17RD_uc011bex.1_Frame_Shift_Ins_p.A151fs NM_017563 NP_060033 Q8NFM7 I17RD_HUMAN interleukin 17 receptor D precursor 295 Extracellular (Potential). Golgi membrane|integral to membrane|plasma membrane receptor activity 0 KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204) GATGGGCCCGGCCCACGGGGAG 0.465 0.10 215 23 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 55 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 141 168 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.40 54 36 STK10 6793 broad.mit.edu 37 5 171532685 171532686 + Frame_Shift_Ins INS - G G A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr5:171532685_171532686insG uc003mbo.1 - 7 1144_1145 c.844_845insC c.(844-846)CGAfs p.R282fs NM_005990 NP_005981 O94804 STK10_HUMAN serine/threonine kinase 10 282 Protein kinase. ATP binding|protein serine/threonine kinase activity ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1) 8 Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094) Medulloblastoma(196;0.00868)|all_neural(177;0.026) Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516) GGCACTGGGTCGGGTTTCTGGG 0.589 0.20 37 9 SRPK2 6733 broad.mit.edu 37 7 104758331 104758332 + Frame_Shift_Ins INS - G G A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr7:104758331_104758332insG uc003vct.2 - 15 2207_2208 c.2020_2021insC c.(2020-2022)CGAfs p.R674fs SRPK2_uc003vcu.2_Frame_Shift_Ins_p.R674fs|SRPK2_uc003vcv.2_Frame_Shift_Ins_p.R685fs|uc003vcr.1_5'Flank|SRPK2_uc003vcs.1_RNA NM_182691 NP_872633 P78362 SRPK2_HUMAN serine/arginine-rich protein-specific kinase 2 674 Protein kinase. angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly cytoplasm|nucleolus 14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1) 6 AGCTGAGGCTCGTTTTTCTGGA 0.446 0.12 166 22 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 2 16 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.45 21 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 654 370 Unknown 0 broad.mit.edu 37 14 23574096 23574098 + In_Frame_Del DEL GCA - - A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr14:23574096_23574098delGCA uc010aki.1 - 1 80_82 c.32_34delTGC c.(31-36)CTGCCG>CCG p.L11del Homo sapiens cDNA clone IMAGE:40134016. ACTAGTGgcggcagcagcagcag 0.448 0.33 8 4 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.42 28 20 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 3 45 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 29 137 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.10 131 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 70 484 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 11 150 SMARCB1 6598 broad.mit.edu 37 22 24145522 24145523 + Frame_Shift_Del DEL TC - - A204_SOFT_TISSUE NA A204_SOFT_TISSUE NA g.chr22:24145522_24145523delTC uc002zyb.2 + 5 748_749 c.541_542delTC c.(541-543)TCTfs p.S181fs SMARCB1_uc002zya.2_Frame_Shift_Del_p.S181fs|SMARCB1_uc002zyc.2_Frame_Shift_Del_p.S172fs|SMARCB1_uc002zyd.2_Frame_Shift_Del_p.S190fs|SMARCB1_uc002zye.1_Frame_Shift_Del_p.S107fs|SMARCB1_uc002zyf.1_RNA|SMARCB1_uc010gue.1_RNA NM_003073 NP_003064 Q12824 SNF5_HUMAN SWI/SNF related, matrix associated, actin 181 DNA-binding (Potential). cell cycle|chromatin remodeling|DNA integration|interspecies interaction between organisms|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|retroviral genome replication|transcription, DNA-dependent nBAF complex|npBAF complex|nucleolus|nucleoplasm|SWI/SNF complex p53 binding p.?(5)|p.S181fs*29(1) soft_tissue(193)|central_nervous_system(172)|haematopoietic_and_lymphoid_tissue(23)|meninges(5)|skin(5)|bone(4)|ovary(2)|endometrium(1)|lung(1)|pancreas(1) 407 Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05) TGAGAACGCATCTCAGCCCGAG 0.554 0.94 3 47 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 A2058_SKIN NA A2058_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 3 49 TPRXL 348825 broad.mit.edu 37 3 14105883 14105885 + In_Frame_Del DEL CAG - - rs113575909 A2058_SKIN NA A2058_SKIN NA g.chr3:14105883_14105885delCAG uc011avd.1 + 3 662_664 c.207_209delCAG c.(205-210)CCCAGC>CCC p.S73del TPRXL_uc003byh.1_In_Frame_Del_p.S73del|TPRXL_uc003byg.2_In_Frame_Del_p.S73del NR_002223 RecName: Full=Putative protein TPRXL; 0 gcagcagccccagcagcagcagc 0.000 0.57 6 8 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes A2058_SKIN NA A2058_SKIN NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.23 98 30 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A A2058_SKIN NA A2058_SKIN NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.11 168 20 BMP2K 55589 broad.mit.edu 37 4 79792119 79792136 + In_Frame_Del DEL CAGCAGCAGCAACAGCAA - - A2058_SKIN NA A2058_SKIN NA g.chr4:79792119_79792136delCAGCAGCAGCAACAGCAA uc003hlk.2 + 11 1580_1597 c.1414_1431delCAGCAGCAGCAACAGCAA c.(1414-1431)CAGCAGCAGCAACAGCAAdel p.QQQQQQ478del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQQQQ478del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 478_483 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 acagcaacagcagcagcagcaacagcaacagcagcagc 0.206 0.13 277 43 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 A2058_SKIN NA A2058_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 28 20 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 A2058_SKIN NA A2058_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.71 123 304 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 A2058_SKIN NA A2058_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 29 88 RASA1 5921 broad.mit.edu 37 5 86672845 86672846 + Frame_Shift_Ins INS - TAAG TAAG A2058_SKIN NA A2058_SKIN NA g.chr5:86672845_86672846insTAAG uc003kiw.2 + 17 2450_2451 c.2332_2333insTAAG c.(2332-2334)ATAfs p.I778fs RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_Frame_Shift_Ins_p.I601fs|RASA1_uc011ctv.1_Frame_Shift_Ins_p.I611fs|RASA1_uc011ctw.1_Frame_Shift_Ins_p.I612fs|RASA1_uc010jaw.2_Frame_Shift_Ins_p.I600fs NM_002890 NP_002881 P20936 RASA1_HUMAN RAS p21 protein activator 1 isoform 1 778 Ras-GAP. cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis cytosol|intrinsic to internal side of plasma membrane glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding upper_aerodigestive_tract(3)|ovary(1)|lung(1) 5 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) TGACAGAGAAATAAGCATGGAA 0.376 0.15 187 34 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 A2058_SKIN NA A2058_SKIN NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.16 221 43 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes A2058_SKIN NA A2058_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.97 1 37 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 A2058_SKIN NA A2058_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 46 PIP5K1B 8395 broad.mit.edu 37 9 71491669 71491670 + In_Frame_Ins INS - ATTTCA ATTTCA A2058_SKIN NA A2058_SKIN NA g.chr9:71491669_71491670insATTTCA uc004agu.2 + 6 582_583 c.277_278insATTTCA c.(277-279)TAT>TATTTCAAT p.93_94insFN PIP5K1B_uc011lrq.1_In_Frame_Ins_p.93_94insFN|PIP5K1B_uc004agv.2_RNA NM_003558 NP_003549 O14986 PI51B_HUMAN phosphatidylinositol-4-phosphate 5-kinase, type 93_94 PIPK. endomembrane system|membrane|uropod 1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding stomach(1) 1 Lung(182;0.133) AGCATTCCGATATTTCAGAGAA 0.371 0.10 223 26 PTEN 5728 broad.mit.edu 37 10 89711904 89711938 + Frame_Shift_Del DEL TGTGTATTATTATAGCTACCTGTTAAAGAATCATC - - rs104894184 A2058_SKIN NA A2058_SKIN NA g.chr10:89711904_89711938delTGTGTATTATTATAGCTACCTGTTAAAGAATCATC uc001kfb.2 + 7 1553_1587 c.522_556delTGTGTATTATTATAGCTACCTGTTAAAGAATCATC c.(520-558)TATGTGTATTATTATAGCTACCTGTTAAAGAATCATCTGfs p.Y174fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 174_186 activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.Y177C(4)|p.R55fs*1(4)|p.?(3)|p.N184fs*6(3)|p.G165fs*9(3)|p.V166fs*17(3)|p.Y174D(2)|p.Y176del(2)|p.L182fs*16(2)|p.Y177*(2)|p.Y27_N212>Y(2)|p.L181P(2)|p.Y27fs*1(2)|p.Y180*(1)|p.L182F(1)|p.N184I(1)|p.V175fs*3(1)|p.Y174N(1)|p.V175L(1)|p.K183fs*6(1)|p.K183fs*7(1)|p.S179fs*3(1)|p.S179I(1)|p.Y177fs*2(1)|p.Y177fs*1(1)|p.Y176*(1)|p.Y174fs*5(1)|p.Y178*(1)|p.Y178fs*5(1)|p.G165_*404del(1)|p.Y174*(1)|p.G165_K342del(1)|p.R172fs*5(1)|p.L182*(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) AGAGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCATCTGGATTATAG 0.366 0.10 228 24 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 A2058_SKIN NA A2058_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.45 620 511 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 A2058_SKIN NA A2058_SKIN NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.69 5 11 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes A2058_SKIN NA A2058_SKIN NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.41 92 65 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C A2058_SKIN NA A2058_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 47 427 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 A2058_SKIN NA A2058_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 128 95 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 A2058_SKIN NA A2058_SKIN NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 269 37 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 A2058_SKIN NA A2058_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 157 678 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 A2058_SKIN NA A2058_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.99 2 135 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 A253_SALIVARY_GLAND NA A253_SALIVARY_GLAND NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 3 35 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 A253_SALIVARY_GLAND NA A253_SALIVARY_GLAND NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 35 43 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 A253_SALIVARY_GLAND NA A253_SALIVARY_GLAND NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 21 42 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 A253_SALIVARY_GLAND NA A253_SALIVARY_GLAND NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 28 CDKN2A 1029 broad.mit.edu 37 9 21974766 21974778 + Frame_Shift_Del DEL CCGCGGCCGTGGC - - A253_SALIVARY_GLAND NA A253_SALIVARY_GLAND NA g.chr9:21974766_21974778delCCGCGGCCGTGGC uc003zpk.2 - 1 261_273 c.49_61delGCCACGGCCGCGG c.(49-63)GCCACGGCCGCGGCCfs p.A17fs MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_Frame_Shift_Del_p.A17fs|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Intron NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 17_21 ANK 1. cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.?(23)|p.L16fs*9(3)|p.A20P(3)|p.A19_A20insTA(3)|p.A20A(2)|p.A20T(2)|p.L16_A17insAT(1)|p.R22fs*14(1)|p.S12fs*20(1)|p.A20E(1)|p.S7_A19del(1)|p.S12fs*6(1)|p.A17_T18insTA(1)|p.T18M(1)|p.M9_A20>X(1)|p.A20fs*26(1)|p.A20_A21del(1)|p.A17fs*5(1)|p.A20S(1)|p.A17T(1)|p.A20fs*6(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) 0.000 0.63 162 278 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 A253_SALIVARY_GLAND NA A253_SALIVARY_GLAND NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 150 82 ATP11A 23250 broad.mit.edu 37 13 113487269 113487270 + Frame_Shift_Ins INS - G G A253_SALIVARY_GLAND NA A253_SALIVARY_GLAND NA g.chr13:113487269_113487270insG uc001vsi.3 + 14 1579_1580 c.1491_1492insG c.(1489-1494)GACGGGfs p.D497fs ATP11A_uc001vsj.3_Frame_Shift_Ins_p.D497fs|ATP11A_uc001vsm.1_Frame_Shift_Ins_p.D373fs NM_015205 NP_056020 P98196 AT11A_HUMAN ATPase, class VI, type 11A isoform a 497_498 Cytoplasmic (Potential). ATP biosynthetic process integral to membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity large_intestine(2)|ovary(2) 4 all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163) all_lung(25;0.134)|all_epithelial(44;0.141) AATCGCCGGACGGGGGGAAATC 0.619 0.27 86 32 SERPINA12 145264 broad.mit.edu 37 14 94962859 94962859 + Frame_Shift_Del DEL G - - A253_SALIVARY_GLAND NA A253_SALIVARY_GLAND NA g.chr14:94962859delG uc001ydj.2 - 4 1552 c.756delC c.(754-756)GACfs p.D252fs NM_173850 NP_776249 Q8IW75 SPA12_HUMAN serine (or cysteine) proteinase inhibitor, clade 252 regulation of proteolysis extracellular region serine-type endopeptidase inhibitor activity central_nervous_system(2)|ovary(1)|lung(1) 4 COAD - Colon adenocarcinoma(157;0.235) AGAGCTTATCGTCATAGCCAA 0.438 0.39 92 58 TP53 7157 broad.mit.edu 37 17 7578391 7578391 + Frame_Shift_Del DEL T - - A253_SALIVARY_GLAND NA A253_SALIVARY_GLAND NA g.chr17:7578391delT uc002gim.2 - 5 733 c.539delA c.(538-540)GAGfs p.E180fs TP53_uc002gig.1_Frame_Shift_Del_p.E180fs|TP53_uc002gih.2_Frame_Shift_Del_p.E180fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.E48fs|TP53_uc010cng.1_Frame_Shift_Del_p.E48fs|TP53_uc002gii.1_Frame_Shift_Del_p.E48fs|TP53_uc010cnh.1_Frame_Shift_Del_p.E180fs|TP53_uc010cni.1_Frame_Shift_Del_p.E180fs|TP53_uc002gij.2_Frame_Shift_Del_p.E180fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.E87fs|TP53_uc002gio.2_Frame_Shift_Del_p.E48fs|TP53_uc010vug.1_Frame_Shift_Del_p.E141fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 180 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). E -> Q (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> K (in LFS; germline mutation and in sporadic cancers; somatic mutation).|E -> G (in a sporadic cancer; somatic mutation).|E -> A (in a sporadic cancer; somatic mutation).|E -> V (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.E180*(13)|p.P177_C182delPHHERC(8)|p.0?(7)|p.E180K(5)|p.C176_R181delCPHHER(3)|p.R175_E180delRCPHHE(3)|p.R174fs*24(3)|p.E180D(3)|p.P177fs*3(2)|p.V173fs*59(2)|p.K164_P219del(1)|p.C176fs*65(1)|p.V173fs*23(1)|p.V172_E180delVVRRCPHHE(1)|p.E180G(1)|p.E180fs*67(1)|p.E180Q(1)|p.R81fs*24(1)|p.E180>DGRCPHQ(1)|p.R174_E180>K(1)|p.P177_E180delPHHE(1)|p.R42fs*24(1)|p.E180_S183del(1)|p.R174fs*3(1)|p.E180fs*6(1)|p.E171fs*61(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) TGAGCAGCGCTCATGGTGGGG 0.632 0.99 1 68 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 A253_SALIVARY_GLAND NA A253_SALIVARY_GLAND NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 12 37 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 A253_SALIVARY_GLAND NA A253_SALIVARY_GLAND NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 54 214 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 A2780_OVARY NA A2780_OVARY NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.24 129 40 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 A2780_OVARY NA A2780_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 3 92 ARID1A 8289 broad.mit.edu 37 1 27105551 27105551 + Frame_Shift_Del DEL G - - A2780_OVARY NA A2780_OVARY NA g.chr1:27105551delG uc001bmv.1 + 20 5535 c.5162delG c.(5161-5163)CGAfs p.R1721fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.R1504fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.R567fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.R49fs|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1721 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.R1721*(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GAATATTTCCGACGATGCCTG 0.443 0.43 120 90 PTCH2 8643 broad.mit.edu 37 1 45293620 45293622 + In_Frame_Del DEL CTC - - A2780_OVARY NA A2780_OVARY NA g.chr1:45293620_45293622delCTC uc010olf.1 - 14 1963_1965 c.1951_1953delGAG c.(1951-1953)GAGdel p.E651del PTCH2_uc010olg.1_In_Frame_Del_p.E349del NM_003738 NP_003729 Q9Y6C5 PTC2_HUMAN patched 2 651 Cytoplasmic (Potential). protein complex assembly|spermatogenesis integral to plasma membrane hedgehog receptor activity lung(6)|breast(6)|central_nervous_system(3)|skin(2)|ovary(1) 18 Acute lymphoblastic leukemia(166;0.155) TCTGCCTTGTCTCCTCCTCCTGG 0.635 0.54 11 13 IDH1 3417 broad.mit.edu 37 2 209116262 209116263 + Frame_Shift_Ins INS - T T A2780_OVARY NA A2780_OVARY NA g.chr2:209116262_209116263insT uc002vcs.2 - 3 259_260 c.13_14insA c.(13-15)ATCfs p.I5fs IDH1_uc002vct.2_Frame_Shift_Ins_p.I5fs|IDH1_uc002vcu.2_Frame_Shift_Ins_p.I5fs NM_005896 NP_005887 O75874 IDHC_HUMAN isocitrate dehydrogenase 1 (NADP+), soluble 5 2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle cytosol|peroxisomal matrix isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1) 2868 Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136) ACCGCCACTGATTTTTTTGGAC 0.317 0.10 203 23 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A A2780_OVARY NA A2780_OVARY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.15 94 16 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 A2780_OVARY NA A2780_OVARY NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.26 115 40 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 A2780_OVARY NA A2780_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.34 33 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 A2780_OVARY NA A2780_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.51 124 128 NIPBL 25836 broad.mit.edu 37 5 37059231 37059233 + In_Frame_Del DEL AAC - - A2780_OVARY NA A2780_OVARY NA g.chr5:37059231_37059233delAAC uc003jkl.3 + 44 8148_8150 c.7649_7651delAAC c.(7648-7653)AAACAA>AAA p.Q2551del NIPBL_uc003jkk.3_In_Frame_Del_p.Q2551del|NIPBL_uc003jkn.2_In_Frame_Del_p.Q244del NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 2551 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) CTCATGTTAAAACAACATTTGAA 0.300 0.38 112 69 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 A2780_OVARY NA A2780_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.51 59 62 PIP5K1P1 206426 broad.mit.edu 37 6 7988220 7988221 + In_Frame_Ins INS - AAC AAC A2780_OVARY NA A2780_OVARY NA g.chr6:7988220_7988221insAAC uc003mxx.3 + 1 1886_1887 c.1451_1452insAAC c.(1450-1452)ATA>ATAACA p.484_485insT TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 TCACAAGTGATAAAGGTGCAAG 0.480 0.38 83 50 PIP5K1P1 206426 broad.mit.edu 37 6 7988269 7988275 + Frame_Shift_Del DEL ACCTCAG - - A2780_OVARY NA A2780_OVARY NA g.chr6:7988269_7988275delACCTCAG uc003mxx.3 + 1 1935_1941 c.1500_1506delACCTCAG c.(1498-1506)TTACCTCAGfs p.L500fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CTGATGTTTTACCTCAGACCTCAGAAT 0.454 0.35 71 38 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 A2780_OVARY NA A2780_OVARY NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.13 54 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes A2780_OVARY NA A2780_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 20 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - A2780_OVARY NA A2780_OVARY NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.37 17 10 CSMD3 114788 broad.mit.edu 37 8 113301714 113301715 + Frame_Shift_Ins INS - C C A2780_OVARY NA A2780_OVARY NA g.chr8:113301714_113301715insC uc003ynu.2 - 57 9186_9187 c.9027_9028insG c.(9025-9030)GAGAAGfs p.E3009fs CSMD3_uc003yns.2_Frame_Shift_Ins_p.E2211fs|CSMD3_uc003ynt.2_Frame_Shift_Ins_p.E2969fs|CSMD3_uc011lhx.1_Frame_Shift_Ins_p.E2840fs NM_198123 NP_937756 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 isoform 1 3009_3010 Sushi 21.|Extracellular (Potential). integral to membrane|plasma membrane ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1) 63 AAAGTATACTTCTCGCCAGACA 0.416 0.53 55 63 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 A2780_OVARY NA A2780_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.87 5 34 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency A2780_OVARY NA A2780_OVARY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.69 210 472 PTEN 5728 broad.mit.edu 37 10 89692896 89692904 + In_Frame_Del DEL GAAAGGGAC - - rs121909218;rs121909224 A2780_OVARY NA A2780_OVARY NA g.chr10:89692896_89692904delGAAAGGGAC uc001kfb.2 + 6 1411_1419 c.380_388delGAAAGGGAC c.(379-390)GGAAAGGGACGA>GGA p.KGR128del NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 128_130 Phosphatase tensin-type. R -> L (in CD and endometrial hyperplasia; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes).|R -> Q (in CD; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes).|R -> G (loss of phosphatase activity towards Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3). R->M: Does not affect the ability to inhibit AKT/PKB activation. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R130G(62)|p.R130*(54)|p.G129R(6)|p.K128N(4)|p.R55fs*1(4)|p.K128_R130del(3)|p.G129*(3)|p.G127E(3)|p.Y27_N212>Y(2)|p.?(2)|p.Y27fs*1(2)|p.K128fs*47(1)|p.R130R(1)|p.G127fs*5(1)|p.F56fs*2(1)|p.G129E(1)|p.A121_F145del(1)|p.G127V(1)|p.G129V(1)|p.G129fs*5(1)|p.G129fs*50(1)|p.G129fs*51(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) TGTAAAGCTGGAAAGGGACGAACTGGTGT 0.411 0.72 40 104 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 A2780_OVARY NA A2780_OVARY NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.92 1 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 A2780_OVARY NA A2780_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 617 140 SIK3 23387 broad.mit.edu 37 11 116729338 116729339 + Frame_Shift_Ins INS - G G A2780_OVARY NA A2780_OVARY NA g.chr11:116729338_116729339insG uc001ppy.2 - 20 2560_2561 c.2524_2525insC c.(2524-2526)CGGfs p.R842fs SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron|SIK3_uc001ppw.2_Intron|SIK3_uc001ppx.2_Intron|SIK3_uc001pqb.2_Frame_Shift_Ins_p.R145fs NM_025164 NP_079440 Q9Y2K2 SIK3_HUMAN serine/threonine-protein kinase QSK 842 Gln-rich. cytoplasm ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1) 12 GGGGGAACCCCGGGACTGGTCC 0.569 0.10 205 23 PCSK7 9159 broad.mit.edu 37 11 117077805 117077806 + Frame_Shift_Ins INS - T T A2780_OVARY NA A2780_OVARY NA g.chr11:117077805_117077806insT uc001pqr.2 - 15 2058_2059 c.1857_1858insA c.(1855-1860)GCAGTAfs p.A619fs uc001pqq.1_RNA|PCSK7_uc001pqs.1_Intron NM_004716 NP_004707 Q16549 PCSK7_HUMAN proprotein convertase subtilisin/kexin type 7 619_620 Extracellular (Potential). peptide hormone processing integral to Golgi membrane serine-type endopeptidase activity 0 all_hematologic(175;0.0487) Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234) BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537) CTGATGTCTACTGCACTCCACA 0.604 0.15 44 8 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency A2780_OVARY NA A2780_OVARY NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.30 58 25 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C A2780_OVARY NA A2780_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 31 469 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 A2780_OVARY NA A2780_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.79 24 91 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 A2780_OVARY NA A2780_OVARY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.10 143 16 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 A2780_OVARY NA A2780_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 85 423 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 A2780_OVARY NA A2780_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 4 164 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 A375_SKIN NA A375_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 74 SPEN 23013 broad.mit.edu 37 1 16260674 16260694 + In_Frame_Del DEL CTCACTGGTCTGGTGAGCGCA - - rs141547279 by1000genomes A375_SKIN NA A375_SKIN NA g.chr1:16260674_16260694delCTCACTGGTCTGGTGAGCGCA uc001axk.1 + 11 8143_8163 c.7939_7959delCTCACTGGTCTGGTGAGCGCA c.(7939-7959)CTCACTGGTCTGGTGAGCGCAdel p.LTGLVSA2647del SPEN_uc010obp.1_In_Frame_Del_p.LTGLVSA2606del NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2647_2653 RID. interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) TCCTCAAACCCTCACTGGTCTGGTGAGCGCACTCACTGGCC 0.534 0.17 50 10 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - A375_SKIN NA A375_SKIN NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.27 382 139 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 A375_SKIN NA A375_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.18 32 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 A375_SKIN NA A375_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.52 12 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 A375_SKIN NA A375_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.33 89 43 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 A375_SKIN NA A375_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.60 16 24 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 A375_SKIN NA A375_SKIN NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.58 108 150 CHD1 1105 broad.mit.edu 37 5 98215316 98215318 + In_Frame_Del DEL TTC - - A375_SKIN NA A375_SKIN NA g.chr5:98215316_98215318delTTC uc003knf.2 - 22 3323_3325 c.3175_3177delGAA c.(3175-3177)GAAdel p.E1059del NM_001270 NP_001261 O14646 CHD1_HUMAN chromodomain helicase DNA binding protein 1 1059 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117) COAD - Colon adenocarcinoma(37;0.0717) Epirubicin(DB00445) CCTTTTGTCTTTCTTCTTCTTCT 0.315 0.37 66 39 CHD1 1105 broad.mit.edu 37 5 98240669 98240672 + Frame_Shift_Del DEL CTGA - - A375_SKIN NA A375_SKIN NA g.chr5:98240669_98240672delCTGA uc003knf.2 - 2 332_335 c.184_187delTCAG c.(184-189)TCAGAGfs p.S62fs NM_001270 NP_001261 O14646 CHD1_HUMAN chromodomain helicase DNA binding protein 1 62_63 Ser-rich. regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117) COAD - Colon adenocarcinoma(37;0.0717) Epirubicin(DB00445) GACTCAGACTCTGACTGACTGCCT 0.466 0.25 177 58 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 A375_SKIN NA A375_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 13 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - A375_SKIN NA A375_SKIN NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 301 34 RCBTB2 1102 broad.mit.edu 37 13 49089459 49089460 + Frame_Shift_Ins INS - C C A375_SKIN NA A375_SKIN NA g.chr13:49089459_49089460insC uc001vch.2 - 6 601_602 c.230_231insG c.(229-231)TGTfs p.C77fs RCBTB2_uc010tgg.1_Frame_Shift_Ins_p.C82fs|RCBTB2_uc001vci.2_Frame_Shift_Ins_p.C53fs|RCBTB2_uc010tgh.1_5'UTR|RCBTB2_uc001vcj.2_Frame_Shift_Ins_p.C81fs|RCBTB2_uc010acv.1_RNA|RCBTB2_uc010tgi.1_Frame_Shift_Ins_p.C53fs NM_001268 NP_001259 O95199 RCBT2_HUMAN regulator of chromosome condensation and BTB 77 RCC1 1. Ran guanyl-nucleotide exchange factor activity ovary(2)|lung(2)|skin(1) 5 all_cancers(8;4.86e-71)|all_epithelial(8;2.11e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;2.3e-10)|Lung NSC(96;1.07e-07)|Breast(56;1.53e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.00826)|Myeloproliferative disorder(33;0.0179)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(99;1.8e-09)|LUSC - Lung squamous cell carcinoma(3;0.116) CTAACCCCAAACAGCCACAGCA 0.421 0.13 141 22 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C A375_SKIN NA A375_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 5 67 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 A375_SKIN NA A375_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.25 33 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 A375_SKIN NA A375_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 30 278 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 A375_SKIN NA A375_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 72 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 A498_KIDNEY NA A498_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 54 ARNT 405 broad.mit.edu 37 1 150799085 150799086 + Frame_Shift_Ins INS - C C A498_KIDNEY NA A498_KIDNEY NA g.chr1:150799085_150799086insC uc001evr.1 - 13 1318_1319 c.1175_1176insG c.(1174-1176)TTAfs p.L392fs ARNT_uc001evs.1_Frame_Shift_Ins_p.L377fs|ARNT_uc009wmb.1_Frame_Shift_Ins_p.L378fs|ARNT_uc009wmc.1_Frame_Shift_Ins_p.L392fs|ARNT_uc009wmd.1_Frame_Shift_Ins_p.L377fs|ARNT_uc009wme.1_Frame_Shift_Ins_p.L392fs|ARNT_uc010pcl.1_Frame_Shift_Ins_p.L376fs NM_001668 NP_001659 P27540 ARNT_HUMAN aryl hydrocarbon receptor nuclear translocator 392 PAS 2. positive regulation of hormone biosynthetic process|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|response to hypoxia aryl hydrocarbon receptor binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity skin(4)|lung(3)|central_nervous_system(1)|kidney(1) 9 all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211) TATTCTTTCCTAAGAGTTCCTA 0.248 0.24 64 20 VHL 7428 broad.mit.edu 37 3 10188283 10188286 + Frame_Shift_Del DEL TGAC - - rs143594610 A498_KIDNEY NA A498_KIDNEY NA g.chr3:10188283_10188286delTGAC uc003bvc.2 + 2 639_642 c.426_429delTGAC c.(424-429)GTTGACfs p.V142fs VHL_uc003bvd.2_Intron NM_000551 NP_000542 P40337 VHL_HUMAN von Hippel-Lindau tumor suppressor isoform 1 142_143 Involved in binding to CCT complex. D -> E (in VHLD; type II). anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus protein binding|transcription factor binding p.V142fs*17(4)|p.G144fs*14(4)|p.N141fs*16(2)|p.D143E(2)|p.V142fs*30(1)|p.V142V(1)|p.Q145fs*30(1)|p.V142fs*1(1)|p.D143fs*16(1)|p.N141fs*30(1)|p.G144fs*19(1) kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1) 1346 Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569) CTCTCAATGTTGACGGACAGCCTA 0.426 1.00 0 47 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes A498_KIDNEY NA A498_KIDNEY NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.54 13 15 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 A498_KIDNEY NA A498_KIDNEY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.33 29 14 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A A498_KIDNEY NA A498_KIDNEY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.13 58 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 A498_KIDNEY NA A498_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 100 147 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 A498_KIDNEY NA A498_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.28 65 25 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes A498_KIDNEY NA A498_KIDNEY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.82 2 9 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes A498_KIDNEY NA A498_KIDNEY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.98 1 46 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 A498_KIDNEY NA A498_KIDNEY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.43 25 19 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 A498_KIDNEY NA A498_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 61 SMARCA2 6595 broad.mit.edu 37 9 2039806 2039807 + In_Frame_Ins INS - CAA CAA A498_KIDNEY NA A498_KIDNEY NA g.chr9:2039806_2039807insCAA uc003zhc.2 + 4 795_796 c.696_697insCAA c.(694-699)insCAA p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.19 1242 298 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 A498_KIDNEY NA A498_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 475 211 NCOR2 9612 broad.mit.edu 37 12 124887058 124887059 + In_Frame_Ins INS - GCTGCT GCTGCT rs35831183;rs67031864 A498_KIDNEY NA A498_KIDNEY NA g.chr12:124887058_124887059insGCTGCT uc010tba.1 - 14 1648_1649 c.1531_1532insAGCAGC c.(1531-1533)CCC>CAGCAGCCC p.510_511insQQ NCOR2_uc010tay.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010taz.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbb.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbc.1_In_Frame_Ins_p.509_510insQQ|NCOR2_uc001ugj.1_In_Frame_Ins_p.510_511insQQ NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 510_511 cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) GCGGGGCATGGgctgctgctgc 0.312 0.17 66 14 MKL2 57496 broad.mit.edu 37 16 14334333 14334334 + Frame_Shift_Ins INS - CC CC A498_KIDNEY NA A498_KIDNEY NA g.chr16:14334333_14334334insCC uc010uza.1 + 10 1226_1227 c.1071_1072insCC c.(1069-1074)GCACCAfs p.A357fs MKL2_uc002dcg.2_Frame_Shift_Ins_p.A357fs|MKL2_uc002dch.2_Frame_Shift_Ins_p.A346fs|MKL2_uc010uzb.1_Frame_Shift_Ins_p.A306fs NM_014048 NP_054767 Q9ULH7 MKL2_HUMAN megakaryoblastic leukemia 2 protein 346_347 cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent identical protein binding|nucleic acid binding|transcription coactivator activity ovary(3)|kidney(1)|pancreas(1) 5 TCCTGCCTGCACCATTCAAGTA 0.500 0.47 10 9 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes A498_KIDNEY NA A498_KIDNEY NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.16 104 20 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C A498_KIDNEY NA A498_KIDNEY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 56 411 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 A498_KIDNEY NA A498_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 44 187 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 A498_KIDNEY NA A498_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 144 831 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 A498_KIDNEY NA A498_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 9 118 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 A549_LUNG NA A549_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 61 TTN 7273 broad.mit.edu 37 2 179613269 179613269 + Frame_Shift_Del DEL G - - A549_LUNG NA A549_LUNG NA g.chr2:179613269delG uc002unb.2 - 46 14082 c.13858delC c.(13858-13860)CAAfs p.Q4620fs TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron NM_133379 NP_596870 Q8WZ42 TITIN_HUMAN titin isoform novex-3 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GAATACATTTGTTTTAGATCA 0.363 0.11 220 28 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes A549_LUNG NA A549_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.53 19 21 TPRXL 348825 broad.mit.edu 37 3 14106310 14106311 + In_Frame_Ins INS - CCAGCACCAGCAGTC CCAGCACCAGCAGTC A549_LUNG NA A549_LUNG NA g.chr3:14106310_14106311insCCAGCACCAGCAGTC uc011avd.1 + 3 1089_1090 c.634_635insCCAGCACCAGCAGTC c.(634-636)TCC>TCCAGCACCAGCAGTCCC p.217_218insSTSSP TPRXL_uc003byh.1_In_Frame_Ins_p.217_218insSTSSP|TPRXL_uc003byg.2_In_Frame_Ins_p.217_218insSTSSP NR_002223 RecName: Full=Putative protein TPRXL; 0 cagcagcagctccagcaccagc 0.213 0.35 11 6 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 A549_LUNG NA A549_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 31 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 A549_LUNG NA A549_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 80 133 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 A549_LUNG NA A549_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.18 99 22 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 A549_LUNG NA A549_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.35 382 203 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes A549_LUNG NA A549_LUNG NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.31 9 4 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT A549_LUNG NA A549_LUNG NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.11 1571 189 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - A549_LUNG NA A549_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.32 17 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 A549_LUNG NA A549_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 2 86 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 A549_LUNG NA A549_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 418 219 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C A549_LUNG NA A549_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.85 16 91 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 A549_LUNG NA A549_LUNG NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.16 47 9 SMARCA4 6597 broad.mit.edu 37 19 11121117 11121139 + Frame_Shift_Del DEL GCAGTCCTACTATGCCGTGGCCC - - A549_LUNG NA A549_LUNG NA g.chr19:11121117_11121139delGCAGTCCTACTATGCCGTGGCCC uc002mqf.3 + 15 2468_2490 c.2184_2206delGCAGTCCTACTATGCCGTGGCCC c.(2182-2208)CTGCAGTCCTACTATGCCGTGGCCCATfs p.L728fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.L728fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.L728fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.L728fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.L728fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.L728fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.L728fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.L728fs|SMARCA4_uc010dxt.1_5'Flank NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 728_736 chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.Q729fs*4(2)|p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) CACGTGGCCTGCAGTCCTACTATGCCGTGGCCCATGCTGTCAC 0.578 0.99 1 68 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 A549_LUNG NA A549_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 168 645 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 A549_LUNG NA A549_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 80 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 A673_BONE NA A673_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 4 50 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 A673_BONE NA A673_BONE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.58 5 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 A673_BONE NA A673_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 101 110 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 A673_BONE NA A673_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 38 61 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes A673_BONE NA A673_BONE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.82 2 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 A673_BONE NA A673_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 3 78 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 A673_BONE NA A673_BONE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.83 7 34 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 A673_BONE NA A673_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 751 99 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes A673_BONE NA A673_BONE NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.17 33 7 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes A673_BONE NA A673_BONE NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.30 87 37 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency A673_BONE NA A673_BONE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.19 51 12 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C A673_BONE NA A673_BONE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 9 78 TP53 7157 broad.mit.edu 37 17 7579332 7579333 + Frame_Shift_Ins INS - TG TG A673_BONE NA A673_BONE NA g.chr17:7579332_7579333insTG uc002gim.2 - 4 548_549 c.354_355insCA c.(352-357)ACAGCCfs p.T118fs TP53_uc002gig.1_Frame_Shift_Ins_p.T118fs|TP53_uc002gih.2_Frame_Shift_Ins_p.T118fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Ins_p.T118fs|TP53_uc010cni.1_Frame_Shift_Ins_p.T118fs|TP53_uc002gij.2_Frame_Shift_Ins_p.T118fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Ins_p.T79fs|TP53_uc010cnk.1_Frame_Shift_Ins_p.T133fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 118_119 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). A -> T (in a sporadic cancer; somatic mutation).|A -> D (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.T118fs*5(4)|p.T118I(3)|p.G59fs*23(3)|p.V73fs*9(1)|p.T118T(1)|p.T118fs*31(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.T118fs*27(1)|p.H115fs*27(1)|p.A119fs*5(1)|p.Y107fs*44(1)|p.T118fs*6(1)|p.T118A(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.T118R(1)|p.L114fs*30(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.96 41 1086 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 A673_BONE NA A673_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.48 47 43 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 A673_BONE NA A673_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 98 454 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 A673_BONE NA A673_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 6 117 PRKX 5613 broad.mit.edu 37 X 3592700 3592715 + Frame_Shift_Del DEL GCTCCTGCTTTAGGCG - - A704_KIDNEY NA A704_KIDNEY NA g.chrX:3592700_3592715delGCTCCTGCTTTAGGCG uc010nde.2 - 2 626_641 c.259_274delCGCCTAAAGCAGGAGC c.(259-276)CGCCTAAAGCAGGAGCAAfs p.R87fs NM_005044 NP_005035 P51817 PRKX_HUMAN protein kinase, X-linked 87_92 Protein kinase. ATP binding|cAMP-dependent protein kinase activity skin(2)|lung(1) 3 all_lung(23;0.000396)|Lung NSC(23;0.00123) 0.000 0.10 178 19 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 A704_KIDNEY NA A704_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.83 9 45 FMN2 56776 broad.mit.edu 37 1 240256066 240256067 + In_Frame_Ins INS - CAG CAG A704_KIDNEY NA A704_KIDNEY NA g.chr1:240256066_240256067insCAG uc010pyd.1 + 1 882_883 c.657_658insCAG c.(655-660)insCAG p.225_226insQ FMN2_uc010pye.1_In_Frame_Ins_p.225_226insQ NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 225_226 Potential.|Gln-rich. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) agctccagcaacagcagcagca 0.465 0.23 30 9 PBRM1 55193 broad.mit.edu 37 3 52651382 52651383 + Frame_Shift_Ins INS - AA AA A704_KIDNEY NA A704_KIDNEY NA g.chr3:52651382_52651383insAA uc003des.2 - 14 1725_1726 c.1713_1714insTT c.(1711-1716)ATTGAGfs p.I571fs PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Ins_p.I571fs|PBRM1_uc003der.2_Frame_Shift_Ins_p.I539fs|PBRM1_uc003det.2_Frame_Shift_Ins_p.I586fs|PBRM1_uc003deu.2_Frame_Shift_Ins_p.I586fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Ins_p.I571fs|PBRM1_uc010hmk.1_Frame_Shift_Ins_p.I571fs|PBRM1_uc003dey.2_Frame_Shift_Ins_p.I571fs|PBRM1_uc003dez.1_Frame_Shift_Ins_p.I571fs|PBRM1_uc003dfb.1_Frame_Shift_Ins_p.I484fs|PBRM1_uc003dfc.2_5'Flank NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 571_572 Bromo 4. chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding p.I571fs*2(1) kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.63 239 413 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A A704_KIDNEY NA A704_KIDNEY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.30 92 39 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 A704_KIDNEY NA A704_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 90 80 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 A704_KIDNEY NA A704_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.89 2 17 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency A704_KIDNEY NA A704_KIDNEY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.31 9 4 COBRA1 25920 broad.mit.edu 37 9 140158792 140158793 + Frame_Shift_Ins INS - T T A704_KIDNEY NA A704_KIDNEY NA g.chr9:140158792_140158793insT uc004cmm.3 + 6 1082_1083 c.879_880insT c.(877-882)GGCCAGfs p.G293fs NM_015456 NP_056271 Q8WX92 NELFB_HUMAN cofactor of BRCA1 293_294 negative regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction cytoplasm|nucleoplasm protein binding 0 all_cancers(76;0.0926) STAD - Stomach adenocarcinoma(284;0.137) OV - Ovarian serous cystadenocarcinoma(145;9.42e-05)|Epithelial(140;0.000766) 0.000 1.00 0 14 RET 5979 broad.mit.edu 37 10 43606860 43606860 + Frame_Shift_Del DEL A - - A704_KIDNEY NA A704_KIDNEY NA g.chr10:43606860delA uc001jal.2 + 7 1659 c.1469delA c.(1468-1470)CAGfs p.Q490fs RET_uc001jak.1_Frame_Shift_Del_p.Q490fs|RET_uc010qez.1_Frame_Shift_Del_p.Q236fs NM_020975 NP_066124 P07949 RET_HUMAN ret proto-oncogene isoform a 490 Extracellular (Potential). homophilic cell adhesion|positive regulation of metanephric glomerulus development|positive regulation of transcription, DNA-dependent|posterior midgut development integral to membrane ATP binding|calcium ion binding|transmembrane receptor protein tyrosine kinase activity thyroid(404)|adrenal_gland(20)|lung(9)|large_intestine(5)|breast(4)|ovary(4)|central_nervous_system(3)|urinary_tract(1)|NS(1) 451 Ovarian(717;0.0423) Sunitinib(DB01268) GCCACCGACCAGCAGACCTCT 0.637 0.28 41 16 DKK1 22943 broad.mit.edu 37 10 54074711 54074712 + Frame_Shift_Del DEL GC - - A704_KIDNEY NA A704_KIDNEY NA g.chr10:54074711_54074712delGC uc001jjr.2 + 2 426_427 c.272_273delGC c.(271-273)TGCfs p.C91fs uc001jjq.1_5'Flank|uc009xox.1_5'Flank NM_012242 NP_036374 O94907 DKK1_HUMAN dickkopf homolog 1 precursor 91 DKK-type Cys-1. negative regulation of peptidyl-serine phosphorylation|negative regulation of protein complex assembly|negative regulation of transcription from RNA polymerase II promoter|positive regulation of heart induction by negative regulation of canonical Wnt receptor signaling pathway|regulation of receptor internalization extracellular space|plasma membrane growth factor activity|low-density lipoprotein particle receptor binding|receptor antagonist activity|signal transducer activity ovary(1)|lung(1)|kidney(1) 3 0.000 0.52 243 268 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 A704_KIDNEY NA A704_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 236 77 PAFAH1B2 5049 broad.mit.edu 37 11 117034520 117034520 + Frame_Shift_Del DEL A - - A704_KIDNEY NA A704_KIDNEY NA g.chr11:117034520delA uc001pqe.1 + 5 425 c.323delA c.(322-324)GAAfs p.E108fs PAFAH1B2_uc009yzk.1_Frame_Shift_Del_p.E108fs|PAFAH1B2_uc009yzl.1_Frame_Shift_Del_p.E108fs|PAFAH1B2_uc009yzm.2_RNA|PAFAH1B2_uc009yzn.2_RNA|PAFAH1B2_uc009yzj.1_RNA NM_002572 NP_002563 P68402 PA1B2_HUMAN platelet-activating factor acetylhydrolase, 108 lipid catabolic process cytoplasm 1-alkyl-2-acetylglycerophosphocholine esterase activity kidney(1) 1 all_hematologic(175;0.0487) Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(192;0.232) BRCA - Breast invasive adenocarcinoma(274;1.68e-05)|Epithelial(105;0.000162)|all cancers(92;0.00111) AATAACCACGAAAATACAGCA 0.433 0.45 155 127 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GAGA GAGA rs141931278 by1000genomes A704_KIDNEY NA A704_KIDNEY NA g.chr12:120190054_120190055insGAGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.26 73 25 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C A704_KIDNEY NA A704_KIDNEY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 9 86 NLRP1 22861 broad.mit.edu 37 17 5418090 5418091 + Frame_Shift_Ins INS - G G A704_KIDNEY NA A704_KIDNEY NA g.chr17:5418090_5418091insG uc002gci.2 - 17 4960_4961 c.4405_4406insC c.(4405-4407)CTGfs p.L1469fs NLRP1_uc002gcg.1_Intron|NLRP1_uc002gck.2_Frame_Shift_Ins_p.L1425fs|NLRP1_uc002gcj.2_Frame_Shift_Ins_p.L1439fs|NLRP1_uc002gcl.2_Frame_Shift_Ins_p.L1395fs|NLRP1_uc002gch.3_Frame_Shift_Ins_p.L1425fs NM_033004 NP_127497 Q9C000 NALP1_HUMAN NLR family, pyrin domain containing 1 isoform 1 1469 defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide cytoplasm|NALP1 inflammasome complex|nucleus ATP binding|caspase activator activity|enzyme binding|protein domain specific binding lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1) 9 Colorectal(1115;3.48e-05) GCTGAGTGGCAGGAGTCCCTTT 0.525 0.11 66 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 A704_KIDNEY NA A704_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.75 9 27 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 A704_KIDNEY NA A704_KIDNEY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.34 86 44 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 A704_KIDNEY NA A704_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 74 471 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 A704_KIDNEY NA A704_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 4 39 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ACHN_KIDNEY NA ACHN_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 22 FLNA 2316 broad.mit.edu 37 X 153588405 153588406 + Frame_Shift_Ins INS - C C ACHN_KIDNEY NA ACHN_KIDNEY NA g.chrX:153588405_153588406insC uc004fkk.2 - 22 4006_4007 c.3757_3758insG c.(3757-3759)GTGfs p.V1253fs FLNA_uc011mzn.1_5'Flank|FLNA_uc010nuu.1_Frame_Shift_Ins_p.V1253fs NM_001110556 NP_001104026 P21333 FLNA_HUMAN filamin A, alpha isoform 2 1253 Filamin 11. actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering cell cortex|cytosol|extracellular region|nucleus|plasma membrane actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding breast(6) 6 all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176) GGAAGTGTCCACCGCAGGTTCC 0.649 0.16 37 7 MPL 4352 broad.mit.edu 37 1 43804946 43804947 + Frame_Shift_Ins INS - C C ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr1:43804946_43804947insC uc001ciw.2 + 4 441_442 c.396_397insC c.(394-399)CTGCCGfs p.L132fs MPL_uc001civ.2_Frame_Shift_Ins_p.L132fs|MPL_uc009vwr.2_Frame_Shift_Ins_p.L125fs NM_005373 NP_005364 P40238 TPOR_HUMAN myeloproliferative leukemia virus oncogene 132_133 Extracellular (Potential).|Fibronectin type-III 1. cell proliferation|platelet activation integral to plasma membrane cytokine receptor activity haematopoietic_and_lymphoid_tissue(361)|upper_aerodigestive_tract(1)|pancreas(1) 363 all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0505) CCTCAGGCCTGCCGGCTCCCCC 0.599 0.12 96 13 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.53 8 9 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.55 5 6 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.50 17 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 102 131 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 17 40 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.52 14 15 EPHB4 2050 broad.mit.edu 37 7 100421476 100421477 + Frame_Shift_Ins INS - G G rs138656609;rs34653459 byFrequency ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr7:100421476_100421477insG uc003uwn.1 - 3 691_692 c.200_201insC c.(199-201)CCGfs p.P67fs EPHB4_uc003uwm.1_5'UTR|EPHB4_uc010lhj.1_Frame_Shift_Ins_p.P67fs|EPHB4_uc011kkf.1_Frame_Shift_Ins_p.P67fs|EPHB4_uc011kkg.1_Frame_Shift_Ins_p.P67fs|EPHB4_uc011kkh.1_Frame_Shift_Ins_p.P67fs NM_004444 NP_004435 P54760 EPHB4_HUMAN EPH receptor B4 precursor 67 Extracellular (Potential). cell proliferation|organ morphogenesis|regulation of angiogenesis cell surface|integral to plasma membrane ATP binding|ephrin receptor activity lung(4)|stomach(3)|skin(3)|central_nervous_system(2)|ovary(2)|breast(1) 15 Lung NSC(181;0.041)|all_lung(186;0.0581) GGGCCTGGCCCGGGGCACGCTG 0.663 0.10 72 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 4 30 WRN 7486 broad.mit.edu 37 8 30925776 30925777 + Frame_Shift_Ins INS - G G ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr8:30925776_30925777insG uc003xio.3 + 7 1445_1446 c.657_658insG c.(655-660)GCTGGTfs p.A219fs NM_000553 NP_000544 Q14191 WRN_HUMAN Werner syndrome protein 219_220 Interaction with WRNIP1 (By similarity).|3'-5' exonuclease. base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance centrosome|nucleolus|nucleoplasm 3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1) 7 Breast(100;0.195) KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192) TTTTATAGGCTGGTTTTATTAT 0.277 0.32 28 13 PREX2 80243 broad.mit.edu 37 8 68995501 68995501 + Frame_Shift_Del DEL G - - ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr8:68995501delG uc003xxv.1 + 18 1932 c.1905delG c.(1903-1905)AAGfs p.K635fs PREX2_uc003xxu.1_Frame_Shift_Del_p.K635fs|PREX2_uc011lez.1_Frame_Shift_Del_p.K570fs NM_024870 NP_079146 Q70Z35 PREX2_HUMAN DEP domain containing 2 isoform a 635 PDZ 1. G-protein coupled receptor protein signaling pathway|intracellular signal transduction intracellular protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1) 17 TCGGGAAAAAGATTTTTGCTA 0.318 0.98 1 57 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 25 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.30 62 26 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 577 310 MBD6 114785 broad.mit.edu 37 12 57919294 57919295 + Frame_Shift_Ins INS - G G ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr12:57919294_57919295insG uc001soj.1 + 6 767_768 c.543_544insG c.(541-546)CCTGGGfs p.P181fs MBD6_uc001sok.1_Frame_Shift_Ins_p.P48fs|MBD6_uc001sol.1_5'Flank NM_052897 NP_443129 Q96DN6 MBD6_HUMAN methyl-CpG binding domain protein 6 181_182 Pro-rich. chromosome|nucleus chromatin binding|DNA binding central_nervous_system(3)|ovary(1) 4 TAGCAGGCCCTGGGGGGCTTTT 0.639 0.17 34 7 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.15 149 26 IRS2 8660 broad.mit.edu 37 13 110436296 110436297 + In_Frame_Ins INS - CGG CGG rs34412495 ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr13:110436296_110436297insCGG uc001vqv.2 - 1 2618_2619 c.2104_2105insCCG c.(2104-2106)GTG>GCCGTG p.701_702insA NM_003749 NP_003740 Q9Y4H2 IRS2_HUMAN insulin receptor substrate 2 701_702 fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus cytosol|plasma membrane insulin receptor binding|signal transducer activity large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|skin(1)|ovary(1)|kidney(1) 8 all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155) Breast(118;0.159) all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147) 0.000 0.69 121 271 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 5 42 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.14 65 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 27 308 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ACHN_KIDNEY NA ACHN_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 88 Unknown 0 broad.mit.edu 37 X 80185321 80185321 + Frame_Shift_Del DEL A - - AGS_STOMACH NA AGS_STOMACH NA g.chrX:80185321delA uc004eec.1 + 1 394 c.220delA c.(220-222)AAAfs p.K74fs SubName: Full=cDNA FLJ16670 fis, clone THYMU3001133, highly similar to Voltage-dependent anion-selective channel protein 1; SubName: Full=Voltage-dependent anion channel 1, isoform CRA_a; TAACACTGGGAAAAAAAATGC 0.483 0.49 163 155 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 AGS_STOMACH NA AGS_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 3 107 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - AGS_STOMACH NA AGS_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.19 346 83 RHOA 387 broad.mit.edu 37 3 49405944 49405946 + In_Frame_Del DEL TCT - - AGS_STOMACH NA AGS_STOMACH NA g.chr3:49405944_49405946delTCT uc003cwu.2 - 3 468_470 c.192_194delAGA c.(190-195)GAAGAT>GAT p.E64del RHOA_uc010hku.2_5'UTR NM_001664 NP_001655 P61586 RHOA_HUMAN ras homolog gene family, member A precursor 64 axon guidance|interspecies interaction between organisms|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of axonogenesis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of neuron differentiation|positive regulation of NF-kappaB import into nucleus|positive regulation of stress fiber assembly|regulation of cell migration|regulation of small GTPase mediated signal transduction|Rho protein signal transduction|spindle assembly involved in mitosis cytoskeleton|cytosol|plasma membrane GTP binding|GTPase activity|myosin binding ovary(2) 2 BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258) Atorvastatin(DB01076)|Simvastatin(DB00641) GCGATCATAATCTTCCTGCCCAG 0.493 0.44 63 50 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A AGS_STOMACH NA AGS_STOMACH NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.25 58 19 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 AGS_STOMACH NA AGS_STOMACH NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.13 46 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 AGS_STOMACH NA AGS_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 99 176 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 AGS_STOMACH NA AGS_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 19 53 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 AGS_STOMACH NA AGS_STOMACH NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.35 22 12 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes AGS_STOMACH NA AGS_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 AGS_STOMACH NA AGS_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 55 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency AGS_STOMACH NA AGS_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.17 111 23 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 AGS_STOMACH NA AGS_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 991 224 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 AGS_STOMACH NA AGS_STOMACH NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.31 9 4 CDH1 999 broad.mit.edu 37 16 68855924 68855925 + Frame_Shift_Ins INS - C C AGS_STOMACH NA AGS_STOMACH NA g.chr16:68855924_68855925insC uc002ewg.1 + 12 1856_1857 c.1732_1733insC c.(1732-1734)ACAfs p.T578fs CDH1_uc010vlj.1_RNA|CDH1_uc010cfg.1_Frame_Shift_Ins_p.T517fs NM_004360 NP_004351 P12830 CADH1_HUMAN cadherin 1, type 1 preproprotein 578 Extracellular (Potential).|Cadherin 4. adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm cell adhesion molecule binding|gamma-catenin binding p.G579fs*9(1) breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1) 243 all_neural(199;0.0189)|Ovarian(137;0.0563) Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261) TGCTACTGGAACAGGGACACTT 0.470 0.94 5 82 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C AGS_STOMACH NA AGS_STOMACH NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 5 57 ATP8B1 5205 broad.mit.edu 37 18 55351319 55351320 + Frame_Shift_Ins INS - CTGT CTGT AGS_STOMACH NA AGS_STOMACH NA g.chr18:55351319_55351320insCTGT uc002lgw.2 - 14 1578_1579 c.1578_1579insACAG c.(1576-1581)CAGTTCfs p.Q526fs uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 526_527 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) AAGAAGAAGAACTGTCGTACTT 0.431 0.76 19 59 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 AGS_STOMACH NA AGS_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 90 387 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 AGS_STOMACH NA AGS_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.47 173 155 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 AGS_STOMACH NA AGS_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 6 104 MYH9 4627 broad.mit.edu 37 22 36716380 36716380 + Frame_Shift_Del DEL T - - AGS_STOMACH NA AGS_STOMACH NA g.chr22:36716380delT uc003apg.2 - 9 1128 c.897delA c.(895-897)AAAfs p.K299fs MYH9_uc003aph.1_Frame_Shift_Del_p.K163fs NM_002473 NP_002464 P35579 MYH9_HUMAN myosin, heavy polypeptide 9, non-muscle 299 Myosin head-like. actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1) 11 GGAAGCGGTATTTGTTGTACG 0.592 0.53 89 100 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 2 28 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.33 24 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 114 178 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 12 28 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 1 14 NOTCH1 4851 broad.mit.edu 37 9 139390772 139390773 + Frame_Shift_Ins INS - CC CC ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:139390772_139390773insCC uc004chz.2 - 34 7418_7419 c.7418_7419insGG c.(7417-7419)GTCfs p.V2473fs NM_017617 NP_060087 P46531 NOTC1_HUMAN notch1 preproprotein 2473 Cytoplasmic (Potential). aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity p.P2475fs*34(2)|p.L2473fs*1(1)|p.L2473fs*7(1)|p.V2474fs*5(1)|p.V2474fs*4(1)|p.P2475fs*5(1) haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1) 856 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06) TCACGGGTGGGACCAGCGAGGA 0.693 0.36 16 9 WT1 7490 broad.mit.edu 37 11 32449588 32449589 + Frame_Shift_Ins INS - GGATGTA GGATGTA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:32449588_32449589insGGATGTA uc001mtn.1 - 3 981_982 c.785_786insTACATCC c.(784-786)TCGfs p.S262fs WT1_uc001mtl.1_Frame_Shift_Ins_p.S50fs|WT1_uc001mtm.1_Frame_Shift_Ins_p.S50fs|WT1_uc001mto.1_Frame_Shift_Ins_p.S262fs|WT1_uc001mtp.1_Frame_Shift_Ins_p.S262fs|WT1_uc001mtq.1_Frame_Shift_Ins_p.S262fs|WT1_uc009yjs.1_RNA NM_024426 NP_077744 P19544 WT1_HUMAN Wilms tumor 1 isoform D 194 adrenal cortex formation|branching involved in ureteric bud morphogenesis|camera-type eye development|cardiac muscle cell fate commitment|cellular response to cAMP|cellular response to gonadotropin stimulus|germ cell development|glomerular basement membrane development|glomerular visceral epithelial cell differentiation|induction of apoptosis|male genitalia development|male gonad development|mesenchymal to epithelial transition|metanephric epithelium development|metanephric S-shaped body morphogenesis|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of female gonad development|negative regulation of metanephric glomerular mesangial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of translation|positive regulation of male gonad development|positive regulation of transcription, DNA-dependent|posterior mesonephric tubule development|regulation of organ formation|RNA splicing|sex determination|vasculogenesis|visceral serous pericardium development cytoplasm|nuclear speck|nucleoplasm C2H2 zinc finger domain binding|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding p.V195fs*32(2)|p.E262A(1) EWSR1/WT1(231) haematopoietic_and_lymphoid_tissue(318)|soft_tissue(231)|kidney(132)|pleura(2)|lung(2)|upper_aerodigestive_tract(1)|peritoneum(1) 687 Breast(20;0.247) OV - Ovarian serous cystadenocarcinoma(30;0.128) GGGGCGGCACCGAGTACTGCTG 0.683 0.18 53 12 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.36 7 4 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 686 280 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.17 90 19 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.45 102 84 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 123 541 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 3 92 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.73 12 32 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 231 90 C1orf106 55765 broad.mit.edu 37 1 200880777 200880778 + Frame_Shift_Ins INS - A A AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr1:200880777_200880778insA uc001gvo.2 + 9 1441_1442 c.1411_1412insA c.(1411-1413)GGCfs p.G471fs C1orf106_uc010ppm.1_Frame_Shift_Ins_p.G386fs NM_018265 NP_060735 Q3KP66 CA106_HUMAN hypothetical protein LOC55765 isoform 1 471 skin(2)|ovary(1) 3 0.000 1.00 0 15 SOX11 6664 broad.mit.edu 37 2 5833281 5833282 + In_Frame_Ins INS - CGGCGG CGGCGG AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr2:5833281_5833282insCGGCGG uc002qyj.2 + 1 483_484 c.428_429insCGGCGG c.(427-429)GCC>GCCGGCGGC p.147_148insGG NM_003108 NP_003099 P35716 SOX11_HUMAN SRY-box 11 147_148 Poly-Gly. cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis cytoplasm|nucleolus enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding central_nervous_system(3) 3 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) OV - Ovarian serous cystadenocarcinoma(76;0.132) 0.000 0.15 769 134 VRK2 7444 broad.mit.edu 37 2 58386688 58386689 + Frame_Shift_Ins INS - ACTT ACTT rs149451697 byFrequency AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr2:58386688_58386689insACTT uc002rzo.2 + 16 2132_2133 c.1387_1388insACTT c.(1387-1389)GACfs p.D463fs VRK2_uc010fcb.2_3'UTR|VRK2_uc002rzs.2_3'UTR|VRK2_uc002rzr.2_3'UTR|VRK2_uc010fcc.2_Frame_Shift_Ins_p.D345fs|VRK2_uc002rzv.2_Frame_Shift_Ins_p.D463fs|VRK2_uc010fcd.2_Frame_Shift_Ins_p.D440fs|VRK2_uc002rzp.2_Frame_Shift_Ins_p.D463fs|VRK2_uc010ypg.1_Frame_Shift_Ins_p.D463fs|VRK2_uc002rzq.2_3'UTR|VRK2_uc002rzu.2_3'UTR|VRK2_uc002rzt.2_Frame_Shift_Ins_p.D345fs|FANCL_uc002rzw.3_3'UTR|FANCL_uc002rzx.3_3'UTR|FANCL_uc010fce.2_3'UTR NM_001130482 NP_001123954 Q86Y07 VRK2_HUMAN vaccinia related kinase 2 isoform 2 463 integral to membrane ATP binding|protein binding|protein serine/threonine kinase activity ovary(1) 1 GGGGATCACAGACTTAGAAAGT 0.391 0.48 84 79 CNTN6 27255 broad.mit.edu 37 3 1427481 1427482 + Splice_Site INS - GTAA GTAA rs140337334;rs148944048 AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr3:1427481_1427482insGTAA uc003boz.2 + 20 2971 c.2704_splice c.e20+1 p.P902_splice CNTN6_uc011asj.1_Splice_Site_p.P830_splice|CNTN6_uc003bpa.2_Splice_Site_p.P902_splice NM_014461 NP_055276 Q9UQ52 CNTN6_HUMAN contactin 6 precursor axon guidance|cell adhesion|central nervous system development|Notch signaling pathway anchored to membrane|plasma membrane skin(3)|lung(2)|breast(2)|pancreas(1) 8 all_cancers(2;0.000164)|all_epithelial(2;0.107) Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139) CAAAAAGTCTCGTAAGTATGCA 0.436 0.25 56 19 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.50 7 7 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.30 78 34 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 94 143 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.37 59 34 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.32 243 115 HMGA1 3159 broad.mit.edu 37 6 34208627 34208627 + Frame_Shift_Del DEL C - - AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr6:34208627delC uc003oit.2 + 3 392 c.70delC c.(70-72)CGGfs p.R24fs HMGA1_uc011dso.1_Frame_Shift_Del_p.R24fs|HMGA1_uc003oiv.2_Frame_Shift_Del_p.R24fs|HMGA1_uc003oiw.2_Frame_Shift_Del_p.R24fs|HMGA1_uc003oiu.2_Frame_Shift_Del_p.R24fs|HMGA1_uc003oiy.2_Frame_Shift_Del_p.R24fs|HMGA1_uc003oiz.2_Frame_Shift_Del_p.R24fs|HMGA1_uc003oja.2_Frame_Shift_Del_p.R24fs|HMGA1_uc003oix.2_Frame_Shift_Del_p.R24fs|HMGA1_uc010jvl.2_RNA|HMGA1_uc003ojc.2_Frame_Shift_Del_p.R24fs|HMGA1_uc011dsp.1_RNA|HMGA1_uc003ojd.2_Frame_Shift_Del_p.R24fs NM_145899 NP_665906 P17096 HMGA1_HUMAN high mobility group AT-hook 1 isoform a 24 A.T hook 1. DNA unwinding involved in replication|initiation of viral infection|interspecies interaction between organisms|loss of chromatin silencing|nucleosome disassembly|protein complex assembly|provirus integration chromatin|cytosol|transcription factor complex AT DNA binding|enzyme binding|ligand-dependent nuclear receptor transcription coactivator activity|peroxisome proliferator activated receptor binding|protein binding|retinoid X receptor binding|sequence-specific DNA binding transcription factor activity 0 0.000 0.49 1726 1676 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 1 10 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.67 4 8 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.27 27 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 23 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.19 29 7 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.58 5 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 598 283 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 7 58 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.53 43 49 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.20 43 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 91 492 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 AM38_CENTRAL_NERVOUS_SYSTEM NA AM38_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 57 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.86 5 32 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.18 58 13 BMP2K 55589 broad.mit.edu 37 4 79792082 79792083 + In_Frame_Ins INS - CAG CAG rs5859654;rs35071794 AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:79792082_79792083insCAG uc003hlk.2 + 11 1543_1544 c.1377_1378insCAG c.(1375-1380)insCAG p.486_487insQ BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Ins_p.486_487insQ|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486_487 Gln/His-rich. nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 GTCATCCTCACcagcagcagca 0.262 0.19 236 57 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 117 190 MAML3 55534 broad.mit.edu 37 4 140810638 140810639 + In_Frame_Ins INS - GCT GCT AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140810638_140810639insGCT uc003ihz.1 - 3 2691_2692 c.1939_1940insAGC c.(1939-1941)CCG>CAGCCG p.646_647insQ MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 646_647 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) TGGAGGTGGCGgctgctgctgc 0.416 0.13 257 38 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.78 11 40 EZH2 2146 broad.mit.edu 37 7 148504775 148504779 + Frame_Shift_Del DEL TTCAG - - AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:148504775_148504779delTTCAG uc003wfd.1 - 20 2366_2370 c.2200_2204delCTGAA c.(2200-2205)CTGAAGfs p.L734fs EZH2_uc011kug.1_Frame_Shift_Del_p.L683fs|EZH2_uc003wfb.1_Frame_Shift_Del_p.L739fs|EZH2_uc003wfc.1_Frame_Shift_Del_p.L695fs|EZH2_uc011kuh.1_Frame_Shift_Del_p.L725fs NM_004456 NP_004447 Q15910 EZH2_HUMAN enhancer of zeste 2 isoform a 734_735 negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent ESC/E(Z) complex DNA binding|histone-lysine N-methyltransferase activity|protein binding haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1) 183 Melanoma(164;0.15) OV - Ovarian serous cystadenocarcinoma(82;0.00239) 0.000 0.28 407 157 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.99 1 71 NOTCH1 4851 broad.mit.edu 37 9 139390863 139390864 + Frame_Shift_Ins INS - CATCCTCTTCC CATCCTCTTCC AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:139390863_139390864insCATCCTCTTCC uc004chz.2 - 34 7327_7328 c.7327_7328insGGAAGAGGATG c.(7327-7329)GTGfs p.V2443fs NM_017617 NP_060087 P46531 NOTC1_HUMAN notch1 preproprotein 2443 Cytoplasmic (Potential). aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity p.V2444fs*37(4)|p.D2443fs*39(3)|p.Q2445fs*65(1)|p.D2443fs*2(1)|p.V2444fs*73(1)|p.D2443fs(1)|p.V2444fs*69(1)|p.D2443fs*35(1)|p.V2444fs*39(1)|p.V2444fs*36(1)|p.V2444fs*35(1)|p.V2444fs*3(1) haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1) 856 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06) 0.000 0.42 339 250 BTRC 8945 broad.mit.edu 37 10 103285822 103285827 + In_Frame_Del DEL ATCACT - - AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:103285822_103285827delATCACT uc001kta.2 + 6 722_727 c.609_614delATCACT c.(607-615)AAATCACTA>AAA p.SL204del BTRC_uc001ktb.2_In_Frame_Del_p.SL168del|BTRC_uc001ktc.2_In_Frame_Del_p.SL178del NM_033637 NP_378663 Q9Y297 FBW1A_HUMAN beta-transducin repeat containing protein 204_205 F-box.|Required for down-regulation of SNAI1. anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|positive regulation of proteolysis|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|viral reproduction|Wnt receptor signaling pathway cytosol|nucleus|SCF ubiquitin ligase complex ovary(1) 1 Colorectal(252;0.234) Epithelial(162;1.05e-08)|all cancers(201;6.59e-07) TGGATGCCAAATCACTATGTGCTGCT 0.481 0.31 252 113 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 897 317 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.34 76 39 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.19 104 25 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.37 37 22 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 60 165 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.20 66 17 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 10 82 ARAF 369 broad.mit.edu 37 X 47426415 47426415 + Frame_Shift_Del DEL C - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chrX:47426415delC uc011mlq.1 + 9 891 c.758delC c.(757-759)ACCfs p.T253fs ARAF_uc011mln.1_RNA|ARAF_uc011mlo.1_Frame_Shift_Del_p.T119fs|ARAF_uc011mlp.1_Frame_Shift_Del_p.T253fs|ARAF_uc004dic.1_Frame_Shift_Del_p.T34fs NM_001654 NP_001645 P10398 ARAF_HUMAN v-raf murine sarcoma 3611 viral oncogene 253 intracellular signal transduction|negative regulation of apoptosis|positive regulation of peptidyl-serine phosphorylation ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity large_intestine(3)|lung(2)|ovary(1)|skin(1) 7 Adenosine triphosphate(DB00171) AGTGATGGAACCCCCCGGGGG 0.652 0.34 92 47 RPS6KA6 27330 broad.mit.edu 37 X 83371254 83371255 + Frame_Shift_Ins INS - A A AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chrX:83371254_83371255insA uc004eej.1 - 12 1067_1068 c.990_991insT c.(988-993)TTTGCAfs p.F330fs RPS6KA6_uc011mqt.1_Frame_Shift_Ins_p.F330fs|RPS6KA6_uc011mqu.1_Frame_Shift_Ins_p.F227fs NM_014496 NP_055311 Q9UK32 KS6A6_HUMAN ribosomal protein S6 kinase polypeptide 6 330_331 AGC-kinase C-terminal. axon guidance|central nervous system development|intracellular protein kinase cascade|synaptic transmission cytosol|nucleoplasm ATP binding|magnesium ion binding|protein serine/threonine kinase activity lung(5)|stomach(1)|central_nervous_system(1)|skin(1) 8 TCAATATTTGCAAAAAACAGAT 0.257 0.50 7 7 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.79 14 54 ODZ1 10178 broad.mit.edu 37 X 123514785 123514785 + Frame_Shift_Del DEL C - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chrX:123514785delC uc004euj.2 - 31 7843 c.7779delG c.(7777-7779)GGGfs p.G2593fs ODZ1_uc011muj.1_Frame_Shift_Del_p.G2599fs|ODZ1_uc010nqy.2_Frame_Shift_Del_p.G2600fs NM_014253 NP_055068 Q9UKZ4 TEN1_HUMAN odz, odd Oz/ten-m homolog 1 isoform 3 2593 Extracellular (Potential). immune response|negative regulation of cell proliferation|nervous system development|signal transduction extracellular region heparin binding ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1) 23 GAATCCGCCTCCCCCCAGTGT 0.498 0.44 150 117 FLNA 2316 broad.mit.edu 37 X 153588492 153588493 + Frame_Shift_Ins INS - G G AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chrX:153588492_153588493insG uc004fkk.2 - 22 3919_3920 c.3670_3671insC c.(3670-3672)CTCfs p.L1224fs FLNA_uc011mzn.1_5'Flank|FLNA_uc010nuu.1_Frame_Shift_Ins_p.L1224fs NM_001110556 NP_001104026 P21333 FLNA_HUMAN filamin A, alpha isoform 2 1224 Filamin 10. actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering cell cortex|cytosol|extracellular region|nucleus|plasma membrane actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding breast(6) 6 all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176) CCCGGGGCAGAGGGGAATGTAG 0.644 0.45 36 29 EPHA2 1969 broad.mit.edu 37 1 16462199 16462199 + Frame_Shift_Del DEL G - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr1:16462199delG uc001aya.1 - 6 1516 c.1379delC c.(1378-1380)CCGfs p.P460fs EPHA2_uc010oca.1_Frame_Shift_Del_p.P460fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 460 Extracellular (Potential).|Fibronectin type-III 2. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) 0.000 0.34 829 431 ARID1A 8289 broad.mit.edu 37 1 27105931 27105931 + Frame_Shift_Del DEL G - - rs140055856 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr1:27105931delG uc001bmv.1 + 20 5915 c.5542delG c.(5542-5544)GGGfs p.G1848fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.G1631fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.G694fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.G176fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.G90fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1848 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.G1848fs*6(3) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GCGGATTGGTGGGGGGGACAC 0.582 0.42 144 104 ARID1A 8289 broad.mit.edu 37 1 27106545 27106568 + In_Frame_Del DEL CTTGGAGATGCTCCGGGAAAACAC - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr1:27106545_27106568delCTTGGAGATGCTCCGGGAAAACAC uc001bmv.1 + 20 6529_6552 c.6156_6179delCTTGGAGATGCTCCGGGAAAACAC c.(6154-6180)TGCTTGGAGATGCTCCGGGAAAACACC>TGC p.LEMLRENT2053del ARID1A_uc001bmu.1_In_Frame_Del_p.LEMLRENT1836del|ARID1A_uc001bmx.1_In_Frame_Del_p.LEMLRENT899del|ARID1A_uc009vsm.1_In_Frame_Del_p.LEMLRENT381del|ARID1A_uc009vsn.1_In_Frame_Del_p.LEMLRENT295del NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 2053_2060 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GGTGGGACTGCTTGGAGATGCTCCGGGAAAACACCTTGGTTACA 0.554 0.24 62 20 CDC42BPA 8476 broad.mit.edu 37 1 227333193 227333194 + Frame_Shift_Ins INS - T T AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr1:227333193_227333194insT uc001hqr.2 - 8 2082_2083 c.1139_1140insA c.(1138-1140)AATfs p.N380fs CDC42BPA_uc001hqs.2_Frame_Shift_Ins_p.N380fs|CDC42BPA_uc009xes.2_Frame_Shift_Ins_p.N380fs|CDC42BPA_uc010pvs.1_Frame_Shift_Ins_p.N380fs NM_003607 NP_003598 Q5VT25 MRCKA_HUMAN CDC42-binding protein kinase alpha isoform B 380 AGC-kinase C-terminal. actin cytoskeleton reorganization|intracellular signal transduction cell leading edge|cell-cell junction|cytoplasm ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1) 11 all_cancers(173;0.156)|Prostate(94;0.0792) TACTTACAGAATTTTTTAAACA 0.322 0.50 17 17 FMN2 56776 broad.mit.edu 37 1 240256637 240256637 + Frame_Shift_Del DEL C - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr1:240256637delC uc010pyd.1 + 1 1453 c.1228delC c.(1228-1230)CCCfs p.P410fs FMN2_uc010pye.1_Frame_Shift_Del_p.P410fs NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 410 actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) CTGTTTCAAGCCCTACCCGCT 0.682 0.49 42 41 SOX11 6664 broad.mit.edu 37 2 5833526 5833528 + In_Frame_Del DEL GAC - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr2:5833526_5833528delGAC uc002qyj.2 + 1 728_730 c.673_675delGAC c.(673-675)GACdel p.D233del NM_003108 NP_003099 P35716 SOX11_HUMAN SRY-box 11 233 Poly-Asp. cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis cytoplasm|nucleolus enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding central_nervous_system(3) 3 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) OV - Ovarian serous cystadenocarcinoma(76;0.132) 0.000 0.35 234 126 GLI2 2736 broad.mit.edu 37 2 121554984 121554984 + Frame_Shift_Del DEL A - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr2:121554984delA uc010flp.2 + 1 118 c.88delA c.(88-90)AAAfs p.K30fs GLI2_uc010yyu.1_Frame_Shift_Del_p.K30fs|GLI2_uc002tmp.1_Frame_Shift_Del_p.K30fs|GLI2_uc010fln.1_RNA|GLI2_uc002tmq.1_5'UTR|GLI2_uc002tmr.1_5'UTR|GLI2_uc002tmt.3_5'UTR|GLI2_uc002tmu.3_5'UTR|GLI2_uc002tmv.1_Frame_Shift_Del_p.K30fs|GLI2_uc010flo.1_5'UTR|GLI2_uc002tmw.1_Frame_Shift_Del_p.K30fs NM_005270 NP_005261 P10070 GLI2_HUMAN GLI-Kruppel family member GLI2 30 axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis nucleus|nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1) 13 Renal(3;0.0496) Prostate(154;0.0623) CGACCCGGGTAAAAAGGCCTC 0.612 0.54 45 53 LRP2 4036 broad.mit.edu 37 2 169997025 169997025 + Frame_Shift_Del DEL G - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr2:169997025delG uc002ues.2 - 72 13352 c.13139delC c.(13138-13140)CCAfs p.P4380fs NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 4380 EGF-like 17.|Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) 0.000 0.49 106 100 DCLK3 85443 broad.mit.edu 37 3 36779824 36779824 + Frame_Shift_Del DEL G - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr3:36779824delG uc003cgi.2 - 2 818 c.327delC c.(325-327)CCCfs p.P109fs NM_033403 NP_208382 Q9C098 DCLK3_HUMAN doublecortin-like kinase 3 109 cytoplasm|nucleus ATP binding|protein serine/threonine kinase activity lung(3)|large_intestine(2)|breast(1)|skin(1)|ovary(1)|kidney(1) 9 TGGCTTCCCTGGGGGGCTTGC 0.562 0.46 156 131 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.31 24 11 PARP9 83666 broad.mit.edu 37 3 122274683 122274683 + Frame_Shift_Del DEL C - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr3:122274683delC uc010hri.2 - 4 585 c.440delG c.(439-441)GGAfs p.G147fs PARP9_uc003eff.3_Frame_Shift_Del_p.G112fs|PARP9_uc011bjs.1_Frame_Shift_Del_p.G112fs|PARP9_uc003efg.2_Intron|PARP9_uc003efi.2_Frame_Shift_Del_p.G112fs|PARP9_uc003efh.2_Frame_Shift_Del_p.G147fs|PARP9_uc003efj.2_Frame_Shift_Del_p.G112fs NM_001146102 NP_001139574 Q8IXQ6 PARP9_HUMAN poly (ADP-ribose) polymerase family, member 9 147 Macro 1. cell migration cytosol|nucleus NAD+ ADP-ribosyltransferase activity|protein binding ovary(1)|pancreas(1)|prostate(1)|skin(1) 4 GBM - Glioblastoma multiforme(114;0.0519) GGCCAGGCCTCCCCCATGCAG 0.483 0.46 155 134 SKIL 6498 broad.mit.edu 37 3 170078197 170078197 + Frame_Shift_Del DEL C - - rs141929354 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr3:170078197delC uc003fgu.2 + 2 790 c.78delC c.(76-78)AGCfs p.S26fs SKIL_uc011bps.1_Frame_Shift_Del_p.S6fs|SKIL_uc003fgv.2_Frame_Shift_Del_p.S26fs|SKIL_uc003fgw.2_Frame_Shift_Del_p.S26fs NM_005414 NP_005405 P12757 SKIL_HUMAN SKI-like isoform 1 26 cell cycle arrest|negative regulation of cell differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of axonogenesis|protein heterotrimerization|protein homotrimerization|regulation of apoptosis|regulation of apoptosis|response to antibiotic|response to growth factor stimulus|skeletal muscle tissue development cytoplasm|PML body chromatin binding|nucleotide binding|protein complex binding|protein domain specific binding|SMAD binding|transcription corepressor activity|transcription repressor activity ovary(2)|skin(1) 3 all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137) Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197) ATGATGGCAGCCCCCCAGCGA 0.413 0.55 14 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 99 182 NIPBL 25836 broad.mit.edu 37 5 37020614 37020615 + Frame_Shift_Ins INS - G G AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr5:37020614_37020615insG uc003jkl.3 + 26 5563_5564 c.5064_5065insG c.(5062-5067)ACAGAAfs p.T1688fs NIPBL_uc003jkk.3_Frame_Shift_Ins_p.T1688fs NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 1688_1689 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) CTCTGGAAACAGAAAAAGCAAT 0.366 0.36 18 10 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.44 41 32 PIK3R1 5295 broad.mit.edu 37 5 67591077 67591088 + In_Frame_Del DEL GAGAAATTGACA - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr5:67591077_67591088delGAGAAATTGACA uc003jva.2 + 13 2230_2241 c.1670_1681delGAGAAATTGACA c.(1669-1683)CGAGAAATTGACAAA>CAA p.557_561REIDK>Q PIK3R1_uc003jvb.2_In_Frame_Del_p.557_561REIDK>Q|PIK3R1_uc003jvc.2_In_Frame_Del_p.257_261REIDK>Q|PIK3R1_uc003jvd.2_In_Frame_Del_p.287_291REIDK>Q|PIK3R1_uc003jve.2_In_Frame_Del_p.236_240REIDK>Q|PIK3R1_uc011crb.1_In_Frame_Del_p.227_231REIDK>Q NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 557_561 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.D560_S565del(1)|p.R557_K561>Q(1)|p.D560Y(1)|p.?(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) GCTGAGTATCGAGAAATTGACAAACGTATGAA 0.349 0.68 17 36 RAD50 10111 broad.mit.edu 37 5 131931451 131931452 + Frame_Shift_Ins INS - A A AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr5:131931451_131931452insA uc003kxi.2 + 13 2543_2544 c.2156_2157insA c.(2155-2157)CTAfs p.L719fs RAD50_uc003kxh.2_Frame_Shift_Ins_p.L580fs NM_005732 NP_005723 Q92878 RAD50_HUMAN RAD50 homolog isoform 1 719 Zinc-hook.|Potential. DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding lung(2)|ovary(1)|skin(1) 4 all_cancers(142;0.0368)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GAATCAGAGCTAAAAAAAAAGG 0.416 0.21 31 8 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.58 8 11 NSD1 64324 broad.mit.edu 37 5 176638443 176638444 + Frame_Shift_Del DEL TG - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr5:176638443_176638444delTG uc003mfr.3 + 5 3181_3182 c.3043_3044delTG c.(3043-3045)TGTfs p.C1015fs NSD1_uc003mft.3_Frame_Shift_Del_p.C746fs|NSD1_uc003mfs.1_Frame_Shift_Del_p.C912fs|NSD1_uc011dfx.1_Frame_Shift_Del_p.C663fs NM_022455 NP_071900 Q96L73 NSD1_HUMAN nuclear receptor binding SET domain protein 1 1015 negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|nucleus androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding ovary(2)|kidney(1) 3 all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002) all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198) Kidney(146;0.235) TCGTTCAGACTGTGTTACTAGG 0.485 0.33 194 97 POU5F1 5460 broad.mit.edu 37 6 31138181 31138182 + Frame_Shift_Ins INS - C C AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr6:31138181_31138182insC uc003nsv.2 - 1 270_271 c.216_217insG c.(214-219)GGGATGfs p.G72fs uc011dng.1_RNA NM_002701 NP_002692 Q01860 PO5F1_HUMAN POU domain, class 5, transcription factor 1 72_73 anatomical structure morphogenesis|blastocyst development|BMP signaling pathway involved in heart induction|cardiac cell fate determination|cell fate commitment involved in formation of primary germ layers|mRNA transcription from RNA polymerase II promoter|negative regulation of gene silencing by miRNA|positive regulation of catenin import into nucleus|positive regulation of SMAD protein import into nucleus|positive regulation of transcription from RNA polymerase II promoter|regulation of asymmetric cell division|regulation of heart induction by regulation of canonical Wnt receptor signaling pathway|regulation of methylation-dependent chromatin silencing|response to wounding|somatic stem cell maintenance|somatic stem cell maintenance cytosol|nucleoplasm|transcription factor complex miRNA binding|sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|ubiquitin protein ligase binding EWSR1/POU5F1(10) skin(7)|salivary_gland(2)|bone(2)|lung(1)|ovary(1) 13 CAGTACGCCATCCCCCCACAGA 0.678 0.51 72 76 DNAH8 1769 broad.mit.edu 37 6 38821018 38821018 + Frame_Shift_Del DEL A - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr6:38821018delA uc003ooe.1 + 39 5577 c.4977delA c.(4975-4977)TTAfs p.L1659fs NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 TGGATTTGTTAAAAATGCAGA 0.328 0.30 66 28 PHF3 23469 broad.mit.edu 37 6 64395352 64395352 + Frame_Shift_Del DEL A - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr6:64395352delA uc003pep.1 + 3 1755 c.1729delA c.(1729-1731)AAAfs p.K577fs PHF3_uc010kaf.1_Frame_Shift_Del_p.K577fs|PHF3_uc003pem.2_Frame_Shift_Del_p.K530fs|PHF3_uc010kag.1_Frame_Shift_Del_p.K489fs|PHF3_uc010kah.1_Frame_Shift_Del_p.K391fs|PHF3_uc003pen.2_Frame_Shift_Del_p.K489fs|PHF3_uc011dxs.1_Intron|PHF3_uc003peo.2_Frame_Shift_Del_p.K577fs NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 577 multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) TTCTGTACTGAAAAAAACATT 0.368 0.71 10 24 FYN 2534 broad.mit.edu 37 6 111983042 111983042 + Frame_Shift_Del DEL T - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr6:111983042delT uc003pvj.2 - 13 1854 c.1514delA c.(1513-1515)AAGfs p.K505fs FYN_uc003pvi.2_Frame_Shift_Del_p.K450fs|FYN_uc003pvk.2_Frame_Shift_Del_p.K505fs|FYN_uc003pvh.2_Frame_Shift_Del_p.K502fs NM_002037 NP_002028 P06241 FYN_HUMAN protein-tyrosine kinase fyn isoform a 505 Protein kinase. axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction cytosol|endosome|plasma membrane ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity lung(5)|central_nervous_system(1)|skin(1) 7 all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211) all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102) Dasatinib(DB01254) TTCAGGGTCCTTTTTCCAGCA 0.562 0.35 229 123 TBP 6908 broad.mit.edu 37 6 170871014 170871016 + In_Frame_Del DEL CAG - - rs72320253 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr6:170871014_170871016delCAG uc003qxt.2 + 3 422_424 c.190_192delCAG c.(190-192)CAGdel p.Q95del TBP_uc003qxu.2_In_Frame_Del_p.Q95del|TBP_uc011ehf.1_In_Frame_Del_p.Q75del|TBP_uc011ehg.1_In_Frame_Del_p.Q95del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 95 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacaacaacagcagcagcagc 0.177 0.28 198 78 DBF4 10926 broad.mit.edu 37 7 87537437 87537437 + Frame_Shift_Del DEL T - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr7:87537437delT uc003ujf.1 + 12 2488 c.1984delT c.(1984-1986)TTTfs p.F662fs DBF4_uc003ujh.1_Frame_Shift_Del_p.F402fs|DBF4_uc003ujg.1_Frame_Shift_Del_p.F438fs|DBF4_uc011khf.1_Frame_Shift_Del_p.F429fs NM_006716 NP_006707 Q9UBU7 DBF4A_HUMAN activator of S phase kinase 662 cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle nucleoplasm enzyme activator activity|nucleic acid binding|protein binding|zinc ion binding lung(2) 2 Esophageal squamous(14;0.00202) Breast(660;0.0334) GTTAACAGCGTTTTTCTCGTC 0.308 0.68 21 45 AKAP9 10142 broad.mit.edu 37 7 91699371 91699372 + Frame_Shift_Ins INS - A A AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr7:91699371_91699372insA uc003ulg.2 + 27 6583_6584 c.6358_6359insA c.(6358-6360)GAAfs p.E2120fs AKAP9_uc003ulf.2_Frame_Shift_Ins_p.E2120fs|AKAP9_uc003uli.2_Frame_Shift_Ins_p.E1743fs|AKAP9_uc003ulj.2_5'UTR NM_005751 NP_005742 Q99996 AKAP9_HUMAN A-kinase anchor protein 9 isoform 2 2132 Potential.|Glu-rich. G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport centrosome|cytosol|Golgi apparatus receptor binding breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1) 26 all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) TCATCTGAAAGAAAAAACAGAC 0.297 0.50 10 10 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.78 4 14 KCNH2 3757 broad.mit.edu 37 7 150656679 150656679 + Frame_Shift_Del DEL G - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr7:150656679delG uc003wic.2 - 3 466 c.453delC c.(451-453)CCCfs p.P151fs KCNH2_uc011kux.1_Frame_Shift_Del_p.P55fs|KCNH2_uc003wie.2_Frame_Shift_Del_p.P151fs NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 151 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) GCCAGCTGGTGGGGGGGCCCC 0.587 0.27 107 39 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.92 1 11 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.12 202 28 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 35 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.18 115 26 MLLT3 4300 broad.mit.edu 37 9 20414277 20414278 + In_Frame_Ins INS - CTG CTG AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr9:20414277_20414278insCTG uc003zoe.2 - 5 825_826 c.566_567insCAG c.(565-567)AGT>AGCAGT p.189_189S>SS MLLT3_uc011lne.1_In_Frame_Ins_p.157_157S>SS|MLLT3_uc011lnf.1_In_Frame_Ins_p.186_186S>SS|MLLT3_uc003zof.2_5'UTR NM_004529 NP_004520 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia 189 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding lung(2)|ovary(1) 3 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) AACTGGTActactgctgctgct 0.183 0.28 331 126 TAF1L 138474 broad.mit.edu 37 9 32633025 32633025 + Frame_Shift_Del DEL T - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr9:32633025delT uc003zrg.1 - 1 2643 c.2553delA c.(2551-2553)AAAfs p.K851fs uc003zrh.1_5'Flank NM_153809 NP_722516 Q8IZX4 TAF1L_HUMAN TBP-associated factor RNA polymerase 1-like 851 male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent transcription factor TFIID complex DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1) 26 LUSC - Lung squamous cell carcinoma(29;0.0181) GBM - Glioblastoma multiforme(74;0.00301) AAGGAAAGGCTTTTTTTATAT 0.443 0.52 73 80 PCDH15 65217 broad.mit.edu 37 10 55581645 55581648 + Frame_Shift_Del DEL TTGT - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr10:55581645_55581648delTTGT uc001jju.1 - 33 6233_6236 c.5838_5841delACAA c.(5836-5841)AAACAAfs p.K1946fs PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Frame_Shift_Del_p.K800fs|PCDH15_uc010qhv.1_Frame_Shift_Del_p.K1943fs|PCDH15_uc010qhw.1_Frame_Shift_Del_p.K1906fs|PCDH15_uc010qhx.1_Frame_Shift_Del_p.K1877fs|PCDH15_uc010qhy.1_Frame_Shift_Del_p.K1953fs|PCDH15_uc010qhz.1_Frame_Shift_Del_p.K1948fs|PCDH15_uc010qia.1_Frame_Shift_Del_p.K1926fs|PCDH15_uc010qib.1_Frame_Shift_Del_p.K1923fs NM_033056 NP_149045 Q96QU1 PCD15_HUMAN protocadherin 15 isoform CD1-4 precursor 1946_1947 Cytoplasmic (Potential). equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse calcium ion binding pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2) 13 Melanoma(3;0.117)|Lung SC(717;0.238) GACTGTGAGATTGTTTTTCAGTTC 0.358 0.67 47 95 MYST4 23522 broad.mit.edu 37 10 76781905 76781906 + In_Frame_Ins INS - GAA GAA rs138589645;rs111976843 by1000genomes AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr10:76781905_76781906insGAA uc001jwn.1 + 16 3781_3782 c.3288_3289insGAA c.(3286-3291)insGAA p.1104_1105insE MYST4_uc001jwm.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwo.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwp.1_In_Frame_Ins_p.921_922insE NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1104_1105 histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) aggaagaagaggaagaagaaga 0.203 0.14 64 10 PTEN 5728 broad.mit.edu 37 10 89692905 89692905 + Frame_Shift_Del DEL G - - rs121913292 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr10:89692905delG uc001kfb.2 + 6 1420 c.389delG c.(388-390)CGAfs p.R130fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 130 Phosphatase tensin-type. R -> L (in CD and endometrial hyperplasia; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes).|R -> Q (in CD; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes).|R -> G (loss of phosphatase activity towards Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3). R->M: Does not affect the ability to inhibit AKT/PKB activation. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R130G(65)|p.R130*(61)|p.R130Q(43)|p.R130fs*4(12)|p.R130L(7)|p.R55fs*1(4)|p.R130P(4)|p.K128_R130del(3)|p.Y27_N212>Y(2)|p.?(2)|p.Y27fs*1(2)|p.R130R(1)|p.K128fs*47(1)|p.A121_F145del(1)|p.R130fs*2(1)|p.T131fs*50(1)|p.F56fs*2(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GGAAAGGGACGAACTGGTGTA 0.403 0.97 4 140 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 906 270 ERC1 23085 broad.mit.edu 37 12 1481069 1481071 + In_Frame_Del DEL AAG - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr12:1481069_1481071delAAG uc001qjb.2 + 16 3092_3094 c.2851_2853delAAG c.(2851-2853)AAGdel p.K953del ERC1_uc001qiz.2_RNA|ERC1_uc001qjc.2_In_Frame_Del_p.K925del|ERC1_uc001qja.2_RNA|ERC1_uc001qjd.2_RNA|ERC1_uc001qjf.2_In_Frame_Del_p.K953del|ERC1_uc010sdv.1_In_Frame_Del_p.K661del|ERC1_uc001qje.2_RNA NM_178040 NP_829884 Q8IUD2 RB6I2_HUMAN RAB6-interacting protein 2 isoform epsilon 953 Potential. I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport Golgi membrane|IkappaB kinase complex|presynaptic membrane leucine zipper domain binding ovary(2)|lung(2)|breast(1) 5 all_epithelial(11;0.0698)|Ovarian(42;0.107) OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567) TTCGTCCTCTAAGAAGAAGACCC 0.493 0.56 15 19 DYRK4 8798 broad.mit.edu 37 12 4714200 4714203 + Frame_Shift_Del DEL ACCC - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr12:4714200_4714203delACCC uc001qmx.2 + 9 1062_1065 c.902_905delACCC c.(901-906)TACCCCfs p.Y301fs DYRK4_uc009zeh.1_Frame_Shift_Del_p.Y416fs|DYRK4_uc001qmy.1_Frame_Shift_Del_p.Y301fs|DYRK4_uc001qmz.1_Frame_Shift_Del_p.Y15fs|DYRK4_uc001qna.1_5'UTR|DYRK4_uc010ser.1_5'UTR NM_003845 NP_003836 Q9NR20 DYRK4_HUMAN dual-specificity tyrosine-(Y)-phosphorylation 301_302 Protein kinase. Golgi apparatus ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(2)|skin(1) 3 Colorectal(7;0.103) TACACGGGCTACCCCCTGTTCCCC 0.657 0.45 46 37 GUCY2C 2984 broad.mit.edu 37 12 14775080 14775081 + Frame_Shift_Del DEL AT - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr12:14775080_14775081delAT uc001rcd.2 - 22 2596_2597 c.2459_2460delAT c.(2458-2460)TATfs p.Y820fs NM_004963 NP_004954 P25092 GUC2C_HUMAN guanylate cyclase 2C precursor 820 Cytoplasmic (Potential). intracellular signal transduction|receptor guanylyl cyclase signaling pathway integral to membrane ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity ovary(4)|skin(2) 6 TAACTTCCTCATATAGTTCCGG 0.411 0.50 79 80 LRRK2 120892 broad.mit.edu 37 12 40702287 40702287 + Frame_Shift_Del DEL A - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr12:40702287delA uc001rmg.3 + 29 4099 c.3978delA c.(3976-3978)TTAfs p.L1326fs LRRK2_uc009zjw.2_Frame_Shift_Del_p.L164fs|LRRK2_uc001rmi.2_Frame_Shift_Del_p.L159fs NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 1326 activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) AACAGCGATTAAAAAAGGCTG 0.313 0.57 16 21 TWF1 5756 broad.mit.edu 37 12 44191239 44191239 + Frame_Shift_Del DEL T - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr12:44191239delT uc001rob.2 - 8 777 c.749delA c.(748-750)AATfs p.N250fs TWF1_uc001rnz.2_Frame_Shift_Del_p.N111fs|TWF1_uc001roa.2_Frame_Shift_Del_p.N243fs|TWF1_uc001roc.2_Frame_Shift_Del_p.N111fs NM_002822 NP_002813 Q12792 TWF1_HUMAN twinfilin 1 209 ADF-H 2. actin cytoskeleton|cytoplasm actin binding|protein tyrosine kinase activity stomach(1) 1 all_cancers(12;0.00125) Lung NSC(34;0.0804)|all_lung(34;0.181) GBM - Glioblastoma multiforme(48;0.0474) TATAATTTCATTTTTTATATC 0.279 0.44 10 8 GLI1 2735 broad.mit.edu 37 12 57860075 57860075 + Frame_Shift_Del DEL G - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr12:57860075delG uc001snx.2 + 8 893 c.815delG c.(814-816)TGGfs p.W272fs GLI1_uc009zpq.2_Frame_Shift_Del_p.W144fs NM_005269 NP_005260 P08151 GLI1_HUMAN GLI family zinc finger 1 isoform 1 272 C2H2-type 2. epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter cytosol|nucleus transcription regulatory region DNA binding|zinc ion binding skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1) 15 GBM - Glioblastoma multiforme(3;3.99e-32) GTGTGCCACTGGGGGGGCTGC 0.597 0.44 242 189 EDNRB 1910 broad.mit.edu 37 13 78475267 78475267 + Frame_Shift_Del DEL A - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr13:78475267delA uc001vko.2 - 4 1135 c.877delT c.(877-879)TATfs p.Y293fs EDNRB_uc001vkq.1_Frame_Shift_Del_p.Y293fs|uc001vkn.1_Intron|EDNRB_uc010aez.1_Frame_Shift_Del_p.Y293fs|EDNRB_uc001vkp.1_Frame_Shift_Del_p.Y376fs NM_001122659 NP_001116131 P24530 EDNRB_HUMAN endothelin receptor type B isoform 1 precursor 293 Helical; Name=5; (Potential). activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction integral to plasma membrane endothelin-B receptor activity|peptide hormone binding 0 Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037) GBM - Glioblastoma multiforme(99;0.0933) Bosentan(DB00559) ATTAGTGTATAAAAAAATGCA 0.343 0.36 27 15 ERCC5 2073 broad.mit.edu 37 13 103524611 103524612 + Frame_Shift_Ins INS - A A AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr13:103524611_103524612insA uc001vpw.2 + 13 3185_3186 c.2742_2743insA c.(2740-2745)GTGAAAfs p.V914fs ERCC5_uc001vpu.1_Frame_Shift_Ins_p.V1368fs|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_Frame_Shift_Ins_p.V746fs NM_000123 NP_000114 P28715 ERCC5_HUMAN XPG-complementing protein 914_915 negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection nucleoplasm bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding ovary(4)|lung(1)|central_nervous_system(1)|skin(1) 7 all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211) ACACCAAAGTGAAAAAAAAATT 0.431 0.36 43 24 IRS2 8660 broad.mit.edu 37 13 110435136 110435136 + Frame_Shift_Del DEL C - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr13:110435136delC uc001vqv.2 - 1 3779 c.3265delG c.(3265-3267)GCCfs p.A1089fs NM_003749 NP_003740 Q9Y4H2 IRS2_HUMAN insulin receptor substrate 2 1089 fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus cytosol|plasma membrane insulin receptor binding|signal transducer activity large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|skin(1)|ovary(1)|kidney(1) 8 all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155) Breast(118;0.159) all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147) 0.000 0.49 317 305 ING1 3621 broad.mit.edu 37 13 111367902 111367903 + Frame_Shift_Ins INS - T T AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr13:111367902_111367903insT uc001vri.2 + 1 544_545 c.112_113insT c.(112-114)CTTfs p.L38fs CARS2_uc010tjm.1_5'Flank|uc001vre.2_5'Flank|ING1_uc001vrf.2_Intron|ING1_uc001vrg.2_Intron|ING1_uc001vrh.2_Intron NM_005537 NP_005528 Q9UK53 ING1_HUMAN inhibitor of growth family, member 1 isoform D 38 cell cycle|negative regulation of cell growth|negative regulation of cell proliferation nucleus zinc ion binding ovary(1) 1 all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148) BRCA - Breast invasive adenocarcinoma(86;0.188) CCGCTGTCTTCTTTTTTCTTTT 0.559 0.52 32 34 CHD8 57680 broad.mit.edu 37 14 21869596 21869596 + Frame_Shift_Del DEL T - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr14:21869596delT uc001was.1 - 21 3396 c.3302delA c.(3301-3303)AAGfs p.K1101fs CHD8_uc001war.1_Frame_Shift_Del_p.K997fs|CHD8_uc001wav.1_Frame_Shift_Del_p.K543fs NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 1380 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) TAGGTCAGCCTTTTTGGCCCA 0.443 0.46 43 37 NOVA1 4857 broad.mit.edu 37 14 27066542 27066543 + Frame_Shift_Del DEL GG - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr14:27066542_27066543delGG uc001wpy.2 - 1 418_419 c.100_101delCC c.(100-102)CCTfs p.P34fs NOVA1_uc001wpz.2_Frame_Shift_Del_p.P34fs|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_Frame_Shift_Del_p.P34fs NM_002515 NP_002506 P51513 NOVA1_HUMAN neuro-oncological ventral antigen 1 isoform 1 34 Bipartite nuclear localization signal (Potential). locomotory behavior|RNA splicing|synaptic transmission nucleus RNA binding skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1) 5 GBM - Glioblastoma multiforme(265;0.0135) 0.000 0.57 603 807 RAB15 376267 broad.mit.edu 37 14 65417684 65417685 + Frame_Shift_Ins INS - G G AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr14:65417684_65417685insG uc001xhz.2 - 4 512_513 c.431_432insC c.(430-432)CCAfs p.P144fs FNTB_uc010tsl.1_Intron|FNTB_uc010tsm.1_Intron|RAB15_uc010aqk.2_RNA NM_198686 NP_941959 P59190 RAB15_HUMAN RAB15, member RAS onocogene family Error:Variant_position_missing_in_P59190_after_alignment protein transport|small GTPase mediated signal transduction plasma membrane GTP binding ovary(1) 1 all cancers(60;0.00136)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.0102) TCCAGGGCTGTGGAAGGCAAAG 0.604 0.10 224 24 PSEN1 5663 broad.mit.edu 37 14 73664814 73664814 + Frame_Shift_Del DEL T - - rs63750050 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr14:73664814delT uc001xnr.2 + 8 1129 c.845delT c.(844-846)CTTfs p.L282fs PSEN1_uc001xnv.2_Frame_Shift_Del_p.L278fs|PSEN1_uc010ark.2_Frame_Shift_Del_p.L278fs|PSEN1_uc001xnt.1_RNA|PSEN1_uc001xnu.2_RNA NM_000021 NP_000012 P49768 PSN1_HUMAN presenilin 1 isoform I-467 282 Cytoplasmic (Potential). L -> R (in AD3). amyloid precursor protein catabolic process|anti-apoptosis|beta-amyloid metabolic process|cell-cell adhesion|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|smooth endoplasmic reticulum calcium ion homeostasis apical plasma membrane|axon|cell cortex|cell surface|centrosome|ciliary rootlet|dendritic shaft|endoplasmic reticulum membrane|gamma-secretase complex|Golgi membrane|growth cone|integral to plasma membrane|kinetochore|lysosomal membrane|membrane raft|mitochondrial inner membrane|neuromuscular junction|neuronal cell body|nuclear outer membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum|smooth endoplasmic reticulum|Z disc aspartic-type endopeptidase activity|beta-catenin binding|cadherin binding|calcium channel activity|PDZ domain binding breast(1)|kidney(1) 2 BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.075) AATGAAACGCTTTTTCCAGCT 0.368 0.39 39 25 TRIP11 9321 broad.mit.edu 37 14 92439199 92439199 + Frame_Shift_Del DEL A - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr14:92439199delA uc001xzy.2 - 20 6369 c.5581delT c.(5581-5583)TCAfs p.S1861fs TRIP11_uc010auf.1_Frame_Shift_Del_p.S1597fs NM_004239 NP_004230 Q15643 TRIPB_HUMAN thyroid hormone receptor interactor 11 1861 transcription from RNA polymerase II promoter cytoskeleton|Golgi apparatus|membrane|nucleus protein binding|transcription coactivator activity ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1) 13 COAD - Colon adenocarcinoma(157;0.223) AAAAGTTCTGAAAAAGACTAA 0.299 0.38 8 5 SRP14 6727 broad.mit.edu 37 15 40328597 40328599 + In_Frame_Del DEL TGC - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr15:40328597_40328599delTGC uc001zkq.2 - 5 418_420 c.346_348delGCA c.(346-348)GCAdel p.A116del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgcggcaggtgctgctgctgct 0.227 0.23 133 40 BUB1B 701 broad.mit.edu 37 15 40477506 40477506 + Frame_Shift_Del DEL C - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr15:40477506delC uc001zkx.3 + 7 1104 c.892delC c.(892-894)CCCfs p.P298fs BUB1B_uc010ucl.1_Frame_Shift_Del_p.P161fs NM_001211 NP_001202 O60566 BUB1B_HUMAN budding uninhibited by benzimidazoles 1 beta 298 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone ATP binding|protein binding|protein serine/threonine kinase activity stomach(2)|ovary(1)|kidney(1) 4 all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556) ATGGATAGCACCCCCCATGCC 0.478 0.41 73 51 SBK1 388228 broad.mit.edu 37 16 28331960 28331961 + Frame_Shift_Ins INS - C C AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr16:28331960_28331961insC uc002dpd.2 + 4 1782_1783 c.993_994insC c.(991-996)AAGCCCfs p.K331fs NM_001024401 NP_001019572 Q52WX2 SBK1_HUMAN SH3-binding kinase 1 331_332 Pro-rich. cytoplasm ATP binding|protein serine/threonine kinase activity ovary(1)|kidney(1) 2 0.000 0.36 57 32 GSG2 83903 broad.mit.edu 37 17 3628460 3628461 + Frame_Shift_Del DEL TC - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr17:3628460_3628461delTC uc002fwp.2 + 1 1264_1265 c.1231_1232delTC c.(1231-1233)TCTfs p.S411fs ITGAE_uc002fwo.3_Intron|ITGAE_uc002fwn.3_5'Flank NM_031965 NP_114171 Q8TF76 HASP_HUMAN haspin 411 cell cycle|chromatin modification|intracellular protein kinase cascade nucleus ATP binding|protein serine/threonine kinase activity 0 CACTGCCACTTCTCTCTCTGGA 0.475 0.31 119 53 RABEP1 9135 broad.mit.edu 37 17 5268420 5268420 + Frame_Shift_Del DEL A - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr17:5268420delA uc002gbm.3 + 11 1896 c.1672delA c.(1672-1674)AAAfs p.K558fs RABEP1_uc010clc.1_Frame_Shift_Del_p.K551fs|RABEP1_uc010cld.1_Frame_Shift_Del_p.K515fs|RABEP1_uc010vsw.1_Frame_Shift_Del_p.K515fs|RABEP1_uc002gbl.3_Frame_Shift_Del_p.K558fs|NUP88_uc002gbn.2_Intron NM_004703 NP_004694 Q15276 RABE1_HUMAN rabaptin, RAB GTPase binding effector protein 1 558 Potential. apoptosis|cellular membrane fusion|endocytosis|protein transport centrosome|early endosome|endocytic vesicle|recycling endosome growth factor activity|GTPase activator activity|protein homodimerization activity large_intestine(1)|ovary(1) 2 0.000 0.49 151 143 TP53 7157 broad.mit.edu 37 17 7579420 7579420 + Frame_Shift_Del DEL G - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr17:7579420delG uc002gim.2 - 4 461 c.267delC c.(265-267)CCCfs p.P89fs TP53_uc002gig.1_Frame_Shift_Del_p.P89fs|TP53_uc002gih.2_Frame_Shift_Del_p.P89fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.P89fs|TP53_uc010cni.1_Frame_Shift_Del_p.P89fs|TP53_uc002gij.2_Frame_Shift_Del_p.P89fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.P50fs|TP53_uc010cnk.1_Frame_Shift_Del_p.P104fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 89 Interaction with WWOX. P -> L (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.A76_S90del15(3)|p.P89S(3)|p.G59fs*23(3)|p.P89fs*60(1)|p.V73fs*9(1)|p.D48fs*55(1)|p.P85fs*58(1)|p.S33fs*23(1)|p.A86fs*33(1)|p.A86fs*32(1)|p.P87fs*54(1)|p.P13fs*18(1)|p.A88fs*52(1)|p.P89L(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGGGCCAGGAGGGGGCTGGTG 0.627 0.50 5 5 MAPK7 5598 broad.mit.edu 37 17 19285630 19285630 + Frame_Shift_Del DEL C - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr17:19285630delC uc002gvn.2 + 5 2400 c.2014delC c.(2014-2016)CCCfs p.P672fs MAPK7_uc002gvo.2_Frame_Shift_Del_p.P533fs|MAPK7_uc002gvq.2_Frame_Shift_Del_p.P672fs|MAPK7_uc002gvp.2_Frame_Shift_Del_p.P672fs|uc010vyt.1_5'Flank NM_139033 NP_620602 Q13164 MK07_HUMAN mitogen-activated protein kinase 7 isoform 1 672 May not be required for kinase activity; required to stimulate MEF2C activity (By similarity).|Pro-rich. cell cycle|cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|MAP kinase activity|protein binding central_nervous_system(4)|lung(3)|stomach(1)|skin(1) 9 all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206) ACTTGTGCCACCCCCTGGGCT 0.697 0.47 16 14 STAT5A 6776 broad.mit.edu 37 17 40453398 40453399 + Frame_Shift_Ins INS - C C rs146398782 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr17:40453398_40453399insC uc002hzj.1 + 10 1737_1738 c.1095_1096insC c.(1093-1098)AATCCCfs p.N365fs STAT5A_uc010cya.1_Frame_Shift_Ins_p.N365fs|STAT5A_uc010cyb.1_Frame_Shift_Ins_p.N365fs|STAT5A_uc010cyc.1_Frame_Shift_Ins_p.N335fs NM_003152 NP_003143 P42229 STA5A_HUMAN signal transducer and activator of transcription 365_366 2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|oxaloacetate metabolic process|succinate metabolic process|taurine metabolic process|valine metabolic process cytosol|nucleoplasm calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity lung(1) 1 all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.128) TGCACATGAATCCCCCCCAGGT 0.564 0.38 157 95 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.25 39 13 ALPK2 115701 broad.mit.edu 37 18 56246440 56246440 + Frame_Shift_Del DEL T - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr18:56246440delT uc002lhj.3 - 4 1782 c.1568delA c.(1567-1569)AAGfs p.K523fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 523 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 CCATAAGTCCTTTCCCCCCAC 0.522 0.44 182 142 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.72 83 214 TP53RK 112858 broad.mit.edu 37 20 45315440 45315440 + Frame_Shift_Del DEL T - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr20:45315440delT uc002xsk.2 - 2 937 c.714delA c.(712-714)AAAfs p.K238fs SLC13A3_uc002xsg.1_5'Flank|SLC13A3_uc010gho.1_5'Flank|TP53RK_uc002xsj.2_3'UTR NM_033550 NP_291028 Q96S44 PRPK_HUMAN p53-related protein kinase 238 Protein kinase. lipopolysaccharide biosynthetic process membrane|nucleus ATP binding|p53 binding|protein serine/threonine kinase activity|protein tyrosine kinase activity 0 Myeloproliferative disorder(115;0.0122) CTTCATCTAATTTTTTTAGCA 0.448 0.42 84 61 GNAS 2778 broad.mit.edu 37 20 57428975 57428975 + Frame_Shift_Del DEL C - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr20:57428975delC uc002xzw.2 + 1 940 c.655delC c.(655-657)CCCfs p.P219fs GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_RNA NM_080425 NP_536350 P63092 GNAS2_HUMAN GNAS complex locus XLas Error:Variant_position_missing_in_P63092_after_alignment activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1) 292 all_lung(29;0.0104) BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109) CTACAGCCCTCCCCCTGAGGA 0.647 0.38 31 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 51 301 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 87 MED15 51586 broad.mit.edu 37 22 20918916 20918918 + In_Frame_Del DEL CAG - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr22:20918916_20918918delCAG uc002zsp.2 + 6 711_713 c.631_633delCAG c.(631-633)CAGdel p.Q218del MED15_uc002zsn.1_In_Frame_Del_p.Q137del|MED15_uc002zso.2_In_Frame_Del_p.Q147del|MED15_uc002zsq.2_In_Frame_Del_p.Q218del|MED15_uc010gso.2_In_Frame_Del_p.Q218del|MED15_uc002zsr.2_In_Frame_Del_p.Q192del|MED15_uc011ahs.1_In_Frame_Del_p.Q192del|MED15_uc011aht.1_In_Frame_Del_p.Q192del|MED15_uc002zss.2_In_Frame_Del_p.Q137del|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 218 Poly-Gln. Missing (in Ref. 4; CAG30423). regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) gcagcagctccagcagcagcagc 0.187 0.33 56 27 MYH9 4627 broad.mit.edu 37 22 36708257 36708257 + Frame_Shift_Del DEL G - - AN3CA_ENDOMETRIUM NA AN3CA_ENDOMETRIUM NA g.chr22:36708257delG uc003apg.2 - 14 1796 c.1565delC c.(1564-1566)CCGfs p.P522fs MYH9_uc003aph.1_Frame_Shift_Del_p.P386fs NM_002473 NP_002464 P35579 MYH9_HUMAN myosin, heavy polypeptide 9, non-muscle 522 Myosin head-like. actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1) 11 CAGAATGCCCGGGGGGCCTGC 0.642 0.34 142 74 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 5 88 GPR112 139378 broad.mit.edu 37 X 135429987 135429987 + Frame_Shift_Del DEL T - - ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chrX:135429987delT uc004ezu.1 + 6 4413 c.4122delT c.(4120-4122)ACTfs p.T1374fs GPR112_uc010nsb.1_Frame_Shift_Del_p.T1169fs|GPR112_uc010nsc.1_Frame_Shift_Del_p.T1141fs NM_153834 NP_722576 Q8IZF6 GP112_HUMAN G-protein coupled receptor 112 1374 Extracellular (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1) 12 Acute lymphoblastic leukemia(192;0.000127) CAATCACCACTTTTTTGTGTC 0.458 0.94 13 202 ARID1A 8289 broad.mit.edu 37 1 27023401 27023401 + Frame_Shift_Del DEL C - - ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr1:27023401delC uc001bmv.1 + 1 880 c.507delC c.(505-507)TTCfs p.F169fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.F169fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.F169fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 169 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.97 4 136 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.35 203 110 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 104 104 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.16 66 13 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.84 3 16 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.67 97 201 CDKN2A 1029 broad.mit.edu 37 9 21971124 21971125 + Frame_Shift_Del DEL GA - - ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr9:21971124_21971125delGA uc003zpk.2 - 2 445_446 c.233_234delTC c.(232-234)CTCfs p.L78fs MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Frame_Shift_Del_p.S133fs NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 78 ANK 3. cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.L78fs*41(17)|p.?(13)|p.E61_L94del(1)|p.L78fs*68(1)|p.A76fs*64(1)|p.T79fs*41(1)|p.L65fs*38(1)|p.L78fs*67(1)|p.A68fs*3(1)|p.L78H(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) 0.000 0.26 390 140 KSR2 283455 broad.mit.edu 37 12 117992990 117992991 + Frame_Shift_Ins INS - T T ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr12:117992990_117992991insT uc001two.2 - 9 1469_1470 c.1414_1415insA c.(1414-1416)ACCfs p.T472fs NM_173598 NP_775869 Q6VAB6 KSR2_HUMAN kinase suppressor of ras 2 501 intracellular signal transduction cytoplasm|membrane ATP binding|metal ion binding|protein serine/threonine kinase activity lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1) 15 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) GATTTTGTTGGTTTTGGGGAGC 0.569 0.64 129 232 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.29 48 20 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.78 7 25 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 2 25 TP53 7157 broad.mit.edu 37 17 7578527 7578527 + Frame_Shift_Del DEL A - - ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr17:7578527delA uc002gim.2 - 5 597 c.403delT c.(403-405)TGCfs p.C135fs TP53_uc002gig.1_Frame_Shift_Del_p.C135fs|TP53_uc002gih.2_Frame_Shift_Del_p.C135fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.C3fs|TP53_uc010cng.1_Frame_Shift_Del_p.C3fs|TP53_uc002gii.1_Frame_Shift_Del_p.C3fs|TP53_uc010cnh.1_Frame_Shift_Del_p.C135fs|TP53_uc010cni.1_Frame_Shift_Del_p.C135fs|TP53_uc002gij.2_Frame_Shift_Del_p.C135fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.C42fs|TP53_uc002gio.2_Frame_Shift_Del_p.C3fs|TP53_uc010vug.1_Frame_Shift_Del_p.C96fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 135 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). C -> S (in sporadic cancers; somatic mutation).|C -> Y (in sporadic cancers; somatic mutation; decreased E6-mediated binding to E6-AP).|C -> T (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> R (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> F (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.C135Y(49)|p.C135F(34)|p.C135W(19)|p.C135S(10)|p.C135fs*35(9)|p.0?(7)|p.C135*(7)|p.C135G(6)|p.C135R(6)|p.C135C(5)|p.C135fs*14(2)|p.N131fs*27(2)|p.F134_T140>S(1)|p.K132_A138delKMFCQLA(1)|p.S127_Q136del10(1)|p.C135T(1)|p.V73fs*9(1)|p.C135fs*36(1)|p.C135fs*15(1)|p.Y126fs*11(1)|p.C135_A138delCQLA(1)|p.M133fs*13(1)|p.C135_T140delCQLAKT(1)|p.C135_Q136insXXXXXX(1)|p.C135_Q136insX(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GCCAGTTGGCAAAACATCTTG 0.567 0.87 11 76 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.72 27 70 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 53 349 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ASPC1_PANCREAS NA ASPC1_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.84 12 65 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.48 17 16 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.33 12 6 MAGI1 9223 broad.mit.edu 37 3 65425586 65425591 + In_Frame_Del DEL TGCTGT - - rs62637700;rs139785185;rs35698502;rs79701778 byFrequency BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:65425586_65425591delTGCTGT uc003dmn.2 - 9 1759_1764 c.1233_1238delACAGCA c.(1231-1239)CAACAGCAG>CAG p.411_413QQQ>Q MAGI1_uc003dmm.2_In_Frame_Del_p.411_413QQQ>Q|MAGI1_uc003dmo.2_In_Frame_Del_p.411_413QQQ>Q|MAGI1_uc003dmp.2_In_Frame_Del_p.411_413QQQ>Q|MAGI1_uc010hny.2_In_Frame_Del_p.296_298QQQ>Q NM_001033057 NP_001028229 Q96QZ7 MAGI1_HUMAN membrane associated guanylate kinase, WW and PDZ 411_413 Poly-Gln. cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly tight junction ATP binding|protein C-terminus binding lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1) 6 Lung NSC(201;0.0016) BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133) ctgctgctgctgctgttgctgctgct 0.354 0.25 87 29 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.34 19 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 107 159 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 17 39 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.18 47 10 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.83 2 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 3 60 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.11 124 15 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.42 69 50 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 724 379 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.18 143 31 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 35 515 KIAA0802 23255 broad.mit.edu 37 18 8825273 8825274 + Frame_Shift_Ins INS - A A BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr18:8825273_8825274insA uc002knr.2 + 15 3907_3908 c.3765_3766insA c.(3763-3768)CGCCCCfs p.R1255fs KIAA0802_uc002knq.2_Frame_Shift_Ins_p.R1214fs|KIAA0802_uc002kns.2_Frame_Shift_Ins_p.R595fs NM_015210 NP_056025 Q9Y4B5 CC165_HUMAN hypothetical protein LOC23255 1565_1566 0 GGGCACGGCGCCCCCTTGATAG 0.634 0.46 58 50 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.72 59 154 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.28 36 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 113 476 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 7 55 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BCPAP_THYROID NA BCPAP_THYROID NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 6 57 ARID1A 8289 broad.mit.edu 37 1 27023909 27023923 + In_Frame_Del DEL GCTGCGGCGGCGGCA - - BCPAP_THYROID NA BCPAP_THYROID NA g.chr1:27023909_27023923delGCTGCGGCGGCGGCA uc001bmv.1 + 1 1388_1402 c.1015_1029delGCTGCGGCGGCGGCA c.(1015-1029)GCTGCGGCGGCGGCAdel p.AAAAA344del ARID1A_uc001bmt.1_In_Frame_Del_p.AAAAA344del|ARID1A_uc001bmu.1_In_Frame_Del_p.AAAAA344del NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 344_348 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.A339fs*24(1)|p.A344_A348del(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.11 85 11 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes BCPAP_THYROID NA BCPAP_THYROID NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.53 9 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BCPAP_THYROID NA BCPAP_THYROID NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 89 154 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BCPAP_THYROID NA BCPAP_THYROID NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.22 64 18 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes BCPAP_THYROID NA BCPAP_THYROID NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.92 1 11 ATXN1 6310 broad.mit.edu 37 6 16327916 16327918 + In_Frame_Del DEL TGC - - rs28555263 BCPAP_THYROID NA BCPAP_THYROID NA g.chr6:16327916_16327918delTGC uc003nbt.2 - 8 1595_1597 c.624_626delGCA c.(622-627)CAGCAT>CAT p.Q208del ATXN1_uc010jpi.2_In_Frame_Del_p.Q208del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 208 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgatgctgatgctgctgctgct 0.379 0.15 56 10 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes BCPAP_THYROID NA BCPAP_THYROID NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 12 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 BCPAP_THYROID NA BCPAP_THYROID NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.67 4 8 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency BCPAP_THYROID NA BCPAP_THYROID NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.11 216 28 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 BCPAP_THYROID NA BCPAP_THYROID NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.47 10 9 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BCPAP_THYROID NA BCPAP_THYROID NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 1 17 CHERP 10523 broad.mit.edu 37 19 16640563 16640564 + In_Frame_Ins INS - GCTGCTGCT GCTGCTGCT BCPAP_THYROID NA BCPAP_THYROID NA g.chr19:16640563_16640564insGCTGCTGCT uc002nei.1 - 8 1098_1099 c.1024_1025insAGCAGCAGC c.(1024-1026)CTC>CAGCAGCAGCTC p.341_342insQQQ MED26_uc002nee.2_Intron NM_006387 NP_006378 Q8IWX8 CHERP_HUMAN calcium homeostasis endoplasmic reticulum 341_342 Gln-rich. cellular calcium ion homeostasis|negative regulation of cell proliferation|nervous system development|RNA processing endoplasmic reticulum|perinuclear region of cytoplasm RNA binding ovary(2) 2 CGGCATCTGGAgctgctgctgc 0.554 0.31 67 30 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BCPAP_THYROID NA BCPAP_THYROID NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 37 399 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BCPAP_THYROID NA BCPAP_THYROID NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 74 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 BCPAP_THYROID NA BCPAP_THYROID NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 0.000 0.15 403 70 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 21 TTN 7273 broad.mit.edu 37 2 179563643 179563643 + Splice_Site DEL T - - BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179563643delT uc010zfg.1 - 109 27175 c.26951_splice c.e109-1 p.V8984_splice TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Splice_Site_p.V5645_splice|TTN_uc010fre.1_Splice_Site_p.V95_splice NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTTTGGTAACTaaaaaaaaaa 0.264 0.13 47 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.17 44 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 79 84 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 30 64 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.18 296 65 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 15 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.27 38 14 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 69 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 263 143 TRIM29 23650 broad.mit.edu 37 11 120008680 120008681 + Frame_Shift_Ins INS - T T BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:120008680_120008681insT uc001pwz.2 - 1 183_184 c.59_60insA c.(58-60)CGGfs p.R20fs TRIM29_uc001pxa.2_RNA NM_012101 NP_036233 Q14134 TRI29_HUMAN tripartite motif protein TRIM29 20 transcription from RNA polymerase II promoter cytoplasm protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1)|breast(1)|kidney(1)|skin(1) 4 Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;5.37e-06) 0.000 1.00 0 11 ZNF384 171017 broad.mit.edu 37 12 6777070 6777081 + In_Frame_Del DEL TGCTGCTGCTGC - - rs151322806;rs111332695;rs78573212;rs1052680;rs149757410;rs72393318 BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:6777070_6777081delTGCTGCTGCTGC uc010sfh.1 - 11 1741_1752 c.1533_1544delGCAGCAGCAGCA c.(1531-1545)CAGCAGCAGCAGCAA>CAA p.511_515QQQQQ>Q ZNF384_uc001qpz.2_In_Frame_Del_p.450_454QQQQQ>Q|ZNF384_uc001qqa.2_In_Frame_Del_p.450_454QQQQQ>Q|ZNF384_uc001qqb.2_In_Frame_Del_p.434_438QQQQQ>Q|ZNF384_uc001qqc.2_In_Frame_Del_p.450_454QQQQQ>Q|ZNF384_uc001qqd.2_In_Frame_Del_p.395_399QQQQQ>Q|ZNF384_uc001qqe.2_In_Frame_Del_p.434_438QQQQQ>Q NM_001135734 NP_001129206 Q8TF68 ZN384_HUMAN nuclear matrix transcription factor 4 isoform d 511_515 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding EWSR1/ZNF384(4) haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1) 8 TGGTGgctgttgctgctgctgctgctgctgct 0.325 0.21 77 20 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 37 266 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.45 51 41 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 139 28 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 153 645 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 5 51 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BEN_LUNG NA BEN_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 32 TTN 7273 broad.mit.edu 37 2 179595488 179595489 + Frame_Shift_Ins INS - T T BEN_LUNG NA BEN_LUNG NA g.chr2:179595488_179595489insT uc010zfg.1 - 58 14263_14264 c.14039_14040insA c.(14038-14040)AAGfs p.K4680fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Ins_p.K1341fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 5607 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTTTCTTCAGCTTTTTGGTGAA 0.327 0.20 131 32 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A BEN_LUNG NA BEN_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.13 47 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BEN_LUNG NA BEN_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 39 46 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BEN_LUNG NA BEN_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.58 8 11 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 BEN_LUNG NA BEN_LUNG NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.84 3 16 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 BEN_LUNG NA BEN_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.50 8 8 ADAM32 203102 broad.mit.edu 37 8 38994213 38994214 + Frame_Shift_Del DEL TG - - BEN_LUNG NA BEN_LUNG NA g.chr8:38994213_38994214delTG uc003xmt.3 + 3 421_422 c.176_177delTG c.(175-177)CTGfs p.L59fs ADAM32_uc011lch.1_Frame_Shift_Del_p.L66fs|ADAM32_uc003xmu.3_Frame_Shift_Del_p.L59fs NM_145004 NP_659441 Q8TC27 ADA32_HUMAN a disintegrin and metalloprotease domain 32 59 proteolysis integral to membrane metalloendopeptidase activity|zinc ion binding ovary(1)|lung(1)|kidney(1) 3 all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503) LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146) GATGAGAAACTGTACACTGTGC 0.282 0.70 24 55 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 BEN_LUNG NA BEN_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency BEN_LUNG NA BEN_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 376 44 PCDH15 65217 broad.mit.edu 37 10 56077145 56077146 + Frame_Shift_Ins INS - T T BEN_LUNG NA BEN_LUNG NA g.chr10:56077145_56077146insT uc001jju.1 - 8 1156_1157 c.761_762insA c.(760-762)GATfs p.D254fs PCDH15_uc010qhq.1_Frame_Shift_Ins_p.D259fs|PCDH15_uc010qhr.1_Frame_Shift_Ins_p.D254fs|PCDH15_uc010qhs.1_Frame_Shift_Ins_p.D259fs|PCDH15_uc010qht.1_Frame_Shift_Ins_p.D254fs|PCDH15_uc010qhu.1_Frame_Shift_Ins_p.D254fs|PCDH15_uc001jjv.1_Frame_Shift_Ins_p.D232fs|PCDH15_uc010qhv.1_Frame_Shift_Ins_p.D254fs|PCDH15_uc010qhw.1_Frame_Shift_Ins_p.D217fs|PCDH15_uc010qhx.1_Frame_Shift_Ins_p.D254fs|PCDH15_uc010qhy.1_Frame_Shift_Ins_p.D259fs|PCDH15_uc010qhz.1_Frame_Shift_Ins_p.D254fs|PCDH15_uc010qia.1_Frame_Shift_Ins_p.D232fs|PCDH15_uc010qib.1_Frame_Shift_Ins_p.D232fs|PCDH15_uc001jjw.2_Frame_Shift_Ins_p.D254fs NM_033056 NP_149045 Q96QU1 PCD15_HUMAN protocadherin 15 isoform CD1-4 precursor 254 Extracellular (Potential).|Cadherin 2. equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse calcium ion binding pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2) 13 Melanoma(3;0.117)|Lung SC(717;0.238) CATCCAGAACATCCACTGTGAG 0.470 0.22 86 24 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BEN_LUNG NA BEN_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 205 105 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 BEN_LUNG NA BEN_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.81 3 13 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BEN_LUNG NA BEN_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 10 126 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT BEN_LUNG NA BEN_LUNG NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.15 412 73 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BEN_LUNG NA BEN_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.48 44 41 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 BEN_LUNG NA BEN_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.20 207 52 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BEN_LUNG NA BEN_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 106 512 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BEN_LUNG NA BEN_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 3 39 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes BEN_LUNG NA BEN_LUNG NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.23 82 24 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 71 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.43 168 129 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 7 5 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.37 19 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 29 37 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.57 17 23 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.75 74 217 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.65 154 290 C9orf96 169436 broad.mit.edu 37 9 136249678 136249680 + In_Frame_Del DEL GGA - - BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr9:136249678_136249680delGGA uc004cdk.2 + 3 274_276 c.213_215delGGA c.(211-216)CTGGAG>CTG p.E73del C9orf96_uc004cdl.2_RNA NM_153710 NP_714921 Q8NE28 SGK71_HUMAN hypothetical protein LOC169436 73 Protein kinase. ATP binding|protein kinase activity stomach(2)|central_nervous_system(2) 4 OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05) GTCAGGCCCTGGAGGAGGTAACT 0.463 0.84 45 232 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.48 29 27 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 165 44 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.16 157 30 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.21 27 7 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.26 78 27 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.95 22 424 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 45 MAPK8IP2 23542 broad.mit.edu 37 22 51042336 51042337 + Frame_Shift_Ins INS - T T rs116947359 by1000genomes BFTC905_URINARY_TRACT NA BFTC905_URINARY_TRACT NA g.chr22:51042336_51042337insT uc003bmx.2 + 5 725_726 c.608_609insT c.(607-609)GGTfs p.G203fs MAPK8IP2_uc003bmy.2_Frame_Shift_Ins_p.G176fs|MAPK8IP2_uc011asc.1_5'Flank NM_012324 NP_036456 Q13387 JIP2_HUMAN mitogen-activated protein kinase 8 interacting 203 JNK-binding domain (JBD). behavioral fear response|dendrite morphogenesis|MAPKKK cascade|nonassociative learning|positive regulation of anti-apoptosis|regulation of excitatory postsynaptic membrane potential|regulation of JNK cascade|regulation of receptor activity|regulation of synaptic transmission, glutamatergic|signal complex assembly|social behavior cytoplasm|postsynaptic density beta-amyloid binding|kinesin binding|MAP-kinase scaffold activity|protein kinase activator activity|protein kinase binding large_intestine(2)|central_nervous_system(1) 3 all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) OV - Ovarian serous cystadenocarcinoma(4;1.28e-70)|Epithelial(4;3.46e-65)|GBM - Glioblastoma multiforme(4;4.83e-06)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247) 0.000 0.14 570 89 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BFTC909_KIDNEY NA BFTC909_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 40 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - BFTC909_KIDNEY NA BFTC909_KIDNEY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.50 136 134 RIF1 55183 broad.mit.edu 37 2 152320713 152320715 + In_Frame_Del DEL AAG - - BFTC909_KIDNEY NA BFTC909_KIDNEY NA g.chr2:152320713_152320715delAAG uc002txm.2 + 30 4809_4811 c.4679_4681delAAG c.(4678-4683)AAAGAA>AAA p.E1562del RIF1_uc002txl.2_In_Frame_Del_p.E1562del|RIF1_uc002txn.2_In_Frame_Del_p.E1562del|RIF1_uc002txo.2_In_Frame_Del_p.E1562del|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1562 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) TCGGAGGCAAAAGAAGAAGGTTC 0.404 0.42 19 14 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A BFTC909_KIDNEY NA BFTC909_KIDNEY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 89 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BFTC909_KIDNEY NA BFTC909_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.49 52 50 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BFTC909_KIDNEY NA BFTC909_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 46 28 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 BFTC909_KIDNEY NA BFTC909_KIDNEY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.10 78 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 BFTC909_KIDNEY NA BFTC909_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BFTC909_KIDNEY NA BFTC909_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 100 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BFTC909_KIDNEY NA BFTC909_KIDNEY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 30 304 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BFTC909_KIDNEY NA BFTC909_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.27 19 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BFTC909_KIDNEY NA BFTC909_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 216 1250 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BFTC909_KIDNEY NA BFTC909_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 50 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BHT101_THYROID NA BHT101_THYROID NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 4 91 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 BHT101_THYROID NA BHT101_THYROID NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.67 30 62 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A BHT101_THYROID NA BHT101_THYROID NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.14 275 45 FAM157A 728262 broad.mit.edu 37 3 197880131 197880136 + In_Frame_Del DEL GCAGCA - - BHT101_THYROID NA BHT101_THYROID NA g.chr3:197880131_197880136delGCAGCA uc011bup.1 + 2 210_215 c.210_215delGCAGCA c.(208-216)TGGCAGCAG>TGG p.QQ83del NM_001145248 NP_001138720 C9JC47 F157A_HUMAN family with sequence similarity 157, member A 83_84 Gln-rich. 0 ACAAGAACTGgcagcagcagcagcag 0.403 0.21 27 7 HTT 3064 broad.mit.edu 37 4 3076604 3076609 + In_Frame_Del DEL CAGCAG - - rs10618869 BHT101_THYROID NA BHT101_THYROID NA g.chr4:3076604_3076609delCAGCAG uc011bvq.1 + 2 203_208 c.58_63delCAGCAG c.(58-63)CAGCAGdel p.QQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagc 0.330 0.22 102 29 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 BHT101_THYROID NA BHT101_THYROID NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.60 19 29 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BHT101_THYROID NA BHT101_THYROID NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.72 85 217 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BHT101_THYROID NA BHT101_THYROID NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 52 133 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes BHT101_THYROID NA BHT101_THYROID NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.91 1 10 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 BHT101_THYROID NA BHT101_THYROID NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.11 351 45 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - BHT101_THYROID NA BHT101_THYROID NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.37 448 261 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes BHT101_THYROID NA BHT101_THYROID NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 3 29 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - BHT101_THYROID NA BHT101_THYROID NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.58 13 18 VPS13B 157680 broad.mit.edu 37 8 100887746 100887775 + In_Frame_Del DEL TGCAAATACCATGCCCTGTGGTGGCTGCAG - - rs73273219 by1000genomes BHT101_THYROID NA BHT101_THYROID NA g.chr8:100887746_100887775delTGCAAATACCATGCCCTGTGGTGGCTGCAG uc003yiv.2 + 62 12032_12061 c.11921_11950delTGCAAATACCATGCCCTGTGGTGGCTGCAG c.(11920-11952)ATGCAAATACCATGCCCTGTGGTGGCTGCAGAA>AAA p.3974_3984MQIPCPVVAAE>K VPS13B_uc003yiw.2_In_Frame_Del_p.3949_3959MQIPCPVVAAE>K NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 3974_3984 protein transport p.A3982D(1) ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TGTTCTTCCATGCAAATACCATGCCCTGTGGTGGCTGCAGAACCTCCCCC 0.474 0.34 61 31 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 BHT101_THYROID NA BHT101_THYROID NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 31 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BHT101_THYROID NA BHT101_THYROID NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 732 342 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency BHT101_THYROID NA BHT101_THYROID NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.18 215 46 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BHT101_THYROID NA BHT101_THYROID NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 76 837 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BHT101_THYROID NA BHT101_THYROID NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.48 88 82 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BHT101_THYROID NA BHT101_THYROID NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 210 630 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BHT101_THYROID NA BHT101_THYROID NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 99 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 31 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.45 123 99 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 62 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.32 26 12 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.83 2 10 CSMD3 114788 broad.mit.edu 37 8 113259328 113259328 + Frame_Shift_Del DEL T - - rs142018478 BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr8:113259328delT uc003ynu.2 - 64 10302 c.10143delA c.(10141-10143)AAAfs p.K3381fs CSMD3_uc003yns.2_Frame_Shift_Del_p.K2583fs|CSMD3_uc003ynt.2_Frame_Shift_Del_p.K3341fs|CSMD3_uc011lhx.1_Frame_Shift_Del_p.K3212fs NM_198123 NP_937756 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 isoform 1 3381 Extracellular (Potential).|Sushi 27. integral to membrane|plasma membrane ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1) 63 GAAGGTGTCCTTTTTTGCAAT 0.408 0.43 85 63 MYST4 23522 broad.mit.edu 37 10 76788645 76788647 + In_Frame_Del DEL GAG - - BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr10:76788645_76788647delGAG uc001jwn.1 + 18 4556_4558 c.4063_4065delGAG c.(4063-4065)GAGdel p.E1368del MYST4_uc001jwo.1_In_Frame_Del_p.E1076del|MYST4_uc001jwp.1_In_Frame_Del_p.E1185del NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1368 Poly-Glu. histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) ggaagaggaagaggaggaggagg 0.241 0.36 61 34 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.62 25 40 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 118 31 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.29 25 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 7 50 TP53 7157 broad.mit.edu 37 17 7579336 7579336 + Frame_Shift_Del DEL C - - BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr17:7579336delC uc002gim.2 - 4 545 c.351delG c.(349-351)GGGfs p.G117fs TP53_uc002gig.1_Frame_Shift_Del_p.G117fs|TP53_uc002gih.2_Frame_Shift_Del_p.G117fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.G117fs|TP53_uc010cni.1_Frame_Shift_Del_p.G117fs|TP53_uc002gij.2_Frame_Shift_Del_p.G117fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.G78fs|TP53_uc010cnk.1_Frame_Shift_Del_p.G132fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 117 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). G -> E (in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.G59fs*23(3)|p.G117E(2)|p.V73fs*9(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.T118fs*27(1)|p.H115fs*27(1)|p.T118fs*6(1)|p.Y107fs*44(1)|p.G117R(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.T118fs*5(1)|p.T118fs*31(1)|p.L114fs*30(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.97 26 979 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.30 30 13 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 101 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 53 415 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BHY_UPPER_AERODIGESTIVE_TRACT NA BHY_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 6 63 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BICR16_UPPER_AERODIGESTIVE_TRACT NA BICR16_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 23 DFFA 1676 broad.mit.edu 37 1 10523556 10523559 + Frame_Shift_Del DEL GACT - - BICR16_UPPER_AERODIGESTIVE_TRACT NA BICR16_UPPER_AERODIGESTIVE_TRACT NA g.chr1:10523556_10523559delGACT uc001arj.2 - 4 658_661 c.560_563delAGTC c.(559-564)CAGTCCfs p.Q187fs DFFA_uc001ark.2_Frame_Shift_Del_p.Q187fs NM_004401 NP_004392 O00273 DFFA_HUMAN DNA fragmentation factor, 45kDa, alpha 187_188 DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction|negative regulation of apoptosis cytosol|mitochondrion|nucleoplasm|plasma membrane deoxyribonuclease activity|identical protein binding 0 Ovarian(185;0.203) all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487) GAGCTGCTTGGACTGACGCACTTC 0.569 0.43 8 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BICR16_UPPER_AERODIGESTIVE_TRACT NA BICR16_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 69 47 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BICR16_UPPER_AERODIGESTIVE_TRACT NA BICR16_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 19 44 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 BICR16_UPPER_AERODIGESTIVE_TRACT NA BICR16_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 32 DTX1 1840 broad.mit.edu 37 12 113515459 113515470 + In_Frame_Del DEL CGCCGGCGCCGC - - rs146714593 BICR16_UPPER_AERODIGESTIVE_TRACT NA BICR16_UPPER_AERODIGESTIVE_TRACT NA g.chr12:113515459_113515470delCGCCGGCGCCGC uc001tuk.1 + 2 826_837 c.490_501delCGCCGGCGCCGC c.(490-501)CGCCGGCGCCGCdel p.RRRR164del NM_004416 NP_004407 Q86Y01 DTX1_HUMAN deltex homolog 1 164_167 WWE 2. negative regulation of neuron differentiation|Notch signaling pathway|regulation of Notch signaling pathway|transcription from RNA polymerase II promoter cytoplasm|nucleus Notch binding|SH3 domain binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding lung(2)|ovary(1)|central_nervous_system(1) 4 CCGCCAGAcgcgccggcgccgccgcctgcgcc 0.538 0.33 27 13 TRPM7 54822 broad.mit.edu 37 15 50920363 50920366 + Frame_Shift_Del DEL AAAC - - BICR16_UPPER_AERODIGESTIVE_TRACT NA BICR16_UPPER_AERODIGESTIVE_TRACT NA g.chr15:50920363_50920366delAAAC uc001zyt.3 - 11 1549_1552 c.1285_1288delGTTT c.(1285-1290)GTTTATfs p.V429fs TRPM7_uc010bew.1_Frame_Shift_Del_p.V429fs NM_017672 NP_060142 Q96QT4 TRPM7_HUMAN transient receptor potential cation channel, 429_430 Cytoplasmic (Potential). cell death integral to membrane ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity ovary(4)|stomach(3)|breast(1)|central_nervous_system(1)|skin(1) 10 all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045) TGCTGTCCATAAACAAATACATGA 0.338 0.42 19 14 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BICR16_UPPER_AERODIGESTIVE_TRACT NA BICR16_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.49 23 22 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BICR16_UPPER_AERODIGESTIVE_TRACT NA BICR16_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 31 266 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BICR16_UPPER_AERODIGESTIVE_TRACT NA BICR16_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 3 85 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.99 1 73 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.52 12 13 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.22 47 13 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.49 18 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 167 166 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.23 31 9 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.28 210 81 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.67 5 10 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 4 134 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 897 376 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 5 91 TP53 7157 broad.mit.edu 37 17 7578410 7578412 + In_Frame_Del DEL TCA - - BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr17:7578410_7578412delTCA uc002gim.2 - 5 712_714 c.518_520delTGA c.(517-522)GTGAGG>GGG p.173_174VR>G TP53_uc002gig.1_In_Frame_Del_p.173_174VR>G|TP53_uc002gih.2_In_Frame_Del_p.173_174VR>G|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_In_Frame_Del_p.41_42VR>G|TP53_uc010cng.1_In_Frame_Del_p.41_42VR>G|TP53_uc002gii.1_In_Frame_Del_p.41_42VR>G|TP53_uc010cnh.1_In_Frame_Del_p.173_174VR>G|TP53_uc010cni.1_In_Frame_Del_p.173_174VR>G|TP53_uc002gij.2_In_Frame_Del_p.173_174VR>G|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_In_Frame_Del_p.80_81VR>G|TP53_uc002gio.2_In_Frame_Del_p.41_42VR>G|TP53_uc010vug.1_In_Frame_Del_p.134_135VR>G NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 173_174 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). R -> M (in sporadic cancers; somatic mutation).|R -> T (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in a sporadic cancer; somatic mutation).|R -> W (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.V173L(50)|p.V173M(39)|p.V173A(8)|p.V173V(8)|p.R174W(8)|p.0?(7)|p.V173G(6)|p.V173fs*1(4)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.K164_P219del(1)|p.V172_R174delVVR(1)|p.V173fs*69(1)|p.P151_V173del23(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.V172_E180delVVRRCPHHE(1)|p.V173E(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.V173W(1)|p.V173fs*8(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*73(1)|p.R174fs*70(1)|p.R174G(1)|p.E171_H179delEVVRRCPHH(1)|p.S149fs*72(1)|p.R174fs*3(1)|p.R174fs*7(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGGCAGCGCCTCACAACCTCCGT 0.655 1.00 1 267 PER1 5187 broad.mit.edu 37 17 8051338 8051339 + Frame_Shift_Ins INS - AG AG BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr17:8051338_8051339insAG uc002gkd.2 - 10 1448_1449 c.1210_1211insCT c.(1210-1212)CTCfs p.L404fs PER1_uc010vuq.1_RNA|PER1_uc010vur.1_Frame_Shift_Ins_p.L388fs NM_002616 NP_002607 O15534 PER1_HUMAN period 1 404 PAS 2. circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus signal transducer activity lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1) 9 0.000 0.13 521 77 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.45 173 141 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 48 521 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BICR31_UPPER_AERODIGESTIVE_TRACT NA BICR31_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 13 219 HUWE1 10075 broad.mit.edu 37 X 53562382 53562384 + In_Frame_Del DEL CTT - - BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chrX:53562382_53562384delCTT uc004dsp.2 - 81 13012_13014 c.12610_12612delAAG c.(12610-12612)AAGdel p.K4204del HUWE1_uc004dsn.2_In_Frame_Del_p.K3012del NM_031407 NP_113584 Q7Z6Z7 HUWE1_HUMAN HECT, UBA and WWE domain containing 1 4204 HECT. base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process cytoplasm|nucleus DNA binding|protein binding|ubiquitin-protein ligase activity p.K4094del(1) ovary(8)|large_intestine(4)|breast(4)|kidney(1) 17 0.000 0.60 493 743 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 5 58 CDK11A 728642 broad.mit.edu 37 1 1635536 1635537 + Frame_Shift_Ins INS - A A BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr1:1635536_1635537insA uc009vks.2 - 16 1843_1844 c.1735_1736insT c.(1735-1737)TACfs p.Y579fs CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agv.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc001ahh.3_Intron|SLC35E2_uc009vkm.1_Intron|CDK11A_uc001ahj.3_Frame_Shift_Ins_p.Y86fs|CDK11A_uc009vkp.2_Frame_Shift_Ins_p.Y196fs|CDK11A_uc009vkq.2_Intron|CDK11A_uc009vkr.2_Frame_Shift_Ins_p.Y569fs NM_024011 NP_076916 Q9UQ88 CD11A_HUMAN cell division cycle 2-like 2 isoform 1 582 Protein kinase. apoptosis|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent cytoplasm|nucleus ATP binding|cyclin-dependent protein kinase activity|protein binding stomach(1) 1 GACCGGGGTGTAGGCCTTCAGA 0.673 0.33 18 9 TGFBR2 7048 broad.mit.edu 37 3 30691871 30691872 + Frame_Shift_Ins INS - A A BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr3:30691871_30691872insA uc003ceo.2 + 3 755_756 c.373_374insA c.(373-375)GAAfs p.E125fs TGFBR2_uc003cen.2_Frame_Shift_Ins_p.E150fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 125 Extracellular (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 CATTATGAAGGAAAAAAAAAAG 0.421 0.72 20 51 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.22 29 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.44 68 53 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 22 35 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.22 206 59 MAML1 9794 broad.mit.edu 37 5 179160388 179160389 + Frame_Shift_Ins INS - G G rs112668028 BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr5:179160388_179160389insG uc003mkm.2 + 1 538_539 c.275_276insG c.(274-276)CTGfs p.L92fs MAML1_uc003mkn.1_Frame_Shift_Ins_p.L92fs NM_014757 NP_055572 Q92585 MAML1_HUMAN mastermind-like 1 92 Required for interaction with NOTCH proteins. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck peptide antigen binding|protein kinase binding|transcription coactivator activity lung(4)|ovary(2) 6 all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218) all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) 0.000 0.47 162 146 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.33 10 5 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 11 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.66 301 586 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 149 32 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 48 476 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.52 13 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 217 569 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BICR56_UPPER_AERODIGESTIVE_TRACT NA BICR56_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 53 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 3 42 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.33 232 115 RIF1 55183 broad.mit.edu 37 2 152320565 152320566 + Frame_Shift_Ins INS - T T BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr2:152320565_152320566insT uc002txm.2 + 30 4661_4662 c.4531_4532insT c.(4531-4533)ATTfs p.I1511fs RIF1_uc002txl.2_Frame_Shift_Ins_p.I1511fs|RIF1_uc002txn.2_Frame_Shift_Ins_p.I1511fs|RIF1_uc002txo.2_Frame_Shift_Ins_p.I1511fs|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1511 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) CCCTGAGAACATTAAGTCTGAG 0.411 0.59 24 34 NEK4 6787 broad.mit.edu 37 3 52773532 52773533 + Frame_Shift_Ins INS - T T BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr3:52773532_52773533insT uc003dfq.3 - 14 2400_2401 c.2211_2212insA c.(2209-2214)AAACTTfs p.K737fs NEK4_uc011bej.1_Frame_Shift_Ins_p.K648fs|NEK4_uc003dfr.2_Frame_Shift_Ins_p.K691fs NM_003157 NP_003148 P51957 NEK4_HUMAN NIMA-related kinase 4 737_738 cell division|mitosis nucleus ATP binding|metal ion binding|protein serine/threonine kinase activity large_intestine(1) 1 BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513) TTCCGATGAAGTTTGAATTCTG 0.426 0.92 10 121 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.43 66 50 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.55 34 42 RECQL4 9401 broad.mit.edu 37 8 145741584 145741585 + Frame_Shift_Ins INS - CTGTGCC CTGTGCC BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145741584_145741585insCTGTGCC uc003zdj.2 - 5 950_951 c.918_919insGGCACAG c.(916-921)CAGCCAfs p.Q306fs LRRC14_uc003zdk.1_5'Flank|LRRC14_uc003zdl.1_5'Flank NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 306_307 DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) GGCTGAGGTGGCTGTGCCTGTA 0.658 0.26 23 8 IFNA2 3440 broad.mit.edu 37 9 21384875 21384876 + Frame_Shift_Del DEL AG - - BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr9:21384875_21384876delAG uc003zpb.2 - 1 521_522 c.453_454delCT c.(451-456)CTCTATfs p.L151fs NM_000605 NP_000596 P01563 IFNA2_HUMAN interferon, alpha 2 precursor 151_152 blood coagulation|cell-cell signaling|induction of apoptosis|inflammatory response|negative regulation of interleukin-13 secretion|negative regulation of interleukin-5 secretion|negative regulation of T cell differentiation|negative regulation of T-helper 2 cell cytokine production|negative regulation of transcription, DNA-dependent|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway extracellular space cytokine activity|interferon-alpha/beta receptor binding breast(1) 1 Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173) Interferon Alfa-2a, Recombinant(DB00034)|Interferon Alfa-2b, Recombinant(DB00105)|Interferon alfa-n1(DB00011)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022) TCTTTCAGATAGAGAGTGATTC 0.455 0.89 18 148 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.88 2 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 123 23 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 9 69 NF1 4763 broad.mit.edu 37 17 29653256 29653267 + In_Frame_Del DEL AAAGTTTCTATT - - rs148540952 BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr17:29653256_29653267delAAAGTTTCTATT uc002hgg.2 + 37 5587_5598 c.5254_5265delAAAGTTTCTATT c.(5254-5265)AAAGTTTCTATTdel p.KVSI1752del NF1_uc002hgh.2_In_Frame_Del_p.KVSI1731del|NF1_uc002hgi.1_In_Frame_Del_p.KVSI764del|NF1_uc010cso.2_5'UTR NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 1752_1755 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) CAAAGACACCAAAGTTTCTATTAAAGTAAGTT 0.429 0.25 116 38 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.46 32 27 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 37 290 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BICR6_UPPER_AERODIGESTIVE_TRACT NA BICR6_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 2 42 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 30 ARID1A 8289 broad.mit.edu 37 1 27101662 27101663 + Frame_Shift_Ins INS - A A BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:27101662_27101663insA uc001bmv.1 + 18 5317_5318 c.4944_4945insA c.(4942-4947)GCCACAfs p.A1648fs ARID1A_uc001bmt.1_Frame_Shift_Ins_p.A1647fs|ARID1A_uc001bmu.1_Frame_Shift_Ins_p.A1431fs|ARID1A_uc001bmw.1_Frame_Shift_Ins_p.A1265fs|ARID1A_uc001bmx.1_Frame_Shift_Ins_p.A494fs|ARID1A_uc009vsm.1_Intron|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1648_1649 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CTGTTGAAGCCACACAGCCTGT 0.564 0.40 58 38 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 1.00 0 26 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.64 4 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 131 175 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 37 72 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.75 3 9 ERCC6 2074 broad.mit.edu 37 10 50732547 50732547 + Frame_Shift_Del DEL T - - BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:50732547delT uc001jhs.3 - 5 1083 c.929delA c.(928-930)AATfs p.N310fs PGBD3_uc001jht.2_5'Flank|PGBD3_uc009xoe.2_Frame_Shift_Del_p.N310fs|PGBD3_uc001jhu.2_Frame_Shift_Del_p.N310fs NM_000124 NP_000115 Q03468 ERCC6_HUMAN excision repair cross-complementing rodent 310 base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair nucleolus|soluble fraction|transcription elongation factor complex ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1) 16 TTTGTTTTTATTTTGCACTGG 0.438 0.49 220 214 TFDP1 7027 broad.mit.edu 37 13 114288284 114288286 + In_Frame_Del DEL AGA - - BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:114288284_114288286delAGA uc001vtw.2 + 7 766_768 c.554_556delAGA c.(553-558)GAGAAG>GAG p.K187del TFDP1_uc010tkd.1_In_Frame_Del_p.K92del|TFDP1_uc010tke.1_In_Frame_Del_p.K92del|TFDP1_uc001vty.3_In_Frame_Del_p.K187del|TFDP1_uc001vtx.2_In_Frame_Del_p.K67del|TFDP1_uc010agx.2_In_Frame_Del_p.K187del NM_007111 NP_009042 Q14186 TFDP1_HUMAN transcription factor Dp-1 187 Potential.|DEF box. cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|regulation of transcription from RNA polymerase II promoter transcription factor complex DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding lung(4)|ovary(2)|skin(1) 7 Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218) all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153) all cancers(43;0.0576) ATCTCCAAGGAGAAGAAGGAGAT 0.502 0.90 10 89 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.35 39 21 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 34 361 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.48 120 112 SIK1 150094 broad.mit.edu 37 21 44836897 44836914 + In_Frame_Del DEL CAGGGCCATCACAGGGGG - - BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:44836897_44836914delCAGGGCCATCACAGGGGG uc002zdf.2 - 14 2187_2204 c.2060_2077delCCCCCTGTGATGGCCCTG c.(2059-2079)GCCCCCTGTGATGGCCCTGGG>GGG p.APCDGP687del NM_173354 NP_775490 P57059 SIK1_HUMAN salt-inducible kinase 1 687_692 anoikis|cell cycle|cell differentiation|intracellular protein kinase cascade|multicellular organismal development|regulation of cell differentiation|regulation of mitotic cell cycle nucleus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity lung(2)|testis(2)|ovary(1)|central_nervous_system(1)|skin(1) 7 0.000 0.43 848 628 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 213 586 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 6 120 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 1 12 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.16 350 67 MSH2 4436 broad.mit.edu 37 2 47641559 47641562 + Splice_Site DEL TAAA - - rs11309117 BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:47641559_47641562delTAAA uc002rvy.1 + 5 1010 c.942_splice c.e5+2 p.Q314_splice MSH2_uc010yoh.1_Splice_Site_p.Q248_splice|MSH2_uc002rvz.2_Splice_Site_p.Q314_splice|MSH2_uc010fbg.2_Intron NM_000251 NP_000242 P43246 MSH2_HUMAN mutS homolog 2 B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes MutSalpha complex|MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding p.?(1) large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1) 55 all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) CTTTTTCAGGTaaaaaaaaaaaaa 0.294 0.17 40 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.37 67 39 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 16 26 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.17 148 30 CCND3 896 broad.mit.edu 37 6 41903755 41903756 + Frame_Shift_Ins INS - G G BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:41903755_41903756insG uc003orn.2 - 5 966_967 c.801_802insC c.(799-804)CCCAAAfs p.P267fs CCND3_uc003orp.2_Frame_Shift_Ins_p.P186fs|CCND3_uc011duk.1_Frame_Shift_Ins_p.P71fs|CCND3_uc003orm.2_Frame_Shift_Ins_p.P217fs|CCND3_uc003oro.2_Frame_Shift_Ins_p.P195fs NM_001760 NP_001751 P30281 CCND3_HUMAN cyclin D3 isoform 2 267_268 cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus protein kinase binding 0 Colorectal(47;0.121) Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152) CGGGGGGCTTTGGGCGCTGGGC 0.649 0.52 41 44 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 198 47 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.40 21 14 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.22 47 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 40 248 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 3 47 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BT474_BREAST NA BT474_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 73 TPM3 7170 broad.mit.edu 37 1 154142916 154142917 + Frame_Shift_Del DEL TC - - BT474_BREAST NA BT474_BREAST NA g.chr1:154142916_154142917delTC uc001fec.1 - 8 849_850 c.734_735delGA c.(733-735)AGAfs p.R245fs TPM3_uc001fdx.1_Frame_Shift_Del_p.R193fs|TPM3_uc010pei.1_Frame_Shift_Del_p.R118fs|TPM3_uc001fdy.1_Frame_Shift_Del_p.R208fs|TPM3_uc001fdz.1_Frame_Shift_Del_p.R208fs|TPM3_uc001fea.1_Frame_Shift_Del_p.R208fs|TPM3_uc001feb.1_Frame_Shift_Del_p.R208fs|TPM3_uc010pej.1_Frame_Shift_Del_p.R141fs|TPM3_uc009wor.2_Intron|TPM3_uc001fed.1_Frame_Shift_Del_p.R208fs NM_152263 NP_689476 P06753 TPM3_HUMAN tropomyosin 3 isoform 1 244 By similarity. cellular component movement|muscle filament sliding|regulation of muscle contraction cytosol|muscle thin filament tropomyosin|stress fiber actin binding TPM3/ALK(33) haematopoietic_and_lymphoid_tissue(22)|soft_tissue(11)|skin(1) 34 all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128) TGGCTACCGATCTCTCAGCAAA 0.436 0.21 877 237 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 BT474_BREAST NA BT474_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.29 75 30 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BT474_BREAST NA BT474_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 154 193 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BT474_BREAST NA BT474_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.76 21 66 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes BT474_BREAST NA BT474_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 17 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - BT474_BREAST NA BT474_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.26 20 7 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 BT474_BREAST NA BT474_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.20 215 54 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 BT474_BREAST NA BT474_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 35 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency BT474_BREAST NA BT474_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.80 37 148 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BT474_BREAST NA BT474_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 268 51 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 BT474_BREAST NA BT474_BREAST NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.71 6 15 HERC2 8924 broad.mit.edu 37 15 28501091 28501092 + Frame_Shift_Del DEL AG - - BT474_BREAST NA BT474_BREAST NA g.chr15:28501091_28501092delAG uc001zbj.2 - 19 2903_2904 c.2797_2798delCT c.(2797-2799)CTTfs p.L933fs HERC2_uc001zbl.1_Frame_Shift_Del_p.L628fs NM_004667 NP_004658 O95714 HERC2_HUMAN hect domain and RLD 2 933 DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process nucleus guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1) 13 all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227) all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199) GCCCACCAGAAGATCAATCATG 0.490 0.22 667 186 FANCA 2175 broad.mit.edu 37 16 89815075 89815075 + Frame_Shift_Del DEL A - - BT474_BREAST NA BT474_BREAST NA g.chr16:89815075delA uc002fou.1 - 33 3382 c.3340delT c.(3340-3342)TCTfs p.S1114fs FANCA_uc010vpn.1_Frame_Shift_Del_p.S1114fs|FANCA_uc010vpo.1_Frame_Shift_Del_p.S200fs NM_000135 NP_000126 O15360 FANCA_HUMAN Fanconi anemia, complementation group A isoform 1114 DNA repair|protein complex assembly cytoplasm|nucleoplasm protein binding ovary(2)|breast(2)|central_nervous_system(1)|skin(1) 6 Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194) BRCA - Breast invasive adenocarcinoma(80;0.028) ACCATCTCAGAGTTGACCAAG 0.602 0.23 230 69 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BT474_BREAST NA BT474_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.23 87 26 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes BT474_BREAST NA BT474_BREAST NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.49 23 22 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 BT474_BREAST NA BT474_BREAST NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.33 243 121 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BT474_BREAST NA BT474_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.95 12 234 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BT474_BREAST NA BT474_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 16 282 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - BT483_BREAST NA BT483_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 332 129 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes BT483_BREAST NA BT483_BREAST NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.45 12 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 BT483_BREAST NA BT483_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.40 15 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BT483_BREAST NA BT483_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 110 145 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BT483_BREAST NA BT483_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 18 32 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes BT483_BREAST NA BT483_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 12 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - BT483_BREAST NA BT483_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.84 5 27 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 BT483_BREAST NA BT483_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 3 80 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency BT483_BREAST NA BT483_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.12 821 117 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039791 + In_Frame_Del DEL CAGCAGCAGCAGCAG - - rs113070757;rs62639301;rs139102413;rs145170448;rs147609454;rs142219087 byFrequency;byFrequency;byFrequency;byFrequency;byFrequency BT483_BREAST NA BT483_BREAST NA g.chr9:2039777_2039791delCAGCAGCAGCAGCAG uc003zhc.2 + 4 766_780 c.667_681delCAGCAGCAGCAGCAG c.(667-681)CAGCAGCAGCAGCAGdel p.QQQQQ233del SMARCA2_uc003zhd.2_In_Frame_Del_p.QQQQQ233del|SMARCA2_uc010mha.2_In_Frame_Del_p.QQQQQ224del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 233_237 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagcagcagcagcagc 0.270 0.31 46 21 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BT483_BREAST NA BT483_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 502 211 UNC13C 440279 broad.mit.edu 37 15 54307731 54307735 + Frame_Shift_Del DEL TTATG - - BT483_BREAST NA BT483_BREAST NA g.chr15:54307731_54307735delTTATG uc002ack.2 + 1 2631_2635 c.2631_2635delTTATG c.(2629-2637)GATTATGTTfs p.D877fs NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 877_879 exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) ATGAAACAGATTATGTTGAAGTCAT 0.385 0.12 76 10 CDH3 1001 broad.mit.edu 37 16 68679613 68679614 + Frame_Shift_Ins INS - A A BT483_BREAST NA BT483_BREAST NA g.chr16:68679613_68679614insA uc002ewf.2 + 2 1252_1253 c.120_121insA c.(118-123)GCGGGAfs p.A40fs CDH3_uc010vli.1_Intron NM_001793 NP_001784 P22223 CADH3_HUMAN cadherin 3, type 1 preproprotein 40_41 adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception integral to membrane calcium ion binding p.?(1) ovary(3)|breast(1)|skin(1) 5 Ovarian(137;0.0564) OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384) 0.000 1.00 0 14 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BT483_BREAST NA BT483_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 31 98 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BT483_BREAST NA BT483_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 56 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 BT549_BREAST NA BT549_BREAST NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.52 49 53 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BT549_BREAST NA BT549_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 6 80 FLNA 2316 broad.mit.edu 37 X 153580614 153580615 + Frame_Shift_Ins INS - C C BT549_BREAST NA BT549_BREAST NA g.chrX:153580614_153580615insC uc004fkk.2 - 41 6952_6953 c.6703_6704insG c.(6703-6705)GAAfs p.E2235fs FLNA_uc004fki.2_Frame_Shift_Ins_p.E278fs|FLNA_uc011mzn.1_Frame_Shift_Ins_p.E368fs|FLNA_uc010nuu.1_Frame_Shift_Ins_p.E2227fs NM_001110556 NP_001104026 P21333 FLNA_HUMAN filamin A, alpha isoform 2 2235 Filamin 21. actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering cell cortex|cytosol|extracellular region|nucleus|plasma membrane actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding breast(6) 6 all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176) GGCTCCCCCTTCCCCTAGGGGC 0.653 0.11 57 7 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - BT549_BREAST NA BT549_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.14 346 54 CASP10 843 broad.mit.edu 37 2 202074072 202074078 + Frame_Shift_Del DEL GCCAAGG - - BT549_BREAST NA BT549_BREAST NA g.chr2:202074072_202074078delGCCAAGG uc002uxl.1 + 9 1620_1626 c.1202_1208delGCCAAGG c.(1201-1209)TGCCAAGGTfs p.C401fs CASP10_uc002uxj.1_Frame_Shift_Del_p.C401fs|CASP10_uc002uxk.1_Frame_Shift_Del_p.C358fs|CASP10_uc010fta.1_Frame_Shift_Del_p.C334fs|CASP10_uc002uxm.1_Frame_Shift_Del_p.C358fs|CASP10_uc010ftb.1_RNA NM_032974 NP_116756 Q92851 CASPA_HUMAN caspase 10 isoform b preproprotein 401_403 apoptosis|induction of apoptosis by extracellular signals|proteolysis cytosol|plasma membrane cysteine-type endopeptidase activity|identical protein binding|protein binding skin(3)|ovary(1)|pancreas(1)|breast(1) 6 ATCCAGGCCTGCCAAGGTGAAGAGATA 0.536 1.00 0 66 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes BT549_BREAST NA BT549_BREAST NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.37 32 19 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 BT549_BREAST NA BT549_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.33 22 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BT549_BREAST NA BT549_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 116 126 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes BT549_BREAST NA BT549_BREAST NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.90 1 9 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes BT549_BREAST NA BT549_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 19 PCM1 5108 broad.mit.edu 37 8 17883149 17883150 + Frame_Shift_Del DEL GA - - BT549_BREAST NA BT549_BREAST NA g.chr8:17883149_17883150delGA uc003wyi.3 + 38 6453_6454 c.6031_6032delGA c.(6031-6033)GAGfs p.E2011fs PCM1_uc011kyh.1_Frame_Shift_Del_p.E2003fs|PCM1_uc003wyj.3_Frame_Shift_Del_p.E1847fs|PCM1_uc011kyi.1_Frame_Shift_Del_p.E810fs|PCM1_uc011kyj.1_Frame_Shift_Del_p.E767fs|PCM1_uc003wyk.3_Frame_Shift_Del_p.E693fs|PCM1_uc011kyk.1_Frame_Shift_Del_p.E627fs NM_006197 NP_006188 Q15154 PCM1_HUMAN pericentriolar material 1 2011 Interaction with BBS4. centrosome organization|cilium assembly|G2/M transition of mitotic cell cycle|interkinetic nuclear migration|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome centriolar satellite|cytosol|nuclear membrane|pericentriolar material identical protein binding PCM1/JAK2(30) haematopoietic_and_lymphoid_tissue(30)|breast(4)|ovary(2) 36 Colorectal(111;0.0789) TGGAAATTCTGAGACACTAAAA 0.297 0.15 45 8 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 BT549_BREAST NA BT549_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.62 15 24 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 BT549_BREAST NA BT549_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 4 69 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - BT549_BREAST NA BT549_BREAST NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.12 195 26 MYST4 23522 broad.mit.edu 37 10 76788480 76788481 + Frame_Shift_Ins INS - C C BT549_BREAST NA BT549_BREAST NA g.chr10:76788480_76788481insC uc001jwn.1 + 18 4391_4392 c.3898_3899insC c.(3898-3900)ACCfs p.T1300fs MYST4_uc001jwo.1_Frame_Shift_Ins_p.T1008fs|MYST4_uc001jwp.1_Frame_Shift_Ins_p.T1117fs NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1300 histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) AGAAGGAAAAACCAGCCCCAGT 0.510 0.20 118 29 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BT549_BREAST NA BT549_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 662 373 IL21R 50615 broad.mit.edu 37 16 27460536 27460546 + Frame_Shift_Del DEL CGGAGCTACCT - - rs142141390 by1000genomes BT549_BREAST NA BT549_BREAST NA g.chr16:27460536_27460546delCGGAGCTACCT uc002doq.1 + 9 1782_1792 c.1549_1559delCGGAGCTACCT c.(1549-1560)CGGAGCTACCTCfs p.R517fs IL21R_uc002dor.1_Frame_Shift_Del_p.R517fs|IL21R_uc002dos.1_Frame_Shift_Del_p.R517fs|uc002dot.2_RNA NM_181078 NP_851564 Q9HBE5 IL21R_HUMAN interleukin 21 receptor precursor 517_520 Cytoplasmic (Potential). natural killer cell activation integral to membrane interleukin-21 receptor activity ovary(2)|lung(1)|breast(1) 4 AGGACCCCCCCGGAGCTACCTCCGCCAGTGG 0.645 0.10 104 11 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes BT549_BREAST NA BT549_BREAST NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.14 100 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BT549_BREAST NA BT549_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 11 105 SMARCE1 6605 broad.mit.edu 37 17 38793755 38793756 + Frame_Shift_Ins INS - TG TG BT549_BREAST NA BT549_BREAST NA g.chr17:38793755_38793756insTG uc002hux.2 - 5 349_350 c.225_226insCA c.(223-228)AGGTACfs p.R75fs SMARCE1_uc010wff.1_Frame_Shift_Ins_p.R40fs|SMARCE1_uc010wfg.1_Frame_Shift_Ins_p.R5fs|SMARCE1_uc002huy.2_Frame_Shift_Ins_p.R40fs|SMARCE1_uc010wfh.1_Frame_Shift_Ins_p.R5fs|SMARCE1_uc010wfi.1_Frame_Shift_Ins_p.R57fs|SMARCE1_uc002huz.1_Frame_Shift_Ins_p.R40fs|SMARCE1_uc010wfj.1_Frame_Shift_Ins_p.R57fs NM_003079 NP_003070 Q969G3 SMCE1_HUMAN SWI/SNF-related matrix-associated 75_76 HMG box. chromatin modification|negative regulation of transcription, DNA-dependent|nervous system development|nucleosome disassembly|regulation of transcription from RNA polymerase II promoter nBAF complex|npBAF complex|nuclear chromosome|SWI/SNF complex|transcriptional repressor complex chromatin binding|DNA binding|N-acetyltransferase activity|protein binding|protein N-terminus binding|transcription coactivator activity 0 Breast(137;0.000812) 0.000 0.94 7 112 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BT549_BREAST NA BT549_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.82 26 118 MYBL2 4605 broad.mit.edu 37 20 42310481 42310482 + Frame_Shift_Ins INS - C C BT549_BREAST NA BT549_BREAST NA g.chr20:42310481_42310482insC uc002xlb.1 + 3 387_388 c.172_173insC c.(172-174)GCCfs p.A58fs MYBL2_uc010zwj.1_Intron|MYBL2_uc002xla.1_Frame_Shift_Ins_p.A58fs NM_002466 NP_002457 P10244 MYBB_HUMAN MYB-related protein B 58 H-T-H motif (By similarity).|HTH myb-type 1. nucleus DNA binding|sequence-specific DNA binding transcription factor activity lung(3)|kidney(2) 5 Myeloproliferative disorder(115;0.00452) COAD - Colon adenocarcinoma(18;0.0031) GAAGTTCCTGGCCAGCCACTTC 0.609 0.21 48 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BT549_BREAST NA BT549_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 127 423 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BT549_BREAST NA BT549_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 11 94 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 31 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.38 103 63 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 18 37 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.14 83 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 29 MAML2 84441 broad.mit.edu 37 11 96074791 96074798 + Frame_Shift_Del DEL CCAGCTTT - - BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:96074791_96074798delCCAGCTTT uc001pfw.1 - 1 1547_1554 c.262_269delAAAGCTGG c.(262-270)AAAGCTGGCfs p.K88fs NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 88_90 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ggtgTGTTTGCCAGCTTTCCTTGCCCCC 0.308 0.54 38 45 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.96 4 88 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.61 13 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 38 279 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 94 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 3 51 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.29 20 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 78 66 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 12 27 BRAF 673 broad.mit.edu 37 7 140477834 140477848 + In_Frame_Del DEL GTGTAGGTGCTGTCA - - BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chr7:140477834_140477848delGTGTAGGTGCTGTCA uc003vwc.3 - 12 1521_1535 c.1460_1474delTGACAGCACCTACAC c.(1459-1476)GTGACAGCACCTACACCT>GCT p.487_492VTAPTP>A NM_004333 NP_004324 P15056 BRAF_HUMAN B-Raf 487_492 Protein kinase. activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission cytosol|nucleus|plasma membrane ATP binding|metal ion binding p.L485_P490>Y(2)|p.N486_P490del(1) KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2) thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1) 18290 Melanoma(164;0.00956) Sorafenib(DB00398) AACTGCTGAGGTGTAGGTGCTGTCACATTCAACAT 0.353 0.13 48 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 2 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 2 34 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 736 147 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.12 92 13 AKAP6 9472 broad.mit.edu 37 14 33015845 33015847 + In_Frame_Del DEL CAT - - BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chr14:33015845_33015847delCAT uc001wrq.2 + 4 2156_2158 c.1986_1988delCAT c.(1984-1989)ACCATC>ACC p.I663del AKAP6_uc010aml.2_In_Frame_Del_p.I660del NM_004274 NP_004265 Q13023 AKAP6_HUMAN A-kinase anchor protein 6 663 protein targeting calcium channel complex|nuclear membrane|sarcoplasmic reticulum protein kinase A binding|receptor binding breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1) 21 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) GBM - Glioblastoma multiforme(265;0.019) GAGGAGAAACCATCCAGAATATT 0.424 0.29 110 44 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.60 17 25 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 23 198 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 99 592 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 BXPC3_PANCREAS NA BXPC3_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 65 HEPH 9843 broad.mit.edu 37 X 65393494 65393495 + Frame_Shift_Ins INS - C C C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chrX:65393494_65393495insC uc011moz.1 + 4 545_546 c.485_486insC c.(484-486)GGCfs p.G162fs HEPH_uc004dwn.2_Frame_Shift_Ins_p.G162fs|HEPH_uc004dwo.2_5'UTR|HEPH_uc010nkr.2_Frame_Shift_Ins_p.G162fs|HEPH_uc011mpa.1_Frame_Shift_Ins_p.G162fs NM_138737 NP_620074 Q9BQS7 HEPH_HUMAN hephaestin isoform a 159 Extracellular (Potential).|Plastocyanin-like 1. cellular iron ion homeostasis|copper ion transport|transmembrane transport integral to membrane|plasma membrane copper ion binding|oxidoreductase activity lung(5)|ovary(4) 9 CCCCCGGGGGGCAGCCATATCT 0.535 0.13 131 20 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 77 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.12 57 8 FGF2 2247 broad.mit.edu 37 4 123748258 123748259 + Frame_Shift_Ins INS - G G C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chr4:123748258_123748259insG uc003iev.1 + 1 396_397 c.328_329insG c.(328-330)CGGfs p.R110fs NM_002006 NP_001997 P09038 FGF2_HUMAN fibroblast growth factor 2 110 activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing extracellular space fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity ovary(1)|lung(1)|central_nervous_system(1) 3 Pentosan Polysulfate(DB00686) 0.000 0.11 73 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.43 167 126 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 36 75 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 1 12 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.11 529 64 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 469 87 CIT 11113 broad.mit.edu 37 12 120270583 120270584 + In_Frame_Ins INS - TGA TGA C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chr12:120270583_120270584insTGA uc001txi.1 - 7 797_798 c.744_745insTCA c.(742-747)insTCA p.248_249insS CIT_uc001txj.1_In_Frame_Ins_p.248_249insS NM_007174 NP_009105 O14578 CTRO_HUMAN citron 248_249 Protein kinase. intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) ACCATCTTGTTTGAATTCATTT 0.386 0.34 460 235 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 20 224 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 22 60 SRMS 6725 broad.mit.edu 37 20 62174799 62174799 + Frame_Shift_Del DEL G - - C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chr20:62174799delG uc002yfi.1 - 3 554 c.513delC c.(511-513)GTCfs p.V171fs NM_080823 NP_543013 Q9H3Y6 SRMS_HUMAN src-related kinase lacking C-terminal regulatory 171 SH2. ATP binding|non-membrane spanning protein tyrosine kinase activity stomach(1)|lung(1) 2 all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13) Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06) CTGCCATGGAGACCCGGTAGT 0.642 0.80 89 355 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 102 690 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 C2BBE1_LARGE_INTESTINE NA C2BBE1_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 23 234 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 C32_SKIN NA C32_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 47 ALK 238 broad.mit.edu 37 2 30143051 30143052 + Frame_Shift_Ins INS - G G C32_SKIN NA C32_SKIN NA g.chr2:30143051_30143052insG uc002rmy.2 - 1 1381_1382 c.474_475insC c.(472-477)CCCGGGfs p.P158fs NM_004304 NP_004295 Q9UM73 ALK_HUMAN anaplastic lymphoma kinase precursor 158_159 Extracellular (Potential). protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2) haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1) 1218 Acute lymphoblastic leukemia(172;0.155) Adenosine triphosphate(DB00171) GCCGCCTCCCCGGGGGGCCCGA 0.673 0.14 84 14 TTN 7273 broad.mit.edu 37 2 179505972 179505973 + Frame_Shift_Ins INS - G G C32_SKIN NA C32_SKIN NA g.chr2:179505972_179505973insG uc010zfg.1 - 169 33148_33149 c.32924_32925insC c.(32923-32925)CCTfs p.P10975fs TTN_uc010zfh.1_Frame_Shift_Ins_p.P4670fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.P4603fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.P4478fs|TTN_uc010fre.1_Frame_Shift_Ins_p.P853fs|TTN_uc002umw.1_Intron|TTN_uc002umx.1_Intron NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 11902 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCCTACCTGCAGGTTTTTTAAC 0.277 0.16 72 14 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes C32_SKIN NA C32_SKIN NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.35 24 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 C32_SKIN NA C32_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 113 212 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 C32_SKIN NA C32_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.37 67 39 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 C32_SKIN NA C32_SKIN NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.37 19 11 AIM1 202 broad.mit.edu 37 6 107001383 107001385 + In_Frame_Del DEL AAC - - rs138855733 byFrequency C32_SKIN NA C32_SKIN NA g.chr6:107001383_107001385delAAC uc003prh.2 + 14 4789_4791 c.4302_4304delAAC c.(4300-4305)GAAACA>GAA p.T1436del AIM1_uc003pri.2_In_Frame_Del_p.T240del NM_001624 NP_001615 Q9Y4K1 AIM1_HUMAN absent in melanoma 1 1436 Beta/gamma crystallin 'Greek key' 9. sugar binding breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1) 9 Breast(9;0.0138)|all_epithelial(6;0.169) all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473) Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305) all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858) GTTTTGAAGAAACAACAAGTCAA 0.360 0.36 79 44 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes C32_SKIN NA C32_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 10 64 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 C32_SKIN NA C32_SKIN NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.22 29 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 C32_SKIN NA C32_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 351 150 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes C32_SKIN NA C32_SKIN NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.12 53 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C C32_SKIN NA C32_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 20 157 PRKCA 5578 broad.mit.edu 37 17 64683333 64683334 + Frame_Shift_Ins INS - C C C32_SKIN NA C32_SKIN NA g.chr17:64683333_64683334insC uc002jfp.1 + 6 678_679 c.634_635insC c.(634-636)ACCfs p.T212fs PRKCA_uc002jfo.1_Frame_Shift_Ins_p.T83fs NM_002737 NP_002728 P17252 KPCA_HUMAN protein kinase C, alpha 212 C2. activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1) 9 BRCA - Breast invasive adenocarcinoma(6;4.68e-09) Phosphatidylserine(DB00144)|Vitamin E(DB00163) CAAGCAAAAAACCAAAACCATC 0.401 0.13 58 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 C32_SKIN NA C32_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.41 96 68 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 C32_SKIN NA C32_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 129 644 CHEK2 11200 broad.mit.edu 37 22 29091227 29091227 + Frame_Shift_Del DEL A - - C32_SKIN NA C32_SKIN NA g.chr22:29091227delA uc003adu.1 - 12 1335 c.1263delT c.(1261-1263)CTTfs p.L421fs CHEK2_uc003ads.1_Frame_Shift_Del_p.L200fs|CHEK2_uc010gvh.1_Frame_Shift_Del_p.L330fs|CHEK2_uc010gvi.1_Intron|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_RNA|CHEK2_uc010gvk.1_RNA|CHEK2_uc003adt.1_Frame_Shift_Del_p.L464fs|CHEK2_uc003adv.1_Frame_Shift_Del_p.L392fs|CHEK2_uc003adw.1_Frame_Shift_Del_p.L421fs|CHEK2_uc003adx.1_Frame_Shift_Del_p.L200fs|CHEK2_uc003ady.1_Intron|CHEK2_uc003adz.1_Frame_Shift_Del_p.L225fs NM_007194 NP_009125 O96017 CHK2_HUMAN protein kinase CHK2 isoform a 421 Protein kinase. cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence PML body ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(17)|stomach(1)|ovary(1)|lung(1) 20 GATACCCACTAAGGCTTAATA 0.398 0.43 66 49 CARD10 29775 broad.mit.edu 37 22 37906357 37906358 + Frame_Shift_Ins INS - G G C32_SKIN NA C32_SKIN NA g.chr22:37906357_37906358insG uc003asx.1 - 4 773_774 c.770_771insC c.(769-771)CCGfs p.P257fs CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_Frame_Shift_Ins_p.P257fs NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 257 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) CCCCAGGGGGCGGGCCCCTGGC 0.515 0.11 459 58 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 46 MAST2 23139 broad.mit.edu 37 1 46496355 46496355 + Frame_Shift_Del DEL A - - CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:46496355delA uc001cov.2 + 22 2913 c.2630delA c.(2629-2631)GAGfs p.E877fs MAST2_uc001cow.2_Frame_Shift_Del_p.E877fs|MAST2_uc001coy.1_Frame_Shift_Del_p.E551fs|MAST2_uc001coz.1_Frame_Shift_Del_p.E762fs|MAST2_uc001cpa.2_RNA NM_015112 NP_055927 Q6P0Q8 MAST2_HUMAN microtubule associated serine/threonine kinase 877 regulation of interleukin-12 biosynthetic process|spermatid differentiation cytoplasm|cytoskeleton|plasma membrane ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity ovary(5)|lung(3)|stomach(2)|breast(1) 11 Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184) AGCCTGAGTGAGGAGAAGGAG 0.642 0.26 35 12 CELF3 11189 broad.mit.edu 37 1 151678722 151678723 + In_Frame_Ins INS - TGC TGC CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:151678722_151678723insTGC uc001eys.1 - 10 1897_1898 c.1103_1104insGCA c.(1102-1104)CAA>CAGCAA p.368_368Q>QQ CELF3_uc010pdh.1_In_Frame_Ins_p.154_154Q>QQ|CELF3_uc001eyr.2_In_Frame_Ins_p.367_367Q>QQ|CELF3_uc009wmy.2_In_Frame_Ins_p.318_318Q>QQ|CELF3_uc009wmx.1_In_Frame_Ins_p.367_367Q>QQ NM_007185 NP_009116 Q5SZQ8 CELF3_HUMAN trinucleotide repeat containing 4 368 Gln-rich. nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome cytoplasm|nucleus mRNA binding|nucleotide binding ovary(1)|central_nervous_system(1) 2 gctgctgctgttgctgctgctg 0.505 0.27 91 33 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.29 17 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.20 43 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 120 181 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.29 49 20 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.70 3 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 19 SLK 9748 broad.mit.edu 37 10 105762994 105762996 + In_Frame_Del DEL TCC - - CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:105762994_105762996delTCC uc001kxo.1 + 9 2092_2094 c.2058_2060delTCC c.(2056-2061)ATTCCA>ATA p.P687del SLK_uc001kxp.1_In_Frame_Del_p.P687del NM_014720 NP_055535 Q9H2G2 SLK_HUMAN serine/threonine kinase 2 687 apoptosis|nucleotide-excision repair cytoplasm|plasma membrane ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity ovary(2)|stomach(2)|skin(2)|lung(1)|kidney(1) 8 Colorectal(252;0.178) Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165) AAAAAGAAATTCCAGTGTCAATT 0.394 0.48 30 28 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.88 3 23 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 910 380 DDX10 1662 broad.mit.edu 37 11 108564298 108564299 + Frame_Shift_Del DEL AT - - CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:108564298_108564299delAT uc001pkm.2 + 9 1259_1260 c.1194_1195delAT c.(1192-1197)ACATATfs p.T398fs DDX10_uc001pkl.1_Frame_Shift_Del_p.T398fs NM_004398 NP_004389 Q13206 DDX10_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 10 398_399 Helicase C-terminal. ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity breast(2)|lung(1)|prostate(1) 4 all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729) BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133) ATGCCAACACATATATTCACAG 0.411 0.48 92 86 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.35 11 6 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.19 48 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 47 194 LMTK3 114783 broad.mit.edu 37 19 49001791 49001792 + Frame_Shift_Ins INS - G G CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:49001791_49001792insG uc002pjk.2 - 12 2621_2622 c.2621_2622insC c.(2620-2622)CCGfs p.P874fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) CCCGGGGCCCCGGGAGTGGGAG 0.718 0.14 108 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 138 495 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 11 99 MED15 51586 broad.mit.edu 37 22 20918916 20918918 + In_Frame_Del DEL CAG - - CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:20918916_20918918delCAG uc002zsp.2 + 6 711_713 c.631_633delCAG c.(631-633)CAGdel p.Q218del MED15_uc002zsn.1_In_Frame_Del_p.Q137del|MED15_uc002zso.2_In_Frame_Del_p.Q147del|MED15_uc002zsq.2_In_Frame_Del_p.Q218del|MED15_uc010gso.2_In_Frame_Del_p.Q218del|MED15_uc002zsr.2_In_Frame_Del_p.Q192del|MED15_uc011ahs.1_In_Frame_Del_p.Q192del|MED15_uc011aht.1_In_Frame_Del_p.Q192del|MED15_uc002zss.2_In_Frame_Del_p.Q137del|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 218 Poly-Gln. Missing (in Ref. 4; CAG30423). regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) gcagcagctccagcagcagcagc 0.187 0.25 89 30 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CADOES1_BONE NA CADOES1_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 61 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - CADOES1_BONE NA CADOES1_BONE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 183 55 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CADOES1_BONE NA CADOES1_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 64 56 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CADOES1_BONE NA CADOES1_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.26 45 16 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 CADOES1_BONE NA CADOES1_BONE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.66 59 113 DST 667 broad.mit.edu 37 6 56426245 56426246 + Frame_Shift_Del DEL GA - - rs148547958 by1000genomes CADOES1_BONE NA CADOES1_BONE NA g.chr6:56426245_56426246delGA uc003pdf.2 - 51 7841_7842 c.7813_7814delTC c.(7813-7815)TCCfs p.S2605fs DST_uc003pcz.3_Frame_Shift_Del_p.S2427fs|DST_uc011dxj.1_Frame_Shift_Del_p.S2456fs|DST_uc011dxk.1_Frame_Shift_Del_p.S2467fs|DST_uc003pcy.3_Frame_Shift_Del_p.S2101fs NM_001144769 NP_001138241 Q03001 DYST_HUMAN dystonin isoform 2 4513 cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1) 14 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) TTGCAATTTGGAGAGTTTAGTG 0.396 0.42 217 155 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CADOES1_BONE NA CADOES1_BONE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.83 2 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 CADOES1_BONE NA CADOES1_BONE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.20 40 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CADOES1_BONE NA CADOES1_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 25 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CADOES1_BONE NA CADOES1_BONE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.30 307 131 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 CADOES1_BONE NA CADOES1_BONE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.60 4 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CADOES1_BONE NA CADOES1_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 216 52 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CADOES1_BONE NA CADOES1_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.52 10 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CADOES1_BONE NA CADOES1_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 123 418 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CADOES1_BONE NA CADOES1_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 53 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 32 ARID1A 8289 broad.mit.edu 37 1 27024001 27024002 + Frame_Shift_Ins INS - G G CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr1:27024001_27024002insG uc001bmv.1 + 1 1480_1481 c.1107_1108insG c.(1105-1110)GGCGGGfs p.G369fs ARID1A_uc001bmt.1_Frame_Shift_Ins_p.G369fs|ARID1A_uc001bmu.1_Frame_Shift_Ins_p.G369fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 369_370 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.Q372fs*19(1)|p.Q372fs*28(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.18 217 48 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 41 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.32 75 36 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 54 26 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.41 213 150 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.60 4 6 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 LETM2 137994 broad.mit.edu 37 8 38250315 38250315 + Frame_Shift_Del DEL G - - CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr8:38250315delG uc003xlm.1 + 3 333 c.162delG c.(160-162)CAGfs p.Q54fs LETM2_uc003xlk.2_Frame_Shift_Del_p.Q101fs|LETM2_uc011lbn.1_5'UTR|LETM2_uc003xll.1_Frame_Shift_Del_p.Q54fs|LETM2_uc003xln.1_5'UTR|LETM2_uc003xlo.1_5'UTR NM_144652 NP_653253 Q2VYF4 LETM2_HUMAN leucine zipper-EF-hand containing transmembrane 101 Mitochondrial intermembrane (Potential). integral to membrane|mitochondrial inner membrane 0 all_cancers(2;6.77e-47)|all_epithelial(2;1.01e-50)|all_lung(3;1.25e-23)|Lung NSC(2;2.76e-23)|Colorectal(12;0.000442)|Esophageal squamous(3;0.00202) all_lung(54;0.0657)|Hepatocellular(245;0.152)|Lung NSC(58;0.175) Epithelial(3;1.17e-42)|all cancers(3;5.44e-38)|BRCA - Breast invasive adenocarcinoma(5;5.44e-27)|LUSC - Lung squamous cell carcinoma(2;7.12e-25)|Lung(2;4.49e-22)|COAD - Colon adenocarcinoma(9;0.114) AACATCCACAGGTGACAAGCC 0.418 0.32 32 15 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.57 30 39 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 21 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.11 615 74 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.40 18 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 105 27 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 6 65 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.59 22 32 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 58 312 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAKI1_KIDNEY NA CAKI1_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 34 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.76 9 29 PDE4DIP 9659 broad.mit.edu 37 1 144886180 144886183 + Frame_Shift_Del DEL TTCT - - CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr1:144886180_144886183delTTCT uc001elw.3 - 23 3342_3345 c.3051_3054delAGAA c.(3049-3054)TTAGAAfs p.L1017fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.L1083fs|PDE4DIP_uc001elv.3_Frame_Shift_Del_p.L24fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 1017_1018 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TCCTCTTCTCTTCTAAGTGCTGGT 0.505 0.15 289 50 DOCK3 1795 broad.mit.edu 37 3 51184025 51184025 + Frame_Shift_Del DEL C - - rs67401724 CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr3:51184025delC uc011bds.1 + 10 815 c.792delC c.(790-792)AACfs p.N264fs NM_004947 NP_004938 Q8IZD9 DOCK3_HUMAN dedicator of cytokinesis 3 264 cytoplasm GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding 0 BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518) GGCCGAGGAACCCAGAGAAGA 0.418 1.00 0 68 PBRM1 55193 broad.mit.edu 37 3 52637730 52637733 + Frame_Shift_Del DEL ATAT - - rs149186835 CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr3:52637730_52637733delATAT uc003des.2 - 17 2595_2598 c.2583_2586delATAT c.(2581-2586)ATATATfs p.I861fs PBRM1_uc003dex.2_Intron|PBRM1_uc003deq.2_Frame_Shift_Del_p.I861fs|PBRM1_uc003der.2_Frame_Shift_Del_p.I829fs|PBRM1_uc003det.2_Frame_Shift_Del_p.I876fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.I876fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.I861fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.I861fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.I861fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.I861fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.I774fs|PBRM1_uc003dfa.1_Frame_Shift_Del_p.I207fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 861_862 Bromo 6. chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.99 2 187 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 112 175 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 12 25 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.39 95 61 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 2 15 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.25 46 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 62 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 395 42 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 626 253 ATN1 1822 broad.mit.edu 37 12 7045892 7045894 + In_Frame_Del DEL CAG - - rs66756893;rs67074116 CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr12:7045892_7045894delCAG uc001qrw.1 + 5 1699_1701 c.1462_1464delCAG c.(1462-1464)CAGdel p.Q502del ATN1_uc001qrx.1_In_Frame_Del_p.Q502del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagc 0.458 0.14 69 11 AKAP6 9472 broad.mit.edu 37 14 33292931 33292931 + Frame_Shift_Del DEL A - - CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr14:33292931delA uc001wrq.2 + 13 6082 c.5912delA c.(5911-5913)GAAfs p.E1971fs NM_004274 NP_004265 Q13023 AKAP6_HUMAN A-kinase anchor protein 6 1971 protein targeting calcium channel complex|nuclear membrane|sarcoplasmic reticulum protein kinase A binding|receptor binding breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1) 21 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) GBM - Glioblastoma multiforme(265;0.019) CACCATTTTGAAAATCAAAGC 0.388 0.95 7 140 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.64 20 36 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 60 954 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 95 258 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.30 44 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 92 473 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 8 129 DDX17 10521 broad.mit.edu 37 22 38897210 38897211 + Frame_Shift_Ins INS - T T CAKI2_KIDNEY NA CAKI2_KIDNEY NA g.chr22:38897210_38897211insT uc003avy.3 - 2 465_466 c.362_363insA c.(361-363)AAGfs p.K121fs DDX17_uc003avx.3_Frame_Shift_Ins_p.K121fs|DDX17_uc011anu.1_Frame_Shift_Ins_p.K34fs NM_001098504 NP_001091974 Q92841 DDX17_HUMAN DEAD box polypeptide 17 isoform 3 42 RNA processing nucleus ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity skin(3)|upper_aerodigestive_tract(1) 4 Melanoma(58;0.0286) 0.000 0.28 484 192 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAL120_BREAST NA CAL120_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.83 8 40 CDK11A 728642 broad.mit.edu 37 1 1635536 1635537 + Frame_Shift_Ins INS - A A CAL120_BREAST NA CAL120_BREAST NA g.chr1:1635536_1635537insA uc009vks.2 - 16 1843_1844 c.1735_1736insT c.(1735-1737)TACfs p.Y579fs CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agv.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc001ahh.3_Intron|SLC35E2_uc009vkm.1_Intron|CDK11A_uc001ahj.3_Frame_Shift_Ins_p.Y86fs|CDK11A_uc009vkp.2_Frame_Shift_Ins_p.Y196fs|CDK11A_uc009vkq.2_Intron|CDK11A_uc009vkr.2_Frame_Shift_Ins_p.Y569fs NM_024011 NP_076916 Q9UQ88 CD11A_HUMAN cell division cycle 2-like 2 isoform 1 582 Protein kinase. apoptosis|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent cytoplasm|nucleus ATP binding|cyclin-dependent protein kinase activity|protein binding stomach(1) 1 GACCGGGGTGTAGGCCTTCAGA 0.673 0.40 40 27 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - CAL120_BREAST NA CAL120_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.35 237 129 TTN 7273 broad.mit.edu 37 2 179485131 179485132 + Frame_Shift_Ins INS - A A CAL120_BREAST NA CAL120_BREAST NA g.chr2:179485131_179485132insA uc010zfg.1 - 197 38636_38637 c.38412_38413insT c.(38410-38415)ATTGTCfs p.I12804fs TTN_uc010zfh.1_Frame_Shift_Ins_p.I6499fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.I6432fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.I6307fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 13731_13732 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CCAGCAGTGACAATGTATTCAC 0.426 0.16 250 46 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes CAL120_BREAST NA CAL120_BREAST NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.35 22 12 ROBO1 6091 broad.mit.edu 37 3 78710241 78710242 + Frame_Shift_Ins INS - G G CAL120_BREAST NA CAL120_BREAST NA g.chr3:78710241_78710242insG uc003dqe.2 - 16 2466_2467 c.2258_2259insC c.(2257-2259)CCTfs p.P753fs ROBO1_uc003dqb.2_Frame_Shift_Ins_p.P714fs|ROBO1_uc003dqc.2_Frame_Shift_Ins_p.P717fs|ROBO1_uc003dqd.2_Frame_Shift_Ins_p.P717fs|ROBO1_uc010hoh.2_5'UTR|ROBO1_uc011bgl.1_Frame_Shift_Ins_p.P325fs|ROBO1_uc003dqf.1_Frame_Shift_Ins_p.P432fs NM_002941 NP_002932 Q9Y6N7 ROBO1_HUMAN roundabout 1 isoform a 753 Extracellular (Potential).|Fibronectin type-III 2. activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway cell surface|cytoplasm|integral to plasma membrane axon guidance receptor activity|identical protein binding|LRR domain binding large_intestine(2) 2 Lung SC(41;0.0257)|Lung NSC(201;0.0439) LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274) CATTAAAAAAAGGGCGAGCCTT 0.411 0.16 65 12 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CAL120_BREAST NA CAL120_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.37 19 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAL120_BREAST NA CAL120_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 90 128 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes CAL120_BREAST NA CAL120_BREAST NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.70 3 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CAL120_BREAST NA CAL120_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.82 2 9 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CAL120_BREAST NA CAL120_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.43 16 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CAL120_BREAST NA CAL120_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 2 31 ZNF503 84858 broad.mit.edu 37 10 77158587 77158587 + Frame_Shift_Del DEL C - - CAL120_BREAST NA CAL120_BREAST NA g.chr10:77158587delC uc001jxg.2 - 2 2197 c.1861delG c.(1861-1863)GCCfs p.A621fs C10orf41_uc010qlf.1_5'Flank NM_032772 NP_116161 Q96F45 ZN503_HUMAN zinc finger protein 503 621 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus nucleic acid binding|zinc ion binding ovary(1) 1 all_cancers(46;0.105)|all_epithelial(25;0.00449)|Prostate(51;0.0112)|Ovarian(15;0.088) 0.000 1.00 0 12 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency CAL120_BREAST NA CAL120_BREAST NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.52 45 48 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CAL120_BREAST NA CAL120_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 58 879 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAL120_BREAST NA CAL120_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 258 776 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAL120_BREAST NA CAL120_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 7 52 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAL12T_LUNG NA CAL12T_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 34 ARHGAP29 9411 broad.mit.edu 37 1 94654492 94654492 + Frame_Shift_Del DEL A - - CAL12T_LUNG NA CAL12T_LUNG NA g.chr1:94654492delA uc001dqj.3 - 15 1951 c.1582delT c.(1582-1584)TCCfs p.S528fs ARHGAP29_uc009wdq.1_RNA|ARHGAP29_uc001dqk.2_Frame_Shift_Del_p.S94fs NM_004815 NP_004806 Q52LW3 RHG29_HUMAN PTPL1-associated RhoGAP 1 528 Rho protein signal transduction cytosol metal ion binding|Rho GTPase activator activity breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1) 11 all_lung(203;0.000732)|Lung NSC(277;0.00328) all cancers(265;0.0187)|Epithelial(280;0.159) CTTATAAAGGAAGGACCTTTA 0.358 0.33 24 12 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes CAL12T_LUNG NA CAL12T_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.69 11 24 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes CAL12T_LUNG NA CAL12T_LUNG NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.34 50 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAL12T_LUNG NA CAL12T_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 108 135 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAL12T_LUNG NA CAL12T_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 61 121 FBN2 2201 broad.mit.edu 37 5 127607738 127607738 + Frame_Shift_Del DEL C - - CAL12T_LUNG NA CAL12T_LUNG NA g.chr5:127607738delC uc003kuu.2 - 62 8352 c.7913delG c.(7912-7914)GGCfs p.G2638fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 2638 EGF-like 45; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) TTGGGGGCAGCCACATCTGTA 0.512 0.91 8 81 HIP1 3092 broad.mit.edu 37 7 75184783 75184794 + In_Frame_Del DEL CCTGCTCCGCAG - - rs141940280 CAL12T_LUNG NA CAL12T_LUNG NA g.chr7:75184783_75184794delCCTGCTCCGCAG uc003uds.1 - 19 1930_1941 c.1889_1900delCTGCGGAGCAGG c.(1888-1902)GCTGCGGAGCAGGTG>GTG p.AAEQ630del HIP1_uc011kfz.1_In_Frame_Del_p.AAEQ507del NM_005338 NP_005329 O00291 HIP1_HUMAN huntingtin interacting protein 1 630_633 Potential. activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1) 8 TCTTGTATCACCTGCTCCGCAGCCTTCCTGGA 0.557 0.30 118 50 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 CAL12T_LUNG NA CAL12T_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.47 20 18 CYP17A1 1586 broad.mit.edu 37 10 104592290 104592290 + Frame_Shift_Del DEL G - - CAL12T_LUNG NA CAL12T_LUNG NA g.chr10:104592290delG uc001kwg.2 - 6 1289 c.1117delC c.(1117-1119)CACfs p.H373fs NM_000102 NP_000093 P05093 CP17A_HUMAN cytochrome P450, family 17 373 H -> L (in AH5). androgen biosynthetic process|glucocorticoid biosynthetic process|sex differentiation|xenobiotic metabolic process endoplasmic reticulum membrane electron carrier activity|heme binding|oxygen binding|steroid 17-alpha-monooxygenase activity 0 Colorectal(252;0.122)|all_hematologic(284;0.152) Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215) NADH(DB00157)|Progesterone(DB00396) TTGGCCTTGTGGGGGATGAGC 0.622 0.31 29 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAL12T_LUNG NA CAL12T_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 865 454 RB1 5925 broad.mit.edu 37 13 49054142 49054147 + In_Frame_Del DEL CGAACA - - CAL12T_LUNG NA CAL12T_LUNG NA g.chr13:49054142_49054147delCGAACA uc001vcb.2 + 27 2888_2893 c.2722_2727delCGAACA c.(2722-2727)CGAACAdel p.RT908del NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 908_909 Interaction with LIMD1.|Domain C; mediates interaction with E4F1. androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.?(7) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) AGCTTCTACTCGAACACGAATGCAAA 0.422 0.24 64 20 TAOK2 9344 broad.mit.edu 37 16 29994855 29994856 + Frame_Shift_Del DEL AG - - CAL12T_LUNG NA CAL12T_LUNG NA g.chr16:29994855_29994856delAG uc002dva.1 + 13 2075_2076 c.1292_1293delAG c.(1291-1293)CAGfs p.Q431fs uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TAOK2_uc002dvb.1_Frame_Shift_Del_p.Q431fs|TAOK2_uc002dvc.1_Frame_Shift_Del_p.Q431fs|TAOK2_uc010bzm.1_Frame_Shift_Del_p.Q438fs|TAOK2_uc002dvd.1_Frame_Shift_Del_p.Q258fs NM_016151 NP_057235 Q9UL54 TAOK2_HUMAN TAO kinase 2 isoform 2 431 actin cytoskeleton organization|activation of MAPKK activity|apoptosis|cell migration|focal adhesion assembly|positive regulation of JNK cascade|protein targeting to membrane|regulation of cell growth|regulation of cell shape|response to stress cytoplasmic vesicle membrane|cytoskeleton|dendrite|integral to membrane|nucleolus ATP binding|protein serine/threonine kinase activity ovary(1) 1 GACCCCTACCAGCCAGAGATAA 0.619 0.36 81 46 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAL12T_LUNG NA CAL12T_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 24 120 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 CAL12T_LUNG NA CAL12T_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.14 42 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAL12T_LUNG NA CAL12T_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 66 791 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAL12T_LUNG NA CAL12T_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 10 133 MED15 51586 broad.mit.edu 37 22 20918915 20918916 + In_Frame_Ins INS - CAG CAG CAL12T_LUNG NA CAL12T_LUNG NA g.chr22:20918915_20918916insCAG uc002zsp.2 + 6 710_711 c.630_631insCAG c.(628-633)insCAG p.218_219insQ MED15_uc002zsn.1_In_Frame_Ins_p.137_138insQ|MED15_uc002zso.2_In_Frame_Ins_p.147_148insQ|MED15_uc002zsq.2_In_Frame_Ins_p.218_219insQ|MED15_uc010gso.2_In_Frame_Ins_p.218_219insQ|MED15_uc002zsr.2_In_Frame_Ins_p.192_193insQ|MED15_uc011ahs.1_In_Frame_Ins_p.192_193insQ|MED15_uc011aht.1_In_Frame_Ins_p.192_193insQ|MED15_uc002zss.2_In_Frame_Ins_p.137_138insQ|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 218_219 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) agcagcagctccagcagcagca 0.178 0.10 458 50 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAL148_BREAST NA CAL148_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.42 26 19 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A CAL148_BREAST NA CAL148_BREAST NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 70 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAL148_BREAST NA CAL148_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 52 66 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAL148_BREAST NA CAL148_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.85 11 60 NSD1 64324 broad.mit.edu 37 5 176638990 176638991 + Frame_Shift_Del DEL AG - - CAL148_BREAST NA CAL148_BREAST NA g.chr5:176638990_176638991delAG uc003mfr.3 + 5 3728_3729 c.3590_3591delAG c.(3589-3591)CAGfs p.Q1197fs NSD1_uc003mft.3_Frame_Shift_Del_p.Q928fs|NSD1_uc003mfs.1_Frame_Shift_Del_p.Q1094fs|NSD1_uc011dfx.1_Frame_Shift_Del_p.Q845fs NM_022455 NP_071900 Q96L73 NSD1_HUMAN nuclear receptor binding SET domain protein 1 1197 negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|nucleus androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding ovary(2)|kidney(1) 3 all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002) all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198) Kidney(146;0.235) 0.000 0.24 120 38 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CAL148_BREAST NA CAL148_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 25 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 CAL148_BREAST NA CAL148_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.38 48 29 TET1 80312 broad.mit.edu 37 10 70333991 70333993 + In_Frame_Del DEL TGT - - CAL148_BREAST NA CAL148_BREAST NA g.chr10:70333991_70333993delTGT uc001jok.3 + 2 2401_2403 c.1896_1898delTGT c.(1894-1899)TCTGTT>TCT p.V635del NM_030625 NP_085128 Q8NFU7 TET1_HUMAN CXXC finger 6 635 Sufficient for binding to genomic CpG islands. DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding ovary(5)|lung(2)|prostate(1)|breast(1) 9 AGAAACCATCTGTTGTTGTGCCT 0.438 0.27 110 41 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 CAL148_BREAST NA CAL148_BREAST NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.93 1 13 ITGA7 3679 broad.mit.edu 37 12 56092191 56092191 + Frame_Shift_Del DEL C - - CAL148_BREAST NA CAL148_BREAST NA g.chr12:56092191delC uc001shh.2 - 7 1400 c.1180delG c.(1180-1182)GACfs p.D394fs ITGA7_uc001shg.2_Frame_Shift_Del_p.D390fs|ITGA7_uc010sps.1_Frame_Shift_Del_p.D297fs|ITGA7_uc009znw.2_5'Flank|ITGA7_uc009znx.2_Frame_Shift_Del_p.D277fs NM_001144996 NP_001138468 Q13683 ITA7_HUMAN integrin alpha 7 isoform 1 precursor 434 Potential.|FG-GAP 6.|Extracellular (Potential). cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development|regulation of cell shape integrin complex receptor activity ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1) 5 0.000 0.10 284 32 MYH11 4629 broad.mit.edu 37 16 15820795 15820797 + In_Frame_Del DEL CTT - - rs149241435 byFrequency CAL148_BREAST NA CAL148_BREAST NA g.chr16:15820795_15820797delCTT uc002ddy.2 - 28 3873_3875 c.3766_3768delAAG c.(3766-3768)AAGdel p.K1256del MYH11_uc002ddv.2_In_Frame_Del_p.K1263del|MYH11_uc002ddw.2_In_Frame_Del_p.K1256del|MYH11_uc002ddx.2_In_Frame_Del_p.K1263del|MYH11_uc010bvg.2_In_Frame_Del_p.K1088del|MYH11_uc010bvh.2_5'Flank NM_002474 NP_002465 P35749 MYH11_HUMAN smooth muscle myosin heavy chain 11 isoform 1256 Potential. Missing (in AAT4). axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction cytosol|melanosome|muscle myosin complex|myosin filament actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1) 15 GCGCCTCCAGCTTCTTCTTCTTA 0.611 0.20 173 43 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CAL148_BREAST NA CAL148_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.75 15 45 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAL148_BREAST NA CAL148_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 4 48 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAL148_BREAST NA CAL148_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.83 4 20 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAL27_UPPER_AERODIGESTIVE_TRACT NA CAL27_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 2 20 CASP8 841 broad.mit.edu 37 2 202137471 202137474 + Frame_Shift_Del DEL AATC - - CAL27_UPPER_AERODIGESTIVE_TRACT NA CAL27_UPPER_AERODIGESTIVE_TRACT NA g.chr2:202137471_202137474delAATC uc002uxr.1 + 5 731_734 c.522_525delAATC c.(520-525)ATAATCfs p.I174fs CASP8_uc010ftc.1_Frame_Shift_Del_p.I174fs|CASP8_uc002uxo.1_Frame_Shift_Del_p.I174fs|CASP8_uc002uxp.1_Frame_Shift_Del_p.I206fs|CASP8_uc002uxq.1_Frame_Shift_Del_p.I174fs|CASP8_uc002uxs.1_Frame_Shift_Del_p.I174fs|CASP8_uc002uxt.1_Frame_Shift_Del_p.I233fs|CASP8_uc002uxu.1_RNA|CASP8_uc010ftd.1_Frame_Shift_Del_p.I71fs|CASP8_uc002uxv.1_Frame_Shift_Del_p.I174fs|CASP8_uc002uxw.1_Frame_Shift_Del_p.I174fs|CASP8_uc002uxy.1_Frame_Shift_Del_p.I174fs|CASP8_uc002uxx.1_Frame_Shift_Del_p.I174fs|CASP8_uc010ftf.2_Frame_Shift_Del_p.I174fs|CASP8_uc010fte.1_Frame_Shift_Del_p.I71fs NM_033355 NP_203519 Q14790 CASP8_HUMAN caspase 8 isoform B precursor 174_175 DED 2. activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor centrosome|cytosol|mitochondrial outer membrane cysteine-type endopeptidase activity|protein binding|protein binding upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1) 5 TGCTGAAGATAATCAACGACTATG 0.422 0.50 40 40 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAL27_UPPER_AERODIGESTIVE_TRACT NA CAL27_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.37 51 30 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAL27_UPPER_AERODIGESTIVE_TRACT NA CAL27_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 54 27 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CAL27_UPPER_AERODIGESTIVE_TRACT NA CAL27_UPPER_AERODIGESTIVE_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.92 1 11 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CAL27_UPPER_AERODIGESTIVE_TRACT NA CAL27_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 1 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAL27_UPPER_AERODIGESTIVE_TRACT NA CAL27_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 334 97 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAL27_UPPER_AERODIGESTIVE_TRACT NA CAL27_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 174 414 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAL27_UPPER_AERODIGESTIVE_TRACT NA CAL27_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 7 69 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAL29_URINARY_TRACT NA CAL29_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 2 86 FANCD2 2177 broad.mit.edu 37 3 10089654 10089655 + Frame_Shift_Del DEL CT - - CAL29_URINARY_TRACT NA CAL29_URINARY_TRACT NA g.chr3:10089654_10089655delCT uc003buw.2 + 16 1410_1411 c.1332_1333delCT c.(1330-1335)CACTCTfs p.H444fs FANCD2_uc003bux.1_Frame_Shift_Del_p.H444fs|FANCD2_uc003buy.1_Frame_Shift_Del_p.H444fs|FANCD2_uc010hcw.1_5'Flank NM_033084 NP_149075 Q9BXW9 FACD2_HUMAN Fanconi anemia complementation group D2 isoform 444_445 DNA repair|response to gamma radiation nucleoplasm protein binding|protein binding central_nervous_system(2)|ovary(1)|skin(1) 4 OV - Ovarian serous cystadenocarcinoma(96;0.148) GTTTGCTTCACTCTCTAGACCA 0.391 0.13 276 42 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CAL29_URINARY_TRACT NA CAL29_URINARY_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.28 21 8 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CAL29_URINARY_TRACT NA CAL29_URINARY_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.23 24 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAL29_URINARY_TRACT NA CAL29_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.67 41 85 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAL29_URINARY_TRACT NA CAL29_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.58 36 50 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CAL29_URINARY_TRACT NA CAL29_URINARY_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CAL29_URINARY_TRACT NA CAL29_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 14 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 CAL29_URINARY_TRACT NA CAL29_URINARY_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.33 42 21 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAL29_URINARY_TRACT NA CAL29_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 59 224 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAL29_URINARY_TRACT NA CAL29_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 93 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 6 51 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.62 5 8 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.23 120 35 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 66 93 TRIO 7204 broad.mit.edu 37 5 14364002 14364004 + In_Frame_Del DEL TCT - - CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr5:14364002_14364004delTCT uc003jff.2 + 14 2559_2561 c.2553_2555delTCT c.(2551-2556)GATCTT>GAT p.L853del TRIO_uc003jfg.2_RNA|TRIO_uc011cna.1_In_Frame_Del_p.L804del|TRIO_uc003jfh.1_In_Frame_Del_p.L502del NM_007118 NP_009049 O75962 TRIO_HUMAN triple functional domain (PTPRF interacting) 853 apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway cytosol ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1) 18 Lung NSC(4;0.000742) AAGGGCAAGATCTTCTGCAGTAT 0.493 0.46 78 67 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 21 36 MSH3 4437 broad.mit.edu 37 5 80160647 80160648 + Frame_Shift_Del DEL CT - - CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr5:80160647_80160648delCT uc003kgz.2 + 22 3269_3270 c.3016_3017delCT c.(3016-3018)CTGfs p.L1006fs NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 1006 maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) ATCCTTAACCCTGTTTGTCACC 0.312 0.42 41 30 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 18 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 147 17 MLLT10 8028 broad.mit.edu 37 10 22016857 22016857 + Frame_Shift_Del DEL G - - CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr10:22016857delG uc001iqs.2 + 17 2459 c.2111delG c.(2110-2112)CGAfs p.R704fs MLLT10_uc001iqt.2_Frame_Shift_Del_p.R688fs|MLLT10_uc001iqv.2_RNA|MLLT10_uc001iqy.2_Frame_Shift_Del_p.R688fs|MLLT10_uc001ira.2_Frame_Shift_Del_p.R145fs|MLLT10_uc001irb.2_RNA NM_004641 NP_004632 P55197 AF10_HUMAN myeloid/lymphoid or mixed-lineage leukemia 704 positive regulation of transcription from RNA polymerase II promoter cytoplasm|nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding lung(1)|skin(1) 2 CTCTCGCCACGGTAAGCGCTA 0.423 0.36 54 31 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.45 22 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 195 60 TP53BP1 7158 broad.mit.edu 37 15 43769885 43769899 + In_Frame_Del DEL TTGTGCAGACAACTG - - CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr15:43769885_43769899delTTGTGCAGACAACTG uc001zrs.2 - 8 980_994 c.832_846delCAGTTGTCTGCACAA c.(832-846)CAGTTGTCTGCACAAdel p.QLSAQ278del TP53BP1_uc010udp.1_In_Frame_Del_p.QLSAQ278del|TP53BP1_uc001zrq.3_In_Frame_Del_p.QLSAQ283del|TP53BP1_uc001zrr.3_In_Frame_Del_p.QLSAQ283del|TP53BP1_uc010udq.1_In_Frame_Del_p.QLSAQ283del NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 278_282 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) CCATAAGTTCTTGTGCAGACAACTGTTCTTTTGCT 0.433 0.22 91 25 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.15 100 18 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.83 12 58 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 6 16 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 85 614 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 61 MYH9 4627 broad.mit.edu 37 22 36696947 36696948 + In_Frame_Ins INS - CTC CTC CAL33_UPPER_AERODIGESTIVE_TRACT NA CAL33_UPPER_AERODIGESTIVE_TRACT NA g.chr22:36696947_36696948insCTC uc003apg.2 - 22 3018_3019 c.2787_2788insGAG c.(2785-2790)insGAG p.929_930insE MYH9_uc003aph.1_In_Frame_Ins_p.793_794insE NM_002473 NP_002464 P35579 MYH9_HUMAN myosin, heavy polypeptide 9, non-muscle 929_930 Potential. actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1) 11 TGCTGGCAGCGCTCCTCCTCCT 0.668 0.30 225 95 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAL51_BREAST NA CAL51_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 60 MCF2 4168 broad.mit.edu 37 X 138697051 138697052 + Frame_Shift_Ins INS - A A CAL51_BREAST NA CAL51_BREAST NA g.chrX:138697051_138697052insA uc004fau.2 - 10 1645_1646 c.1351_1352insT c.(1351-1353)TCAfs p.S451fs MCF2_uc004fav.2_Frame_Shift_Ins_p.S451fs|MCF2_uc011mwl.1_Frame_Shift_Ins_p.S412fs|MCF2_uc010nsh.1_Frame_Shift_Ins_p.S451fs|MCF2_uc011mwm.1_Frame_Shift_Ins_p.S412fs|MCF2_uc011mwn.1_Frame_Shift_Ins_p.S596fs|MCF2_uc004faw.2_Frame_Shift_Ins_p.S511fs|MCF2_uc011mwo.1_Frame_Shift_Ins_p.S511fs NM_005369 NP_005360 P10911 MCF2_HUMAN MCF.2 cell line derived transforming sequence 451 apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytoskeleton|cytosol|membrane|membrane fraction protein binding|Rho guanyl-nucleotide exchange factor activity lung(1)|pleura(1) 2 Acute lymphoblastic leukemia(192;0.000127) TTGTTTAGATGAAAAAAATGGT 0.371 0.50 57 58 PINK1 65018 broad.mit.edu 37 1 20960379 20960379 + Frame_Shift_Del DEL A - - CAL51_BREAST NA CAL51_BREAST NA g.chr1:20960379delA uc001bdm.2 + 1 432 c.338delA c.(337-339)GAAfs p.E113fs NM_032409 NP_115785 Q9BXM7 PINK1_HUMAN PTEN induced putative kinase 1 precursor 113 Cytoplasmic (Potential). cell death|intracellular protein kinase cascade|mitochondrion degradation|peptidyl-serine phosphorylation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of release of cytochrome c from mitochondria|regulation of protein complex assembly|regulation of protein ubiquitination|response to stress cytosol|integral to membrane|mitochondrial outer membrane ATP binding|C3HC4-type RING finger domain binding|calcium-dependent protein kinase activity|magnesium ion binding|protein serine/threonine kinase activity|ubiquitin protein ligase binding ovary(2)|central_nervous_system(1) 3 all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199) 0.000 0.24 640 204 ARID1A 8289 broad.mit.edu 37 1 27105931 27105931 + Frame_Shift_Del DEL G - - rs140055856 CAL51_BREAST NA CAL51_BREAST NA g.chr1:27105931delG uc001bmv.1 + 20 5915 c.5542delG c.(5542-5544)GGGfs p.G1848fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.G1631fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.G694fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.G176fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.G90fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1848 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.G1848fs*6(3) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GCGGATTGGTGGGGGGGACAC 0.582 0.38 80 48 OBSCN 84033 broad.mit.edu 37 1 228526003 228526004 + Frame_Shift_Ins INS - G G CAL51_BREAST NA CAL51_BREAST NA g.chr1:228526003_228526004insG uc009xez.1 + 68 17058_17059 c.17014_17015insG c.(17014-17016)TGGfs p.W5672fs OBSCN_uc001hsn.2_Frame_Shift_Ins_p.W5672fs|OBSCN_uc001hsr.1_Frame_Shift_Ins_p.W300fs NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 5672 apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) GTCACCTGAGTGGGGGGCCGCT 0.644 0.44 10 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAL51_BREAST NA CAL51_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.37 103 61 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAL51_BREAST NA CAL51_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.31 44 20 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 CAL51_BREAST NA CAL51_BREAST NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.28 200 79 NSD1 64324 broad.mit.edu 37 5 176638344 176638344 + Frame_Shift_Del DEL G - - CAL51_BREAST NA CAL51_BREAST NA g.chr5:176638344delG uc003mfr.3 + 5 3082 c.2944delG c.(2944-2946)GGGfs p.G982fs NSD1_uc003mft.3_Frame_Shift_Del_p.G713fs|NSD1_uc003mfs.1_Frame_Shift_Del_p.G879fs|NSD1_uc011dfx.1_Frame_Shift_Del_p.G630fs NM_022455 NP_071900 Q96L73 NSD1_HUMAN nuclear receptor binding SET domain protein 1 982 negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|nucleus androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding ovary(2)|kidney(1) 3 all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002) all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198) Kidney(146;0.235) TAGCCCTAGTGGGGGTGACTC 0.512 0.32 80 37 BAI3 577 broad.mit.edu 37 6 70098782 70098782 + Frame_Shift_Del DEL A - - CAL51_BREAST NA CAL51_BREAST NA g.chr6:70098782delA uc003pev.3 + 32 5016 c.4568delA c.(4567-4569)TAAfs p.*1523fs BAI3_uc010kak.2_Frame_Shift_Del_p.*1523fs|BAI3_uc011dxx.1_Frame_Shift_Del_p.*729fs NM_001704 NP_001695 O60242 BAI3_HUMAN brain-specific angiogenesis inhibitor 3 1523 negative regulation of angiogenesis|neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1) 50 all_lung(197;0.212) ACAGAAGTTTAAAAAAATCAA 0.418 0.35 17 9 CDK14 5218 broad.mit.edu 37 7 90528642 90528642 + Frame_Shift_Del DEL G - - CAL51_BREAST NA CAL51_BREAST NA g.chr7:90528642delG uc003uky.2 + 7 898 c.676delG c.(676-678)GGGfs p.G226fs CDK14_uc003ukz.1_Frame_Shift_Del_p.G208fs|CDK14_uc010les.1_Frame_Shift_Del_p.G180fs|CDK14_uc011khl.1_Frame_Shift_Del_p.G97fs NM_012395 NP_036527 O94921 CDK14_HUMAN PFTAIRE protein kinase 1 226 Protein kinase. cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane ATP binding|cyclin binding|cyclin-dependent protein kinase activity lung(3)|ovary(1) 4 CAAGCACCCTGGGGGGCTGCA 0.353 0.29 114 46 KCNH2 3757 broad.mit.edu 37 7 150655465 150655465 + Frame_Shift_Del DEL G - - CAL51_BREAST NA CAL51_BREAST NA g.chr7:150655465delG uc003wic.2 - 4 611 c.598delC c.(598-600)CTGfs p.L200fs KCNH2_uc003wib.2_5'Flank|KCNH2_uc011kux.1_Frame_Shift_Del_p.L104fs|KCNH2_uc003wid.2_5'Flank|KCNH2_uc003wie.2_Frame_Shift_Del_p.L200fs NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 200 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) 0.000 0.47 639 565 VPS13B 157680 broad.mit.edu 37 8 100832327 100832329 + In_Frame_Del DEL ATT - - rs56413739 CAL51_BREAST NA CAL51_BREAST NA g.chr8:100832327_100832329delATT uc003yiv.2 + 49 9157_9159 c.9046_9048delATT c.(9046-9048)ATTdel p.I3018del VPS13B_uc003yiw.2_In_Frame_Del_p.I2993del NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 3018 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TGCTGGCAAAATTATTATTCCTC 0.355 0.11 98 12 CEP110 11064 broad.mit.edu 37 9 123924525 123924525 + Frame_Shift_Del DEL A - - CAL51_BREAST NA CAL51_BREAST NA g.chr9:123924525delA uc004bkx.1 + 32 5430 c.5399delA c.(5398-5400)GAAfs p.E1800fs CEP110_uc004blb.1_Frame_Shift_Del_p.E469fs|CEP110_uc010mvp.1_Intron NM_007018 NP_008949 Q7Z7A1 CNTRL_HUMAN centrosomal protein 110kDa 1800 Potential. cell division|G2/M transition of mitotic cell cycle centrosome|cytosol protein binding 0 GACATTTGGGAAAAAAAGTTG 0.383 0.47 8 7 PTEN 5728 broad.mit.edu 37 10 89720712 89720712 + Frame_Shift_Del DEL A - - CAL51_BREAST NA CAL51_BREAST NA g.chr10:89720712delA uc001kfb.2 + 9 1894 c.863delA c.(862-864)GAAfs p.E288fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 288 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.E288fs*3(6)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.E288*(2)|p.G165_*404del(1)|p.S287fs*1(1)|p.G165_K342del(1)|p.E288fs*8(1)|p.S287fs*8(1)|p.W274_F341del(1)|p.E288K(1)|p.E288fs*9(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GAAACCTCAGAAAAAGTAGAA 0.299 0.48 59 55 PTEN 5728 broad.mit.edu 37 10 89720811 89720812 + Frame_Shift_Ins INS - A A CAL51_BREAST NA CAL51_BREAST NA g.chr10:89720811_89720812insA uc001kfb.2 + 9 1993_1994 c.962_963insA c.(961-963)ACAfs p.T321fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 321 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.T321fs*23(9)|p.T321fs*3(7)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.N323fs*2(2)|p.T319_K332del(1)|p.T321fs*22(1)|p.G165_*404del(1)|p.G165_K342del(1)|p.L316fs*1(1)|p.W274_F341del(1)|p.V317_K322del(1)|p.T321fs*4(1)|p.T321fs*6(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) CTTACTTTAACAAAAAATGATC 0.327 0.35 93 49 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 CAL51_BREAST NA CAL51_BREAST NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.82 2 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAL51_BREAST NA CAL51_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 182 41 CHEK1 1111 broad.mit.edu 37 11 125514123 125514123 + Frame_Shift_Del DEL T - - CAL51_BREAST NA CAL51_BREAST NA g.chr11:125514123delT uc009zbo.2 + 10 1953 c.1061delT c.(1060-1062)CTTfs p.L354fs CHEK1_uc010sbh.1_Frame_Shift_Del_p.L370fs|CHEK1_uc010sbi.1_Frame_Shift_Del_p.L354fs|CHEK1_uc001qcf.3_Frame_Shift_Del_p.L354fs|CHEK1_uc009zbp.2_Frame_Shift_Del_p.L354fs|CHEK1_uc001qcg.3_Frame_Shift_Del_p.L354fs|CHEK1_uc009zbq.2_Frame_Shift_Del_p.L354fs|CHEK1_uc001qci.1_RNA|CHEK1_uc001qcj.2_Frame_Shift_Del_p.L2fs NM_001114122 NP_001107594 O14757 CHK1_HUMAN checkpoint kinase 1 354 cellular response to mechanical stimulus|DNA repair|DNA replication|gamete generation|negative regulation of cell proliferation|reciprocal meiotic recombination|regulation of cyclin-dependent protein kinase activity|replicative senescence condensed nuclear chromosome|microtubule organizing center|nucleoplasm ATP binding|protein binding|protein serine/threonine kinase activity central_nervous_system(3)|lung(2)|skin(1) 6 all_hematologic(175;0.228) Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748) GATCATATGCTTTTGAATAGT 0.413 0.46 105 91 CHD8 57680 broad.mit.edu 37 14 21859633 21859633 + Frame_Shift_Del DEL G - - CAL51_BREAST NA CAL51_BREAST NA g.chr14:21859633delG uc001was.1 - 36 6311 c.6217delC c.(6217-6219)CGAfs p.R2073fs CHD8_uc001war.1_Frame_Shift_Del_p.R1969fs NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 2352 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) GCTAGAAATCGGGGATCAACA 0.483 0.43 62 46 Unknown 0 broad.mit.edu 37 15 20651258 20651259 + Frame_Shift_Ins INS - AG AG CAL51_BREAST NA CAL51_BREAST NA g.chr15:20651258_20651259insAG uc001ytg.2 - 17 2398_2399 c.1689_1690insCT c.(1687-1692)TCTGCTfs p.S563fs uc010tyx.1_RNA|uc001yth.3_Frame_Shift_Ins_p.S563fs|uc010tyy.1_Frame_Shift_Ins_p.S563fs RecName: Full=Putative HERC2-like protein 3; GCACCTTGAGCAGAAGCATTCA 0.495 0.41 34 24 RBL2 5934 broad.mit.edu 37 16 53476704 53476704 + Frame_Shift_Del DEL T - - CAL51_BREAST NA CAL51_BREAST NA g.chr16:53476704delT uc002ehi.3 + 3 624 c.506delT c.(505-507)ATTfs p.I169fs RBL2_uc010vgv.1_Frame_Shift_Del_p.I95fs NM_005611 NP_005602 Q08999 RBL2_HUMAN retinoblastoma-like 2 (p130) 169 cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleolus DNA binding|protein binding ovary(2)|lung(2)|upper_aerodigestive_tract(1) 5 TATGAACCCATTTTTCAGGAC 0.413 0.42 124 91 MAP2K4 6416 broad.mit.edu 37 17 11984670 11984671 + Splice_Site INS - AG AG CAL51_BREAST NA CAL51_BREAST NA g.chr17:11984670_11984671insAG uc002gnj.2 + 3 288 c.219_splice c.e3-2 p.I73_splice MAP2K4_uc002gnk.2_Splice_Site_p.I84_splice|MAP2K4_uc010vvi.1_Splice_Site|MAP2K4_uc010vvj.1_Intron|MIR744_hsa-mir-744|MI0005559_5'Flank NM_003010 NP_003001 P45985 MP2K4_HUMAN mitogen-activated protein kinase kinase 4 cellular response to mechanical stimulus|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|JUN kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity large_intestine(14)|breast(12)|lung(8)|ovary(8)|pancreas(8)|stomach(2)|central_nervous_system(1)|biliary_tract(1)|testis(1)|endometrium(1)|urinary_tract(1)|skin(1) 58 all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163) Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681) AATATTTTAACAGAGAGAGACT 0.351 0.46 36 31 CPAMD8 27151 broad.mit.edu 37 19 17081703 17081703 + Frame_Shift_Del DEL G - - CAL51_BREAST NA CAL51_BREAST NA g.chr19:17081703delG uc002nfb.2 - 18 2384 c.2352delC c.(2350-2352)CCCfs p.P784fs NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 737 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 0.000 0.59 220 323 ZNF780B 163131 broad.mit.edu 37 19 40540442 40540442 + Frame_Shift_Del DEL T - - CAL51_BREAST NA CAL51_BREAST NA g.chr19:40540442delT uc002omu.2 - 5 2389 c.2324delA c.(2323-2325)CATfs p.H775fs ZNF780B_uc002omv.2_Frame_Shift_Del_p.H627fs NM_001005851 NP_001005851 Q9Y6R6 Z780B_HUMAN zinc finger protein 780B 775 C2H2-type 22; degenerate. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1)|pancreas(1) 2 all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925) CTCACCAGTATGAATACTCTG 0.418 0.47 10 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAL51_BREAST NA CAL51_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.52 10 11 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 CAL51_BREAST NA CAL51_BREAST NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.18 84 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAL51_BREAST NA CAL51_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.96 19 428 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAL54_KIDNEY NA CAL54_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 5 60 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAL54_KIDNEY NA CAL54_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 79 110 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAL54_KIDNEY NA CAL54_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.36 49 28 MCM4 4173 broad.mit.edu 37 8 48880047 48880048 + Splice_Site INS - A A CAL54_KIDNEY NA CAL54_KIDNEY NA g.chr8:48880047_48880048insA uc003xqk.1 + 10 1269 c.1174_splice c.e10+2 p.G392_splice MCM4_uc003xql.1_Splice_Site_p.G392_splice|MCM4_uc011ldi.1_Splice_Site_p.G379_splice NM_182746 NP_877423 P33991 MCM4_HUMAN minichromosome maintenance complex component 4 cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle MCM complex ATP binding|DNA binding|helicase activity|protein binding ovary(2)|skin(2) 4 all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354) ATGTTACAGGTAAGAGTGTAGG 0.495 0.66 92 182 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 CAL54_KIDNEY NA CAL54_KIDNEY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.64 21 37 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CAL54_KIDNEY NA CAL54_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 28 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CAL54_KIDNEY NA CAL54_KIDNEY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.69 257 561 RAG1 5896 broad.mit.edu 37 11 36597900 36597900 + Frame_Shift_Del DEL G - - CAL54_KIDNEY NA CAL54_KIDNEY NA g.chr11:36597900delG uc001mwu.3 + 2 3170 c.3046delG c.(3046-3048)GGGfs p.G1016fs RAG1_uc001mwt.2_Intron NM_000448 NP_000439 P15918 RAG1_HUMAN recombination activating gene 1 1016 histone monoubiquitination|immune response|pre-B cell allelic exclusion|protein autoubiquitination|T cell differentiation in thymus|V(D)J recombination nucleus endonuclease activity|histone binding|protein homodimerization activity|sequence-specific DNA binding|ubiquitin-protein ligase activity|zinc ion binding ovary(1)|pancreas(1)|lung(1)|kidney(1)|skin(1) 5 all_lung(20;0.226) all_hematologic(20;0.107) AAAAACCTCTGGGTTTACCAT 0.433 0.45 191 159 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAL54_KIDNEY NA CAL54_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 282 68 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CAL54_KIDNEY NA CAL54_KIDNEY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 6 39 MYH8 4626 broad.mit.edu 37 17 10297636 10297639 + Frame_Shift_Del DEL TCTG - - CAL54_KIDNEY NA CAL54_KIDNEY NA g.chr17:10297636_10297639delTCTG uc002gmm.2 - 35 5188_5191 c.5093_5096delCAGA c.(5092-5097)ACAGAGfs p.T1698fs uc002gml.1_Intron NM_002472 NP_002463 P13535 MYH8_HUMAN myosin, heavy chain 8, skeletal muscle, 1698_1699 Potential. muscle filament sliding cytosol|muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle skin(6)|ovary(3)|breast(2) 11 CCTGCTTCTCTCTGTCTGTTCCAG 0.588 0.58 5 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAL54_KIDNEY NA CAL54_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.16 37 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAL54_KIDNEY NA CAL54_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 73 471 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAL54_KIDNEY NA CAL54_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 66 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAL62_THYROID NA CAL62_THYROID NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 62 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAL62_THYROID NA CAL62_THYROID NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 49 58 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAL62_THYROID NA CAL62_THYROID NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 24 35 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 CAL62_THYROID NA CAL62_THYROID NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.14 289 49 STAG3 10734 broad.mit.edu 37 7 99796511 99796515 + Frame_Shift_Del DEL GCAAC - - CAL62_THYROID NA CAL62_THYROID NA g.chr7:99796511_99796515delGCAAC uc003utx.1 + 14 1553_1557 c.1398_1402delGCAAC c.(1396-1404)GAGCAACGCfs p.E466fs STAG3_uc010lgs.1_Frame_Shift_Del_p.E254fs|STAG3_uc011kjk.1_Frame_Shift_Del_p.E408fs|STAG3_uc003uub.1_5'Flank NM_012447 NP_036579 Q9UJ98 STAG3_HUMAN stromal antigen 3 466_468 chromosome segregation|synaptonemal complex assembly chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex binding ovary(4)|skin(2)|lung(1)|kidney(1) 8 Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439) GTGGAAGAGAGCAACGCCAGAGCCC 0.532 0.66 12 23 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 CAL62_THYROID NA CAL62_THYROID NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.36 36 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CAL62_THYROID NA CAL62_THYROID NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.89 2 17 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - CAL62_THYROID NA CAL62_THYROID NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.11 356 45 KLF6 1316 broad.mit.edu 37 10 3822362 3822381 + Frame_Shift_Del DEL CATCACTTCTTGCAAAACGC - - CAL62_THYROID NA CAL62_THYROID NA g.chr10:3822362_3822381delCATCACTTCTTGCAAAACGC uc001iha.2 - 3 984_1003 c.717_736delGCGTTTTGCAAGAAGTGATG c.(715-738)TGGCGTTTTGCAAGAAGTGATGAGfs p.W239fs KLF6_uc010qaj.1_Intron|KLF6_uc010qak.1_RNA|KLF6_uc010qal.1_Frame_Shift_Del_p.W197fs NM_001300 NP_001291 Q99612 KLF6_HUMAN Kruppel-like factor 6 isoform A 239_246 C2H2-type 2. B cell differentiation nucleus zinc ion binding central_nervous_system(3)|lung(1) 4 Colorectal(1;0.238) CTGGTTAACTCATCACTTCTTGCAAAACGCCACTCACACC 0.555 0.51 38 40 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAL62_THYROID NA CAL62_THYROID NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 207 51 SRP14 6727 broad.mit.edu 37 15 40328564 40328575 + In_Frame_Del DEL TGCTGTTGTTGG - - rs16924521;rs8874;rs7535 by1000genomes CAL62_THYROID NA CAL62_THYROID NA g.chr15:40328564_40328575delTGCTGTTGTTGG uc001zkq.2 - 5 442_453 c.370_381delCCAACAACAGCA c.(370-381)CCAACAACAGCAdel p.PTTA124del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 124_127 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgttgttgctgctgttgttggtgctgttgct 0.231 0.74 9 26 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAL62_THYROID NA CAL62_THYROID NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.63 13 22 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 CAL62_THYROID NA CAL62_THYROID NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 160 31 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAL62_THYROID NA CAL62_THYROID NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 36 285 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAL62_THYROID NA CAL62_THYROID NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.99 1 72 EP300 2033 broad.mit.edu 37 22 41568504 41568504 + Frame_Shift_Del DEL A - - CAL62_THYROID NA CAL62_THYROID NA g.chr22:41568504delA uc003azl.3 + 28 4849 c.4454delA c.(4453-4455)GATfs p.D1485fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1485 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 TTTTCACAGGATATTTTTAAA 0.328 0.98 1 47 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAL851_BREAST NA CAL851_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 67 PI4KB 5298 broad.mit.edu 37 1 151288451 151288471 + In_Frame_Del DEL GTTGCGAAAGCAGAAGAGCCG - - CAL851_BREAST NA CAL851_BREAST NA g.chr1:151288451_151288471delGTTGCGAAAGCAGAAGAGCCG uc001ext.2 - 2 902_922 c.487_507delCGGCTCTTCTGCTTTCGCAAC c.(487-507)CGGCTCTTCTGCTTTCGCAACdel p.RLFCFRN163del PI4KB_uc001exr.2_In_Frame_Del_p.RLFCFRN175del|PI4KB_uc001exs.2_In_Frame_Del_p.RLFCFRN163del|PI4KB_uc001exu.2_In_Frame_Del_p.RLFCFRN163del|PI4KB_uc010pcw.1_Intron|PI4KB_uc009wmq.1_In_Frame_Del_p.RLFCFRN175del NM_002651 NP_002642 Q9UBF8 PI4KB_HUMAN catalytic phosphatidylinositol 4-kinase beta 163_169 phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|receptor-mediated endocytosis endosome|Golgi apparatus|mitochondrial outer membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum membrane 1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding p.F179C(1) ovary(2)|skin(2) 4 Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181) CCACGTCCTCGTTGCGAAAGCAGAAGAGCCGGTTGCCAATG 0.498 0.21 262 69 FMN2 56776 broad.mit.edu 37 1 240371080 240371112 + In_Frame_Del DEL CCCCCACTTCCCGGAGCGGGCATACCCCCTCCG - - rs71646826;rs71646827;rs71646887;rs11586155;rs71170719;rs71646889 CAL851_BREAST NA CAL851_BREAST NA g.chr1:240371080_240371112delCCCCCACTTCCCGGAGCGGGCATACCCCCTCCG uc010pyd.1 + 5 3193_3225 c.2968_3000delCCCCCACTTCCCGGAGCGGGCATACCCCCTCCG c.(2968-3000)CCCCCACTTCCCGGAGCGGGCATACCCCCTCCGdel p.PPLPGAGIPPP1089del FMN2_uc010pye.1_In_Frame_Del_p.PPLPGAGIPPP1093del NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 1089_1099 Pro-rich.|FH1. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) ACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTTC 0.717 0.24 42 13 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes CAL851_BREAST NA CAL851_BREAST NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.32 15 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CAL851_BREAST NA CAL851_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.56 24 30 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A CAL851_BREAST NA CAL851_BREAST NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 163 44 HTT 3064 broad.mit.edu 37 4 3076604 3076609 + In_Frame_Del DEL CAGCAG - - rs10618869 CAL851_BREAST NA CAL851_BREAST NA g.chr4:3076604_3076609delCAGCAG uc011bvq.1 + 2 203_208 c.58_63delCAGCAG c.(58-63)CAGCAGdel p.QQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagc 0.330 0.15 40 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAL851_BREAST NA CAL851_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.74 102 285 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAL851_BREAST NA CAL851_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 40 116 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 CAL851_BREAST NA CAL851_BREAST NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.46 34 29 FOXO3 2309 broad.mit.edu 37 6 108882647 108882648 + In_Frame_Ins INS - CGG CGG CAL851_BREAST NA CAL851_BREAST NA g.chr6:108882647_108882648insCGG uc003psk.2 + 2 552_553 c.236_237insCGG c.(235-237)ATC>ATCGGC p.84_85insG FOXO3_uc003psn.2_In_Frame_Ins_p.84_85insG|FOXO3_uc003psm.2_In_Frame_Ins_p.84_85insG NM_201559 NP_963853 O43524 FOXO3_HUMAN forkhead box O3A 84_85 antral ovarian follicle growth|apoptosis|embryo development|glucose homeostasis|induction of apoptosis|initiation of primordial ovarian follicle growth|insulin receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|oocyte maturation|ovulation from ovarian follicle|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding central_nervous_system(4)|lung(2) 6 all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152) Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718) 0.000 0.27 615 226 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 CAL851_BREAST NA CAL851_BREAST NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.16 220 41 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 CAL851_BREAST NA CAL851_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.39 60 39 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CAL851_BREAST NA CAL851_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 33 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CAL851_BREAST NA CAL851_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.47 128 114 PIPSL 266971 broad.mit.edu 37 10 95720932 95720933 + Frame_Shift_Ins INS - T T CAL851_BREAST NA CAL851_BREAST NA g.chr10:95720932_95720933insT uc009xuj.2 - 1 740_741 c.221_222insA c.(220-222)AACfs p.N74fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CAGGGGTCAGGTTGCTCCCTTC 0.510 0.94 32 498 BRCA2 675 broad.mit.edu 37 13 32912870 32912870 + Frame_Shift_Del DEL T - - CAL851_BREAST NA CAL851_BREAST NA g.chr13:32912870delT uc001uub.1 + 11 4605 c.4378delT c.(4378-4380)TTTfs p.F1460fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 1460 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) ATTGCATAACTTTTCCTTAAA 0.289 0.41 183 127 RB1 5925 broad.mit.edu 37 13 48878107 48878120 + Frame_Shift_Del DEL CCCCGGCACCGCCG - - rs34437965 CAL851_BREAST NA CAL851_BREAST NA g.chr13:48878107_48878120delCCCCGGCACCGCCG uc001vcb.2 + 1 225_238 c.59_72delCCCCGGCACCGCCG c.(58-72)CCCCCGGCACCGCCGfs p.P20fs RB1_uc010acs.1_RNA|uc001vca.2_5'Flank NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 20_24 Poly-Pro. androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.0?(13)|p.P21fs*5(1)|p.?(1)|p.A16fs*3(1) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) 0.000 0.99 6 735 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CAL851_BREAST NA CAL851_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 17 156 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAL851_BREAST NA CAL851_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.23 177 53 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAL851_BREAST NA CAL851_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 77 782 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAL851_BREAST NA CAL851_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 6 75 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CALU1_LUNG NA CALU1_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 5 130 TTN 7273 broad.mit.edu 37 2 179395826 179395828 + In_Frame_Del DEL AGA - - CALU1_LUNG NA CALU1_LUNG NA g.chr2:179395826_179395828delAGA uc010zfg.1 - 307 98034_98036 c.97810_97812delTCT c.(97810-97812)TCTdel p.S32604del uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.S26299del|TTN_uc010zfi.1_In_Frame_Del_p.S26232del|TTN_uc010zfj.1_In_Frame_Del_p.S26107del|TTN_uc002umq.2_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 33531 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GGTGGCGGGCAGAAGTACTTAGC 0.517 0.60 324 486 ZNF717 100131827 broad.mit.edu 37 3 75790811 75790812 + Frame_Shift_Ins INS - T T rs76346895 CALU1_LUNG NA CALU1_LUNG NA g.chr3:75790811_75790812insT uc011bgi.1 - 3 456_457 c.133_134insA c.(133-135)ACCfs p.T45fs ZNF717_uc003dpw.3_RNA NM_001128223 NP_001121695 C9JSV9 C9JSV9_HUMAN zinc finger protein 717 45 regulation of transcription, DNA-dependent intracellular nucleic acid binding|zinc ion binding 0 CCTGTACAGGGTCCTCTGAGCA 0.515 0.80 2 8 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A CALU1_LUNG NA CALU1_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 330 61 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CALU1_LUNG NA CALU1_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.49 53 50 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CALU1_LUNG NA CALU1_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.49 136 133 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CALU1_LUNG NA CALU1_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.22 150 43 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 CALU1_LUNG NA CALU1_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.17 231 47 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 CALU1_LUNG NA CALU1_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.24 29 9 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CALU1_LUNG NA CALU1_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 11 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 CALU1_LUNG NA CALU1_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.53 9 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CALU1_LUNG NA CALU1_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 235 37 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CALU1_LUNG NA CALU1_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 12 169 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CALU1_LUNG NA CALU1_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.57 19 25 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes CALU1_LUNG NA CALU1_LUNG NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.54 6 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CALU1_LUNG NA CALU1_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 87 322 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CALU1_LUNG NA CALU1_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 8 208 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CALU6_LUNG NA CALU6_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.80 8 32 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CALU6_LUNG NA CALU6_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 46 63 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CALU6_LUNG NA CALU6_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.84 8 42 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CALU6_LUNG NA CALU6_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 2 22 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 CALU6_LUNG NA CALU6_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.77 3 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CALU6_LUNG NA CALU6_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 179 69 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CALU6_LUNG NA CALU6_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 51 402 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CALU6_LUNG NA CALU6_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.67 17 35 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 CALU6_LUNG NA CALU6_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.35 26 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CALU6_LUNG NA CALU6_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 90 271 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CALU6_LUNG NA CALU6_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 39 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAMA1_BREAST NA CAMA1_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 51 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - CAMA1_BREAST NA CAMA1_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.41 412 282 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CAMA1_BREAST NA CAMA1_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.35 13 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CAMA1_BREAST NA CAMA1_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.14 49 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAMA1_BREAST NA CAMA1_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 147 195 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAMA1_BREAST NA CAMA1_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.34 53 27 NRG2 9542 broad.mit.edu 37 5 139422531 139422532 + In_Frame_Ins INS - GCTGCTGCT GCTGCTGCT CAMA1_BREAST NA CAMA1_BREAST NA g.chr5:139422531_139422532insGCTGCTGCT uc003lex.1 - 1 348_349 c.123_124insAGCAGCAGC c.(121-126)insAGCAGCAGC p.41_42insSSS NRG2_uc003lev.1_In_Frame_Ins_p.41_42insSSS|NRG2_uc003lew.1_In_Frame_Ins_p.41_42insSSS|NRG2_uc003ley.1_In_Frame_Ins_p.41_42insSSS NM_004883 NP_004874 O14511 NRG2_HUMAN neuregulin 2 isoform 1 41_42 Poly-Ser. embryo development extracellular region|integral to membrane|plasma membrane growth factor activity pancreas(2)|breast(2)|ovary(1)|skin(1) 6 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) ctgccgctctcgctgctgctgc 0.287 0.26 82 29 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes CAMA1_BREAST NA CAMA1_BREAST NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.54 6 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CAMA1_BREAST NA CAMA1_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.82 5 23 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G CAMA1_BREAST NA CAMA1_BREAST NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.12 678 95 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CAMA1_BREAST NA CAMA1_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.90 11 96 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CAMA1_BREAST NA CAMA1_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.35 564 302 PTEN 5728 broad.mit.edu 37 10 89720683 89720686 + Frame_Shift_Del DEL CTTC - - CAMA1_BREAST NA CAMA1_BREAST NA g.chr10:89720683_89720686delCTTC uc001kfb.2 + 9 1865_1868 c.834_837delCTTC c.(832-837)TTCTTCfs p.F278fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 278_279 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.D268_F279>VGQNVSLLGKYI(2)|p.G165_*404del(1)|p.G165_K342del(1)|p.W274_F341del(1)|p.T277fs*13(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) TAAATACATTCTTCATACCAGGAC 0.265 0.31 31 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAMA1_BREAST NA CAMA1_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 385 194 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CAMA1_BREAST NA CAMA1_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 39 370 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAMA1_BREAST NA CAMA1_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.79 42 154 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAMA1_BREAST NA CAMA1_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 110 421 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAMA1_BREAST NA CAMA1_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 8 130 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAOV3_OVARY NA CAOV3_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 5 47 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes CAOV3_OVARY NA CAOV3_OVARY NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.47 19 17 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CAOV3_OVARY NA CAOV3_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.39 48 31 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CAOV3_OVARY NA CAOV3_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.48 14 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAOV3_OVARY NA CAOV3_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 64 100 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAOV3_OVARY NA CAOV3_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 15 43 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 CAOV3_OVARY NA CAOV3_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.85 32 178 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CAOV3_OVARY NA CAOV3_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 5 40 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CAOV3_OVARY NA CAOV3_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 53 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAOV3_OVARY NA CAOV3_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 830 334 ATN1 1822 broad.mit.edu 37 12 7045892 7045894 + In_Frame_Del DEL CAG - - rs66756893;rs67074116 CAOV3_OVARY NA CAOV3_OVARY NA g.chr12:7045892_7045894delCAG uc001qrw.1 + 5 1699_1701 c.1462_1464delCAG c.(1462-1464)CAGdel p.Q502del ATN1_uc001qrx.1_In_Frame_Del_p.Q502del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagc 0.458 0.12 121 16 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAOV3_OVARY NA CAOV3_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 116 87 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 CAOV3_OVARY NA CAOV3_OVARY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.29 63 26 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAOV3_OVARY NA CAOV3_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 31 315 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAOV3_OVARY NA CAOV3_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 9 254 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAOV4_OVARY NA CAOV4_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 19 AKR7A2 8574 broad.mit.edu 37 1 19630781 19630781 + Frame_Shift_Del DEL C - - CAOV4_OVARY NA CAOV4_OVARY NA g.chr1:19630781delC uc001bbw.2 - 7 1040 c.1018delG c.(1018-1020)GTGfs p.V340fs AKR7A2_uc001bbx.2_Frame_Shift_Del_p.V305fs NM_003689 NP_003680 O43488 ARK72_HUMAN aldo-keto reductase family 7, member A2 340 carbohydrate metabolic process|cellular aldehyde metabolic process Golgi apparatus alditol:NADP+ 1-oxidoreductase activity|electron carrier activity central_nervous_system(1) 1 Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.00461)|BRCA - Breast invasive adenocarcinoma(304;1.83e-05)|Kidney(64;0.000167)|GBM - Glioblastoma multiforme(114;0.00115)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649) 0.000 0.71 7 17 OR2T2 401992 broad.mit.edu 37 1 248616417 248616418 + Frame_Shift_Ins INS - C C rs149125804 byFrequency CAOV4_OVARY NA CAOV4_OVARY NA g.chr1:248616417_248616418insC uc001iek.1 + 1 319_320 c.319_320insC c.(319-321)ACCfs p.T107fs NM_001004136 NP_001004136 Q6IF00 OR2T2_HUMAN olfactory receptor, family 2, subfamily T, 107 Helical; Name=3; (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity skin(1) 1 all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0265) CCTCTACCTGACCCTGATTGGA 0.545 0.50 13 13 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A CAOV4_OVARY NA CAOV4_OVARY NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 1.00 0 17 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A CAOV4_OVARY NA CAOV4_OVARY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.14 102 17 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CAOV4_OVARY NA CAOV4_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.38 10 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAOV4_OVARY NA CAOV4_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.33 58 28 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAOV4_OVARY NA CAOV4_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 24 43 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes CAOV4_OVARY NA CAOV4_OVARY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.67 5 10 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CAOV4_OVARY NA CAOV4_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.64 4 7 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 CAOV4_OVARY NA CAOV4_OVARY NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.56 7 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAOV4_OVARY NA CAOV4_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 113 21 TRIM29 23650 broad.mit.edu 37 11 120008680 120008681 + Frame_Shift_Ins INS - T T CAOV4_OVARY NA CAOV4_OVARY NA g.chr11:120008680_120008681insT uc001pwz.2 - 1 183_184 c.59_60insA c.(58-60)CGGfs p.R20fs TRIM29_uc001pxa.2_RNA NM_012101 NP_036233 Q14134 TRI29_HUMAN tripartite motif protein TRIM29 20 transcription from RNA polymerase II promoter cytoplasm protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1)|breast(1)|kidney(1)|skin(1) 4 Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;5.37e-06) 0.000 1.00 0 13 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 CAOV4_OVARY NA CAOV4_OVARY NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.69 4 9 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CAOV4_OVARY NA CAOV4_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 41 362 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAOV4_OVARY NA CAOV4_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.62 27 45 ZNF324 25799 broad.mit.edu 37 19 58983120 58983120 + Frame_Shift_Del DEL G - - CAOV4_OVARY NA CAOV4_OVARY NA g.chr19:58983120delG uc002qsw.1 + 4 1355 c.1261delG c.(1261-1263)GGCfs p.G421fs ZNF324_uc002qsx.1_Frame_Shift_Del_p.G198fs NM_014347 NP_055162 O75467 Z324A_HUMAN zinc finger protein 324 421 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding 0 all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232) UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179) 0.000 0.35 11 6 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAOV4_OVARY NA CAOV4_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 474 1342 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAOV4_OVARY NA CAOV4_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 5 61 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 33 EPHB2 2048 broad.mit.edu 37 1 23237042 23237042 + Frame_Shift_Del DEL C - - CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr1:23237042delC uc009vqj.1 + 14 2815 c.2670delC c.(2668-2670)CTCfs p.L890fs EPHB2_uc001bge.2_Frame_Shift_Del_p.L891fs|EPHB2_uc001bgf.2_Frame_Shift_Del_p.L890fs|EPHB2_uc010odu.1_Frame_Shift_Del_p.L832fs NM_017449 NP_059145 P29323 EPHB2_HUMAN ephrin receptor EphB2 isoform 1 precursor 890 Cytoplasmic (Potential). axon guidance integral to plasma membrane ATP binding|transmembrane-ephrin receptor activity ovary(3)|lung(1)|pancreas(1) 5 Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258) UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153) CCAACAGCCTCAAAGCCATGG 0.622 0.38 73 45 LRRC7 57554 broad.mit.edu 37 1 70504692 70504693 + Frame_Shift_Ins INS - A A CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr1:70504692_70504693insA uc001dep.2 + 19 3101_3102 c.3071_3072insA c.(3070-3072)ACAfs p.T1024fs LRRC7_uc009wbg.2_Frame_Shift_Ins_p.T308fs|LRRC7_uc001deq.2_Frame_Shift_Ins_p.T265fs NM_020794 NP_065845 Q96NW7 LRRC7_HUMAN leucine rich repeat containing 7 1024 centrosome|focal adhesion|nucleolus protein binding ovary(9)|breast(2)|central_nervous_system(2)|liver(1) 14 GCTTCTATGACAAAAAAAGTCT 0.450 0.20 88 22 MST1R 4486 broad.mit.edu 37 3 49940433 49940467 + Frame_Shift_Del DEL CCAGTGAGGATGCCACGTAGAAATAGGAGGCCTGG - - CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr3:49940433_49940467delCCAGTGAGGATGCCACGTAGAAATAGGAGGCCTGG uc003cxy.3 - 1 840_874 c.576_610delCCAGGCCTCCTATTTCTACGTGGCATCCTCACTGG c.(574-612)GGCCAGGCCTCCTATTTCTACGTGGCATCCTCACTGGACfs p.G192fs MST1R_uc011bdd.1_Frame_Shift_Del_p.G192fs|MST1R_uc011bde.1_Frame_Shift_Del_p.G192fs|MST1R_uc011bdf.1_Frame_Shift_Del_p.G192fs|MST1R_uc011bdg.1_Frame_Shift_Del_p.G192fs NM_002447 NP_002438 Q04912 RON_HUMAN macrophage stimulating 1 receptor precursor 192_204 Extracellular (Potential).|Sema. cellular component movement|defense response|multicellular organismal development|positive regulation of cell proliferation|single fertilization|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|macrophage colony-stimulating factor receptor activity|protein binding ovary(5)|lung(1) 6 BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625) ACGGCTGCGTCCAGTGAGGATGCCACGTAGAAATAGGAGGCCTGGCCTTGCTCAA 0.626 0.12 237 33 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.24 42 13 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 30 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 93 149 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 11 29 NRG2 9542 broad.mit.edu 37 5 139422531 139422532 + In_Frame_Ins INS - GCT GCT CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr5:139422531_139422532insGCT uc003lex.1 - 1 348_349 c.123_124insAGC c.(121-126)insAGC p.41_42insS NRG2_uc003lev.1_In_Frame_Ins_p.41_42insS|NRG2_uc003lew.1_In_Frame_Ins_p.41_42insS|NRG2_uc003ley.1_In_Frame_Ins_p.41_42insS NM_004883 NP_004874 O14511 NRG2_HUMAN neuregulin 2 isoform 1 41_42 Poly-Ser. embryo development extracellular region|integral to membrane|plasma membrane growth factor activity pancreas(2)|breast(2)|ovary(1)|skin(1) 6 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) ctgccgctctcgctgctgctgc 0.287 0.32 56 26 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 1 13 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 24 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 3 78 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 1096 376 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.27 77 29 SRP14 6727 broad.mit.edu 37 15 40328596 40328597 + In_Frame_Ins INS - TGC TGC CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr15:40328596_40328597insTGC uc001zkq.2 - 5 420_421 c.348_349insGCA c.(346-351)insGCA p.116_117insA SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116_117 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) gctgcggcaggtgctgctgctg 0.228 0.23 123 37 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.25 55 18 TRADD 8717 broad.mit.edu 37 16 67189014 67189014 + Frame_Shift_Del DEL G - - CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr16:67189014delG uc002eri.1 - 4 693 c.613delC c.(613-615)CAGfs p.Q205fs TRADD_uc002erh.1_Frame_Shift_Del_p.Q145fs NM_003789 NP_003780 Q15628 TRADD_HUMAN TNFRSF1A-associated via death domain 205 Death. activation of caspase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|tumor necrosis factor-mediated signaling pathway cytoskeleton|cytosol|receptor complex binding, bridging|death domain binding|identical protein binding|kinase binding|signal transducer activity lung(1) 1 Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184) 0.000 0.37 294 175 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 67 192 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 53 206 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAPAN1_PANCREAS NA CAPAN1_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 4 143 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 33 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.50 7 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.49 93 91 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.30 51 22 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.88 5 35 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 2 30 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.49 182 174 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 482 71 SACS 26278 broad.mit.edu 37 13 23905377 23905378 + Frame_Shift_Del DEL TC - - CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr13:23905377_23905378delTC uc001uon.2 - 10 13226_13227 c.12637_12638delGA c.(12637-12639)GAAfs p.E4213fs SACS_uc001uoo.2_Frame_Shift_Del_p.E4066fs|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 4213 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) GTCAGCATCTTCTCTTTCAACT 0.327 0.47 67 60 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.53 7 8 RNF43 54894 broad.mit.edu 37 17 56436148 56436148 + Frame_Shift_Del DEL C - - CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr17:56436148delC uc002iwf.2 - 8 2945 c.989delG c.(988-990)CGAfs p.R330fs RNF43_uc010wnv.1_Frame_Shift_Del_p.R289fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.R330fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.R330fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.R203fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 330 Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.98 15 942 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.63 20 34 ZMYND8 23613 broad.mit.edu 37 20 45867566 45867567 + In_Frame_Ins INS - TGC TGC CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr20:45867566_45867567insTGC uc002xta.1 - 15 2794_2795 c.2540_2541insGCA c.(2539-2541)CAA>CAGCAA p.847_847Q>QQ ZMYND8_uc010ghq.1_Intron|ZMYND8_uc010ghr.1_Intron|ZMYND8_uc002xst.1_Intron|ZMYND8_uc002xsu.1_Intron|ZMYND8_uc002xsv.1_In_Frame_Ins_p.775_775Q>QQ|ZMYND8_uc002xsw.1_Intron|ZMYND8_uc002xsx.1_Intron|ZMYND8_uc002xsy.1_Intron|ZMYND8_uc002xsz.1_Intron|ZMYND8_uc010zxy.1_In_Frame_Ins_p.874_874Q>QQ|ZMYND8_uc002xtb.1_Intron|ZMYND8_uc002xss.2_In_Frame_Ins_p.847_847Q>QQ|ZMYND8_uc010zxz.1_Intron|ZMYND8_uc002xtc.1_Intron|ZMYND8_uc002xtd.1_Intron|ZMYND8_uc002xte.1_Intron|ZMYND8_uc010zya.1_In_Frame_Ins_p.847_847Q>QQ|ZMYND8_uc002xtf.1_In_Frame_Ins_p.867_867Q>QQ|ZMYND8_uc002xtg.2_In_Frame_Ins_p.841_841Q>QQ|ZMYND8_uc010ghs.1_In_Frame_Ins_p.841_841Q>QQ|ZMYND8_uc002xsr.1_Intron NM_012408 NP_036540 Q9ULU4 PKCB1_HUMAN zinc finger, MYND-type containing 8 isoform b 847 Poly-Gln. protein binding|zinc ion binding central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1) 5 Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154) gctgctggttttgctgctgctg 0.426 0.50 6 6 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.66 268 522 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAPAN2_PANCREAS NA CAPAN2_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 33 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 27 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.30 217 92 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.13 186 28 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.38 48 29 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.56 43 55 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.65 72 134 CYCS 54205 broad.mit.edu 37 7 25163567 25163568 + Splice_Site INS - A A CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr7:25163567_25163568insA uc003sxl.2 - 2 314 c.169_splice c.e2+1 p.G57_splice NM_018947 NP_061820 P99999 CYC_HUMAN cytochrome c activation of caspase activity by cytochrome c|DNA fragmentation involved in apoptotic nuclear change|induction of apoptosis by intracellular signals|respiratory electron transport chain|transport cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|mitochondrial matrix|nucleus|protein phosphatase type 2A complex|respiratory chain electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity|heme binding|protein binding ovary(1)|lung(1) 2 Melatonin(DB01065)|Minocycline(DB01017) AAGTGACTCTTACCTTTGTTCT 0.441 0.27 243 88 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.54 263 310 MYST4 23522 broad.mit.edu 37 10 76781905 76781906 + In_Frame_Ins INS - GAA GAA rs138589645;rs111976843 by1000genomes CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr10:76781905_76781906insGAA uc001jwn.1 + 16 3781_3782 c.3288_3289insGAA c.(3286-3291)insGAA p.1104_1105insE MYST4_uc001jwm.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwo.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwp.1_In_Frame_Ins_p.921_922insE NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1104_1105 histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) aggaagaagaggaagaagaaga 0.203 0.39 43 27 PTEN 5728 broad.mit.edu 37 10 89720706 89720706 + Frame_Shift_Del DEL C - - CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr10:89720706delC uc001kfb.2 + 9 1888 c.857delC c.(856-858)ACCfs p.T286fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 286 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.G165_K342del(1)|p.W274_F341del(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) CCAGAGGAAACCTCAGAAAAA 0.299 0.99 6 419 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 236 25 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.73 3 8 FLCN 201163 broad.mit.edu 37 17 17122367 17122368 + Frame_Shift_Ins INS - G G CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr17:17122367_17122368insG uc002gra.3 - 9 1531_1532 c.1027_1028insC c.(1027-1029)CTGfs p.L343fs PLD6_uc010cpn.2_RNA NM_144997 NP_659434 Q8NFG4 FLCN_HUMAN folliculin isoform 1 343 regulation of protein phosphorylation cytoplasm|nucleus|plasma membrane protein binding thyroid(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1) 3 GAAGACTGGCAGCTTCCGGGGC 0.663 0.11 67 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.70 13 30 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 151 376 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CAS1_CENTRAL_NERVOUS_SYSTEM NA CAS1_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 4 49 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 58 EPHB3 2049 broad.mit.edu 37 3 184280041 184280042 + Frame_Shift_Ins INS - C C CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA g.chr3:184280041_184280042insC uc003foz.2 + 1 455_456 c.18_19insC c.(16-21)CCGCCGfs p.P6fs NM_004443 NP_004434 P54753 EPHB3_HUMAN ephrin receptor EphB3 precursor 6_7 integral to plasma membrane ATP binding|ephrin receptor activity lung(5)|breast(2)|upper_aerodigestive_tract(1)|stomach(1)|skin(1)|ovary(1) 11 all_cancers(143;1.89e-10)|Ovarian(172;0.0339) Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22) 0.000 0.14 68 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 73 83 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 22 40 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.48 112 104 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.31 11 5 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 12 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.75 3 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 178 52 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.68 9 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.94 29 436 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA CCFSTTG1_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 56 HUWE1 10075 broad.mit.edu 37 X 53657968 53657969 + Frame_Shift_Del DEL TG - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chrX:53657968_53657969delTG uc004dsp.2 - 12 1182_1183 c.780_781delCA c.(778-783)CACATAfs p.H260fs NM_031407 NP_113584 Q7Z6Z7 HUWE1_HUMAN HECT, UBA and WWE domain containing 1 260_261 base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process cytoplasm|nucleus DNA binding|protein binding|ubiquitin-protein ligase activity ovary(8)|large_intestine(4)|breast(4)|kidney(1) 17 0.000 0.47 216 189 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 8 60 GPR112 139378 broad.mit.edu 37 X 135427196 135427197 + Frame_Shift_Ins INS - A A CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chrX:135427196_135427197insA uc004ezu.1 + 6 1622_1623 c.1331_1332insA c.(1330-1332)GGAfs p.G444fs GPR112_uc010nsb.1_Frame_Shift_Ins_p.G239fs|GPR112_uc010nsc.1_Frame_Shift_Ins_p.G211fs NM_153834 NP_722576 Q8IZF6 GP112_HUMAN G-protein coupled receptor 112 444 Extracellular (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1) 12 Acute lymphoblastic leukemia(192;0.000127) ACAGCTGCCGGAACTGTACCTT 0.480 0.19 181 42 MCF2 4168 broad.mit.edu 37 X 138684569 138684569 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chrX:138684569delA uc004fau.2 - 16 2126 c.1832delT c.(1831-1833)TTCfs p.F611fs MCF2_uc004fav.2_Frame_Shift_Del_p.F627fs|MCF2_uc011mwl.1_Frame_Shift_Del_p.F588fs|MCF2_uc010nsh.1_Frame_Shift_Del_p.F611fs|MCF2_uc011mwm.1_Frame_Shift_Del_p.F572fs|MCF2_uc011mwn.1_Frame_Shift_Del_p.F756fs|MCF2_uc004faw.2_Frame_Shift_Del_p.F671fs|MCF2_uc011mwo.1_Frame_Shift_Del_p.F687fs NM_005369 NP_005360 P10911 MCF2_HUMAN MCF.2 cell line derived transforming sequence 611 DH. apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytoskeleton|cytosol|membrane|membrane fraction protein binding|Rho guanyl-nucleotide exchange factor activity lung(1)|pleura(1) 2 Acute lymphoblastic leukemia(192;0.000127) CTGTACCTGGAAAAATGCGCA 0.299 0.36 45 25 F8 2157 broad.mit.edu 37 X 154158790 154158790 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chrX:154158790delT uc004fmt.2 - 14 3446 c.3275delA c.(3274-3276)AACfs p.N1092fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1092 B. acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) CATTTCCATGTTTTTTGATGA 0.368 0.22 226 62 TAL1 6886 broad.mit.edu 37 1 47691376 47691376 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr1:47691376delC uc001cqx.2 - 2 762 c.185delG c.(184-186)GGCfs p.G62fs TAL1_uc009vyq.2_5'Flank|TAL1_uc001cqy.2_Frame_Shift_Del_p.G62fs|TAL1_uc001cra.1_Intron|TAL1_uc001cqz.1_Intron NM_003189 NP_003180 P17542 TAL1_HUMAN T-cell acute lymphocytic leukemia 1 62 basophil differentiation|cell fate commitment|cell proliferation|embryonic hemopoiesis|erythrocyte differentiation|megakaryocyte differentiation|positive regulation of cell division|positive regulation of chromatin assembly or disassembly|positive regulation of erythrocyte differentiation|positive regulation of mitotic cell cycle|positive regulation of protein complex assembly|positive regulation of transcription from RNA polymerase II promoter nuclear chromatin E-box binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity lung(1) 1 0.000 0.38 185 113 NFIA 4774 broad.mit.edu 37 1 61798223 61798223 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr1:61798223delT uc001czw.2 + 4 1149 c.665delT c.(664-666)GTTfs p.V222fs NFIA_uc001czy.2_Frame_Shift_Del_p.V214fs|NFIA_uc010oos.1_Frame_Shift_Del_p.V267fs|NFIA_uc001czv.2_Frame_Shift_Del_p.V222fs NM_001134673 NP_001128145 Q12857 NFIA_HUMAN nuclear factor I/A isoform 1 222 DNA replication|viral genome replication cell junction|nucleus DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding pancreas(1)|skin(1) 2 ACATCAGGTGTTTTTAGTGTC 0.383 0.22 168 47 PKN2 5586 broad.mit.edu 37 1 89279292 89279292 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr1:89279292delT uc001dmn.2 + 16 2497 c.2155delT c.(2155-2157)TTTfs p.F719fs PKN2_uc010osp.1_Frame_Shift_Del_p.F703fs|PKN2_uc010osq.1_Frame_Shift_Del_p.F562fs|PKN2_uc009wcv.2_Frame_Shift_Del_p.F671fs|PKN2_uc010osr.1_Frame_Shift_Del_p.F384fs NM_006256 NP_006247 Q16513 PKN2_HUMAN protein kinase N2 719 Protein kinase. signal transduction cytoplasm ATP binding|histone deacetylase binding|protein kinase C activity large_intestine(1)|lung(1)|skin(1) 3 Lung NSC(277;0.123) all cancers(265;0.0136)|Epithelial(280;0.0301) AAGGCATCCCTTTTTGGTGAA 0.338 0.48 93 85 TRIM33 51592 broad.mit.edu 37 1 115053195 115053195 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr1:115053195delC uc001eew.2 - 1 587 c.503delG c.(502-504)GGCfs p.G168fs TRIM33_uc001eex.2_Frame_Shift_Del_p.G168fs NM_015906 NP_056990 Q9UPN9 TRI33_HUMAN tripartite motif-containing 33 protein isoform 168 negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent nucleus co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 11 all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184) all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05) Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133) GCCGTTGCTGCCCCCCGGGAT 0.697 0.47 8 7 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 132 51 LEMD1 93273 broad.mit.edu 37 1 205388453 205388453 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr1:205388453delT uc001hcj.1 - 3 212 c.110delA c.(109-111)AAGfs p.K37fs LEMD1_uc001hci.1_Frame_Shift_Del_p.K37fs|LEMD1_uc001hck.1_RNA|LEMD1_uc001hcl.1_Intron|LEMD1_uc001hcm.1_Intron|LEMD1_uc001hcn.1_Intron Q68G75 LEMD1_HUMAN RecName: Full=LEM domain-containing protein 1; Short=LEMP-1; AltName: Full=Cancer/testis antigen 50; Short=CT50; 37 LEM. integral to membrane|nuclear envelope 0 Breast(84;0.247) BRCA - Breast invasive adenocarcinoma(75;0.0938) CTGTACTAACTTTTTTTCATA 0.433 0.47 90 81 IKBKE 9641 broad.mit.edu 37 1 206652294 206652294 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr1:206652294delT uc001hdz.1 + 10 1369 c.1001delT c.(1000-1002)ATTfs p.I334fs IKBKE_uc009xbv.1_Frame_Shift_Del_p.I334fs|IKBKE_uc001hea.1_Frame_Shift_Del_p.I249fs NM_014002 NP_054721 Q14164 IKKE_HUMAN IKK-related kinase epsilon 334 DNA damage response, signal transduction resulting in induction of apoptosis|innate immune response|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|endosome membrane|plasma membrane|PML body ATP binding|IkappaB kinase activity|NF-kappaB-inducing kinase activity|protein binding ovary(3)|lung(3)|central_nervous_system(1)|skin(1) 8 Breast(84;0.137) AGGATAGCCATTTTCCAGGAG 0.627 0.22 29 8 OR2L13 284521 broad.mit.edu 37 1 248263376 248263376 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr1:248263376delA uc001ids.2 + 3 1036 c.699delA c.(697-699)AGAfs p.R233fs NM_175911 NP_787107 Q8N349 OR2LD_HUMAN olfactory receptor, family 2, subfamily L, 233 Cytoplasmic (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity|protein binding central_nervous_system(2)|ovary(1)|skin(1) 4 all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0132) AGGAGGGGAGAAAAAAGGCCT 0.443 0.48 139 126 RRM2 6241 broad.mit.edu 37 2 10268984 10268985 + Frame_Shift_Del DEL TG - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr2:10268984_10268985delTG uc002rah.2 + 8 999_1000 c.808_809delTG c.(808-810)TGTfs p.C270fs NM_001034 NP_001025 P31350 RIR2_HUMAN ribonucleotide reductase M2 polypeptide isoform 270 deoxyribonucleoside diphosphate metabolic process|deoxyribonucleotide biosynthetic process|DNA replication|nucleobase, nucleoside and nucleotide interconversion|regulation of transcription involved in G1/S phase of mitotic cell cycle cytosol ribonucleoside-diphosphate reductase activity|transition metal ion binding 0 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) Epithelial(75;0.188)|OV - Ovarian serous cystadenocarcinoma(76;0.221) GGGTTTACACTGTGATTTTGCT 0.371 0.48 16 15 IL1R2 7850 broad.mit.edu 37 2 102638649 102638649 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr2:102638649delA uc002tbm.2 + 6 918 c.689delA c.(688-690)AAAfs p.K230fs IL1R2_uc002tbn.2_Frame_Shift_Del_p.K230fs|IL1R2_uc002tbo.1_Frame_Shift_Del_p.K230fs NM_004633 NP_004624 P27930 IL1R2_HUMAN interleukin 1 receptor, type II precursor 230 Extracellular (Potential). immune response integral to membrane|plasma membrane interleukin-1, Type II, blocking receptor activity ovary(1)|breast(1) 2 Anakinra(DB00026) TCTTTCTCAGAAAAAAAAGAA 0.438 0.36 97 55 LRP2 4036 broad.mit.edu 37 2 169997025 169997025 + Frame_Shift_Del DEL G - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr2:169997025delG uc002ues.2 - 72 13352 c.13139delC c.(13138-13140)CCAfs p.P4380fs NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 4380 EGF-like 17.|Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) 0.000 0.23 240 72 MYO3B 140469 broad.mit.edu 37 2 171240259 171240259 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr2:171240259delC uc002ufy.2 + 12 1368 c.1225delC c.(1225-1227)CCCfs p.P409fs MYO3B_uc002ufv.2_Frame_Shift_Del_p.P396fs|MYO3B_uc010fqb.1_Frame_Shift_Del_p.P396fs|MYO3B_uc002ufz.2_Frame_Shift_Del_p.P409fs|MYO3B_uc002ufw.2_RNA|MYO3B_uc002ufx.2_RNA|MYO3B_uc002ugb.2_RNA NM_138995 NP_620482 Q8WXR4 MYO3B_HUMAN myosin IIIB isoform 2 409 Myosin head-like. response to stimulus|visual perception cytoplasm|myosin complex actin binding|ATP binding|motor activity|protein serine/threonine kinase activity lung(8)|ovary(6)|skin(4)|central_nervous_system(1) 19 CGCCTCCAATCCCCCCCACAT 0.463 0.41 77 54 HOXD11 3237 broad.mit.edu 37 2 176972335 176972335 + Frame_Shift_Del DEL G - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr2:176972335delG uc002uki.2 + 1 252 c.252delG c.(250-252)GCGfs p.A84fs HOXD11_uc010fqx.2_Intron NM_021192 NP_067015 P31277 HXD11_HUMAN homeobox D11 84 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678) 0.000 0.41 20 14 TTN 7273 broad.mit.edu 37 2 179424782 179424783 + Frame_Shift_Ins INS - T T CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr2:179424782_179424783insT uc010zfg.1 - 275 78596_78597 c.78372_78373insA c.(78370-78375)AAATCTfs p.K26124fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Ins_p.K19819fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.K19752fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.K19627fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 27051_27052 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GTGTCATCAGATTTTTTGTATT 0.411 0.47 138 121 TTN 7273 broad.mit.edu 37 2 179477976 179477976 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr2:179477976delT uc010zfg.1 - 213 42080 c.41856delA c.(41854-41856)AAAfs p.K13952fs uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.K7647fs|TTN_uc010zfi.1_Frame_Shift_Del_p.K7580fs|TTN_uc010zfj.1_Frame_Shift_Del_p.K7455fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 14879 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GGAATCTGTATTTTTTCTTAT 0.353 0.48 56 51 STK36 27148 broad.mit.edu 37 2 219555202 219555202 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr2:219555202delT uc002viu.2 + 14 1954 c.1688delT c.(1687-1689)CTTfs p.L563fs STK36_uc002viv.2_Frame_Shift_Del_p.L563fs NM_015690 NP_056505 Q9NRP7 STK36_HUMAN serine/threonine kinase 36 563 cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus ATP binding|protein serine/threonine kinase activity|transcription factor binding ovary(4)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1) 11 Renal(207;0.0915) Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984) GCTGCCAACCTTTTTCTGGAC 0.512 0.23 111 33 CCR4 1233 broad.mit.edu 37 3 32995888 32995888 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr3:32995888delT uc003cfg.1 + 2 1142 c.974delT c.(973-975)CTTfs p.L325fs NM_005508 NP_005499 P51679 CCR4_HUMAN chemokine (C-C motif) receptor 4 325 Cytoplasmic (Potential). chemotaxis|elevation of cytosolic calcium ion concentration|immune response|inflammatory response integral to plasma membrane lung(1) 1 TGCAGGGGCCTTTTTGTGCTC 0.478 0.47 140 124 OXSR1 9943 broad.mit.edu 37 3 38263085 38263085 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr3:38263085delT uc003chy.2 + 6 849 c.507delT c.(505-507)GCTfs p.A169fs OXSR1_uc010hhb.2_Frame_Shift_Del_p.A103fs|OXSR1_uc010hha.1_Frame_Shift_Del_p.A101fs NM_005109 NP_005100 O95747 OXSR1_HUMAN oxidative-stress responsive 1 169 Protein kinase. intracellular protein kinase cascade|response to oxidative stress ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity skin(1) 1 KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738) GGGTTAGTGCTTTTTTAGCAA 0.383 0.42 71 51 ROBO1 6091 broad.mit.edu 37 3 78710235 78710235 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr3:78710235delA uc003dqe.2 - 16 2473 c.2265delT c.(2263-2265)TTTfs p.F755fs ROBO1_uc003dqb.2_Frame_Shift_Del_p.F716fs|ROBO1_uc003dqc.2_Frame_Shift_Del_p.F719fs|ROBO1_uc003dqd.2_Frame_Shift_Del_p.F719fs|ROBO1_uc010hoh.2_5'UTR|ROBO1_uc011bgl.1_Frame_Shift_Del_p.F327fs|ROBO1_uc003dqf.1_Frame_Shift_Del_p.F434fs NM_002941 NP_002932 Q9Y6N7 ROBO1_HUMAN roundabout 1 isoform a 755 Extracellular (Potential).|Fibronectin type-III 2. activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway cell surface|cytoplasm|integral to plasma membrane axon guidance receptor activity|identical protein binding|LRR domain binding large_intestine(2) 2 Lung SC(41;0.0257)|Lung NSC(201;0.0439) LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274) GAAATTCATTAAAAAAAGGGC 0.398 0.15 83 15 PIK3R4 30849 broad.mit.edu 37 3 130454762 130454762 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr3:130454762delA uc003enj.2 - 3 1399 c.818delT c.(817-819)TTCfs p.F273fs NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 273 Protein kinase. fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 TTGTTCAGGGAAAAAATGTCC 0.338 0.60 29 43 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.31 46 21 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.40 76 51 MAML3 55534 broad.mit.edu 37 4 140810639 140810641 + In_Frame_Del DEL GCT - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr4:140810639_140810641delGCT uc003ihz.1 - 3 2689_2691 c.1937_1939delAGC c.(1936-1941)CAGCCG>CCG p.Q646del MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 646 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) GGAGGTGGCGgctgctgctgctg 0.419 0.14 75 12 NKD2 85409 broad.mit.edu 37 5 1038446 1038447 + In_Frame_Ins INS - CAC CAC rs3840989 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr5:1038446_1038447insCAC uc003jbt.1 + 10 1319_1320 c.1314_1315insCAC c.(1312-1317)insCAC p.447_448insH NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 447_448 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.31 125 56 CLPTM1L 81037 broad.mit.edu 37 5 1334458 1334458 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr5:1334458delA uc003jch.2 - 7 883 c.837delT c.(835-837)TTTfs p.F279fs CLPTM1L_uc003jcg.2_Frame_Shift_Del_p.F146fs NM_030782 NP_110409 Q96KA5 CLP1L_HUMAN CLPTM1-like 279 Extracellular (Potential). apoptosis integral to membrane breast(1)|central_nervous_system(1) 2 Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09) Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181) KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208) TGGTATCTACAAAAATTCCTT 0.453 0.11 54 7 SKP2 6502 broad.mit.edu 37 5 36153056 36153056 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr5:36153056delC uc003jkc.1 + 2 374 c.192delC c.(190-192)AGCfs p.S64fs SKP2_uc011cou.1_5'UTR|SKP2_uc003jkd.2_Frame_Shift_Del_p.S64fs|LMBRD2_uc003jkb.1_5'Flank NM_005983 NP_005974 Q13309 SKP2_HUMAN S-phase kinase-associated protein 2 isoform 1 64 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G1/S transition of mitotic cell cycle|S phase of mitotic cell cycle nucleoplasm|SCF ubiquitin ligase complex protein binding central_nervous_system(2)|ovary(1)|breast(1) 4 all_lung(31;5.63e-05) Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202) ACCCGGAGAGCCCCCCACGGA 0.562 0.65 18 33 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.18 55 12 MAST4 375449 broad.mit.edu 37 5 66396328 66396330 + In_Frame_Del DEL CTT - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr5:66396328_66396330delCTT uc003jut.1 + 7 479_481 c.411_413delCTT c.(409-414)CACTTC>CAC p.F138del MAST4_uc003jus.2_In_Frame_Del_p.F138del|MAST4_uc003juu.1_In_Frame_Del_p.F148del|MAST4_uc011cra.1_In_Frame_Del_p.F121del|MAST4_uc010ixa.2_RNA|MAST4_uc003juv.2_In_Frame_Del_p.F133del|MAST4_uc003juw.2_In_Frame_Del_p.F133del NM_015183 NP_055998 O15021 MAST4_HUMAN microtubule associated serine/threonine kinase 330 cytoplasm ATP binding|magnesium ion binding|protein serine/threonine kinase activity lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1) 13 Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245) Lung(70;0.011) ACGAGTTACACTTCTTATCAAAA 0.493 0.55 47 57 FER 2241 broad.mit.edu 37 5 108290522 108290522 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr5:108290522delA uc003kop.1 + 12 1806 c.1422delA c.(1420-1422)TTAfs p.L474fs FER_uc011cvf.1_RNA|FER_uc011cvg.1_Frame_Shift_Del_p.L299fs NM_005246 NP_005237 P16591 FER_HUMAN fer (fps/fes related) tyrosine kinase 474 SH2. intracellular signal transduction|peptidyl-tyrosine phosphorylation cytoplasm|nucleus ATP binding|non-membrane spanning protein tyrosine kinase activity lung(2)|stomach(1)|ovary(1)|kidney(1) 5 all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152) OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174) AAGAACTGTTAAAAAAACAAG 0.408 0.44 37 29 CAMK4 814 broad.mit.edu 37 5 110710554 110710554 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr5:110710554delA uc011cvj.1 + 4 346 c.247delA c.(247-249)AAAfs p.K83fs CAMK4_uc003kpf.2_Frame_Shift_Del_p.K83fs|CAMK4_uc010jbv.2_Intron NM_001744 NP_001735 Q16566 KCC4_HUMAN calcium/calmodulin-dependent protein kinase IV 83 Protein kinase. activation of phospholipase C activity|nerve growth factor receptor signaling pathway|synaptic transmission cytosol|nucleoplasm ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity ovary(3)|lung(2) 5 all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244) OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109) TTAGGTGGACAAAAAAATCGT 0.373 0.68 19 40 PGGT1B 5229 broad.mit.edu 37 5 114588934 114588934 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr5:114588934delA uc003kqw.3 - 2 180 c.159delT c.(157-159)TTTfs p.F53fs PGGT1B_uc003kqx.3_5'UTR|PGGT1B_uc010jch.2_Frame_Shift_Del_p.F53fs NM_005023 NP_005014 P53609 PGTB1_HUMAN geranylgeranyltransferase type 1 beta 53 protein geranylgeranylation CAAX-protein geranylgeranyltransferase complex CAAX-protein geranylgeranyltransferase activity 0 all_cancers(142;0.000523)|all_epithelial(76;6.45e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195) Epithelial(69;2.95e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.98e-08)|all cancers(49;3.1e-06) Pravastatin(DB00175) CGGAGAGTGCAAAAAATGCAA 0.358 0.30 28 12 RAD50 10111 broad.mit.edu 37 5 131931451 131931452 + Frame_Shift_Ins INS - A A CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr5:131931451_131931452insA uc003kxi.2 + 13 2543_2544 c.2156_2157insA c.(2155-2157)CTAfs p.L719fs RAD50_uc003kxh.2_Frame_Shift_Ins_p.L580fs NM_005732 NP_005723 Q92878 RAD50_HUMAN RAD50 homolog isoform 1 719 Zinc-hook.|Potential. DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding lung(2)|ovary(1)|skin(1) 4 all_cancers(142;0.0368)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GAATCAGAGCTAAAAAAAAAGG 0.416 0.16 43 8 AFF4 27125 broad.mit.edu 37 5 132232616 132232616 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr5:132232616delT uc003kyd.2 - 11 2114 c.1706delA c.(1705-1707)AAGfs p.K569fs AFF4_uc011cxk.1_Frame_Shift_Del_p.K247fs|AFF4_uc003kye.1_Frame_Shift_Del_p.K569fs NM_014423 NP_055238 Q9UHB7 AFF4_HUMAN ALL1 fused gene from 5q31 569 transcription from RNA polymerase II promoter mitochondrion|nucleolus protein binding|sequence-specific DNA binding transcription factor activity ovary(2)|kidney(2)|skin(1) 5 all_cancers(142;0.145)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) CTTCTCAGCCTTTTTGGGTTG 0.507 0.31 337 148 NR3C1 2908 broad.mit.edu 37 5 142661474 142661475 + Frame_Shift_Ins INS - T T CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr5:142661474_142661475insT uc003lmz.2 - 9 2805_2806 c.2313_2314insA c.(2311-2316)AAACTTfs p.K771fs NR3C1_uc003lmy.2_Frame_Shift_Ins_p.K772fs|NR3C1_uc003lna.2_Intron|NR3C1_uc003lnb.2_Frame_Shift_Ins_p.K771fs|NR3C1_uc011dbk.1_Frame_Shift_Ins_p.K374fs|NR3C1_uc003lnc.2_Frame_Shift_Ins_p.K771fs|NR3C1_uc003lnd.2_Frame_Shift_Ins_p.K771fs|NR3C1_uc003lne.2_Frame_Shift_Ins_p.K771fs|NR3C1_uc003lnf.2_Frame_Shift_Ins_p.K772fs NM_000176 NP_000167 P04150 GCR_HUMAN glucocorticoid receptor isoform alpha 771_772 Steroid-binding. chromatin modification|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus|transcription from RNA polymerase II promoter mitochondrial matrix|nucleoplasm glucocorticoid receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding ovary(2) 2 Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361) KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176) Amcinonide(DB00288)|Betamethasone(DB00443)|Budesonide(DB01222)|Dexamethasone(DB01234)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluticasone Propionate(DB00588)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol Etabonate(DB00873)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Prednisone(DB00635) TGAAACAGAAGTTTTTTGATAT 0.312 0.64 17 30 PTTG1 9232 broad.mit.edu 37 5 159854837 159854837 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr5:159854837delC uc003lyj.2 + 5 531 c.486delC c.(484-486)GGCfs p.G162fs PTTG1_uc003lyk.2_Frame_Shift_Del_p.G162fs NM_004219 NP_004210 O95997 PTTG1_HUMAN pituitary tumor-transforming protein 1 162 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|chromosome organization|chromosome segregation|DNA repair|mitosis|spermatogenesis|transcription from RNA polymerase II promoter cytosol|nucleus cysteine-type endopeptidase inhibitor activity|sequence-specific DNA binding transcription factor activity|SH3 domain binding 0 Renal(175;0.00196) Medulloblastoma(196;0.0354)|all_neural(177;0.116) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) OV - Ovarian serous cystadenocarcinoma(192;0.00219)|Epithelial(171;0.00348)|all cancers(165;0.0104) TTCAGCTGGGCCCCCCTTCAC 0.527 0.11 137 17 FLT4 2324 broad.mit.edu 37 5 180053023 180053023 + Frame_Shift_Del DEL G - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr5:180053023delG uc003mma.3 - 10 1346 c.1267delC c.(1267-1269)CAGfs p.Q423fs FLT4_uc003mlz.3_Frame_Shift_Del_p.Q423fs|FLT4_uc003mmb.1_5'UTR|FLT4_uc011dgy.1_Frame_Shift_Del_p.Q423fs NM_002020 NP_002011 P35916 VGFR3_HUMAN fms-related tyrosine kinase 4 isoform 2 423 Ig-like C2-type 5.|Extracellular (Potential). positive regulation of cell proliferation integral to plasma membrane ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1) 15 all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114) all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) all cancers(165;0.134) Sorafenib(DB00398)|Sunitinib(DB01268) TCATGTATCTGGGGGGGCACT 0.672 0.24 26 8 ATXN1 6310 broad.mit.edu 37 6 16327910 16327924 + In_Frame_Del DEL TGCTGATGCTGCTGC - - rs11969612;rs28555263;rs142039862 by1000genomes;by1000genomes CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr6:16327910_16327924delTGCTGATGCTGCTGC uc003nbt.2 - 8 1589_1603 c.618_632delGCAGCAGCATCAGCA c.(616-633)CAGCAGCAGCATCAGCAT>CAT p.QQQHQ206del ATXN1_uc010jpi.2_In_Frame_Del_p.QQQHQ206del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 206_210 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgatgctgatgctgctgctgctgctgct 0.395 0.33 12 6 ATXN1 6310 broad.mit.edu 37 6 16328049 16328049 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr6:16328049delC uc003nbt.2 - 8 1464 c.493delG c.(493-495)GCCfs p.A165fs ATXN1_uc010jpi.2_Frame_Shift_Del_p.A165fs|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 165 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) GGAGTGGTGGCCCCTGCGGCC 0.617 0.38 8 5 NOTCH4 4855 broad.mit.edu 37 6 32163554 32163554 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr6:32163554delC uc003obb.2 - 30 5811 c.5672delG c.(5671-5673)GGCfs p.G1891fs GPSM3_uc003oax.3_5'Flank|GPSM3_uc003oay.3_5'Flank|GPSM3_uc003oaz.2_5'Flank|NOTCH4_uc011dpt.1_3'UTR|NOTCH4_uc003oba.2_Frame_Shift_Del_p.G551fs|NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 1891 Cytoplasmic (Potential). cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 0.000 0.23 546 161 TTBK1 84630 broad.mit.edu 37 6 43252891 43252891 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr6:43252891delC uc003ouq.1 + 15 4022 c.3743delC c.(3742-3744)TCCfs p.S1248fs NM_032538 NP_115927 Q5TCY1 TTBK1_HUMAN tau tubulin kinase 1 1248 Pro-rich. cell junction|cytoplasm|nucleus ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1) 9 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399) 0.000 0.38 401 247 PHF3 23469 broad.mit.edu 37 6 64394982 64394987 + In_Frame_Del DEL TATAGA - - rs112493279 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr6:64394982_64394987delTATAGA uc003pep.1 + 3 1385_1390 c.1359_1364delTATAGA c.(1357-1365)GCTATAGAA>GCA p.IE454del PHF3_uc010kaf.1_In_Frame_Del_p.IE454del|PHF3_uc003pem.2_In_Frame_Del_p.IE407del|PHF3_uc010kag.1_In_Frame_Del_p.IE366del|PHF3_uc010kah.1_In_Frame_Del_p.IE268del|PHF3_uc003pen.2_In_Frame_Del_p.IE366del|PHF3_uc011dxs.1_Intron|PHF3_uc003peo.2_In_Frame_Del_p.IE454del NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 454_455 multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) AGTTGAATGCTATAGAAAGTACTAAA 0.369 0.47 51 46 TTK 7272 broad.mit.edu 37 6 80751897 80751898 + Frame_Shift_Del DEL AA - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr6:80751897_80751898delAA uc003pjc.2 + 22 2626_2627 c.2552_2553delAA c.(2551-2553)GAAfs p.E851fs TTK_uc003pjb.3_Frame_Shift_Del_p.E850fs NM_003318 NP_003309 P33981 TTK_HUMAN TTK protein kinase 851 mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation spindle ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity p.R838fs*4(3) ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1) 11 all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2) BRCA - Breast invasive adenocarcinoma(397;0.0321) AAGACTTTTGAAAAAAAAAGGG 0.297 0.27 24 9 GLI3 2737 broad.mit.edu 37 7 42005573 42005573 + Frame_Shift_Del DEL G - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr7:42005573delG uc011kbh.1 - 15 3189 c.3098delC c.(3097-3099)CCGfs p.P1033fs GLI3_uc011kbg.1_Frame_Shift_Del_p.P974fs NM_000168 NP_000159 P10071 GLI3_HUMAN GLI-Kruppel family member GLI3 1033 negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis cilium|cytosol|nucleolus beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1) 19 GGCCATCGCCGGGGGGTTGCA 0.701 0.48 12 11 DBF4 10926 broad.mit.edu 37 7 87507389 87507389 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr7:87507389delA uc003ujf.1 + 2 572 c.68delA c.(67-69)GAAfs p.E23fs SLC25A40_uc003uje.2_5'Flank|DBF4_uc003ujh.1_5'UTR|DBF4_uc003ujg.1_5'UTR|DBF4_uc011khf.1_5'UTR NM_006716 NP_006707 Q9UBU7 DBF4A_HUMAN activator of S phase kinase 23 cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle nucleoplasm enzyme activator activity|nucleic acid binding|protein binding|zinc ion binding lung(2) 2 Esophageal squamous(14;0.00202) Breast(660;0.0334) GTCAAAAATGAAAAAAACAGA 0.299 0.43 29 22 CDK14 5218 broad.mit.edu 37 7 90528642 90528642 + Frame_Shift_Del DEL G - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr7:90528642delG uc003uky.2 + 7 898 c.676delG c.(676-678)GGGfs p.G226fs CDK14_uc003ukz.1_Frame_Shift_Del_p.G208fs|CDK14_uc010les.1_Frame_Shift_Del_p.G180fs|CDK14_uc011khl.1_Frame_Shift_Del_p.G97fs NM_012395 NP_036527 O94921 CDK14_HUMAN PFTAIRE protein kinase 1 226 Protein kinase. cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane ATP binding|cyclin binding|cyclin-dependent protein kinase activity lung(3)|ovary(1) 4 CAAGCACCCTGGGGGGCTGCA 0.353 0.35 48 26 GRM8 2918 broad.mit.edu 37 7 126173278 126173278 + Frame_Shift_Del DEL G - - rs77499554 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr7:126173278delG uc003vlr.2 - 8 2469 c.2158delC c.(2158-2160)CACfs p.H720fs GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Frame_Shift_Del_p.H720fs|GRM8_uc010lkz.1_RNA NM_000845 NP_000836 O00222 GRM8_HUMAN glutamate receptor, metabotropic 8 isoform a 720 Extracellular (Potential). negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception integral to plasma membrane lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1) 23 Prostate(267;0.186) L-Glutamic Acid(DB00142) 0.000 0.46 453 386 SMO 6608 broad.mit.edu 37 7 128852004 128852004 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr7:128852004delC uc003vor.2 + 12 2356 c.2076delC c.(2074-2076)CACfs p.H692fs SMO_uc003vos.2_3'UTR NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 692 Cytoplasmic (Potential). adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 CTGAGCTTCACCCCCCTGCCC 0.592 0.57 6 8 BAG4 9530 broad.mit.edu 37 8 38067777 38067778 + Frame_Shift_Ins INS - A A CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr8:38067777_38067778insA uc003xky.1 + 5 1422_1423 c.1140_1141insA c.(1138-1143)ATTAAAfs p.I380fs BAG4_uc003xkz.1_Frame_Shift_Ins_p.I344fs NM_004874 NP_004865 O95429 BAG4_HUMAN BCL2-associated athanogene 4 380_381 BAG. anti-apoptosis|apoptosis|protein folding cytoplasm|nucleus receptor signaling protein activity ovary(1) 1 Colorectal(12;0.000442) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121) CTCCGAGTATTAAAAAAATCAT 0.396 0.41 58 40 BAG4 9530 broad.mit.edu 37 8 38067995 38067995 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr8:38067995delA uc003xky.1 + 5 1640 c.1358delA c.(1357-1359)GAAfs p.E453fs BAG4_uc003xkz.1_Frame_Shift_Del_p.E417fs NM_004874 NP_004865 O95429 BAG4_HUMAN BCL2-associated athanogene 4 453 BAG. anti-apoptosis|apoptosis|protein folding cytoplasm|nucleus receptor signaling protein activity ovary(1) 1 Colorectal(12;0.000442) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121) GAAAAATTAGAAAAAAAAGGA 0.398 0.56 12 15 PRKDC 5591 broad.mit.edu 37 8 48740816 48740817 + Frame_Shift_Ins INS - T T CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr8:48740816_48740817insT uc003xqi.2 - 63 8546_8547 c.8489_8490insA c.(8488-8490)AACfs p.N2830fs PRKDC_uc003xqj.2_Frame_Shift_Ins_p.N2830fs|PRKDC_uc011ldh.1_Intron NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic 2830 KIP-binding. cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) GAGTGATGTTGTTTTTTTCAGA 0.356 0.35 47 25 PLAG1 5324 broad.mit.edu 37 8 57079754 57079754 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr8:57079754delT uc003xsq.3 - 3 1002 c.551delA c.(550-552)AAGfs p.K184fs PLAG1_uc003xsr.3_Frame_Shift_Del_p.K184fs|PLAG1_uc010lyi.2_Frame_Shift_Del_p.K184fs|PLAG1_uc010lyj.2_Frame_Shift_Del_p.K102fs NM_001114635 NP_001108107 Q6DJT9 PLAG1_HUMAN pleiomorphic adenoma gene 1 isoform b 184 Decreased nuclear import with localization in the nucleus but also in the cytoplasm. nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding CTNNB1/PLAG1(60)|FGFR1_ENST00000447712/PLAG1(28)|CHCHD7/PLAG1(12)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|COL1A2/PLAG1(3)|TCEA1_ENST00000521604/PLAG1(3) salivary_gland(113)|soft_tissue(13)|lung(1)|central_nervous_system(1)|breast(1) 129 all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125) Epithelial(17;0.00179)|all cancers(17;0.0125) GCACTGGTGCTTTTTTTCTTT 0.483 0.48 140 131 VPS13B 157680 broad.mit.edu 37 8 100654346 100654346 + Frame_Shift_Del DEL A - - rs141211386 byFrequency CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr8:100654346delA uc003yiv.2 + 34 5714 c.5603delA c.(5602-5604)GAAfs p.E1868fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.E1843fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 1868 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) AAGAATAATGAAAAAACAGAC 0.373 0.44 57 44 RIMS2 9699 broad.mit.edu 37 8 104927779 104927779 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr8:104927779delA uc003yls.2 + 5 1444 c.1203delA c.(1201-1203)GTAfs p.V401fs RIMS2_uc003ylp.2_Frame_Shift_Del_p.V623fs|RIMS2_uc003ylw.2_Frame_Shift_Del_p.V431fs|RIMS2_uc003ylq.2_Frame_Shift_Del_p.V431fs|RIMS2_uc003ylr.2_Frame_Shift_Del_p.V478fs|RIMS2_uc003ylt.2_Frame_Shift_Del_p.V24fs|RIMS2_uc003ylu.1_Frame_Shift_Del_p.V14fs|RIMS2_uc003ylv.1_Frame_Shift_Del_p.V14fs NM_014677 NP_055492 Q9UQ26 RIMS2_HUMAN regulating synaptic membrane exocytosis 2 701 PDZ. intracellular protein transport cell junction|presynaptic membrane metal ion binding|Rab GTPase binding ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1) 15 OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229) TTACTAAAGTAAAAAAAGGAA 0.323 0.45 66 53 MAPK15 225689 broad.mit.edu 37 8 144804319 144804319 + Frame_Shift_Del DEL G - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr8:144804319delG uc003yzj.2 + 14 1574 c.1533delG c.(1531-1533)CAGfs p.Q511fs NM_139021 NP_620590 Q8TD08 MK15_HUMAN mitogen-activated protein kinase 15 511 protein autophosphorylation extracellular region ATP binding|MAP kinase activity|SH3 domain binding lung(2) 2 all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146) 0.000 0.56 402 507 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 31 MLLT3 4300 broad.mit.edu 37 9 20414377 20414379 + In_Frame_Del DEL CTG - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr9:20414377_20414379delCTG uc003zoe.2 - 5 724_726 c.465_467delCAG c.(463-468)AGCAGT>AGT p.155_156SS>S MLLT3_uc011lne.1_In_Frame_Del_p.123_124SS>S|MLLT3_uc011lnf.1_In_Frame_Del_p.152_153SS>S|MLLT3_uc003zof.2_5'UTR|MLLT3_uc011lng.1_Splice_Site_p.T124_splice NM_004529 NP_004520 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia 155_156 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding lung(2)|ovary(1) 3 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) gctgctgctactgctgctgctgc 0.148 0.35 67 36 TAF1L 138474 broad.mit.edu 37 9 32633025 32633025 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr9:32633025delT uc003zrg.1 - 1 2643 c.2553delA c.(2551-2553)AAAfs p.K851fs uc003zrh.1_5'Flank NM_153809 NP_722516 Q8IZX4 TAF1L_HUMAN TBP-associated factor RNA polymerase 1-like 851 male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent transcription factor TFIID complex DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1) 26 LUSC - Lung squamous cell carcinoma(29;0.0181) GBM - Glioblastoma multiforme(74;0.00301) AAGGAAAGGCTTTTTTTATAT 0.443 0.31 147 66 PAX5 5079 broad.mit.edu 37 9 37015030 37015031 + Frame_Shift_Ins INS - CA CA CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr9:37015030_37015031insCA uc003zzo.1 - 3 821_822 c.373_374insTG c.(373-375)GACfs p.D125fs PAX5_uc011lpw.1_Frame_Shift_Ins_p.D125fs|PAX5_uc011lpx.1_Intron|PAX5_uc011lpy.1_Frame_Shift_Ins_p.D17fs|PAX5_uc010mls.1_Frame_Shift_Ins_p.D125fs|PAX5_uc011lpz.1_Frame_Shift_Ins_p.D125fs|PAX5_uc011lqa.1_Frame_Shift_Ins_p.D17fs|PAX5_uc010mlq.1_RNA|PAX5_uc011lqb.1_RNA|PAX5_uc010mlo.1_Frame_Shift_Ins_p.D125fs|PAX5_uc010mlp.1_Frame_Shift_Ins_p.D125fs|PAX5_uc011lqc.1_Frame_Shift_Ins_p.D125fs|PAX5_uc010mlr.1_Frame_Shift_Ins_p.D125fs|PAX5_uc011lqd.1_Intron|PAX5_uc011lqe.1_RNA|PAX5_uc011lqf.1_Intron|PAX5_uc011lqg.1_RNA NM_016734 NP_057953 Q02548 PAX5_HUMAN paired box 5 125 Paired. cell differentiation|humoral immune response|nervous system development|organ morphogenesis|spermatogenesis|transcription from RNA polymerase II promoter nucleus DNA binding p.?(32) PAX5/JAK2(18) haematopoietic_and_lymphoid_tissue(142)|lung(3)|central_nervous_system(2) 147 all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44) GBM - Glioblastoma multiforme(29;0.0108) GGTGTCATTGTCACACACCCGC 0.569 0.37 99 57 OMD 4958 broad.mit.edu 37 9 95179799 95179799 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr9:95179799delA uc004asd.3 - 2 411 c.42delT c.(40-42)TTTfs p.F14fs CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron NM_005014 NP_005005 Q99983 OMD_HUMAN osteomodulin precursor 14 cell adhesion proteinaceous extracellular matrix ovary(2) 2 CTTTGACTCCAAAAAAGAAGA 0.338 0.29 49 20 WNK2 65268 broad.mit.edu 37 9 96054880 96054880 + Frame_Shift_Del DEL G - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr9:96054880delG uc004ati.1 + 23 5244 c.5244delG c.(5242-5244)GTGfs p.V1748fs WNK2_uc011lud.1_Frame_Shift_Del_p.V1711fs|WNK2_uc004atj.2_Frame_Shift_Del_p.V1711fs|WNK2_uc004atk.2_Frame_Shift_Del_p.V1348fs|WNK2_uc004atl.1_Frame_Shift_Del_p.V305fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 1748 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 TGGGCACAGTGGGGGGCCAGG 0.637 0.30 44 19 ERCC6 2074 broad.mit.edu 37 10 50736555 50736555 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr10:50736555delT uc001jhs.3 - 4 714 c.560delA c.(559-561)AAGfs p.K187fs PGBD3_uc009xoe.2_Frame_Shift_Del_p.K187fs|PGBD3_uc001jhu.2_Frame_Shift_Del_p.K187fs NM_000124 NP_000115 Q03468 ERCC6_HUMAN excision repair cross-complementing rodent 187 base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair nucleolus|soluble fraction|transcription elongation factor complex ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1) 16 TGCAGTGATCTTTTTTAGCTG 0.373 0.42 83 59 MYST4 23522 broad.mit.edu 37 10 76781905 76781906 + In_Frame_Ins INS - GAA GAA rs138589645;rs111976843 by1000genomes CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr10:76781905_76781906insGAA uc001jwn.1 + 16 3781_3782 c.3288_3289insGAA c.(3286-3291)insGAA p.1104_1105insE MYST4_uc001jwm.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwo.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwp.1_In_Frame_Ins_p.921_922insE NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1104_1105 histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) aggaagaagaggaagaagaaga 0.203 0.25 41 14 BMPR1A 657 broad.mit.edu 37 10 88649922 88649922 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr10:88649922delT uc001kdy.2 + 4 719 c.171delT c.(169-171)CCTfs p.P57fs NM_004329 NP_004320 P36894 BMR1A_HUMAN bone morphogenetic protein receptor, type IA 57 Extracellular (Potential). BMP signaling pathway|immune response|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway integral to membrane|plasma membrane ATP binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta receptor activity lung(3)|large_intestine(1)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1) 8 ATACCTTGCCTTTTTTAAAGT 0.403 0.41 63 44 TNKS2 80351 broad.mit.edu 37 10 93601945 93601946 + Frame_Shift_Ins INS - A A CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr10:93601945_93601946insA uc001khp.2 + 16 2153_2154 c.1856_1857insA c.(1855-1857)ACAfs p.T619fs NM_025235 NP_079511 Q9H2K2 TNKS2_HUMAN tankyrase, TRF1-interacting ankyrin-related 619 ANK 12. positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm NAD+ ADP-ribosyltransferase activity|protein binding kidney(3)|skin(3)|ovary(1)|lung(1) 8 Colorectal(252;0.162) GCAGACCCTACAAAAAAAAACA 0.391 0.58 8 11 CHUK 1147 broad.mit.edu 37 10 101961894 101961895 + Frame_Shift_Ins INS - T T CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr10:101961894_101961895insT uc001kqp.2 - 14 1574_1575 c.1519_1520insA c.(1519-1521)ATGfs p.M507fs NM_001278 NP_001269 O15111 IKKA_HUMAN conserved helix-loop-helix ubiquitous kinase 507 I-kappaB phosphorylation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway CD40 receptor complex|cytosol|internal side of plasma membrane|nucleus ATP binding|identical protein binding|IkappaB kinase activity ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|breast(1) 7 Colorectal(252;0.117) Epithelial(162;2.05e-10)|all cancers(201;1.91e-08) TGCTTTTAGCATTTTTTCTGAA 0.351 0.48 67 61 NLRP6 171389 broad.mit.edu 37 11 284292 284292 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr11:284292delC uc010qvs.1 + 6 2264 c.2264delC c.(2263-2265)GCCfs p.A755fs NLRP6_uc010qvt.1_Frame_Shift_Del_p.A754fs NM_138329 NP_612202 P59044 NALP6_HUMAN NLR family, pyrin domain containing 6 755 LRR 3. cytoplasm ATP binding upper_aerodigestive_tract(1)|skin(1) 2 all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122) CTGAGGGCAGCCCCCGCACTG 0.647 0.27 19 7 BRSK2 9024 broad.mit.edu 37 11 1466879 1466880 + Frame_Shift_Ins INS - C C CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr11:1466879_1466880insC uc001lti.2 + 11 1442_1443 c.1056_1057insC c.(1054-1059)CTGCCCfs p.L352fs BRSK2_uc009ycv.1_Frame_Shift_Ins_p.L352fs|BRSK2_uc001lth.1_Frame_Shift_Ins_p.L352fs|BRSK2_uc001ltj.2_Frame_Shift_Ins_p.L352fs|BRSK2_uc001ltk.2_RNA|BRSK2_uc001ltl.2_Frame_Shift_Ins_p.L352fs|BRSK2_uc001ltm.2_Frame_Shift_Ins_p.L398fs|BRSK2_uc001ltn.2_RNA|BRSK2_uc010qwx.1_RNA NM_003957 NP_003948 Q8IWQ3 BRSK2_HUMAN BR serine/threonine kinase 2 352_353 establishment of cell polarity|neuron differentiation ATP binding|magnesium ion binding|protein serine/threonine kinase activity 0 all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842) ATGAGGACCTGCCCCCCCGGAA 0.649 0.29 17 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 258 88 ATN1 1822 broad.mit.edu 37 12 7045885 7045886 + In_Frame_Ins INS - CAG CAG CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr12:7045885_7045886insCAG uc001qrw.1 + 5 1692_1693 c.1455_1456insCAG c.(1453-1458)insCAG p.502_503insQ ATN1_uc001qrx.1_In_Frame_Ins_p.502_503insQ|ATN1_uc001qry.1_In_Frame_Ins_p.486_487insQ NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502_503 cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 ACCACcagcaacagcaacagca 0.441 0.26 32 11 CNTN1 1272 broad.mit.edu 37 12 41337447 41337448 + Frame_Shift_Ins INS - A A CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr12:41337447_41337448insA uc001rmm.1 + 13 1541_1542 c.1428_1429insA c.(1426-1431)AGGAATfs p.R476fs CNTN1_uc009zjy.1_Frame_Shift_Ins_p.R476fs|CNTN1_uc001rmn.1_Frame_Shift_Ins_p.R465fs|CNTN1_uc001rmo.2_Frame_Shift_Ins_p.R476fs NM_001843 NP_001834 Q12860 CNTN1_HUMAN contactin 1 isoform 1 precursor 476_477 Ig-like C2-type 5. axon guidance|cell adhesion|Notch signaling pathway anchored to membrane|membrane fraction|plasma membrane lung(4)|ovary(3)|large_intestine(1)|skin(1) 9 all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716) Lung NSC(34;0.0211)|all_lung(34;0.0294) ACATTACAAGGAATGATGGAGG 0.337 0.19 64 15 AMHR2 269 broad.mit.edu 37 12 53819645 53819645 + Frame_Shift_Del DEL G - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr12:53819645delG uc001scx.1 + 6 872 c.794delG c.(793-795)CGGfs p.R265fs AMHR2_uc009zmy.1_Frame_Shift_Del_p.R265fs NM_020547 NP_065434 Q16671 AMHR2_HUMAN anti-Mullerian hormone receptor, type II isoform 265 Cytoplasmic (Potential).|Protein kinase. Mullerian duct regression ATP binding|hormone binding|metal ion binding ovary(1)|skin(1) 2 Adenosine triphosphate(DB00171) ACTGCCAGCCGGGGGGGTCCT 0.512 0.36 86 48 ZMYM2 7750 broad.mit.edu 37 13 20657094 20657094 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr13:20657094delA uc001umr.2 + 24 4040 c.3742delA c.(3742-3744)AAAfs p.K1248fs ZMYM2_uc001ums.2_Frame_Shift_Del_p.K1248fs|ZMYM2_uc001umt.2_Frame_Shift_Del_p.K1248fs|ZMYM2_uc001umv.2_Frame_Shift_Del_p.K628fs|ZMYM2_uc001umw.2_Frame_Shift_Del_p.K701fs NM_003453 NP_003444 Q9UBW7 ZMYM2_HUMAN zinc finger protein 198 1248 regulation of transcription, DNA-dependent|transcription, DNA-dependent PML body ubiquitin conjugating enzyme binding|zinc ion binding lung(3)|ovary(2)|prostate(1) 6 all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856) TAGGCATTGGAAAAAAAATCC 0.363 0.50 55 56 CDK8 1024 broad.mit.edu 37 13 26975408 26975408 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr13:26975408delT uc001uqr.1 + 11 1060 c.1034delT c.(1033-1035)GTTfs p.V345fs CDK8_uc001uqs.1_Frame_Shift_Del_p.V345fs|CDK8_uc001uqt.1_Frame_Shift_Del_p.V172fs NM_001260 NP_001251 P49336 CDK8_HUMAN cyclin-dependent kinase 8 345 regulation of transcription, DNA-dependent|transcription, DNA-dependent mediator complex ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity lung(2)|large_intestine(1)|ovary(1)|skin(1) 5 Colorectal(5;0.000442) Lung SC(185;0.0156)|Breast(139;0.147) all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188) ATGATCAGCGTTTTTGCCGGT 0.323 0.54 36 43 GPR183 1880 broad.mit.edu 37 13 99948213 99948213 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr13:99948213delT uc001vog.2 - 2 361 c.187delA c.(187-189)ATCfs p.I63fs UBAC2_uc001voa.3_Intron|UBAC2_uc010tiu.1_Intron|UBAC2_uc001vob.3_Intron|UBAC2_uc010tiv.1_Intron|UBAC2_uc001vod.2_Intron|UBAC2_uc001voc.2_Intron|UBAC2_uc010tiw.1_Intron NM_004951 NP_004942 P32249 GP183_HUMAN EBV-induced G protein-coupled receptor 2 63 Cytoplasmic (Potential). humoral immune response|mature B cell differentiation involved in immune response integral to plasma membrane purinergic nucleotide receptor activity, G-protein coupled 0 GTAGAGTTGATTTTTTTCCTG 0.428 0.41 138 96 CHD8 57680 broad.mit.edu 37 14 21896301 21896301 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr14:21896301delT uc001was.1 - 4 585 c.491delA c.(490-492)AAGfs p.K164fs CHD8_uc001war.1_Frame_Shift_Del_p.K60fs NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 443 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) CATTCCTGTCTTTCCCCCCGA 0.537 0.24 67 21 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.45 11 9 EIF2AK4 440275 broad.mit.edu 37 15 40270334 40270334 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr15:40270334delA uc001zkm.1 + 13 2355 c.2305delA c.(2305-2307)AAAfs p.K769fs EIF2AK4_uc010bbj.1_Frame_Shift_Del_p.K498fs NM_001013703 NP_001013725 Q9P2K8 E2AK4_HUMAN eukaryotic translation initiation factor 2 alpha 769 Protein kinase 2. translation cytosolic ribosome aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity lung(2)|stomach(1)|skin(1) 4 all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119) GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616) TGAGAACAGTAAAAGTCAGAA 0.308 0.47 18 16 SRP14 6727 broad.mit.edu 37 15 40328596 40328597 + In_Frame_Ins INS - TGC TGC CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr15:40328596_40328597insTGC uc001zkq.2 - 5 420_421 c.348_349insGCA c.(346-351)insGCA p.116_117insA SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116_117 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) gctgcggcaggtgctgctgctg 0.228 0.18 32 7 TRPM7 54822 broad.mit.edu 37 15 50925140 50925140 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr15:50925140delT uc001zyt.3 - 9 1321 c.1057delA c.(1057-1059)ACAfs p.T353fs TRPM7_uc010bew.1_Frame_Shift_Del_p.T353fs NM_017672 NP_060142 Q96QT4 TRPM7_HUMAN transient receptor potential cation channel, 353 Cytoplasmic (Potential). cell death integral to membrane ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity ovary(4)|stomach(3)|breast(1)|central_nervous_system(1)|skin(1) 10 all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045) AAGTTAAATGTTTTTTTGATA 0.338 0.52 32 35 RASGRF1 5923 broad.mit.edu 37 15 79317766 79317767 + Frame_Shift_Ins INS - C C CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr15:79317766_79317767insC uc002beq.2 - 10 1806_1807 c.1431_1432insG c.(1429-1434)GGGCGCfs p.G477fs RASGRF1_uc002bep.2_Frame_Shift_Ins_p.G477fs|RASGRF1_uc010blm.1_Frame_Shift_Ins_p.G399fs|RASGRF1_uc002ber.3_Frame_Shift_Ins_p.G477fs NM_002891 NP_002882 Q13972 RGRF1_HUMAN Ras protein-specific guanine 477_478 PH 2. activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission cytosol|growth cone|plasma membrane|synaptosome Rho guanyl-nucleotide exchange factor activity skin(4)|ovary(1)|central_nervous_system(1) 6 GACCCCAGGCGCCCCCTGGTGA 0.559 0.56 52 67 CREBBP 1387 broad.mit.edu 37 16 3929878 3929878 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr16:3929878delT uc002cvv.2 - 1 244 c.40delA c.(40-42)AGAfs p.R14fs CREBBP_uc002cvw.2_Frame_Shift_Del_p.R14fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 14 cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) AGTTTGGCTCTTTTGGGGTTG 0.438 0.43 12 9 PALB2 79728 broad.mit.edu 37 16 23646553 23646553 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr16:23646553delT uc002dlx.1 - 4 1514 c.1314delA c.(1312-1314)AAAfs p.K438fs NM_024675 NP_078951 Q86YC2 PALB2_HUMAN partner and localizer of BRCA2 438 double-strand break repair via homologous recombination nucleoplasm DNA binding|protein binding lung(3)|breast(3)|ovary(2)|skin(1)|kidney(1)|pancreas(1) 11 GBM - Glioblastoma multiforme(48;0.0167) TTTTAAACCCTTTTTTCTTGA 0.383 0.23 141 41 PLK1 5347 broad.mit.edu 37 16 23701329 23701331 + In_Frame_Del DEL TGG - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr16:23701329_23701331delTGG uc002dlz.1 + 10 1810_1812 c.1757_1759delTGG c.(1756-1761)ATGGTG>ATG p.V587del NM_005030 NP_005021 P53350 PLK1_HUMAN polo-like kinase 1 587 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G2/M transition DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic prophase|negative regulation of cyclin-dependent protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|protein localization to chromatin|protein ubiquitination|regulation of mitotic anaphase|regulation of protein binding centrosome|condensed nuclear chromosome outer kinetochore|cytosol|nucleoplasm|spindle microtubule|spindle midzone|spindle pole anaphase-promoting complex binding|ATP binding|polo kinase kinase activity|protein kinase binding lung(1)|skin(1) 2 GBM - Glioblastoma multiforme(48;0.0156) GCCCGCACTATGGTGGACAAGCT 0.645 0.41 60 41 ZNF668 79759 broad.mit.edu 37 16 31072732 31072732 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr16:31072732delC uc010caf.2 - 3 1874 c.1517delG c.(1516-1518)GGTfs p.G506fs ZNF668_uc002eao.2_Frame_Shift_Del_p.G506fs NM_024706 NP_078982 Q96K58 ZN668_HUMAN zinc finger protein 668 506 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(4) 4 AGCCTCCTCACCCCCCGCCTC 0.652 0.33 22 11 TRADD 8717 broad.mit.edu 37 16 67189036 67189037 + In_Frame_Ins INS - GGC GGC CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr16:67189036_67189037insGGC uc002eri.1 - 4 670_671 c.590_591insGCC c.(589-591)CCA>CCGCCA p.197_197P>PP TRADD_uc002erh.1_In_Frame_Ins_p.137_137P>PP NM_003789 NP_003780 Q15628 TRADD_HUMAN TNFRSF1A-associated via death domain 197 Poly-Pro.|Death. activation of caspase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|tumor necrosis factor-mediated signaling pathway cytoskeleton|cytosol|receptor complex binding, bridging|death domain binding|identical protein binding|kinase binding|signal transducer activity lung(1) 1 Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184) 0.000 0.14 785 129 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 10 71 STAT3 6774 broad.mit.edu 37 17 40476849 40476850 + Frame_Shift_Ins INS - A A rs1141119 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr17:40476849_40476850insA uc002hzl.1 - 17 1719_1720 c.1479_1480insT c.(1477-1482)TTTACCfs p.F493fs STAT3_uc002hzk.1_Frame_Shift_Ins_p.F493fs|STAT3_uc002hzm.1_Frame_Shift_Ins_p.F493fs|STAT3_uc010wgh.1_Frame_Shift_Ins_p.F395fs|STAT3_uc002hzn.1_Frame_Shift_Ins_p.F493fs NM_139276 NP_644805 P40763 STAT3_HUMAN signal transducer and activator of transcription 493_494 cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis cytosol|nucleus|plasma membrane calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding ovary(1)|lung(1)|breast(1)|central_nervous_system(1) 4 all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135) BRCA - Breast invasive adenocarcinoma(366;0.139) GGGGGCTTGGTAAAAAAGTTTA 0.495 0.46 53 46 WNK4 65266 broad.mit.edu 37 17 40947909 40947909 + Frame_Shift_Del DEL G - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr17:40947909delG uc002ibj.2 + 16 3310 c.3289delG c.(3289-3291)GGGfs p.G1097fs WNK4_uc010wgx.1_Frame_Shift_Del_p.G761fs|CCDC56_uc010wgz.1_Frame_Shift_Del_p.Q117fs|CNTD1_uc002ibm.3_5'Flank|CNTD1_uc010wha.1_5'Flank NM_032387 NP_115763 Q96J92 WNK4_HUMAN WNK lysine deficient protein kinase 4 1097 intracellular protein kinase cascade tight junction ATP binding|protein serine/threonine kinase activity ovary(3)|skin(3)|stomach(1) 7 Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.0749) ACCCCAAGTTGGGGGCAGCCC 0.612 0.39 25 16 RNF43 54894 broad.mit.edu 37 17 56435161 56435161 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr17:56435161delC uc002iwf.2 - 8 3932 c.1976delG c.(1975-1977)GGTfs p.G659fs RNF43_uc010wnv.1_Frame_Shift_Del_p.G618fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.G659fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.G659fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.G532fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 659 Pro-rich.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.41 212 150 TEX14 56155 broad.mit.edu 37 17 56663316 56663316 + Frame_Shift_Del DEL G - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr17:56663316delG uc010dcz.1 - 18 3052 c.2934delC c.(2932-2934)CCCfs p.P978fs TEX14_uc002iwr.1_Frame_Shift_Del_p.P972fs|TEX14_uc002iws.1_Frame_Shift_Del_p.P972fs|TEX14_uc010dda.1_Frame_Shift_Del_p.P752fs NM_198393 NP_938207 Q8IWB6 TEX14_HUMAN testis expressed sequence 14 isoform a 978 cytoplasm ATP binding|protein kinase activity stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1) 17 Medulloblastoma(34;0.127)|all_neural(34;0.237) GGCTCCTAATGGGGGGCTGCA 0.522 0.42 195 139 CLTC 1213 broad.mit.edu 37 17 57738871 57738873 + In_Frame_Del DEL CTC - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr17:57738871_57738873delCTC uc002ixq.1 + 8 1678_1680 c.1235_1237delCTC c.(1234-1239)TCTCCT>TCT p.P413del CLTC_uc002ixp.2_In_Frame_Del_p.P413del|CLTC_uc002ixr.1_In_Frame_Del_p.P417del NM_004859 NP_004850 Q00610 CLH1_HUMAN clathrin heavy chain 1 413 Globular terminal domain. axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle protein binding|structural molecule activity CLTC/ALK(44)|CLTC/TFE3(2) haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1) 48 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) GGTCAAACTTCTCCTCTACTTCA 0.468 0.39 88 57 NOTCH3 4854 broad.mit.edu 37 19 15276861 15276861 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr19:15276861delC uc002nan.2 - 30 5480 c.5404delG c.(5404-5406)GCTfs p.A1802fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 1802 Cytoplasmic (Potential). Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) GGCTCCAGAGCCCCCCCACAG 0.572 0.45 69 57 FFAR2 2867 broad.mit.edu 37 19 35941423 35941423 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr19:35941423delC uc002nzg.2 + 2 887 c.807delC c.(805-807)GACfs p.D269fs FFAR2_uc010eea.2_Frame_Shift_Del_p.D269fs NM_005306 NP_005297 O15552 FFAR2_HUMAN free fatty acid receptor 2 269 Helical; Name=7; (Potential). integral to plasma membrane G-protein coupled receptor activity|lipid binding central_nervous_system(1) 1 all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0724) CCAGTCTGGACCCCCTGCTCT 0.582 0.40 55 36 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.48 28 26 CIC 23152 broad.mit.edu 37 19 42799098 42799098 + Frame_Shift_Del DEL C - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr19:42799098delC uc002otf.1 + 20 4622 c.4582delC c.(4582-4584)CCCfs p.P1528fs NM_015125 NP_055940 Q96RK0 CIC_HUMAN capicua homolog 1528 Pro-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1) 11 Prostate(69;0.00682) CACGGAGCAGCCCCCTGGAGC 0.388 0.49 44 42 LMTK3 114783 broad.mit.edu 37 19 49002059 49002061 + In_Frame_Del DEL GGG - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr19:49002059_49002061delGGG uc002pjk.2 - 12 2352_2354 c.2352_2354delCCC c.(2350-2355)CCCCCG>CCG p.784_785PP>P NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.27 259 94 LMTK3 114783 broad.mit.edu 37 19 49002845 49002846 + Frame_Shift_Ins INS - C C CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr19:49002845_49002846insC uc002pjk.2 - 12 1567_1568 c.1567_1568insG c.(1567-1569)GCAfs p.A523fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.21 457 125 TP53RK 112858 broad.mit.edu 37 20 45315440 45315440 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr20:45315440delT uc002xsk.2 - 2 937 c.714delA c.(712-714)AAAfs p.K238fs SLC13A3_uc002xsg.1_5'Flank|SLC13A3_uc010gho.1_5'Flank|TP53RK_uc002xsj.2_3'UTR NM_033550 NP_291028 Q96S44 PRPK_HUMAN p53-related protein kinase 238 Protein kinase. lipopolysaccharide biosynthetic process membrane|nucleus ATP binding|p53 binding|protein serine/threonine kinase activity|protein tyrosine kinase activity 0 Myeloproliferative disorder(115;0.0122) CTTCATCTAATTTTTTTAGCA 0.448 0.51 96 99 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 33 293 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 7 82 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.18 71 16 CHEK2 11200 broad.mit.edu 37 22 29121281 29121281 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr22:29121281delT uc003adu.1 - 3 466 c.394delA c.(394-396)AGAfs p.R132fs CHEK2_uc003ads.1_5'UTR|CHEK2_uc010gvh.1_Intron|CHEK2_uc010gvi.1_Frame_Shift_Del_p.R132fs|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_RNA|CHEK2_uc010gvk.1_RNA|CHEK2_uc003adt.1_Frame_Shift_Del_p.R175fs|CHEK2_uc003adv.1_Frame_Shift_Del_p.R132fs|CHEK2_uc003adw.1_Frame_Shift_Del_p.R132fs|CHEK2_uc003adx.1_5'UTR|CHEK2_uc003ady.1_Frame_Shift_Del_p.R132fs|CHEK2_uc003adz.1_5'UTR NM_007194 NP_009125 O96017 CHK2_HUMAN protein kinase CHK2 isoform a 132 FHA. cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence PML body ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(17)|stomach(1)|ovary(1)|lung(1) 20 TTATCTGTTCTTTTCAGCAGT 0.388 0.46 69 59 NF2 4771 broad.mit.edu 37 22 30050708 30050708 + Frame_Shift_Del DEL A - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr22:30050708delA uc003age.3 + 5 953 c.510delA c.(508-510)CCAfs p.P170fs NF2_uc003afy.3_Frame_Shift_Del_p.P170fs|NF2_uc003afz.3_Frame_Shift_Del_p.P87fs|NF2_uc003agf.3_Frame_Shift_Del_p.P170fs|NF2_uc003agb.3_Frame_Shift_Del_p.P93fs|NF2_uc003agc.3_Frame_Shift_Del_p.P132fs|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Frame_Shift_Del_p.P170fs|NF2_uc003aga.3_Frame_Shift_Del_p.P128fs|NF2_uc003agh.3_Frame_Shift_Del_p.P129fs|NF2_uc003agi.3_Frame_Shift_Del_p.P87fs|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Frame_Shift_Del_p.P132fs NM_000268 NP_000259 P35240 MERL_HUMAN neurofibromin 2 isoform 1 170 FERM. actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane cytoskeletal protein binding|protein binding p.L127_D382del(1)|p.P170fs*4(1)|p.L140_P252del(1)|p.?(1)|p.P170fs*29(1) meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1) 728 AATTGCTTCCAAAAAGGGTAA 0.423 0.45 54 45 DDX17 10521 broad.mit.edu 37 22 38897211 38897211 + Frame_Shift_Del DEL T - - CCK81_LARGE_INTESTINE NA CCK81_LARGE_INTESTINE NA g.chr22:38897211delT uc003avy.3 - 2 465 c.362delA c.(361-363)AAGfs p.K121fs DDX17_uc003avx.3_Frame_Shift_Del_p.K121fs|DDX17_uc011anu.1_Frame_Shift_Del_p.K34fs NM_001098504 NP_001091974 Q92841 DDX17_HUMAN DEAD box polypeptide 17 isoform 3 42 RNA processing nucleus ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity skin(3)|upper_aerodigestive_tract(1) 4 Melanoma(58;0.0286) 0.000 0.23 425 129 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 5 35 EPHA2 1969 broad.mit.edu 37 1 16462198 16462199 + Frame_Shift_Ins INS - G G CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr1:16462198_16462199insG uc001aya.1 - 6 1516_1517 c.1379_1380insC c.(1378-1380)CCGfs p.P460fs EPHA2_uc010oca.1_Frame_Shift_Ins_p.P460fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 460 Extracellular (Potential).|Fibronectin type-III 2. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) 0.000 0.39 671 436 FAM171B 165215 broad.mit.edu 37 2 187559029 187559030 + In_Frame_Ins INS - CAGCAG CAGCAG CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr2:187559029_187559030insCAGCAG uc002ups.2 + 1 241_242 c.129_130insCAGCAG c.(127-132)insCAGCAG p.55_56insQQ FAM171B_uc002upr.1_In_Frame_Ins_p.55_56insQQ NM_177454 NP_803237 Q6P995 F171B_HUMAN KIAA1946 55_56 Extracellular (Potential).|Gln-rich. integral to membrane DNA binding ovary(6)|breast(3)|central_nervous_system(1) 10 GCCTCATCcaacagcagcagca 0.520 0.50 5 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 96 95 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.54 36 42 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 28 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.43 26 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 29 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.67 144 288 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.58 5 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 543 181 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.65 19 36 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 33 328 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.27 85 32 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 150 525 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CFPAC1_PANCREAS NA CFPAC1_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 6 69 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CGTHW1_THYROID NA CGTHW1_THYROID NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 4 51 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.36 314 175 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.33 14 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.19 38 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 92 140 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 30 60 DLC1 10395 broad.mit.edu 37 8 12957033 12957033 + Frame_Shift_Del DEL T - - CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr8:12957033delT uc003wwm.2 - 9 3257 c.2813delA c.(2812-2814)GACfs p.D938fs DLC1_uc003wwk.1_Frame_Shift_Del_p.D501fs|DLC1_uc003wwl.1_Frame_Shift_Del_p.D535fs|DLC1_uc011kxx.1_Frame_Shift_Del_p.D427fs NM_182643 NP_872584 Q96QB1 RHG07_HUMAN deleted in liver cancer 1 isoform 1 938 actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction caveola|cytosol|focal adhesion|nucleus Rho GTPase activator activity|SH2 domain binding ovary(3)|pancreas(2)|lung(1)|kidney(1) 7 AGAGACCGAGTCCAGGGCTGA 0.572 0.15 102 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 35 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.21 495 133 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 674 288 BMP4 652 broad.mit.edu 37 14 54417128 54417128 + Frame_Shift_Del DEL G - - CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr14:54417128delG uc001xal.3 - 3 1036 c.849delC c.(847-849)GCCfs p.A283fs BMP4_uc010aoh.2_Frame_Shift_Del_p.A283fs|BMP4_uc001xao.3_Frame_Shift_Del_p.A283fs|BMP4_uc001xan.3_Frame_Shift_Del_p.A283fs NM_130851 NP_570912 P12644 BMP4_HUMAN bone morphogenetic protein 4 preproprotein 283 activation of MAPKK activity|blood vessel endothelial cell proliferation involved in sprouting angiogenesis|BMP signaling pathway involved in heart induction|BMP signaling pathway involved in nephric duct formation|branching involved in ureteric bud morphogenesis|bronchus development|bud dilation involved in lung branching|cardiac septum development|cartilage development|endocardial cushion development|epithelial cell proliferation involved in lung morphogenesis|intermediate mesodermal cell differentiation|lung alveolus development|lymphoid progenitor cell differentiation|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway|negative regulation of branching involved in ureteric bud morphogenesis|negative regulation of cell proliferation involved in heart morphogenesis|negative regulation of glomerular mesangial cell proliferation|negative regulation of glomerulus development|negative regulation of immature T cell proliferation in thymus|negative regulation of MAP kinase activity|negative regulation of metanephric comma-shaped body morphogenesis|negative regulation of metanephric S-shaped body morphogenesis|negative regulation of mitosis|negative regulation of myoblast differentiation|negative regulation of phosphorylation|negative regulation of striated muscle tissue development|negative regulation of thymocyte apoptosis|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of apoptosis|positive regulation of bone mineralization|positive regulation of cardiac muscle fiber development|positive regulation of cartilage development|positive regulation of collagen biosynthetic process|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of kidney development|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|protein localization to nucleus|pulmonary artery endothelial tube morphogenesis|secondary heart field specification|SMAD protein signal transduction|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway|steroid hormone mediated signaling pathway extracellular space|proteinaceous extracellular matrix BMP receptor binding|chemoattractant activity|cytokine activity|growth factor activity 0 GTCGGGTCAAGGCATGGCCCC 0.612 0.26 73 26 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 28 333 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.42 83 60 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 105 21 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.40 296 198 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CGTHW1_THYROID NA CGTHW1_THYROID NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 7 123 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.84 4 21 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 29 13 LPP 4026 broad.mit.edu 37 3 188327007 188327008 + Frame_Shift_Ins INS - A A CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chr3:188327007_188327008insA uc003frs.1 + 6 734_735 c.488_489insA c.(487-489)AGAfs p.R163fs LPP_uc011bsg.1_Frame_Shift_Ins_p.R163fs|LPP_uc011bsi.1_Frame_Shift_Ins_p.R163fs|LPP_uc003frt.2_Frame_Shift_Ins_p.R163fs|LPP_uc011bsj.1_5'UTR NM_005578 NP_005569 Q93052 LPP_HUMAN LIM domain containing preferred translocation 163 Pro-rich. cell adhesion cytoplasm|focal adhesion|nucleus protein binding|zinc ion binding HMGA2/LPP(161) soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1) 165 all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088) all_lung(153;0.00139)|Lung NSC(153;0.00202) GBM - Glioblastoma multiforme(93;0.00602) GGACACAAGAGAATGGTCATCC 0.485 0.63 18 31 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.59 12 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 141 192 NKD2 85409 broad.mit.edu 37 5 1038447 1038449 + In_Frame_Del DEL CAC - - rs3840989 CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chr5:1038447_1038449delCAC uc003jbt.1 + 10 1320_1322 c.1315_1317delCAC c.(1315-1317)CACdel p.H447del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) ccaccacgagcaccaccaccacc 0.522 0.46 7 6 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.76 5 16 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 16 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 62 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 1014 363 NTRK3 4916 broad.mit.edu 37 15 88472607 88472607 + Frame_Shift_Del DEL C - - CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chr15:88472607delC uc002bme.1 - 16 2110 c.1948delG c.(1948-1950)GAGfs p.E650fs NTRK3_uc002bmh.2_Frame_Shift_Del_p.E642fs|NTRK3_uc002bmf.1_Frame_Shift_Del_p.E650fs|NTRK3_uc010upl.1_Frame_Shift_Del_p.E552fs|NTRK3_uc010bnh.1_Frame_Shift_Del_p.E642fs NM_001012338 NP_001012338 Q16288 NTRK3_HUMAN neurotrophic tyrosine kinase, receptor, type 3 650 Cytoplasmic (Potential).|Protein kinase. transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ETV6/NTRK3(234) soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1) 281 BRCA - Breast invasive adenocarcinoma(143;0.211) AGCCCCAGCTCACCCTTGGCC 0.602 0.51 145 149 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.14 49 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 41 263 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CHAGOK1_LUNG NA CHAGOK1_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 91 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 42 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 406 109 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.70 6 14 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.18 47 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 80 189 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 29 60 RIOK2 55781 broad.mit.edu 37 5 96504513 96504523 + Frame_Shift_Del DEL TCATAAAGAAA - - CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr5:96504513_96504523delTCATAAAGAAA uc003kmz.2 - 7 923_933 c.813_823delTTTCTTTATGA c.(811-825)GATTTCTTTATGAAAfs p.D271fs RIOK2_uc003kna.3_Frame_Shift_Del_p.D271fs NM_018343 NP_060813 Q9BVS4 RIOK2_HUMAN RIO kinase 2 isoform 1 271_275 Protein kinase. ATP binding|protein serine/threonine kinase activity kidney(1) 1 all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105) COAD - Colon adenocarcinoma(37;0.0657) CTGAAACGTTTCATAAAGAAATCTTTAATGC 0.322 0.46 56 47 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.14 138 23 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 16 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.70 3 7 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 28 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.45 217 174 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.42 7 5 MEF2A 4205 broad.mit.edu 37 15 100252710 100252712 + In_Frame_Del DEL CAG - - CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr15:100252710_100252712delCAG uc010urw.1 + 11 1617_1619 c.1258_1260delCAG c.(1258-1260)CAGdel p.Q430del MEF2A_uc010urv.1_In_Frame_Del_p.Q360del|MEF2A_uc010bos.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvf.2_In_Frame_Del_p.Q422del|MEF2A_uc002bve.2_In_Frame_Del_p.Q428del|MEF2A_uc002bvg.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvi.2_In_Frame_Del_p.Q420del|MEF2A_uc010bot.2_In_Frame_Del_p.Q352del NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 430 Gln/Pro-rich. Missing (in Ref. 4; AAB17195/AAB17196). apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) ATCGGGCTTCcagcagcagcagc 0.493 0.35 17 9 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 34 268 MPRIP 23164 broad.mit.edu 37 17 17039561 17039562 + In_Frame_Ins INS - CAG CAG rs147897313;rs148686165 by1000genomes CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr17:17039561_17039562insCAG uc002gqu.1 + 6 589_590 c.533_534insCAG c.(532-534)ACC>ACCAGC p.189_190insS MPRIP_uc002gqv.1_In_Frame_Ins_p.189_190insS|MPRIP_uc002gqw.1_5'UTR NM_201274 NP_958431 Q6WCQ1 MPRIP_HUMAN myosin phosphatase-Rho interacting protein 189_190 Ser-rich.|Interaction with F-actin (By similarity). cytoplasm|cytoskeleton actin binding 0 GTGGCTGTTACcagcagcagca 0.485 0.67 14 29 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.84 22 113 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 126 547 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 8 105 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes CHP126_AUTONOMIC_GANGLIA NA CHP126_AUTONOMIC_GANGLIA NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.10 212 24 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.50 53 52 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 59 PASK 23178 broad.mit.edu 37 2 242065751 242065751 + Frame_Shift_Del DEL G - - CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr2:242065751delG uc002wao.1 - 10 2671 c.2579delC c.(2578-2580)CCAfs p.P860fs PASK_uc010zol.1_Frame_Shift_Del_p.P674fs|PASK_uc010zom.1_Frame_Shift_Del_p.P825fs|PASK_uc010fzl.1_Frame_Shift_Del_p.P860fs|PASK_uc010zon.1_Frame_Shift_Del_p.P641fs|PASK_uc002wap.2_Frame_Shift_Del_p.P403fs|PASK_uc002waq.2_Frame_Shift_Del_p.P860fs NM_015148 NP_055963 Q96RG2 PASK_HUMAN PAS domain containing serine/threonine kinase 860 regulation of transcription, DNA-dependent Golgi apparatus ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity ovary(4)|lung(1)|skin(1) 6 all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968) CTCTGCTGATGGGCACGTGTC 0.617 0.49 123 118 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.38 10 6 N4BP2 55728 broad.mit.edu 37 4 40103919 40103919 + Frame_Shift_Del DEL A - - CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr4:40103919delA uc003guy.3 + 4 792 c.454delA c.(454-456)AAAfs p.K152fs N4BP2_uc010ifq.2_Frame_Shift_Del_p.K72fs|N4BP2_uc010ifr.2_Frame_Shift_Del_p.K72fs NM_018177 NP_060647 Q86UW6 N4BP2_HUMAN Nedd4 binding protein 2 152 Potential. cytoplasm ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding lung(3)|breast(2)|kidney(2)|ovary(1) 8 TGCTTTTGAGAAATTGAACTC 0.343 0.10 83 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 126 165 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 25 53 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.26 150 52 HOXA13 3209 broad.mit.edu 37 7 27239320 27239337 + In_Frame_Del DEL GCAGCGGCAGCCGCGGCA - - rs35861510 CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr7:27239320_27239337delGCAGCGGCAGCCGCGGCA uc003szb.1 - 1 389_406 c.360_377delTGCCGCGGCTGCCGCTGC c.(358-378)GCTGCCGCGGCTGCCGCTGCA>GCA p.120_126AAAAAAA>A uc003szc.1_5'Flank NM_000522 NP_000513 P31271 HXA13_HUMAN homeobox A13 120_126 Poly-Ala. skeletal system development nucleus sequence-specific DNA binding breast(1) 1 0.000 0.54 328 389 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 2 30 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 4 60 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.91 1 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 753 290 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.11 56 7 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.11 85 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 11 141 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CHP212_AUTONOMIC_GANGLIA NA CHP212_AUTONOMIC_GANGLIA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 9 146 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 4 77 RNASEL 6041 broad.mit.edu 37 1 182555260 182555260 + Frame_Shift_Del DEL G - - CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:182555260delG uc001gpj.1 - 1 849 c.682delC c.(682-684)CATfs p.H228fs RNASEL_uc009wxz.1_Frame_Shift_Del_p.H228fs|RNASEL_uc001gpk.2_Frame_Shift_Del_p.H228fs|RNASEL_uc009wya.1_Frame_Shift_Del_p.H228fs NM_021133 NP_066956 Q05823 RN5A_HUMAN ribonuclease L 228 ANK 6. mRNA processing|response to virus|type I interferon-mediated signaling pathway mitochondrion ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding ovary(4)|stomach(1) 5 TCAGCCCCATGGTCCAGCAGC 0.527 0.46 174 148 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 77 17 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.17 40 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 135 189 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 32 47 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 3 18 FNTA 2339 broad.mit.edu 37 8 42914321 42914322 + Splice_Site INS - T T CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:42914321_42914322insT uc003xps.2 + 2 334 c.286_splice c.e2+1 p.F96_splice FNTA_uc003xpt.2_Intron|FNTA_uc003xpu.2_Intron|FNTA_uc003xpv.2_Intron NM_002027 NP_002018 P49354 FNTA_HUMAN farnesyltransferase, CAAX box, alpha isoform a cellular component disassembly involved in apoptosis|positive regulation of deacetylase activity|positive regulation of tubulin deacetylation|protein farnesylation|protein geranylgeranylation|transforming growth factor beta receptor signaling pathway cytosol|microtubule associated complex alpha-tubulin binding|CAAX-protein geranylgeranyltransferase activity|microtubule binding|protein farnesyltransferase activity ovary(1) 1 Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184) all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129) Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17) AGTGACAAATGTAAGTTTGTTT 0.381 0.50 60 60 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) agcagcagcaacagcagcagca 0.267 0.13 107 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 1166 202 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.13 80 12 SRP14 6727 broad.mit.edu 37 15 40328597 40328602 + In_Frame_Del DEL TGCTGC - - CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:40328597_40328602delTGCTGC uc001zkq.2 - 5 415_420 c.343_348delGCAGCA c.(343-348)GCAGCAdel p.AA115del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 115_116 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgcggcaggtgctgctgctgctgct 0.238 0.16 86 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 11 130 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 142 428 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 6 124 MED15 51586 broad.mit.edu 37 22 20918915 20918916 + In_Frame_Ins INS - CAG CAG CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:20918915_20918916insCAG uc002zsp.2 + 6 710_711 c.630_631insCAG c.(628-633)insCAG p.218_219insQ MED15_uc002zsn.1_In_Frame_Ins_p.137_138insQ|MED15_uc002zso.2_In_Frame_Ins_p.147_148insQ|MED15_uc002zsq.2_In_Frame_Ins_p.218_219insQ|MED15_uc010gso.2_In_Frame_Ins_p.218_219insQ|MED15_uc002zsr.2_In_Frame_Ins_p.192_193insQ|MED15_uc011ahs.1_In_Frame_Ins_p.192_193insQ|MED15_uc011aht.1_In_Frame_Ins_p.192_193insQ|MED15_uc002zss.2_In_Frame_Ins_p.137_138insQ|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 218_219 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) agcagcagctccagcagcagca 0.178 0.15 104 19 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CJM_SKIN NA CJM_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 37 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - CJM_SKIN NA CJM_SKIN NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.57 106 140 ALPK1 80216 broad.mit.edu 37 4 113352620 113352629 + Frame_Shift_Del DEL TTCATTGCAT - - rs13148353 byFrequency;by1000genomes CJM_SKIN NA CJM_SKIN NA g.chr4:113352620_113352629delTTCATTGCAT uc003iap.3 + 11 2196_2205 c.1917_1926delTTCATTGCAT c.(1915-1926)CATTCATTGCATfs p.H639fs ALPK1_uc003ian.3_Frame_Shift_Del_p.H639fs|ALPK1_uc011cfx.1_Frame_Shift_Del_p.H561fs|ALPK1_uc003iao.3_Intron|ALPK1_uc010imo.2_Frame_Shift_Del_p.H467fs NM_025144 NP_079420 Q96QP1 ALPK1_HUMAN alpha-kinase 1 639_642 ATP binding|protein serine/threonine kinase activity ovary(5) 5 Ovarian(17;0.0446)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.00325) GAGCTATGCATTCATTGCATTCACAGCTTC 0.490 0.25 109 37 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CJM_SKIN NA CJM_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.25 93 31 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CJM_SKIN NA CJM_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.43 40 30 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 CJM_SKIN NA CJM_SKIN NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.84 25 135 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CJM_SKIN NA CJM_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 MLL3 58508 broad.mit.edu 37 7 151875096 151875097 + Splice_Site INS - T T CJM_SKIN NA CJM_SKIN NA g.chr7:151875096_151875097insT uc003wla.2 - 38 7662 c.7443_splice c.e38-1 p.R2481_splice MLL3_uc003wkz.2_Splice_Site_p.R1542_splice|MLL3_uc003wky.2_Splice_Site NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) AAATCCAAATCTTTTaaaaaaa 0.332 0.53 21 24 TCEA1 6917 broad.mit.edu 37 8 54900712 54900712 + Frame_Shift_Del DEL T - - CJM_SKIN NA CJM_SKIN NA g.chr8:54900712delT uc003xru.2 - 5 751 c.428delA c.(427-429)AAGfs p.K143fs TCEA1_uc003xrv.2_Frame_Shift_Del_p.K122fs|TCEA1_uc011ldw.1_Intron|TCEA1_uc003xrw.1_RNA NM_006756 NP_006747 P23193 TCEA1_HUMAN transcription elongation factor A 1 isoform 1 143 TFIIS central. positive regulation of viral transcription|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction nucleoplasm DNA binding|translation elongation factor activity|zinc ion binding 0 Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181) OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699) CTCCCTACACTTCAACCGCAC 0.493 0.30 104 45 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 CJM_SKIN NA CJM_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.29 56 23 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CJM_SKIN NA CJM_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CJM_SKIN NA CJM_SKIN NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.75 220 666 PCDH15 65217 broad.mit.edu 37 10 55582178 55582204 + In_Frame_Del DEL CAGGAGGAGGAGCAAGAGGAGCAGGAG - - rs58461416 byFrequency;by1000genomes CJM_SKIN NA CJM_SKIN NA g.chr10:55582178_55582204delCAGGAGGAGGAGCAAGAGGAGCAGGAG uc001jju.1 - 33 5677_5703 c.5282_5308delCTCCTGCTCCTCTTGCTCCTCCTCCTG c.(5281-5310)GCTCCTGCTCCTCTTGCTCCTCCTCCTGAC>GAC p.APAPLAPPP1761del PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_In_Frame_Del_p.APAPLAPPP1758del|PCDH15_uc010qhw.1_In_Frame_Del_p.APAPLAPPP1721del|PCDH15_uc010qhx.1_In_Frame_Del_p.APAPLAPPP1692del|PCDH15_uc010qhy.1_In_Frame_Del_p.APAPLAPPP1768del|PCDH15_uc010qhz.1_In_Frame_Del_p.APAPLAPPP1763del|PCDH15_uc010qia.1_In_Frame_Del_p.APAPLAPPP1741del|PCDH15_uc010qib.1_In_Frame_Del_p.APAPLAPPP1738del NM_033056 NP_149045 Q96QU1 PCD15_HUMAN protocadherin 15 isoform CD1-4 precursor 1761_1769 Cytoplasmic (Potential). equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse calcium ion binding pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2) 13 Melanoma(3;0.117)|Lung SC(717;0.238) ggagaaatgtcaggaggaggagcaagaggagcaggagcaggaggagg 0.137 0.42 67 49 CSNK2A1P 283106 broad.mit.edu 37 11 11373701 11373701 + Frame_Shift_Del DEL G - - CJM_SKIN NA CJM_SKIN NA g.chr11:11373701delG uc001mjp.2 - 1 1204 c.966delC c.(964-966)CCCfs p.P322fs GALNTL4_uc001mjo.2_Intron NM_177559 NP_808227 casein kinase II alpha 1 subunit isoform a 0 TGTAGAAATAGGGGTGCTCCA 0.547 0.22 101 29 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CJM_SKIN NA CJM_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 95 15 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CJM_SKIN NA CJM_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.97 1 36 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CJM_SKIN NA CJM_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 38 295 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CJM_SKIN NA CJM_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 11 128 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.58 20 28 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 295 80 TTN 7273 broad.mit.edu 37 2 179436257 179436259 + In_Frame_Del DEL TTG - - rs72646898 CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr2:179436257_179436259delTTG uc010zfg.1 - 275 67120_67122 c.66896_66898delCAA c.(66895-66900)ACAATA>ATA p.T22299del uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.T15994del|TTN_uc010zfi.1_In_Frame_Del_p.T15927del|TTN_uc010zfj.1_In_Frame_Del_p.T15802del NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 23226 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CAAGCCTTTATTGTTGTCCTTGC 0.404 0.67 52 107 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.36 9 5 BMP2K 55589 broad.mit.edu 37 4 79792119 79792136 + In_Frame_Del DEL CAGCAGCAGCAACAGCAA - - CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr4:79792119_79792136delCAGCAGCAGCAACAGCAA uc003hlk.2 + 11 1580_1597 c.1414_1431delCAGCAGCAGCAACAGCAA c.(1414-1431)CAGCAGCAGCAACAGCAAdel p.QQQQQQ478del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQQQQ478del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 478_483 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 acagcaacagcagcagcagcaacagcaacagcagcagc 0.206 0.28 113 44 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.58 5 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 70 82 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.86 7 42 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.15 76 13 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.37 86 50 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.92 1 11 WHSC1L1 54904 broad.mit.edu 37 8 38133960 38133961 + Frame_Shift_Ins INS - TCTT TCTT CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr8:38133960_38133961insTCTT uc003xli.2 - 23 4443_4444 c.3925_3926insAAGA c.(3925-3927)AGAfs p.R1309fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R1298fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R1260fs|WHSC1L1_uc003xlh.2_Frame_Shift_Ins_p.R88fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 1309 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) GATCTTTCGTCTCTTCTGTTTT 0.411 0.83 25 123 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.55 9 11 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.36 115 64 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.46 13 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.62 65 106 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 50 130 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CL14_LARGE_INTESTINE NA CL14_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.79 8 30 POLA1 5422 broad.mit.edu 37 X 24861780 24861780 + Frame_Shift_Del DEL A - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chrX:24861780delA uc004dbl.2 + 34 4038 c.4015delA c.(4015-4017)AAAfs p.K1339fs NM_016937 NP_058633 P09884 DPOLA_HUMAN DNA-directed DNA polymerase alpha 1 1339 Potential. cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding ovary(2)|skin(1) 3 Clofarabine(DB00631)|Fludarabine(DB01073) 0.000 0.55 288 348 ARAF 369 broad.mit.edu 37 X 47426415 47426415 + Frame_Shift_Del DEL C - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chrX:47426415delC uc011mlq.1 + 9 891 c.758delC c.(757-759)ACCfs p.T253fs ARAF_uc011mln.1_RNA|ARAF_uc011mlo.1_Frame_Shift_Del_p.T119fs|ARAF_uc011mlp.1_Frame_Shift_Del_p.T253fs|ARAF_uc004dic.1_Frame_Shift_Del_p.T34fs NM_001654 NP_001645 P10398 ARAF_HUMAN v-raf murine sarcoma 3611 viral oncogene 253 intracellular signal transduction|negative regulation of apoptosis|positive regulation of peptidyl-serine phosphorylation ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity large_intestine(3)|lung(2)|ovary(1)|skin(1) 7 Adenosine triphosphate(DB00171) AGTGATGGAACCCCCCGGGGG 0.652 0.33 82 41 PORCN 64840 broad.mit.edu 37 X 48371078 48371078 + Frame_Shift_Del DEL C - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chrX:48371078delC uc010nie.1 + 6 815 c.657delC c.(655-657)ATCfs p.I219fs PORCN_uc004djr.1_Frame_Shift_Del_p.I219fs|PORCN_uc004djs.1_Frame_Shift_Del_p.I219fs|PORCN_uc004djt.1_Frame_Shift_Del_p.I148fs|PORCN_uc011mlx.1_Frame_Shift_Del_p.I148fs|PORCN_uc004dju.1_Frame_Shift_Del_p.I88fs|PORCN_uc004djv.1_Frame_Shift_Del_p.I219fs|PORCN_uc004djw.1_Frame_Shift_Del_p.I219fs NM_203475 NP_982301 Q9H237 PORCN_HUMAN porcupine isoform D 219 Helical; (Potential). Wnt receptor signaling pathway endoplasmic reticulum membrane|integral to membrane acyltransferase activity ovary(2)|central_nervous_system(1) 3 CGTACTTCATCCCCCTCAACG 0.662 0.43 303 226 TFE3 7030 broad.mit.edu 37 X 48887952 48887952 + Frame_Shift_Del DEL C - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chrX:48887952delC uc004dmb.3 - 10 1683 c.1445delG c.(1444-1446)GGAfs p.G482fs TFE3_uc004dmc.3_Frame_Shift_Del_p.G377fs NM_006521 NP_006512 P19532 TFE3_HUMAN transcription factor E3 482 humoral immune response|positive regulation of transcription from RNA polymerase II promoter cytoplasm|nucleus sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding ASPSCR1/TFE3(161)|PRCC/TFE3(25)|SFPQ/TFE3(6)|NONO/TFE3(2)|CLTC/TFE3(2) soft_tissue(120)|kidney(76)|central_nervous_system(1) 197 CTGGGCAGGTCCCCCCCCTAC 0.647 0.33 12 6 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.20 108 27 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 4 69 TNFRSF4 7293 broad.mit.edu 37 1 1147320 1147321 + Splice_Site INS - C C CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr1:1147320_1147321insC uc001ade.2 - 5 639 c.634_splice c.e5+1 p.G212_splice TNFRSF4_uc001adf.2_Splice_Site_p.G216_splice NM_003327 NP_003318 P43489 TNR4_HUMAN tumor necrosis factor receptor superfamily, immune response|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|positive regulation of B cell proliferation|positive regulation of immunoglobulin secretion|T cell proliferation integral to plasma membrane tumor necrosis factor receptor activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199) 0.000 0.34 161 83 LRRC7 57554 broad.mit.edu 37 1 70460251 70460252 + Frame_Shift_Ins INS - A A CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr1:70460251_70460252insA uc001dep.2 + 9 855_856 c.825_826insA c.(823-828)TTGAAAfs p.L275fs LRRC7_uc009wbg.2_5'UTR NM_020794 NP_065845 Q96NW7 LRRC7_HUMAN leucine rich repeat containing 7 275_276 centrosome|focal adhesion|nucleolus protein binding ovary(9)|breast(2)|central_nervous_system(2)|liver(1) 14 0.000 0.38 381 230 INSRR 3645 broad.mit.edu 37 1 156810756 156810757 + Frame_Shift_Ins INS - C C CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr1:156810756_156810757insC uc010pht.1 - 22 4056_4057 c.3802_3803insG c.(3802-3804)GCCfs p.A1268fs NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron NM_014215 NP_055030 P14616 INSRR_HUMAN insulin receptor-related receptor precursor 1268 Cytoplasmic (Potential). protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity lung(11)|ovary(5)|skin(2)|kidney(1)|central_nervous_system(1) 20 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) GGAGCCCCGGGCCCCCCGGCAT 0.639 0.23 23 7 CDC42BPA 8476 broad.mit.edu 37 1 227182597 227182597 + Frame_Shift_Del DEL G - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr1:227182597delG uc001hqr.2 - 35 5898 c.4955delC c.(4954-4956)CCGfs p.P1652fs CDC42BPA_uc001hqq.2_Frame_Shift_Del_p.P951fs|CDC42BPA_uc001hqs.2_Frame_Shift_Del_p.P1571fs|CDC42BPA_uc009xes.2_Frame_Shift_Del_p.P1624fs|CDC42BPA_uc010pvs.1_Frame_Shift_Del_p.P1632fs|CDC42BPA_uc001hqp.2_Frame_Shift_Del_p.P870fs NM_003607 NP_003598 Q5VT25 MRCKA_HUMAN CDC42-binding protein kinase alpha isoform B 1665 actin cytoskeleton reorganization|intracellular signal transduction cell leading edge|cell-cell junction|cytoplasm ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1) 11 all_cancers(173;0.156)|Prostate(94;0.0792) GCCCTCTGACGGGGAGGGCAT 0.587 0.29 60 24 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.33 14 7 TGFBR2 7048 broad.mit.edu 37 3 30691807 30691807 + Frame_Shift_Del DEL C - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr3:30691807delC uc003ceo.2 + 3 691 c.309delC c.(307-309)GACfs p.D103fs TGFBR2_uc003cen.2_Frame_Shift_Del_p.D128fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 103 Extracellular (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 TTTGCCATGACCCCAAGCTCC 0.433 0.38 45 27 TGFBR2 7048 broad.mit.edu 37 3 30691872 30691873 + Frame_Shift_Del DEL AA - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr3:30691872_30691873delAA uc003ceo.2 + 3 756_757 c.374_375delAA c.(373-375)GAAfs p.E125fs TGFBR2_uc003cen.2_Frame_Shift_Del_p.E150fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 125 Extracellular (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 ATTATGAAGGAAAAAAAAAAGC 0.426 0.51 52 55 PXK 54899 broad.mit.edu 37 3 58389621 58389621 + Frame_Shift_Del DEL A - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr3:58389621delA uc003djz.1 + 13 1313 c.1214delA c.(1213-1215)GAAfs p.E405fs PXK_uc003djx.1_Frame_Shift_Del_p.E405fs|PXK_uc003djy.1_Frame_Shift_Del_p.E388fs|PXK_uc003dka.1_Frame_Shift_Del_p.E405fs|PXK_uc003dkb.1_Frame_Shift_Del_p.E322fs|PXK_uc003dkc.1_Frame_Shift_Del_p.E388fs|PXK_uc011bfe.1_Frame_Shift_Del_p.E372fs|PXK_uc010hnj.1_Frame_Shift_Del_p.E372fs|PXK_uc003dkd.1_Frame_Shift_Del_p.E268fs|PXK_uc010hnk.1_Frame_Shift_Del_p.E179fs NM_017771 NP_060241 Q7Z7A4 PXK_HUMAN PX domain containing serine/threonine kinase 405 Protein kinase. cell communication|inflammatory response|negative regulation of ATPase activity|negative regulation of ion transport|regulation of synaptic transmission centrosome|cytoplasm|nucleus|plasma membrane actin binding|ATP binding|phosphatidylinositol binding|phosphatidylinositol binding|protein C-terminus binding|protein kinase activity ovary(1) 1 BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22) ACCACTTCTGAAAAACCACAG 0.318 0.45 48 39 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.23 27 8 KALRN 8997 broad.mit.edu 37 3 124103865 124103866 + Frame_Shift_Ins INS - CA CA CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr3:124103865_124103866insCA uc003ehg.2 + 11 2065_2066 c.1938_1939insCA c.(1936-1941)TTCCACfs p.F646fs KALRN_uc010hrv.1_Frame_Shift_Ins_p.F646fs|KALRN_uc003ehf.1_Frame_Shift_Ins_p.F646fs|KALRN_uc011bjy.1_Frame_Shift_Ins_p.F646fs|KALRN_uc003ehh.1_Frame_Shift_Ins_p.F5fs NM_001024660 NP_001019831 O60229 KALRN_HUMAN kalirin, RhoGEF kinase isoform 1 646_647 apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport actin cytoskeleton|cytosol ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1) 6 CTGTTTCCTTCCACACACACAC 0.564 0.43 32 24 LPP 4026 broad.mit.edu 37 3 188202394 188202394 + Frame_Shift_Del DEL C - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr3:188202394delC uc003frs.1 + 4 454 c.208delC c.(208-210)CCCfs p.P70fs LPP_uc011bsg.1_Frame_Shift_Del_p.P70fs|LPP_uc011bsi.1_Frame_Shift_Del_p.P70fs|LPP_uc003frt.2_Frame_Shift_Del_p.P70fs NM_005578 NP_005569 Q93052 LPP_HUMAN LIM domain containing preferred translocation 70 Pro-rich. cell adhesion cytoplasm|focal adhesion|nucleus protein binding|zinc ion binding HMGA2/LPP(161) soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1) 165 all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088) all_lung(153;0.00139)|Lung NSC(153;0.00202) GBM - Glioblastoma multiforme(93;0.00602) TTTTCTTCCACCCCCACCTCC 0.408 0.42 72 53 N4BP2 55728 broad.mit.edu 37 4 40144449 40144449 + Frame_Shift_Del DEL A - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr4:40144449delA uc003guy.3 + 15 5280 c.4942delA c.(4942-4944)AAAfs p.K1648fs N4BP2_uc010ifq.2_Frame_Shift_Del_p.K1568fs|N4BP2_uc010ifr.2_Frame_Shift_Del_p.K1551fs NM_018177 NP_060647 Q86UW6 N4BP2_HUMAN Nedd4 binding protein 2 1648 cytoplasm ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding lung(3)|breast(2)|kidney(2)|ovary(1) 8 TCGGATAGGGAAAAAAAATGT 0.398 0.52 37 40 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 111 176 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 32 20 APC 324 broad.mit.edu 37 5 112175951 112175952 + Frame_Shift_Ins INS - A A CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr5:112175951_112175952insA uc010jby.2 + 16 5040_5041 c.4660_4661insA c.(4660-4662)GAAfs p.E1554fs APC_uc011cvt.1_Frame_Shift_Ins_p.E1536fs|APC_uc003kpz.3_Frame_Shift_Ins_p.E1554fs|APC_uc003kpy.3_Frame_Shift_Ins_p.E1554fs|APC_uc010jbz.2_Frame_Shift_Ins_p.E1271fs|APC_uc010jca.2_Frame_Shift_Ins_p.E854fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1554 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.T1556fs*3(35)|p.E1554fs*5(2)|p.E1554*(2)|p.?(1)|p.T1556fs*9(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1554fs*11(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GAAAGAGGCAGAAAAAACTATT 0.342 0.40 6 4 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.40 6 4 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.33 29 14 TTK 7272 broad.mit.edu 37 6 80720629 80720630 + Frame_Shift_Ins INS - A A CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr6:80720629_80720630insA uc003pjc.2 + 5 642_643 c.568_569insA c.(568-570)CAAfs p.Q190fs TTK_uc003pjb.3_Frame_Shift_Ins_p.Q190fs NM_003318 NP_003309 P33981 TTK_HUMAN TTK protein kinase 190 mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation spindle ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1) 11 all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2) BRCA - Breast invasive adenocarcinoma(397;0.0321) 0.000 0.52 259 279 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.83 3 15 NOS3 4846 broad.mit.edu 37 7 150698398 150698398 + Frame_Shift_Del DEL G - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr7:150698398delG uc003wif.2 + 11 1609 c.1313delG c.(1312-1314)AGGfs p.R438fs NOS3_uc011kuy.1_Frame_Shift_Del_p.R232fs|NOS3_uc011kuz.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kva.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kvb.1_Frame_Shift_Del_p.R438fs NM_000603 NP_000594 P29474 NOS3_HUMAN nitric oxide synthase 3 isoform 1 438 Interaction with NOSIP. anti-apoptosis|arginine catabolic process|blood vessel remodeling|endothelial cell migration|mitochondrion organization|negative regulation of muscle hyperplasia|negative regulation of platelet activation|nitric oxide biosynthetic process|platelet activation|positive regulation of angiogenesis|positive regulation of guanylate cyclase activity|positive regulation of vasodilation|regulation of blood vessel size|regulation of nitric-oxide synthase activity|regulation of systemic arterial blood pressure by endothelin|response to fluid shear stress|response to heat|smooth muscle hyperplasia caveola|cytoskeleton|cytosol|Golgi membrane actin monomer binding|arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding central_nervous_system(5)|large_intestine(2)|skin(1) 8 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) L-Arginine(DB00125)|L-Citrulline(DB00155)|Rosuvastatin(DB01098)|Tetrahydrobiopterin(DB00360) CAGAAGGCCAGGGGGGGCTGC 0.617 0.37 32 19 STAR 6770 broad.mit.edu 37 8 38006212 38006212 + Frame_Shift_Del DEL C - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr8:38006212delC uc003xkv.1 - 2 389 c.125delG c.(124-126)GGCfs p.G42fs STAR_uc010lwc.1_Intron NM_001007243 NP_001007244 P49675 STAR_HUMAN steroidogenic acute regulatory protein isoform 42 C21-steroid hormone biosynthetic process mitochondrial intermembrane space cholesterol transporter activity ovary(1) 1 Colorectal(12;0.000442) all_lung(54;0.0151)|Lung NSC(58;0.0295) READ - Rectum adenocarcinoma(644;0.188) AGGGGTGGGGCCCCCCAGGGC 0.587 0.44 96 76 SULF1 23213 broad.mit.edu 37 8 70488249 70488249 + Frame_Shift_Del DEL G - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr8:70488249delG uc010lza.1 + 6 934 c.217delG c.(217-219)GGGfs p.G73fs SULF1_uc003xyd.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xye.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xyf.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xyg.2_Frame_Shift_Del_p.G73fs NM_015170 NP_055985 Q8IWU6 SULF1_HUMAN sulfatase 1 precursor 73 apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway cell surface|endoplasmic reticulum|extracellular space|Golgi stack arylsulfatase activity|calcium ion binding central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1) 7 Breast(64;0.0654) Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534) TATGGAACATGGGGGGGCCAC 0.493 0.45 52 42 TG 7038 broad.mit.edu 37 8 133975283 133975283 + Frame_Shift_Del DEL G - - rs2069561 byFrequency;by1000genomes CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr8:133975283delG uc003ytw.2 + 29 5553 c.5512delG c.(5512-5514)GACfs p.D1838fs TG_uc010mdw.2_Frame_Shift_Del_p.D597fs|TG_uc011ljb.1_Frame_Shift_Del_p.D207fs|TG_uc011ljc.1_5'Flank|TG_uc010mdx.1_RNA NM_003235 NP_003226 P01266 THYG_HUMAN thyroglobulin precursor 1838 Type IIIB. hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation extracellular space hormone activity ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1) 15 Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155) Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735) BRCA - Breast invasive adenocarcinoma(115;0.000701) KIRC - Kidney renal clear cell carcinoma(542;0.0546) ATGTAGAAAAGACACAGTGCC 0.488 0.49 40 38 WNK2 65268 broad.mit.edu 37 9 96051831 96051831 + Frame_Shift_Del DEL G - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr9:96051831delG uc004ati.1 + 20 4906 c.4906delG c.(4906-4908)GGGfs p.G1636fs WNK2_uc011lud.1_Frame_Shift_Del_p.G1599fs|WNK2_uc004atj.2_Frame_Shift_Del_p.G1599fs|WNK2_uc004atk.2_Frame_Shift_Del_p.G1236fs|WNK2_uc004atl.1_Frame_Shift_Del_p.G194fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 1636 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 AGAGGTCTGCGGGGGGGACCT 0.687 0.43 21 16 TSC1 7248 broad.mit.edu 37 9 135781157 135781157 + Frame_Shift_Del DEL G - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr9:135781157delG uc004cca.2 - 15 2042 c.1808delC c.(1807-1809)CCGfs p.P603fs TSC1_uc004ccb.3_Frame_Shift_Del_p.P602fs|TSC1_uc011mcq.1_Frame_Shift_Del_p.P552fs|TSC1_uc011mcr.1_Intron NM_000368 NP_000359 Q92574 TSC1_HUMAN tuberous sclerosis 1 protein isoform 1 603 activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus cell cortex|lamellipodium|membrane|TSC1-TSC2 complex chaperone binding|protein N-terminus binding p.?(1) lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1) 14 OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06) ATGATCATACGGGGGAGGCTG 0.488 0.38 88 53 NUP98 4928 broad.mit.edu 37 11 3765751 3765751 + Frame_Shift_Del DEL G - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr11:3765751delG uc001lyh.2 - 12 1687 c.1396delC c.(1396-1398)CAGfs p.Q466fs NUP98_uc001lyi.2_Frame_Shift_Del_p.Q466fs|NUP98_uc001lyj.1_Frame_Shift_Del_p.Q466fs|NUP98_uc001lyk.1_Frame_Shift_Del_p.Q483fs NM_016320 NP_057404 P52948 NUP98_HUMAN nucleoporin 98kD isoform 1 483 carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex protein binding|structural constituent of nuclear pore|transporter activity breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1) 12 Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227) BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199) 0.000 0.48 197 182 RELA 5970 broad.mit.edu 37 11 65421971 65421972 + Frame_Shift_Ins INS - G G CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr11:65421971_65421972insG uc001ofg.2 - 11 1673_1674 c.1533_1534insC c.(1531-1536)CCCGACfs p.P511fs RELA_uc001ofh.2_Frame_Shift_Ins_p.P508fs|RELA_uc010ron.1_Frame_Shift_Ins_p.P522fs|RELA_uc009yqr.2_Frame_Shift_Ins_p.P458fs|RELA_uc001ofe.2_3'UTR|RELA_uc001off.2_Frame_Shift_Ins_p.P408fs NM_021975 NP_068810 Q04206 TF65_HUMAN v-rel reticuloendotheliosis viral oncogene 511_512 anti-apoptosis|cellular defense response|cytokine-mediated signaling pathway|defense response to virus|inflammatory response|innate immune response|interspecies interaction between organisms|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription, DNA-dependent|nerve growth factor receptor signaling pathway|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of inflammatory response|response to interleukin-1|response to UV-B|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|transcription factor complex activating transcription factor binding|chromatin binding|identical protein binding|NF-kappaB binding|phosphate binding|protein kinase binding|protein N-terminus binding|repressing transcription factor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|ubiquitin protein ligase binding lung(3)|ovary(1) 4 GGAGCTGGGTCGGGGGGCCTCT 0.624 0.33 61 30 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 886 289 PCSK7 9159 broad.mit.edu 37 11 117079625 117079626 + Frame_Shift_Ins INS - G G rs145981335 by1000genomes CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr11:117079625_117079626insG uc001pqr.2 - 13 1879_1880 c.1678_1679insC c.(1678-1680)CGCfs p.R560fs PCSK7_uc001pqs.1_5'Flank NM_004716 NP_004707 Q16549 PCSK7_HUMAN proprotein convertase subtilisin/kexin type 7 560 Homo B/P.|Extracellular (Potential). peptide hormone processing integral to Golgi membrane serine-type endopeptidase activity 0 all_hematologic(175;0.0487) Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234) BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537) GTCCATGCTGCGGGGGGCGCCG 0.594 0.25 213 72 ETV6 2120 broad.mit.edu 37 12 12038958 12038964 + Splice_Site DEL CAGGTAG - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr12:12038958_12038964delCAGGTAG uc001qzz.2 + 7 1527 c.1253_splice c.e7+1 p.R418_splice ETV6_uc001raa.1_Intron NM_001987 NP_001978 P41212 ETV6_HUMAN ets variant 6 cytoplasm|nucleolus protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity p.?(1) ETV6/NTRK3(234)|ETV6/JAK2(11) soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1) 250 all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36) GGCTTTTGTTCAGGTAGCACTTCCTTT 0.444 0.27 37 14 GLI1 2735 broad.mit.edu 37 12 57860075 57860075 + Frame_Shift_Del DEL G - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr12:57860075delG uc001snx.2 + 8 893 c.815delG c.(814-816)TGGfs p.W272fs GLI1_uc009zpq.2_Frame_Shift_Del_p.W144fs NM_005269 NP_005260 P08151 GLI1_HUMAN GLI family zinc finger 1 isoform 1 272 C2H2-type 2. epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter cytosol|nucleus transcription regulatory region DNA binding|zinc ion binding skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1) 15 GBM - Glioblastoma multiforme(3;3.99e-32) GTGTGCCACTGGGGGGGCTGC 0.597 0.46 333 285 DLL4 54567 broad.mit.edu 37 15 41224557 41224557 + Frame_Shift_Del DEL C - - rs76686366 by1000genomes CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr15:41224557delC uc001zng.1 + 6 1082 c.762delC c.(760-762)ATCfs p.I254fs NM_019074 NP_061947 Q9NR61 DLL4_HUMAN delta-like 4 protein precursor 254 EGF-like 2.|Extracellular (Potential). blood circulation|cell communication|cell differentiation|Notch receptor processing|Notch signaling pathway integral to membrane|plasma membrane calcium ion binding|Notch binding breast(2) 2 all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946) GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164) ACGAATGCATCCCCCACAATG 0.627 0.50 52 53 TP53BP1 7158 broad.mit.edu 37 15 43749408 43749408 + Frame_Shift_Del DEL A - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr15:43749408delA uc001zrs.2 - 12 1531 c.1383delT c.(1381-1383)TTTfs p.F461fs TP53BP1_uc010udp.1_Frame_Shift_Del_p.F461fs|TP53BP1_uc001zrq.3_Frame_Shift_Del_p.F466fs|TP53BP1_uc001zrr.3_Frame_Shift_Del_p.F466fs|TP53BP1_uc010udq.1_Frame_Shift_Del_p.F466fs NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 461 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) GGGAAGGAATAAAAATGTCCT 0.308 0.36 35 20 UNC13C 440279 broad.mit.edu 37 15 54626040 54626040 + Frame_Shift_Del DEL T - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr15:54626040delT uc002ack.2 + 14 4570 c.4570delT c.(4570-4572)TTTfs p.F1524fs UNC13C_uc002acl.2_Frame_Shift_Del_p.F354fs NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 1524 exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) AAGTATCACCTTTTTTAGGAT 0.368 0.47 47 42 CYP1A2 1544 broad.mit.edu 37 15 75047263 75047289 + In_Frame_Del DEL TCCTGGCCAAGTGGGAGATCTTCCTCT - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr15:75047263_75047289delTCCTGGCCAAGTGGGAGATCTTCCTCT uc002ayr.1 + 7 1449_1475 c.1385_1411delTCCTGGCCAAGTGGGAGATCTTCCTCT c.(1384-1413)GTCCTGGCCAAGTGGGAGATCTTCCTCTTC>GTC p.LAKWEIFLF463del NM_000761 NP_000752 P05177 CP1A2_HUMAN cytochrome P450, family 1, subfamily A, 463_471 alkaloid metabolic process|exogenous drug catabolic process|methylation|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative deethylation|oxidative demethylation|steroid catabolic process|toxin biosynthetic process|xenobiotic metabolic process endoplasmic reticulum membrane|microsome aromatase activity|caffeine oxidase activity|demethylase activity|electron carrier activity|enzyme binding|heme binding|oxygen binding ovary(3)|breast(1) 4 Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Aciclovir(DB00787)|Alosetron(DB00969)|Aminophenazone(DB01424)|Amitriptyline(DB00321)|Anagrelide(DB00261)|Azelastine(DB00972)|Bortezomib(DB00188)|Caffeine(DB00201)|Carmustine(DB00262)|Chlordiazepoxide(DB00475)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Ciprofloxacin(DB00537)|Clomipramine(DB01242)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Desloratadine(DB00967)|Diazepam(DB00829)|Dibucaine(DB00527)|Diclofenac(DB00586)|Duloxetine(DB00476)|Enoxacin(DB00467)|Esomeprazole(DB00736)|Estradiol(DB00783)|Estrone(DB00655)|Fluorouracil(DB00544)|Flutamide(DB00499)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Grepafloxacin(DB00365)|Haloperidol(DB00502)|Hesperetin(DB01094)|Imipramine(DB00458)|Ketoconazole(DB01026)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Melatonin(DB01065)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mirtazapine(DB00370)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pefloxacin(DB00487)|Pimozide(DB01100)|Propafenone(DB01182)|Propranolol(DB00571)|Quinidine(DB00908)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifampin(DB01045)|Riluzole(DB00740)|Rofecoxib(DB00533)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Tacrine(DB00382)|Telithromycin(DB00976)|Terfenadine(DB00342)|Theophylline(DB00277)|Thiabendazole(DB00730)|Tizanidine(DB00697)|Tolbutamide(DB01124)|Verapamil(DB00661)|Warfarin(DB00682)|Zileuton(DB00744)|Zolmitriptan(DB00315) ATCGGGGAAGTCCTGGCCAAGTGGGAGATCTTCCTCTTCCTGGCCAT 0.604 0.13 326 48 FES 2242 broad.mit.edu 37 15 91436591 91436591 + Frame_Shift_Del DEL G - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr15:91436591delG uc002bpv.2 + 16 2088 c.1992delG c.(1990-1992)GTGfs p.V664fs FES_uc010uqj.1_Frame_Shift_Del_p.V536fs|FES_uc010uqk.1_Frame_Shift_Del_p.V646fs|FES_uc002bpw.2_RNA|FES_uc010bny.2_Frame_Shift_Del_p.V523fs|FES_uc002bpx.2_Frame_Shift_Del_p.V594fs|FES_uc002bpy.2_Frame_Shift_Del_p.V606fs NM_002005 NP_001996 P07332 FES_HUMAN feline sarcoma oncogene isoform 1 664 Protein kinase. axon guidance|cell proliferation|peptidyl-tyrosine phosphorylation cytosol ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(2) 2 Lung NSC(78;0.0771)|all_lung(78;0.137) Lung(145;0.229) TGCAGATGGTGGGGGATGCAG 0.682 0.30 124 52 CREBBP 1387 broad.mit.edu 37 16 3817720 3817721 + Splice_Site INS - T T CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr16:3817720_3817721insT uc002cvv.2 - 16 3454 c.3250_splice c.e16+1 p.I1084_splice CREBBP_uc002cvw.2_Splice_Site_p.I1046_splice NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) AAATGGCCTACTTTTTTTGCGC 0.401 0.48 82 77 IL21R 50615 broad.mit.edu 37 16 27460529 27460530 + Frame_Shift_Ins INS - C C CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr16:27460529_27460530insC uc002doq.1 + 9 1775_1776 c.1542_1543insC c.(1540-1545)GGACCCfs p.G514fs IL21R_uc002dor.1_Frame_Shift_Ins_p.G514fs|IL21R_uc002dos.1_Frame_Shift_Ins_p.G514fs|uc002dot.2_RNA NM_181078 NP_851564 Q9HBE5 IL21R_HUMAN interleukin 21 receptor precursor 514_515 Cytoplasmic (Potential). natural killer cell activation integral to membrane interleukin-21 receptor activity ovary(2)|lung(1)|breast(1) 4 GGGACGAAGGACCCCCCCGGAG 0.639 0.38 131 81 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 48 689 TP53 7157 broad.mit.edu 37 17 7572963 7572963 + Frame_Shift_Del DEL T - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr17:7572963delT uc002gim.2 - 11 1340 c.1146delA c.(1144-1146)AAAfs p.K382fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Intron|TP53_uc010cne.1_RNA|TP53_uc010cnf.1_3'UTR|TP53_uc010cng.1_3'UTR|TP53_uc002gii.1_Frame_Shift_Del_p.K250fs|TP53_uc010cnh.1_3'UTR|TP53_uc010cni.1_3'UTR|TP53_uc002gij.2_Frame_Shift_Del_p.K382fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 382 Basic (repression of DNA-binding).|Interaction with CARM1. K->R: Abolishes monomethylation by SETD8.|K->A: Abolishes acetylation by CREBBP. activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.K382fs*40(3)|p.K382fs*13(2)|p.?(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.54 333 389 MAP2K4 6416 broad.mit.edu 37 17 11924240 11924240 + Frame_Shift_Del DEL G - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr17:11924240delG uc002gnj.2 + 1 106 c.37delG c.(37-39)GGGfs p.G13fs MAP2K4_uc002gnk.2_Frame_Shift_Del_p.G13fs NM_003010 NP_003001 P45985 MP2K4_HUMAN mitogen-activated protein kinase kinase 4 13 Gly/Ser-rich. cellular response to mechanical stimulus|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|JUN kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity p.0?(10)|p.?(1) large_intestine(14)|breast(12)|lung(8)|ovary(8)|pancreas(8)|stomach(2)|central_nervous_system(1)|biliary_tract(1)|testis(1)|endometrium(1)|urinary_tract(1)|skin(1) 58 all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163) Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681) 0.000 0.44 73 58 TAF15 8148 broad.mit.edu 37 17 34165493 34165493 + Frame_Shift_Del DEL G - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr17:34165493delG uc002hkd.2 + 11 935 c.849delG c.(847-849)AAGfs p.K283fs TAF15_uc010ctw.1_RNA|TAF15_uc002hkc.2_Frame_Shift_Del_p.K280fs NM_139215 NP_631961 Q92804 RBP56_HUMAN TBP-associated factor 15 isoform 1 283 RRM. positive regulation of transcription, DNA-dependent cytoplasm|nucleus DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding TAF15/NR4A3(33) bone(33)|lung(1)|skin(1) 35 Ovarian(249;0.17) UCEC - Uterine corpus endometrioid carcinoma (308;0.0193) GAAAGCCAAAGGGGGAGGCAA 0.418 0.32 28 13 VEZF1 7716 broad.mit.edu 37 17 56056605 56056610 + In_Frame_Del DEL TGCTGC - - rs61731354;rs73995411;rs145983359 byFrequency;by1000genomes;byFrequency CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr17:56056605_56056610delTGCTGC uc002ivf.1 - 5 1184_1189 c.1041_1046delGCAGCA c.(1039-1047)CAGCAGCAA>CAA p.347_349QQQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.197_199QQQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 347_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgctgct 0.311 0.45 18 15 TRIM37 4591 broad.mit.edu 37 17 57140004 57140004 + Frame_Shift_Del DEL A - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr17:57140004delA uc002iwy.3 - 11 1310 c.866delT c.(865-867)TTGfs p.L289fs TRIM37_uc002iwz.3_Frame_Shift_Del_p.L289fs|TRIM37_uc002ixa.3_Frame_Shift_Del_p.L167fs|TRIM37_uc010woc.1_Frame_Shift_Del_p.L255fs NM_001005207 NP_001005207 O94972 TRI37_HUMAN tripartite motif-containing 37 protein 289 MATH. perinuclear region of cytoplasm|peroxisome ligase activity|protein binding|zinc ion binding lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1) 7 Medulloblastoma(34;0.0922)|all_neural(34;0.101) TCTCTGACGCAAAGTGCTAAC 0.373 0.61 7 11 LAMA1 284217 broad.mit.edu 37 18 7034575 7034575 + Frame_Shift_Del DEL T - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr18:7034575delT uc002knm.2 - 14 2048 c.1954delA c.(1954-1956)AGGfs p.R652fs LAMA1_uc010wzj.1_Frame_Shift_Del_p.R128fs NM_005559 NP_005550 P25391 LAMA1_HUMAN laminin, alpha 1 precursor 652 Laminin IV type A 1. axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development extracellular space|laminin-1 complex|laminin-3 complex extracellular matrix structural constituent|receptor binding ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1) 21 Colorectal(10;0.172) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) TCAATCTGCCTTTTGCTGTGA 0.433 0.54 101 118 ATP8B1 5205 broad.mit.edu 37 18 55329760 55329760 + Frame_Shift_Del DEL A - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr18:55329760delA uc002lgw.2 - 20 2373 c.2373delT c.(2371-2373)TTTfs p.F791fs uc002lgu.1_Intron|uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 791 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) CACCGGGTGGAAAAAAAGATT 0.443 0.59 30 44 ATP8B1 5205 broad.mit.edu 37 18 55365039 55365040 + Frame_Shift_Ins INS - T T CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr18:55365039_55365040insT uc002lgw.2 - 6 614_615 c.614_615insA c.(613-615)AATfs p.N205fs uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 205 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) 0.000 0.48 31 29 PIP5K1C 23396 broad.mit.edu 37 19 3653520 3653520 + Frame_Shift_Del DEL C - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr19:3653520delC uc002lyj.1 - 7 746 c.689delG c.(688-690)GGCfs p.G230fs PIP5K1C_uc010xhq.1_Frame_Shift_Del_p.G230fs|PIP5K1C_uc010xhr.1_Frame_Shift_Del_p.G230fs NM_012398 NP_036530 O60331 PI51C_HUMAN phosphatidylinositol-4-phosphate 5-kinase, type 230 PIPK. axon guidance cytosol|plasma membrane 1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding stomach(2)|skin(2) 4 Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183) GATGTTCTTGCCCCCCGACTG 0.632 0.34 135 71 MAST3 23031 broad.mit.edu 37 19 18260077 18260077 + Frame_Shift_Del DEL C - - CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr19:18260077delC uc002nhz.3 + 27 3471 c.3471delC c.(3469-3471)CGCfs p.R1157fs NM_015016 NP_055831 O60307 MAST3_HUMAN microtubule associated serine/threonine kinase 1157 ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity large_intestine(2)|ovary(2)|stomach(1) 5 GCCACACCCGCCCCAGCTCCC 0.622 0.43 16 12 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 107 80 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 191 477 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 107 ZNRF3 84133 broad.mit.edu 37 22 29445818 29445819 + In_Frame_Ins INS - CAG CAG CL34_LARGE_INTESTINE NA CL34_LARGE_INTESTINE NA g.chr22:29445818_29445819insCAG uc003aeg.2 + 8 1514_1515 c.1349_1350insCAG c.(1348-1350)GAC>GACAGC p.457_458insS ZNRF3_uc003aeh.1_In_Frame_Ins_p.457_458insS NM_032173 NP_115549 Q9ULT6 ZNRF3_HUMAN zinc and ring finger 3 557_558 Cytoplasmic (Potential). integral to membrane zinc ion binding ovary(1) 1 0.000 0.44 377 300 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.36 52 29 CSRNP1 64651 broad.mit.edu 37 3 39185095 39185096 + Frame_Shift_Ins INS - T T CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr3:39185095_39185096insT uc003cjg.2 - 5 1434_1435 c.1220_1221insA c.(1219-1221)GAGfs p.E407fs CSRNP1_uc003cjh.2_Frame_Shift_Ins_p.E407fs NM_033027 NP_149016 Q96S65 CSRN1_HUMAN AXIN1 up-regulated 1 407 apoptosis|positive regulation of transcription from RNA polymerase II promoter nucleus DNA binding|sequence-specific DNA binding transcription factor activity ovary(4)|skin(1) 5 0.000 0.83 4 19 PIK3CA 5290 broad.mit.edu 37 3 178916938 178916940 + In_Frame_Del DEL GAA - - CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr3:178916938_178916940delGAA uc003fjk.2 + 2 482_484 c.325_327delGAA c.(325-327)GAAdel p.E110del NM_006218 NP_006209 P42336 PK3CA_HUMAN phosphoinositide-3-kinase, catalytic, alpha 110 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity p.E109del(2)|p.G106_R108del(1)|p.E110K(1) breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1) 3553 all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155) OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282) AGGCAACCGTGAAGAAAAGATCC 0.340 0.45 12 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 33 43 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.92 5 55 APC 324 broad.mit.edu 37 5 112175686 112175686 + Frame_Shift_Del DEL T - - CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr5:112175686delT uc010jby.2 + 16 4775 c.4395delT c.(4393-4395)AGTfs p.S1465fs APC_uc011cvt.1_Frame_Shift_Del_p.S1447fs|APC_uc003kpz.3_Frame_Shift_Del_p.S1465fs|APC_uc003kpy.3_Frame_Shift_Del_p.S1465fs|APC_uc010jbz.2_Frame_Shift_Del_p.S1182fs|APC_uc010jca.2_Frame_Shift_Del_p.S765fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1465 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.S1465fs*3(64)|p.S1465fs*8(4)|p.?(1)|p.K1454fs*3(1)|p.K1192fs*3(1)|p.S1465fs*5(1)|p.S1465fs*4(1)|p.G1466fs*8(1)|p.S1465fs*9(1)|p.S1465R(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) AGAGAGAGAGTGGACCTAAGC 0.453 0.51 17 18 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.93 2 27 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 11 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.30 444 187 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 192 38 RAD51L1 5890 broad.mit.edu 37 14 68758642 68758659 + In_Frame_Del DEL CCTGGCTTCTCAGGCAGA - - CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr14:68758642_68758659delCCTGGCTTCTCAGGCAGA uc001xkf.1 + 8 862_879 c.798_815delCCTGGCTTCTCAGGCAGA c.(796-816)GCCCTGGCTTCTCAGGCAGAC>GCC p.LASQAD267del RAD51L1_uc001xkd.2_In_Frame_Del_p.LASQAD267del|RAD51L1_uc010aqr.2_In_Frame_Del_p.LASQAD148del|RAD51L1_uc001xke.2_In_Frame_Del_p.LASQAD267del|RAD51L1_uc010aqs.1_In_Frame_Del_p.LASQAD267del|RAD51L1_uc001xkg.1_In_Frame_Del_p.LASQAD267del NM_133509 NP_598193 O15315 RA51B_HUMAN RAD51-like 1 isoform 3 267_272 blood coagulation|DNA repair|reciprocal meiotic recombination nucleoplasm ATP binding|DNA binding|DNA-dependent ATPase activity 0 UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421) TGAGTGGAGCCCTGGCTTCTCAGGCAGACCTGGTGTCT 0.528 0.18 169 38 MAP2K7 5609 broad.mit.edu 37 19 7977066 7977068 + In_Frame_Del DEL ATA - - CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr19:7977066_7977068delATA uc002mit.2 + 10 1177_1179 c.1112_1114delATA c.(1111-1116)TATAAT>TAT p.N372del MAP2K7_uc002miv.2_In_Frame_Del_p.N379del|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_In_Frame_Del_p.N379del|MAP2K7_uc010dvv.2_In_Frame_Del_p.N247del NM_145185 NP_660186 O14733 MP2K7_HUMAN mitogen-activated protein kinase kinase 7 372 Protein kinase. activation of JUN kinase activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleus ATP binding|JUN kinase kinase activity|magnesium ion binding|protein binding|protein kinase binding|protein phosphatase binding|protein serine/threonine kinase activity|protein tyrosine kinase activity large_intestine(7)|central_nervous_system(2)|ovary(1)|lung(1) 11 Etoposide(DB00773) AGACCAAAGTATAATAAGCTACT 0.591 0.35 11 6 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.59 15 22 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 167 437 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CL40_LARGE_INTESTINE NA CL40_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.87 3 20 GATA1 2623 broad.mit.edu 37 X 48649520 48649521 + Frame_Shift_Del DEL GA - - CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:48649520_48649521delGA uc004dkq.3 + 2 95_96 c.4_5delGA c.(4-6)GAGfs p.E2fs NM_002049 NP_002040 P15976 GATA1_HUMAN GATA binding protein 1 2 basophil differentiation|eosinophil differentiation|erythrocyte development|megakaryocyte differentiation|platelet aggregation|platelet formation|positive regulation of anti-apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|regulation of glycoprotein biosynthetic process|transcription from RNA polymerase II promoter nuclear membrane|nucleolus|nucleoplasm C2H2 zinc finger domain binding|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding p.M1fs(7)|p.E2*(4)|p.E2fs*37(1)|p.E2fs*444(1)|p.E2G(1) haematopoietic_and_lymphoid_tissue(246)|lung(2) 248 AGGCTCCATGGAGTTCCCTGGC 0.530 0.95 2 35 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 4 71 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.46 579 488 LRP2 4036 broad.mit.edu 37 2 170063198 170063200 + In_Frame_Del DEL GTT - - CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:170063198_170063200delGTT uc002ues.2 - 39 7243_7245 c.7030_7032delAAC c.(7030-7032)AACdel p.N2344del NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 2344 EGF-like 9.|Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) CCAAGCAAGGGTTGTTGTTGACC 0.507 0.42 676 480 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.38 35 21 CCR5 1234 broad.mit.edu 37 3 46414729 46414729 + Frame_Shift_Del DEL C - - CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:46414729delC uc003cpo.3 + 3 458 c.336delC c.(334-336)TTCfs p.F112fs CCR5_uc010hjd.2_Frame_Shift_Del_p.F112fs NM_001100168 NP_001093638 P51681 CCR5_HUMAN chemokine (C-C motif) receptor 5 112 Helical; Name=3; (Potential). cell-cell signaling|cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|immune response|inflammatory response|initiation of viral infection endosome|external side of plasma membrane|integral to plasma membrane actin binding|C-C chemokine receptor activity|coreceptor activity|phosphatidylinositol phospholipase C activity lung(4)|upper_aerodigestive_tract(1)|central_nervous_system(1) 6 BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02) Maraviroc(DB04835) TTATAGGCTTCTTCTCTGGAA 0.488 0.25 682 223 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.44 46 36 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 173 38 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 41 30 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 222 415 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.50 6 6 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.97 1 38 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 73 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.10 256 29 SALL1 6299 broad.mit.edu 37 16 51175655 51175656 + In_Frame_Ins INS - GCT GCT rs113614842 CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:51175655_51175656insGCT uc010vgs.1 - 2 508_509 c.477_478insAGC c.(475-480)insAGC p.159_160insS SALL1_uc010vgr.1_In_Frame_Ins_p.62_63insS|SALL1_uc010cbv.2_Intron NM_002968 NP_002959 Q9NSC2 SALL1_HUMAN sal-like 1 isoform a 159_160 Poly-Gly. adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development chromocenter|cytoplasm|heterochromatin|nucleus beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding skin(5)|ovary(3) 8 all_cancers(37;0.0322) COAD - Colon adenocarcinoma(2;0.24) ccgccgccgccgctgctgctgc 0.460 0.27 33 12 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.14 49 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.44 288 222 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 179 655 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 12 189 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.65 16 30 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.59 7 10 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 24 11 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.81 3 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 86 144 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 14 39 APC 324 broad.mit.edu 37 5 112175951 112175952 + Frame_Shift_Ins INS - A A COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr5:112175951_112175952insA uc010jby.2 + 16 5040_5041 c.4660_4661insA c.(4660-4662)GAAfs p.E1554fs APC_uc011cvt.1_Frame_Shift_Ins_p.E1536fs|APC_uc003kpz.3_Frame_Shift_Ins_p.E1554fs|APC_uc003kpy.3_Frame_Shift_Ins_p.E1554fs|APC_uc010jbz.2_Frame_Shift_Ins_p.E1271fs|APC_uc010jca.2_Frame_Shift_Ins_p.E854fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1554 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.T1556fs*3(35)|p.E1554fs*5(2)|p.E1554*(2)|p.?(1)|p.T1556fs*9(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1554fs*11(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GAAAGAGGCAGAAAAAACTATT 0.342 0.80 2 8 ATXN1 6310 broad.mit.edu 37 6 16327907 16327909 + In_Frame_Del DEL TGA - - rs59310777 by1000genomes COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr6:16327907_16327909delTGA uc003nbt.2 - 8 1604_1606 c.633_635delTCA c.(631-636)CATCAG>CAG p.H211del ATXN1_uc010jpi.2_In_Frame_Del_p.H211del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 211 Poly-Gln. H -> HQ (in Ref. 1; CAA55793). cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgctgatgctgatgct 0.384 0.22 32 9 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.21 42 11 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 24 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.86 2 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 35 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 680 335 IRS2 8660 broad.mit.edu 37 13 110435294 110435302 + In_Frame_Del DEL GGCGGCGGT - - rs9583424 by1000genomes COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr13:110435294_110435302delGGCGGCGGT uc001vqv.2 - 1 3613_3621 c.3099_3107delACCGCCGCC c.(3097-3108)CCACCGCCGCCG>CCG p.1033_1036PPPP>P NM_003749 NP_003740 Q9Y4H2 IRS2_HUMAN insulin receptor substrate 2 1033_1036 Poly-Pro. fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus cytosol|plasma membrane insulin receptor binding|signal transducer activity large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|skin(1)|ovary(1)|kidney(1) 8 all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155) Breast(118;0.159) all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147) 0.000 0.51 185 194 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.58 16 22 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.47 92 82 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.24 22 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 30 167 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COLO201_LARGE_INTESTINE NA COLO201_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 5 47 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COLO320_LARGE_INTESTINE NA COLO320_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.85 5 29 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 COLO320_LARGE_INTESTINE NA COLO320_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 6 16 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 COLO320_LARGE_INTESTINE NA COLO320_LARGE_INTESTINE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.70 92 211 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency COLO320_LARGE_INTESTINE NA COLO320_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.33 598 289 BRCA2 675 broad.mit.edu 37 13 32914438 32914438 + Frame_Shift_Del DEL T - - rs80359550 COLO320_LARGE_INTESTINE NA COLO320_LARGE_INTESTINE NA g.chr13:32914438delT uc001uub.1 + 11 6173 c.5946delT c.(5944-5946)AGTfs p.S1982fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 1982 BRCA2 7. cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding p.S1982fs*22(1) ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) GCACAGCAAGTGGAAAATCTG 0.353 0.20 202 50 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C COLO320_LARGE_INTESTINE NA COLO320_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 20 170 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 COLO320_LARGE_INTESTINE NA COLO320_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.33 45 22 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COLO320_LARGE_INTESTINE NA COLO320_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 111 602 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COLO320_LARGE_INTESTINE NA COLO320_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 40 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 COLO668_LUNG NA COLO668_LUNG NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.53 16 18 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COLO668_LUNG NA COLO668_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 33 CLSPN 63967 broad.mit.edu 37 1 36202556 36202557 + Frame_Shift_Del DEL GA - - COLO668_LUNG NA COLO668_LUNG NA g.chr1:36202556_36202557delGA uc001bzi.2 - 24 3947_3948 c.3867_3868delTC c.(3865-3870)TCTCCTfs p.S1289fs CLSPN_uc009vux.2_Frame_Shift_Del_p.S1225fs NM_022111 NP_071394 Q9HAW4 CLSPN_HUMAN claspin 1289_1290 activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation nucleoplasm anaphase-promoting complex binding|DNA binding breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1) 8 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887) 0.000 0.38 352 218 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - COLO668_LUNG NA COLO668_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.12 135 18 LRP1B 53353 broad.mit.edu 37 2 141773434 141773434 + Frame_Shift_Del DEL C - - COLO668_LUNG NA COLO668_LUNG NA g.chr2:141773434delC uc002tvj.1 - 13 2993 c.2021delG c.(2020-2022)GGAfs p.G674fs LRP1B_uc010fnl.1_Intron NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 674 Extracellular (Potential).|LDL-receptor class B 7. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) CTCAATCCTTCCCACGCTGTC 0.413 0.29 52 21 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 COLO668_LUNG NA COLO668_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.32 13 6 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A COLO668_LUNG NA COLO668_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 46 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COLO668_LUNG NA COLO668_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.76 20 62 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - COLO668_LUNG NA COLO668_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.96 1 24 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 COLO668_LUNG NA COLO668_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.33 8 4 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency COLO668_LUNG NA COLO668_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.39 457 292 CSNK2A1P 283106 broad.mit.edu 37 11 11374466 11374468 + In_Frame_Del DEL AAC - - COLO668_LUNG NA COLO668_LUNG NA g.chr11:11374466_11374468delAAC uc001mjp.2 - 1 437_439 c.199_201delGTT c.(199-201)GTTdel p.V67del GALNTL4_uc001mjo.2_Intron NM_177559 NP_808227 casein kinase II alpha 1 subunit isoform a 0 TGAGAATTTTAACAACAACTTTT 0.365 0.32 32 15 RB1 5925 broad.mit.edu 37 13 48941701 48941701 + Frame_Shift_Del DEL G - - COLO668_LUNG NA COLO668_LUNG NA g.chr13:48941701delG uc001vcb.2 + 10 1177 c.1011delG c.(1009-1011)TTGfs p.L337fs RB1_uc010act.1_Frame_Shift_Del_p.L38fs NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 337 androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.?(6) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) GATTATTTTTGGATCATGATA 0.284 0.49 35 33 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 COLO668_LUNG NA COLO668_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.18 77 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COLO668_LUNG NA COLO668_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 245 636 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COLO668_LUNG NA COLO668_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 56 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COLO679_SKIN NA COLO679_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 4 56 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 COLO679_SKIN NA COLO679_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.18 55 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COLO679_SKIN NA COLO679_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 99 159 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 COLO679_SKIN NA COLO679_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 27 58 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes COLO679_SKIN NA COLO679_SKIN NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.33 8 4 DBN1 1627 broad.mit.edu 37 5 176885346 176885347 + Frame_Shift_Ins INS - G G COLO679_SKIN NA COLO679_SKIN NA g.chr5:176885346_176885347insG uc003mgy.2 - 12 1660_1661 c.1488_1489insC c.(1486-1491)CCCACGfs p.P496fs DBN1_uc011dga.1_Frame_Shift_Ins_p.P228fs|DBN1_uc003mgx.2_Frame_Shift_Ins_p.P498fs|DBN1_uc010jkn.1_Frame_Shift_Ins_p.P446fs|DBN1_uc003mgz.1_Frame_Shift_Ins_p.P479fs NM_004395 NP_004386 Q16643 DREB_HUMAN drebrin 1 isoform a 496_497 actin filament organization|regulation of dendrite development|regulation of neuronal synaptic plasticity actomyosin|cytoplasm|dendrite actin binding|profilin binding breast(3)|ovary(1)|lung(1)|skin(1) 6 all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025) all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GAGGGTGGCGTGGGGGCCCTGG 0.683 0.15 111 19 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC COLO679_SKIN NA COLO679_SKIN NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.19 65 15 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes COLO679_SKIN NA COLO679_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 2 18 KIAA1462 57608 broad.mit.edu 37 10 30316500 30316501 + In_Frame_Ins INS - CTG CTG COLO679_SKIN NA COLO679_SKIN NA g.chr10:30316500_30316501insCTG uc001iux.2 - 2 2635_2636 c.2576_2577insCAG c.(2575-2577)AGT>AGCAGT p.859_859S>SS KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_In_Frame_Ins_p.721_721S>SS|KIAA1462_uc009xle.1_In_Frame_Ins_p.859_859S>SS NM_020848 NP_065899 Q9P266 K1462_HUMAN hypothetical protein LOC57608 859 Ser-rich. ovary(4) 4 CACTCTCCTCActgctgctgct 0.460 0.50 5 5 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 COLO679_SKIN NA COLO679_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.38 805 492 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 COLO679_SKIN NA COLO679_SKIN NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.55 14 17 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 COLO679_SKIN NA COLO679_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 102 64 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COLO679_SKIN NA COLO679_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 55 363 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COLO679_SKIN NA COLO679_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 11 194 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.42 19 14 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 4 37 LOC642587 642587 broad.mit.edu 37 1 209605636 209605637 + In_Frame_Ins INS - AGC AGC rs146499758;rs3842530 by1000genomes COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr1:209605636_209605637insAGC uc009xcn.2 + 4 634_635 c.251_252insAGC c.(250-252)GTA>GTAGCA p.97_98insA NM_001104548 NP_001098018 hypothetical protein LOC642587 0 OV - Ovarian serous cystadenocarcinoma(81;0.0422) gccaccaccgTagcagcagcag 0.272 0.33 12 6 MYO3B 140469 broad.mit.edu 37 2 171400488 171400488 + Frame_Shift_Del DEL T - - COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr2:171400488delT uc002ufy.2 + 32 3866 c.3723delT c.(3721-3723)CCTfs p.P1241fs MYO3B_uc010fqb.1_3'UTR|MYO3B_uc002ufz.2_Frame_Shift_Del_p.P1214fs|MYO3B_uc002ufw.2_RNA|MYO3B_uc002ufx.2_RNA|MYO3B_uc002ugb.2_RNA NM_138995 NP_620482 Q8WXR4 MYO3B_HUMAN myosin IIIB isoform 2 1241 response to stimulus|visual perception cytoplasm|myosin complex actin binding|ATP binding|motor activity|protein serine/threonine kinase activity lung(8)|ovary(6)|skin(4)|central_nervous_system(1) 19 GGGGAGCCCCTCAAAAGCCTG 0.463 0.40 159 104 COL3A1 1281 broad.mit.edu 37 2 189849608 189849616 + In_Frame_Del DEL GACGATCAA - - rs112714742 COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr2:189849608_189849616delGACGATCAA uc002uqj.1 + 2 319_327 c.202_210delGACGATCAA c.(202-210)GACGATCAAdel p.DDQ68del NM_000090 NP_000081 P02461 CO3A1_HUMAN collagen type III alpha 1 preproprotein 68_70 VWFC. axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway collagen type III|extracellular space extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding central_nervous_system(7)|ovary(4)|large_intestine(2) 13 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141) Collagenase(DB00048)|Palifermin(DB00039) CATAATATGTGACGATCAAGAATTAGACT 0.445 0.37 177 103 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.48 11 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.39 58 37 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.31 44 20 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.91 8 77 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 353 78 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.42 23 17 FSCB 84075 broad.mit.edu 37 14 44975587 44975588 + Frame_Shift_Del DEL TT - - COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr14:44975587_44975588delTT uc001wvn.2 - 1 912_913 c.603_604delAA c.(601-606)GCAACAfs p.A201fs NM_032135 NP_115511 Q5H9T9 FSCB_HUMAN fibrous sheath CABYR binding protein 201_202 cilium lung(3)|breast(3)|ovary(2)|central_nervous_system(1) 9 GBM - Glioblastoma multiforme(112;0.128) TTGCTGTTTGTTGCTGGTTGAA 0.406 0.32 335 159 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 9 100 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.66 13 25 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 38 486 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COLO680N_OESOPHAGUS NA COLO680N_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 70 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 67 PRKAA2 5563 broad.mit.edu 37 1 57157094 57157094 + Frame_Shift_Del DEL T - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr1:57157094delT uc001cyk.3 + 3 335 c.264delT c.(262-264)GATfs p.D88fs NM_006252 NP_006243 P54646 AAPK2_HUMAN AMP-activated protein kinase alpha 2 catalytic 88 Protein kinase. carnitine shuttle|cell cycle arrest|cholesterol biosynthetic process|energy reserve metabolic process|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleoplasm ATP binding|metal ion binding breast(4)|ovary(1)|stomach(1) 6 CTCCAACAGATTTTTTTATGG 0.328 0.63 14 24 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.13 345 50 TGFB2 7042 broad.mit.edu 37 1 218609371 218609371 + Frame_Shift_Del DEL A - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr1:218609371delA uc001hlm.2 + 5 1467 c.814delA c.(814-816)AAAfs p.K272fs TGFB2_uc001hln.2_Frame_Shift_Del_p.K300fs|TGFB2_uc010pue.1_Intron|TGFB2_uc001hlo.2_Intron NM_003238 NP_003229 P61812 TGFB2_HUMAN transforming growth factor, beta 2 isoform 2 272 activation of protein kinase activity|angiogenesis|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cardioblast differentiation|catagen|cell cycle arrest|cell death|cell growth|cell-cell junction organization|cell-cell signaling|collagen fibril organization|dopamine biosynthetic process|embryonic digestive tract development|eye development|glial cell migration|hair follicle morphogenesis|hemopoiesis|menstrual cycle phase|negative regulation of alkaline phosphatase activity|negative regulation of cell growth|negative regulation of epithelial cell proliferation|negative regulation of immune response|negative regulation of macrophage cytokine production|neuron development|neutrophil chemotaxis|odontogenesis|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of cardioblast differentiation|positive regulation of catagen|positive regulation of cell adhesion mediated by integrin|positive regulation of cell cycle|positive regulation of cell division|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of epithelial cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of heart contraction|positive regulation of immune response|positive regulation of integrin biosynthetic process|positive regulation of neuron apoptosis|positive regulation of ossification|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein secretion|positive regulation of stress-activated MAPK cascade|regulation of transforming growth factor-beta2 production|response to hypoxia|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein import into nucleus|somatic stem cell division|transforming growth factor beta receptor signaling pathway axon|extracellular matrix|extracellular space|neuronal cell body|platelet alpha granule lumen beta-amyloid binding|cytokine activity|growth factor activity|protein heterodimerization activity|protein homodimerization activity|receptor signaling protein serine/threonine kinase activity|type II transforming growth factor beta receptor binding 0 all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776) GTCCACTAGGAAAAAAAACAG 0.433 0.29 98 40 EHBP1 23301 broad.mit.edu 37 2 62991442 62991444 + In_Frame_Del DEL TGT - - rs143106870 COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr2:62991442_62991444delTGT uc002sby.2 + 4 686_688 c.204_206delTGT c.(202-207)GGTGTT>GGT p.V71del EHBP1_uc010fcp.2_In_Frame_Del_p.V71del|EHBP1_uc010fcq.1_In_Frame_Del_p.V71del|EHBP1_uc002sbx.2_In_Frame_Del_p.V71del|EHBP1_uc002sbz.2_In_Frame_Del_p.V71del|EHBP1_uc002scb.2_In_Frame_Del_p.V71del|EHBP1_uc002sca.2_In_Frame_Del_p.V71del NM_015252 NP_056067 Q8NDI1 EHBP1_HUMAN EH domain binding protein 1 isoform 1 71 cytoplasm|membrane ovary(1)|breast(1) 2 Lung NSC(7;0.0951)|all_lung(7;0.169) LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189) CCTATCGTGGTGTTGTTGTGTGG 0.340 0.29 55 23 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.38 20 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 82 119 PIK3R1 5295 broad.mit.edu 37 5 67591114 67591115 + In_Frame_Ins INS - CTT CTT COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr5:67591114_67591115insCTT uc003jva.2 + 13 2267_2268 c.1707_1708insCTT c.(1705-1710)insCTT p.570_571insL PIK3R1_uc003jvb.2_In_Frame_Ins_p.570_571insL|PIK3R1_uc003jvc.2_In_Frame_Ins_p.270_271insL|PIK3R1_uc003jvd.2_In_Frame_Ins_p.300_301insL|PIK3R1_uc003jve.2_In_Frame_Ins_p.249_250insL|PIK3R1_uc011crb.1_In_Frame_Ins_p.240_241insL NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 570_571 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.L570_D578del(1)|p.L570P(1)|p.?(1)|p.L570_Q572del(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) TTAAACCAGACCTTATCCAGCT 0.371 0.44 31 24 MSH3 4437 broad.mit.edu 37 5 79970915 79970916 + Frame_Shift_Del DEL AA - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr5:79970915_79970916delAA uc003kgz.2 + 7 1394_1395 c.1141_1142delAA c.(1141-1143)AAAfs p.K381fs NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 381 maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) TGTTAGGGACAAAAAAAAGGGC 0.347 0.38 40 25 PHF3 23469 broad.mit.edu 37 6 64423096 64423097 + Frame_Shift_Del DEL CT - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr6:64423096_64423097delCT uc003pep.1 + 15 5638_5639 c.5612_5613delCT c.(5611-5613)CCTfs p.P1871fs PHF3_uc003pen.2_Frame_Shift_Del_p.P1783fs|PHF3_uc011dxs.1_Frame_Shift_Del_p.P1140fs NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 1871 multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) ATGATGGGTCCTCTCTCACAAG 0.525 0.47 50 45 GRM8 2918 broad.mit.edu 37 7 126544156 126544156 + Frame_Shift_Del DEL T - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr7:126544156delT uc003vlr.2 - 4 1199 c.888delA c.(886-888)AAAfs p.K296fs GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Frame_Shift_Del_p.K296fs|GRM8_uc010lkz.1_RNA|GRM8_uc003vlu.1_Frame_Shift_Del_p.K17fs NM_000845 NP_000836 O00222 GRM8_HUMAN glutamate receptor, metabotropic 8 isoform a 296 Extracellular (Potential). negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception integral to plasma membrane lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1) 23 Prostate(267;0.186) L-Glutamic Acid(DB00142) 0.000 0.64 214 379 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.83 3 15 FASTK 10922 broad.mit.edu 37 7 150774993 150774993 + Frame_Shift_Del DEL A - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr7:150774993delA uc003wix.1 - 5 1110 c.1012delT c.(1012-1014)TCCfs p.S338fs uc011kvf.1_5'Flank|FASTK_uc003wiw.1_Frame_Shift_Del_p.S99fs|FASTK_uc003wiy.1_Frame_Shift_Del_p.S197fs|FASTK_uc003wiz.1_Frame_Shift_Del_p.S311fs|FASTK_uc003wja.1_3'UTR NM_006712 NP_006703 Q14296 FASTK_HUMAN Fas-activated serine/threonine kinase isoform 1 338 apoptosis|induction of apoptosis by extracellular signals|regulation of RNA splicing ATP binding|Fas-activated serine/threonine kinase activity|protein binding lung(2)|stomach(2) 4 OV - Ovarian serous cystadenocarcinoma(82;0.00989) UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138) AAGCCAGGGGAAAAAACAAAG 0.622 0.55 129 159 SGK3 23678 broad.mit.edu 37 8 67748054 67748055 + Frame_Shift_Ins INS - A A COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr8:67748054_67748055insA uc003xwr.2 + 9 881_882 c.582_583insA c.(580-585)CAGAAAfs p.Q194fs SGK3_uc003xwp.2_Frame_Shift_Ins_p.Q188fs|SGK3_uc003xwt.2_Frame_Shift_Ins_p.Q194fs|SGK3_uc003xwu.2_Frame_Shift_Ins_p.Q194fs NM_001033578 NP_001028750 Q96BR1 SGK3_HUMAN serum/glucocorticoid regulated kinase 3 isoform 194_195 Protein kinase.|Nuclear localization signal (By similarity). cell communication|response to stress cytoplasmic membrane-bounded vesicle|early endosome ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity ovary(1)|large_intestine(1)|lung(1)|breast(1) 4 Breast(64;0.186) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206) 0.000 0.17 78 16 SGK3 23678 broad.mit.edu 37 8 67763085 67763086 + Frame_Shift_Ins INS - T T COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr8:67763085_67763086insT uc003xwr.2 + 16 1549_1550 c.1250_1251insT c.(1249-1251)CCTfs p.P417fs SGK3_uc003xwp.2_Frame_Shift_Ins_p.P411fs|SGK3_uc003xwt.2_Frame_Shift_Ins_p.P417fs|SGK3_uc003xwu.2_Frame_Shift_Ins_p.P385fs NM_001033578 NP_001028750 Q96BR1 SGK3_HUMAN serum/glucocorticoid regulated kinase 3 isoform 417 Protein kinase. cell communication|response to stress cytoplasmic membrane-bounded vesicle|early endosome ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity ovary(1)|large_intestine(1)|lung(1)|breast(1) 4 Breast(64;0.186) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206) CAGAATCATCCTTTTTTTGAAT 0.307 0.23 41 12 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.30 320 135 TNKS2 80351 broad.mit.edu 37 10 93601945 93601946 + Frame_Shift_Ins INS - A A COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr10:93601945_93601946insA uc001khp.2 + 16 2153_2154 c.1856_1857insA c.(1855-1857)ACAfs p.T619fs NM_025235 NP_079511 Q9H2K2 TNKS2_HUMAN tankyrase, TRF1-interacting ankyrin-related 619 ANK 12. positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm NAD+ ADP-ribosyltransferase activity|protein binding kidney(3)|skin(3)|ovary(1)|lung(1) 8 Colorectal(252;0.162) GCAGACCCTACAAAAAAAAACA 0.391 0.70 3 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 869 207 HOXC13 3229 broad.mit.edu 37 12 54333021 54333021 + Frame_Shift_Del DEL C - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr12:54333021delC uc001sei.2 + 1 446 c.331delC c.(331-333)CCCfs p.P111fs HOXC13_uc010sop.1_RNA NM_017410 NP_059106 P31276 HXC13_HUMAN homeobox C13 111 nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity breast(1) 1 0.000 0.42 227 167 XPO4 64328 broad.mit.edu 37 13 21436912 21436912 + Frame_Shift_Del DEL T - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr13:21436912delT uc001unq.3 - 3 297 c.261delA c.(259-261)AAAfs p.K87fs XPO4_uc010tcr.1_Frame_Shift_Del_p.K13fs NM_022459 NP_071904 Q9C0E2 XPO4_HUMAN exportin 4 87 protein transport cytoplasm|nucleus protein binding large_intestine(1)|ovary(1)|kidney(1) 3 all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244) all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548) CGATGCTACCTTTTTCCAAGA 0.433 0.95 6 105 RB1 5925 broad.mit.edu 37 13 48881489 48881490 + Frame_Shift_Del DEL AG - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr13:48881489_48881490delAG uc001vcb.2 + 2 377_378 c.211_212delAG c.(211-213)AGAfs p.R71fs RB1_uc010acs.1_Intron NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 71 androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.0?(13)|p.?(3)|p.V70fs*39(1) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) AGATCATGTCAGAGAGAGAGCT 0.297 0.93 3 37 NIN 51199 broad.mit.edu 37 14 51237236 51237236 + Frame_Shift_Del DEL T - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr14:51237236delT uc001wym.2 - 12 1495 c.1304delA c.(1303-1305)AATfs p.N435fs NIN_uc001wyi.2_Frame_Shift_Del_p.N435fs|NIN_uc001wyj.2_RNA|NIN_uc001wyk.2_Frame_Shift_Del_p.N435fs|NIN_uc010tqp.1_Frame_Shift_Del_p.N441fs|NIN_uc001wyo.2_Frame_Shift_Del_p.N435fs|NIN_uc001wyp.1_Frame_Shift_Del_p.N397fs NM_182946 NP_891991 Q8N4C6 NIN_HUMAN ninein isoform 5 435 Potential. centrosome localization centrosome|microtubule calcium ion binding|GTP binding|protein binding skin(3)|ovary(1)|kidney(1)|central_nervous_system(1) 6 all_epithelial(31;0.00244)|Breast(41;0.127) TCGGAGTTCATTTTTTAAGGC 0.438 0.57 142 192 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.43 56 43 MGA 23269 broad.mit.edu 37 15 42059448 42059448 + Frame_Shift_Del DEL G - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr15:42059448delG uc010ucy.1 + 24 9349 c.9168delG c.(9166-9168)TCGfs p.S3056fs MGA_uc010ucz.1_Frame_Shift_Del_p.S2847fs NM_001164273 NP_001157745 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 1 3017 MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) TGGGCAACTCGGGGGCCTCAC 0.502 0.41 114 79 TAF15 8148 broad.mit.edu 37 17 34169406 34169406 + Frame_Shift_Del DEL T - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr17:34169406delT uc002hkd.2 + 12 1035 c.949delT c.(949-951)TTTfs p.F317fs TAF15_uc010ctw.1_RNA|TAF15_uc002hkc.2_Frame_Shift_Del_p.F314fs NM_139215 NP_631961 Q92804 RBP56_HUMAN TBP-associated factor 15 isoform 1 317 RRM. positive regulation of transcription, DNA-dependent cytoplasm|nucleus DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding TAF15/NR4A3(33) bone(33)|lung(1)|skin(1) 35 Ovarian(249;0.17) UCEC - Uterine corpus endometrioid carcinoma (308;0.0193) TAAAGTGTCCTTTGCCACTAG 0.318 0.50 60 60 TOP2A 7153 broad.mit.edu 37 17 38546381 38546381 + Frame_Shift_Del DEL T - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr17:38546381delT uc002huq.2 - 34 4429 c.4303delA c.(4303-4305)AGGfs p.R1435fs NM_001067 NP_001058 P11388 TOP2A_HUMAN DNA topoisomerase II, alpha isozyme 1435 apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1) 7 Breast(137;0.00328) STAD - Stomach adenocarcinoma(5;0.00183) Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385) GGGGCAGCCCTTTTTTTGGCA 0.413 0.36 79 44 WNK4 65266 broad.mit.edu 37 17 40939869 40939870 + Frame_Shift_Ins INS - G G COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr17:40939869_40939870insG uc002ibj.2 + 8 1836_1837 c.1815_1816insG c.(1813-1818)CCTGGGfs p.P605fs WNK4_uc010wgx.1_Frame_Shift_Ins_p.P269fs|WNK4_uc002ibk.1_Frame_Shift_Ins_p.P377fs|WNK4_uc010wgy.1_Intron NM_032387 NP_115763 Q96J92 WNK4_HUMAN WNK lysine deficient protein kinase 4 605_606 intracellular protein kinase cascade tight junction ATP binding|protein serine/threonine kinase activity ovary(3)|skin(3)|stomach(1) 7 Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.0749) TTCAGCCCCCTGGGGGGGTGCC 0.634 0.36 74 42 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.30 160 69 GSK3A 2931 broad.mit.edu 37 19 42737312 42737313 + Frame_Shift_Ins INS - G G COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr19:42737312_42737313insG uc002otb.1 - 8 1166_1167 c.1047_1048insC c.(1045-1050)CCCAACfs p.P349fs GSK3A_uc002ota.1_Frame_Shift_Ins_p.P267fs|GSK3A_uc002otc.2_RNA NM_019884 NP_063937 P49840 GSK3A_HUMAN glycogen synthase kinase 3 alpha 349_350 Protein kinase. insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of insulin receptor signaling pathway|negative regulation of transferase activity|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process beta-catenin destruction complex|cytosol ATP binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|tau-protein kinase activity ovary(2)|lung(2) 4 Prostate(69;0.00682) TCCGTGTAGTTGGGGTTCATCT 0.599 0.59 38 55 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 176 416 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 6 73 MKL1 57591 broad.mit.edu 37 22 40807831 40807831 + Frame_Shift_Del DEL G - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr22:40807831delG uc003ayv.1 - 12 2566 c.2359delC c.(2359-2361)CTGfs p.L787fs MKL1_uc003ayw.1_Frame_Shift_Del_p.L787fs|MKL1_uc010gye.1_Frame_Shift_Del_p.P790fs|MKL1_uc010gyf.1_Frame_Shift_Del_p.L737fs NM_020831 NP_065882 Q969V6 MKL1_HUMAN megakaryoblastic leukemia 1 protein 787 Pro-rich. positive regulation of transcription from RNA polymerase II promoter|smooth muscle cell differentiation|transcription, DNA-dependent cytoplasm|nucleus actin monomer binding|leucine zipper domain binding|nucleic acid binding|transcription coactivator activity ovary(2)|lung(1)|breast(1)|central_nervous_system(1) 5 TGTGCTGCCAGGGGGGACCCA 0.612 0.41 36 25 EP300 2033 broad.mit.edu 37 22 41566525 41566525 + Frame_Shift_Del DEL A - - COLO684_ENDOMETRIUM NA COLO684_ENDOMETRIUM NA g.chr22:41566525delA uc003azl.3 + 27 4797 c.4402delA c.(4402-4404)AAAfs p.K1468fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1468 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding p.M1470fs*3(3) haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 GGAATGGTACAAAAAAATGCT 0.473 0.84 14 76 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COLO699_LUNG NA COLO699_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.99 1 75 CLSPN 63967 broad.mit.edu 37 1 36226108 36226108 + Frame_Shift_Del DEL C - - COLO699_LUNG NA COLO699_LUNG NA g.chr1:36226108delC uc001bzi.2 - 8 1494 c.1414delG c.(1414-1416)GAAfs p.E472fs CLSPN_uc009vux.2_Frame_Shift_Del_p.E472fs NM_022111 NP_071394 Q9HAW4 CLSPN_HUMAN claspin 472 activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation nucleoplasm anaphase-promoting complex binding|DNA binding breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1) 8 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887) 0.000 0.18 995 223 SNRK 54861 broad.mit.edu 37 3 43389943 43389947 + Frame_Shift_Del DEL TGCAG - - COLO699_LUNG NA COLO699_LUNG NA g.chr3:43389943_43389947delTGCAG uc003cms.3 + 7 2524_2528 c.2192_2196delTGCAG c.(2191-2196)CTGCAGfs p.L731fs SNRK_uc003cmt.3_Frame_Shift_Del_p.L731fs|SNRK_uc010hik.2_Frame_Shift_Del_p.L731fs|SNRK_uc011azr.1_Frame_Shift_Del_p.L525fs NM_017719 NP_060189 Q9NRH2 SNRK_HUMAN SNF related kinase 731_732 myeloid cell differentiation nucleus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity ovary(3)|stomach(1)|breast(1)|skin(1) 6 KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792) AATAACGTGCTGCAGCTACCTCTGT 0.522 0.60 67 99 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COLO699_LUNG NA COLO699_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 42 42 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 COLO699_LUNG NA COLO699_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 24 35 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 COLO699_LUNG NA COLO699_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency COLO699_LUNG NA COLO699_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.65 258 484 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 COLO699_LUNG NA COLO699_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 136 41 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C COLO699_LUNG NA COLO699_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 11 124 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 COLO699_LUNG NA COLO699_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.86 2 12 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 COLO699_LUNG NA COLO699_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.32 82 39 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COLO699_LUNG NA COLO699_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 179 662 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COLO699_LUNG NA COLO699_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 4 178 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COLO741_SKIN NA COLO741_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 4 43 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - COLO741_SKIN NA COLO741_SKIN NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 354 115 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 COLO741_SKIN NA COLO741_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.45 12 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 COLO741_SKIN NA COLO741_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.44 18 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COLO741_SKIN NA COLO741_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.51 91 93 ATXN1 6310 broad.mit.edu 37 6 16327907 16327909 + In_Frame_Del DEL TGA - - rs59310777 by1000genomes COLO741_SKIN NA COLO741_SKIN NA g.chr6:16327907_16327909delTGA uc003nbt.2 - 8 1604_1606 c.633_635delTCA c.(631-636)CATCAG>CAG p.H211del ATXN1_uc010jpi.2_In_Frame_Del_p.H211del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 211 Poly-Gln. H -> HQ (in Ref. 1; CAA55793). cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgctgatgctgatgct 0.384 0.11 58 7 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - COLO741_SKIN NA COLO741_SKIN NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.93 2 27 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 COLO741_SKIN NA COLO741_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 COLO741_SKIN NA COLO741_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 307 133 NLRP1 22861 broad.mit.edu 37 17 5463133 5463133 + Frame_Shift_Del DEL G - - COLO741_SKIN NA COLO741_SKIN NA g.chr17:5463133delG uc002gci.2 - 4 1438 c.883delC c.(883-885)CTGfs p.L295fs NLRP1_uc002gcg.1_Frame_Shift_Del_p.L295fs|NLRP1_uc002gck.2_Frame_Shift_Del_p.L295fs|NLRP1_uc002gcj.2_Frame_Shift_Del_p.L295fs|NLRP1_uc002gcl.2_Frame_Shift_Del_p.L295fs|NLRP1_uc002gch.3_Frame_Shift_Del_p.L295fs|NLRP1_uc010clh.2_Frame_Shift_Del_p.L295fs NM_033004 NP_127497 Q9C000 NALP1_HUMAN NLR family, pyrin domain containing 1 isoform 1 295 defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide cytoplasm|NALP1 inflammasome complex|nucleus ATP binding|caspase activator activity|enzyme binding|protein domain specific binding lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1) 9 Colorectal(1115;3.48e-05) CTCTTGACCAGGGGATCTTGG 0.478 0.95 15 298 TP53 7157 broad.mit.edu 37 17 7576882 7576883 + Frame_Shift_Ins INS - TT TT COLO741_SKIN NA COLO741_SKIN NA g.chr17:7576882_7576883insTT uc002gim.2 - 9 1157_1158 c.963_964insAA c.(961-966)AAACCAfs p.K321fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Frame_Shift_Ins_p.K321fs|TP53_uc010cne.1_RNA|TP53_uc010cnf.1_Frame_Shift_Ins_p.K189fs|TP53_uc010cng.1_Frame_Shift_Ins_p.K189fs|TP53_uc002gii.1_Frame_Shift_Ins_p.K189fs|TP53_uc010cnh.1_Frame_Shift_Ins_p.K321fs|TP53_uc010cni.1_Frame_Shift_Ins_p.K321fs|TP53_uc002gij.2_Frame_Shift_Ins_p.K321fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 321_322 Interaction with HIPK1 (By similarity).|Interaction with CARM1.|Interaction with HIPK2. P -> R (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.K321fs*24(4)|p.K321*(2)|p.P318fs*21(1)|p.S315fs*22(1)|p.?(1)|p.P322fs*23(1)|p.L308fs*15(1)|p.K321K(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) CCATCCAGTGGTTTCTTCTTTG 0.450 0.93 10 128 PRKAR1A 5573 broad.mit.edu 37 17 66511643 66511644 + Frame_Shift_Ins INS - T T COLO741_SKIN NA COLO741_SKIN NA g.chr17:66511643_66511644insT uc002jhg.2 + 2 283_284 c.103_104insT c.(103-105)ATTfs p.I35fs PRKAR1A_uc002jhh.2_Frame_Shift_Ins_p.I35fs|PRKAR1A_uc002jhi.2_Frame_Shift_Ins_p.I35fs|PRKAR1A_uc002jhj.2_Frame_Shift_Ins_p.I35fs|PRKAR1A_uc002jhk.2_5'UTR|PRKAR1A_uc002jhl.2_Frame_Shift_Ins_p.I35fs|PRKAR1A_uc002jhm.2_Frame_Shift_Ins_p.I35fs NM_212471 NP_997636 P10644 KAP0_HUMAN cAMP-dependent protein kinase, regulatory 35 Dimerization and phosphorylation. activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter|transmembrane transport|water transport cAMP-dependent protein kinase complex|cytosol cAMP binding|cAMP-dependent protein kinase regulator activity|protein binding adrenal_gland(4)|lung(3)|thyroid(2)|soft_tissue(2)|breast(1) 12 Breast(10;1.64e-13) CAAAGATTCTATTGTGCAGTTG 0.505 0.95 14 279 MATK 4145 broad.mit.edu 37 19 3779060 3779061 + Frame_Shift_Ins INS - C C COLO741_SKIN NA COLO741_SKIN NA g.chr19:3779060_3779061insC uc002lyt.2 - 12 1526_1527 c.1126_1127insG c.(1126-1128)GCCfs p.A376fs MATK_uc002lyv.2_Frame_Shift_Ins_p.A377fs|MATK_uc002lyu.2_Frame_Shift_Ins_p.A335fs|MATK_uc010dtq.2_Frame_Shift_Ins_p.A376fs NM_139355 NP_647612 P42679 MATK_HUMAN megakaryocyte-associated tyrosine kinase isoform 376 Protein kinase. cell proliferation|mesoderm development|positive regulation of cell proliferation cytoplasm|nucleus ATP binding|non-membrane spanning protein tyrosine kinase activity stomach(2)|ovary(1)|lung(1)|large_intestine(1) 5 Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18) CTTCCGCTCGGCTTTGGCCAGG 0.658 0.10 64 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 COLO741_SKIN NA COLO741_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 18 74 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COLO741_SKIN NA COLO741_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 111 462 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COLO741_SKIN NA COLO741_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 101 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COLO783_SKIN NA COLO783_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 6 85 CTNNB1 1499 broad.mit.edu 37 3 41266134 41266136 + In_Frame_Del DEL CTT - - rs121913407 COLO783_SKIN NA COLO783_SKIN NA g.chr3:41266134_41266136delCTT uc010hia.1 + 4 287_289 c.131_133delCTT c.(130-135)CCTTCT>CCT p.S45del CTNNB1_uc003ckp.2_In_Frame_Del_p.S45del|CTNNB1_uc003ckq.2_In_Frame_Del_p.S45del|CTNNB1_uc003ckr.2_In_Frame_Del_p.S45del|CTNNB1_uc011azf.1_In_Frame_Del_p.S38del|CTNNB1_uc011azg.1_Intron|uc010hib.1_RNA NM_001904 NP_001895 P35222 CTNB1_HUMAN beta-catenin 45 Missing (in colorectal cancer).|S -> P (in hepatocellular carcinoma).|S -> F (in hepatocellular carcinoma). adherens junction assembly|androgen receptor signaling pathway|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell-cell adhesion|cell-matrix adhesion|cellular component disassembly involved in apoptosis|cellular response to growth factor stimulus|cellular response to indole-3-methanol|central nervous system vasculogenesis|cytoskeletal anchoring at plasma membrane|determination of dorsal/ventral asymmetry|dorsal/ventral axis specification|ectoderm development|embryonic axis specification|embryonic foregut morphogenesis|embryonic leg joint morphogenesis|endodermal cell fate commitment|endothelial tube morphogenesis|epithelial to mesenchymal transition|gastrulation with mouth forming second|glial cell fate determination|hair follicle morphogenesis|hair follicle placode formation|hindbrain development|liver development|lung cell differentiation|lung induction|lung-associated mesenchyme development|male genitalia development|mesenchymal cell proliferation involved in lung development|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of osteoclast differentiation|negative regulation of transcription from RNA polymerase II promoter|nephron tubule formation|odontogenesis of dentine-containing tooth|oocyte development|pancreas development|positive regulation of anti-apoptosis|positive regulation of apoptosis|positive regulation of branching involved in lung morphogenesis|positive regulation of epithelial cell proliferation involved in prostate gland development|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of muscle cell differentiation|positive regulation of osteoblast differentiation|positive regulation of transcription from RNA polymerase II promoter|protein localization at cell surface|proximal/distal pattern formation|regulation of angiogenesis|regulation of calcium ion import|regulation of centriole-centriole cohesion|regulation of centromeric sister chromatid cohesion|regulation of fibroblast proliferation|regulation of nephron tubule epithelial cell differentiation|regulation of protein localization at cell surface|regulation of smooth muscle cell proliferation|regulation of T cell proliferation|renal inner medulla development|renal outer medulla development|renal vesicle formation|response to drug|response to estradiol stimulus|Schwann cell proliferation|smooth muscle cell differentiation|synapse organization|synaptic vesicle transport|T cell differentiation in thymus|thymus development|trachea formation APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin-TCF7L2 complex|catenin complex|cell cortex|cell-substrate adherens junction|centrosome|dendritic shaft|desmosome|fascia adherens|internal side of plasma membrane|lamellipodium|lateral plasma membrane|microvillus membrane|perinuclear region of cytoplasm|protein-DNA complex|synapse|transcription factor complex|Z disc|zonula adherens alpha-catenin binding|androgen receptor binding|cadherin binding|estrogen receptor binding|I-SMAD binding|ion channel binding|protein binding|protein C-terminus binding|protein kinase binding|protein phosphatase binding|R-SMAD binding|RPTP-like protein binding|signal transducer activity|specific RNA polymerase II transcription factor activity|structural molecule activity|transcription coactivator activity|transcription regulatory region DNA binding p.S45F(396)|p.S45P(163)|p.S45del(79)|p.A5_A80del(63)|p.S45Y(21)|p.S45C(18)|p.S45A(10)|p.H24_S47del(9)|p.A5_A80>D(7)|p.A5_Q143del(7)|p.Q28_H134del(5)|p.W25_I140del(4)|p.T3_A126del(2)|p.M5_N141>D(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.V22_L139>V(2)|p.A5_Y142>D(2)|p.?(2)|p.L10_N141del(2)|p.P44L(2)|p.E9_S47del(1)|p.Q28_Q61del(1)|p.A20_R151del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.Y30_A97del(1)|p.A20_A80del(1)|p.E15_I140>V(1)|p.D17_P128del(1)|p.H24_M131del(1)|p.L7_I140del(1)|p.G38_S45del(1)|p.K19_Y142>V(1)|p.A20_L148del(1)|p.V22_A80del(1)|p.V22_G80>NNNNN(1)|p.P44del(1)|p.A20_Q143del(1)|p.A43_E53del(1)|p.A13_R151del(1)|p.S23_I140del(1)|p.M1_A87del(1)|p.P44_N51del(1)|p.V22_T102del(1)|p.S45fs*2(1)|p.S45E(1)|p.A21_A80del(1)|p.S45T(1)|p.S45S(1)|p.D6_I140del(1)|p.Q28_I140del(1)|p.E9_A80del(1)|p.I35_K170del(1)|p.S45_S47>C(1)|p.M14_S45del(1)|p.M8_G50del(1)|p.A5_G80>(1)|p.T42_G48del(1)|p.S45_G48del(1)|p.S45_D58del(1)|p.P16_K133del(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.A5_R90del(1)|p.P44_S45>AP(1)|p.M8_A80del(1)|p.P44_S45insGATTTAP(1)|p.E9_I140del(1)|p.S45_E54del(1)|p.A5_Q143>E(1)|p.H36_E53>L(1)|p.A43_E54del(1)|p.A5_Q72del(1)|p.Y30_A80del(1)|p.S45_L46del(1)|p.D6_K133del(1)|p.V22_Y64del(1)|p.A5_D144>D(1)|p.D17_A126del(1)|p.A5_E54del(1)|p.V22_S71>A(1)|p.W25_A80del(1)|p.A20_Q72del(1)|p.A20_S111del(1) CTNNB1/PLAG1(60) liver(806)|soft_tissue(609)|large_intestine(243)|endometrium(222)|kidney(172)|stomach(157)|central_nervous_system(139)|ovary(104)|skin(97)|pancreas(91)|adrenal_gland(85)|pituitary(81)|salivary_gland(62)|haematopoietic_and_lymphoid_tissue(57)|thyroid(55)|biliary_tract(41)|lung(38)|prostate(24)|bone(20)|small_intestine(17)|cervix(9)|parathyroid(9)|urinary_tract(8)|breast(7)|oesophagus(5)|NS(3)|pleura(2)|upper_aerodigestive_tract(2)|eye(1) 3166 KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294) Lithium(DB01356) ACCACAGCTCCTTCTCTGAGTGG 0.502 0.51 35 37 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 COLO783_SKIN NA COLO783_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.34 25 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COLO783_SKIN NA COLO783_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 75 66 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 COLO783_SKIN NA COLO783_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 15 28 AIM1 202 broad.mit.edu 37 6 106968314 106968315 + Frame_Shift_Ins INS - A A COLO783_SKIN NA COLO783_SKIN NA g.chr6:106968314_106968315insA uc003prh.2 + 2 2494_2495 c.2007_2008insA c.(2005-2010)GTTACAfs p.V669fs NM_001624 NP_001615 Q9Y4K1 AIM1_HUMAN absent in melanoma 1 669_670 sugar binding breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1) 9 Breast(9;0.0138)|all_epithelial(6;0.169) all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473) Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305) all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858) ATCAGACTGTTACAAATGGCCA 0.470 0.95 9 155 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 COLO783_SKIN NA COLO783_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.32 26 12 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 COLO783_SKIN NA COLO783_SKIN NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.65 7 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 COLO783_SKIN NA COLO783_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 205 37 CDKN1B 1027 broad.mit.edu 37 12 12870812 12870816 + Frame_Shift_Del DEL GGAGC - - rs2066828 COLO783_SKIN NA COLO783_SKIN NA g.chr12:12870812_12870816delGGAGC uc001rat.2 + 1 511_515 c.39_43delGGAGC c.(37-45)CTGGAGCGGfs p.L13fs NM_004064 NP_004055 P46527 CDN1B_HUMAN cyclin-dependent kinase inhibitor 1B 13_15 autophagic cell death|cell cycle arrest|cellular response to lithium ion|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of transcription, DNA-dependent|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process|S phase of mitotic cell cycle cytosol|endosome|nucleoplasm cyclin-dependent protein kinase inhibitor activity|protein phosphatase binding|transforming growth factor beta receptor, cytoplasmic mediator activity ovary(1)|lung(1) 2 Prostate(47;0.0322)|all_epithelial(100;0.159) BRCA - Breast invasive adenocarcinoma(232;0.0336) GCCCTAGCCTGGAGCGGATGGACGC 0.595 0.34 41 21 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C COLO783_SKIN NA COLO783_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 3 28 NF1 4763 broad.mit.edu 37 17 29687605 29687629 + Frame_Shift_Del DEL CCCTCCTGACTCCCACATCTCCTTA - - COLO783_SKIN NA COLO783_SKIN NA g.chr17:29687605_29687629delCCCTCCTGACTCCCACATCTCCTTA uc002hgg.2 + 57 8594_8618 c.8261_8285delCCCTCCTGACTCCCACATCTCCTTA c.(8260-8286)TCCCTCCTGACTCCCACATCTCCTTACfs p.S2754fs NF1_uc002hgh.2_Frame_Shift_Del_p.S2733fs|NF1_uc010cso.2_Frame_Shift_Del_p.S942fs|NF1_uc010wbt.1_Frame_Shift_Del_p.S232fs|NF1_uc010wbu.1_RNA NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 2754_2762 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.S2751fs*27(1) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) AGTGAAGAATCCCTCCTGACTCCCACATCTCCTTACCCTCCTGCA 0.458 0.15 105 18 PAK4 10298 broad.mit.edu 37 19 39664276 39664278 + In_Frame_Del DEL TCC - - COLO783_SKIN NA COLO783_SKIN NA g.chr19:39664276_39664278delTCC uc002okj.1 + 6 1185_1187 c.724_726delTCC c.(724-726)TCCdel p.S247del PAK4_uc002okl.1_In_Frame_Del_p.S247del|PAK4_uc002okn.1_In_Frame_Del_p.S247del|PAK4_uc002okm.1_In_Frame_Del_p.S94del|PAK4_uc002oko.1_In_Frame_Del_p.S94del|PAK4_uc002okp.1_In_Frame_Del_p.S157del NM_001014831 NP_001014831 O96013 PAK4_HUMAN p21-activated kinase 4 isoform 1 247 Linker. cellular component movement|signal transduction Golgi apparatus ATP binding|protein binding|protein serine/threonine kinase activity lung(3)|ovary(1) 4 all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454) Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113) 0.000 0.21 281 74 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 COLO783_SKIN NA COLO783_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.52 16 17 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COLO783_SKIN NA COLO783_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 82 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COLO792_SKIN NA COLO792_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 2 22 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 COLO792_SKIN NA COLO792_SKIN NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.21 84 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COLO792_SKIN NA COLO792_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.29 79 33 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 COLO792_SKIN NA COLO792_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 19 36 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 COLO792_SKIN NA COLO792_SKIN NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.41 234 162 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes COLO792_SKIN NA COLO792_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.81 3 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency COLO792_SKIN NA COLO792_SKIN NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.71 341 829 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - COLO792_SKIN NA COLO792_SKIN NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 308 36 FNBP1 23048 broad.mit.edu 37 9 132719669 132719674 + In_Frame_Del DEL GTCAGC - - COLO792_SKIN NA COLO792_SKIN NA g.chr9:132719669_132719674delGTCAGC uc004byw.1 - 6 697_702 c.478_483delGCTGAC c.(478-483)GCTGACdel p.AD160del FNBP1_uc011mbv.1_In_Frame_Del_p.AD160del|FNBP1_uc011mbw.1_In_Frame_Del_p.AD160del|FNBP1_uc004bza.2_In_Frame_Del_p.AD160del|FNBP1_uc004byz.1_In_Frame_Del_p.AD160del|FNBP1_uc004byx.1_In_Frame_Del_p.AD81del|FNBP1_uc004byy.1_In_Frame_Del_p.AD81del NM_015033 NP_055848 Q96RU3 FNBP1_HUMAN formin binding protein 1 160_161 Interaction with microtubules (By similarity).|Self-association, lipid-binding and induction of membrane tubulation.|Potential. endocytosis cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane identical protein binding|lipid binding 0 Ovarian(14;0.000536) GBM - Glioblastoma multiforme(294;0.0378) TGACATTGATGTCAGCGTCCATTTTC 0.330 0.41 109 75 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 COLO792_SKIN NA COLO792_SKIN NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.55 5 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 COLO792_SKIN NA COLO792_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 148 34 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes COLO792_SKIN NA COLO792_SKIN NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.29 30 12 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C COLO792_SKIN NA COLO792_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.85 25 139 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 COLO792_SKIN NA COLO792_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.64 20 35 TIAM1 7074 broad.mit.edu 37 21 32537324 32537334 + Frame_Shift_Del DEL CTCGGTCTCCT - - COLO792_SKIN NA COLO792_SKIN NA g.chr21:32537324_32537334delCTCGGTCTCCT uc002yow.1 - 17 3408_3418 c.2936_2946delAGGAGACCGAG c.(2935-2946)GAGGAGACCGAGfs p.E979fs TIAM1_uc011adk.1_Frame_Shift_Del_p.E979fs|TIAM1_uc011adl.1_Frame_Shift_Del_p.E919fs NM_003253 NP_003244 Q13009 TIAM1_HUMAN T-cell lymphoma invasion and metastasis 1 979_982 apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cell-cell junction|cytosol receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity lung(3)|breast(3)|ovary(2)|large_intestine(2) 10 AGTCTGGCCCCTCGGTCTCCTCTGGAGCGGT 0.498 0.52 54 59 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COLO792_SKIN NA COLO792_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 258 697 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COLO792_SKIN NA COLO792_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 65 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COLO829_SKIN NA COLO829_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.99 1 97 IL1R2 7850 broad.mit.edu 37 2 102626147 102626147 + Frame_Shift_Del DEL G - - COLO829_SKIN NA COLO829_SKIN NA g.chr2:102626147delG uc002tbm.2 + 3 420 c.191delG c.(190-192)CGCfs p.R64fs IL1R2_uc002tbn.2_Frame_Shift_Del_p.R64fs|IL1R2_uc002tbo.1_Frame_Shift_Del_p.R64fs NM_004633 NP_004624 P27930 IL1R2_HUMAN interleukin 1 receptor, type II precursor 64 Extracellular (Potential).|Ig-like C2-type 1. immune response integral to membrane|plasma membrane interleukin-1, Type II, blocking receptor activity ovary(1)|breast(1) 2 Anakinra(DB00026) GTCAGCCCCCGCATCAACCTG 0.607 0.56 8 10 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes COLO829_SKIN NA COLO829_SKIN NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.59 14 20 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 COLO829_SKIN NA COLO829_SKIN NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.10 89 10 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A COLO829_SKIN NA COLO829_SKIN NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 297 72 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 COLO829_SKIN NA COLO829_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.17 115 23 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COLO829_SKIN NA COLO829_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.67 184 371 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 COLO829_SKIN NA COLO829_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 50 79 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes COLO829_SKIN NA COLO829_SKIN NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.65 6 11 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes COLO829_SKIN NA COLO829_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 5 30 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 COLO829_SKIN NA COLO829_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 51 CDKN2A 1029 broad.mit.edu 37 9 21971154 21971155 + Frame_Shift_Del DEL CG - - COLO829_SKIN NA COLO829_SKIN NA g.chr9:21971154_21971155delCG uc003zpk.2 - 2 415_416 c.203_204delCG c.(202-204)GCGfs p.A68fs MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Frame_Shift_Del_p.R123fs NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 68 ANK 2. Missing (in melanoma; loss of CDK4 binding).|A -> T (in an esophagus tumor).|A -> V.|A -> L (in CMM2; requires 2 nucleotide substitutions). cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.?(13)|p.A68T(5)|p.A68V(3)|p.A68A(2)|p.E61fs*49(2)|p.E61fs*50(1)|p.A68E(1)|p.L65fs*38(1)|p.A68fs*51(1)|p.L64_E69>Q(1)|p.V59fs*45(1)|p.E61_L94del(1)|p.L65fs*77(1)|p.A68fs*3(1)|p.L63fs*75(1)|p.A68fs*78(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) AGTTGGGCTCCGCGCCGTGGAG 0.708 0.82 2 9 GOLGA5 9950 broad.mit.edu 37 14 93277987 93277989 + In_Frame_Del DEL AGA - - COLO829_SKIN NA COLO829_SKIN NA g.chr14:93277987_93277989delAGA uc001yaz.1 + 6 1390_1392 c.1208_1210delAGA c.(1207-1212)GAGAAG>GAG p.K405del NM_005113 NP_005104 Q8TBA6 GOGA5_HUMAN Golgi autoantigen, golgin subfamily a, 5 405 Cytoplasmic (Potential).|Potential. Golgi organization cis-Golgi network|integral to membrane ATP binding|protein homodimerization activity|protein tyrosine kinase activity|Rab GTPase binding ovary(2)|lung(1) 3 all_cancers(154;0.0934) COAD - Colon adenocarcinoma(157;0.222) TACTCAGATGAGAAGAAGAGGGT 0.414 0.27 257 97 FES 2242 broad.mit.edu 37 15 91436556 91436557 + Frame_Shift_Ins INS - C C COLO829_SKIN NA COLO829_SKIN NA g.chr15:91436556_91436557insC uc002bpv.2 + 16 2053_2054 c.1957_1958insC c.(1957-1959)GCCfs p.A653fs FES_uc010uqj.1_Frame_Shift_Ins_p.A525fs|FES_uc010uqk.1_Frame_Shift_Ins_p.A635fs|FES_uc002bpw.2_RNA|FES_uc010bny.2_Frame_Shift_Ins_p.A512fs|FES_uc002bpx.2_Frame_Shift_Ins_p.A583fs|FES_uc002bpy.2_Frame_Shift_Ins_p.A595fs NM_002005 NP_001996 P07332 FES_HUMAN feline sarcoma oncogene isoform 1 653 Protein kinase. axon guidance|cell proliferation|peptidyl-tyrosine phosphorylation cytosol ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(2) 2 Lung NSC(78;0.0771)|all_lung(78;0.137) Lung(145;0.229) CACGGAGGGGGCCCGCCTGCGG 0.673 0.10 122 14 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C COLO829_SKIN NA COLO829_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 8 96 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 COLO829_SKIN NA COLO829_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 48 208 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COLO829_SKIN NA COLO829_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 99 490 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COLO829_SKIN NA COLO829_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 7 254 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CORL23_LUNG NA CORL23_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 3 105 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - CORL23_LUNG NA CORL23_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 645 206 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CORL23_LUNG NA CORL23_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.25 49 16 CXCL9 4283 broad.mit.edu 37 4 76924801 76924804 + Frame_Shift_Del DEL CTTT - - CORL23_LUNG NA CORL23_LUNG NA g.chr4:76924801_76924804delCTTT uc003hjh.1 - 4 364_367 c.325_328delAAAG c.(325-330)AAAGTTfs p.K109fs NM_002416 NP_002407 Q07325 CXCL9_HUMAN small inducible cytokine B9 precursor 109_110 cell-cell signaling|cellular defense response|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response extracellular space chemokine activity ovary(1) 1 Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934) ACTTTCAGAACTTTCTTTTTTTGA 0.328 0.89 48 395 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CORL23_LUNG NA CORL23_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.43 38 29 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CORL23_LUNG NA CORL23_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.49 86 81 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 CORL23_LUNG NA CORL23_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.26 100 36 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CORL23_LUNG NA CORL23_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.54 245 291 XPA 7507 broad.mit.edu 37 9 100447271 100447273 + In_Frame_Del DEL CTT - - CORL23_LUNG NA CORL23_LUNG NA g.chr9:100447271_100447273delCTT uc004axr.3 - 5 722_724 c.605_607delAAG c.(604-609)GAAGCA>GCA p.E202del XPA_uc004axs.3_RNA NM_000380 NP_000371 P23025 XPA_HUMAN xeroderma pigmentosum, complementation group A 202 nucleotide-excision repair, DNA damage removal nucleoplasm damaged DNA binding|metal ion binding|nucleotide binding|protein domain specific binding|protein homodimerization activity breast(1) 1 Acute lymphoblastic leukemia(62;0.158) ACTTCCTTTGCTTCTTCTAATGC 0.345 0.47 239 209 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CORL23_LUNG NA CORL23_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 169 26 SMARCA4 6597 broad.mit.edu 37 19 11118633 11118635 + In_Frame_Del DEL AGA - - CORL23_LUNG NA CORL23_LUNG NA g.chr19:11118633_11118635delAGA uc002mqf.3 + 14 2341_2343 c.2057_2059delAGA c.(2056-2061)GAGAAG>GAG p.K689del SMARCA4_uc010dxp.2_In_Frame_Del_p.K689del|SMARCA4_uc010dxo.2_In_Frame_Del_p.K689del|SMARCA4_uc002mqg.1_In_Frame_Del_p.K689del|SMARCA4_uc010dxq.2_In_Frame_Del_p.K689del|SMARCA4_uc010dxr.2_In_Frame_Del_p.K689del|SMARCA4_uc002mqj.3_In_Frame_Del_p.K689del|SMARCA4_uc010dxs.2_In_Frame_Del_p.K689del NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 689 chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.K687E(1)|p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) CCCGTGGAGGAGAAGAAGAAGAT 0.586 0.38 40 24 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CORL23_LUNG NA CORL23_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 82 240 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - CORL24_LUNG NA CORL24_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 209 59 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 CORL24_LUNG NA CORL24_LUNG NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.46 7 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CORL24_LUNG NA CORL24_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 36 52 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CORL24_LUNG NA CORL24_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 7 16 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 CORL24_LUNG NA CORL24_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.76 18 57 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CORL24_LUNG NA CORL24_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 2 23 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CORL24_LUNG NA CORL24_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 269 29 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - CORL24_LUNG NA CORL24_LUNG NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.40 80 53 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CORL24_LUNG NA CORL24_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 161 89 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 CORL24_LUNG NA CORL24_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.59 12 17 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 CORL24_LUNG NA CORL24_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.32 40 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CORL24_LUNG NA CORL24_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 86 302 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CORL24_LUNG NA CORL24_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 68 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CORL279_LUNG NA CORL279_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 40 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A CORL279_LUNG NA CORL279_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 68 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CORL279_LUNG NA CORL279_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 51 46 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CORL279_LUNG NA CORL279_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 10 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CORL279_LUNG NA CORL279_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 31 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CORL279_LUNG NA CORL279_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 309 35 TP53 7157 broad.mit.edu 37 17 7578546 7578558 + Splice_Site DEL AGGGGAGTACTGT - - CORL279_LUNG NA CORL279_LUNG NA g.chr17:7578546_7578558delAGGGGAGTACTGT uc002gim.2 - 5 570 c.376_splice c.e5-1 p.Y126_splice TP53_uc002gig.1_Splice_Site_p.Y126_splice|TP53_uc002gih.2_Splice_Site_p.Y126_splice|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'UTR|TP53_uc010cng.1_5'UTR|TP53_uc002gii.1_5'UTR|TP53_uc010cnh.1_Splice_Site_p.Y126_splice|TP53_uc010cni.1_Splice_Site_p.Y126_splice|TP53_uc002gij.2_Splice_Site_p.Y126_splice|TP53_uc010cnj.1_5'UTR|TP53_uc002gin.2_Splice_Site_p.Y33_splice|TP53_uc002gio.2_Splice_Site|TP53_uc010vug.1_Splice_Site_p.Y87_splice NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.?(50)|p.S127F(18)|p.Y126*(11)|p.S127Y(8)|p.0?(7)|p.P128S(7)|p.Y126_K132delYSPALNK(6)|p.Y126N(6)|p.P128fs*42(4)|p.Y126C(4)|p.S127P(3)|p.Y126D(3)|p.P128L(3)|p.Y126_N131delYSPALN(3)|p.S127T(2)|p.Y126S(2)|p.Y126Y(1)|p.S127S(1)|p.S127_Q136del10(1)|p.T125_Y126insX(1)|p.Y33*(1)|p.S127C(1)|p.V73fs*9(1)|p.S127fs*43(1)|p.S127fs*42(1)|p.P128del(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.Y126fs*18(1)|p.S127fs*36(1)|p.P128fs*18(1)|p.P128A(1)|p.P128P(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) TGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGA 0.559 0.73 16 44 MYH13 8735 broad.mit.edu 37 17 10247203 10247204 + Frame_Shift_Ins INS - G G CORL279_LUNG NA CORL279_LUNG NA g.chr17:10247203_10247204insG uc002gmk.1 - 16 1897_1898 c.1807_1808insC c.(1807-1809)CTGfs p.L603fs MYH13_uc010vvf.1_Frame_Shift_Ins_p.L278fs NM_003802 NP_003793 Q9UKX3 MYH13_HUMAN myosin, heavy polypeptide 13, skeletal muscle 603 Myosin head-like. muscle contraction muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|microfilament motor activity ovary(4)|skin(2) 6 AGTCTCGTTCAGGGGGTCCTTG 0.540 0.36 48 27 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 CORL279_LUNG NA CORL279_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 52 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CORL279_LUNG NA CORL279_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 176 415 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CORL279_LUNG NA CORL279_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 82 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CORL311_LUNG NA CORL311_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 58 TPRXL 348825 broad.mit.edu 37 3 14105871 14105885 + In_Frame_Del DEL CAGCAGCAGCCCCAG - - rs4684179;rs113575909 by1000genomes CORL311_LUNG NA CORL311_LUNG NA g.chr3:14105871_14105885delCAGCAGCAGCCCCAG uc011avd.1 + 3 650_664 c.195_209delCAGCAGCAGCCCCAG c.(193-210)CCCAGCAGCAGCCCCAGC>CCC p.SSSPS71del TPRXL_uc003byh.1_In_Frame_Del_p.SSSPS71del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSPS71del NR_002223 RecName: Full=Putative protein TPRXL; 0 gcagcagccccagcagcagccccagcagcagcagc 0.033 0.54 6 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 CORL311_LUNG NA CORL311_LUNG NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.21 77 21 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CORL311_LUNG NA CORL311_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.24 48 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CORL311_LUNG NA CORL311_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.72 73 190 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes CORL311_LUNG NA CORL311_LUNG NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.50 5 5 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes CORL311_LUNG NA CORL311_LUNG NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.15 148 26 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 CORL311_LUNG NA CORL311_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.61 28 43 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 CORL311_LUNG NA CORL311_LUNG NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.17 465 93 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CORL311_LUNG NA CORL311_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 3 25 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CORL311_LUNG NA CORL311_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.55 18 22 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CORL311_LUNG NA CORL311_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 33 ATN1 1822 broad.mit.edu 37 12 7045892 7045894 + In_Frame_Del DEL CAG - - rs66756893;rs67074116 CORL311_LUNG NA CORL311_LUNG NA g.chr12:7045892_7045894delCAG uc001qrw.1 + 5 1699_1701 c.1462_1464delCAG c.(1462-1464)CAGdel p.Q502del ATN1_uc001qrx.1_In_Frame_Del_p.Q502del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagc 0.458 0.42 84 60 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 CORL311_LUNG NA CORL311_LUNG NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.50 10 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CORL311_LUNG NA CORL311_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 16 96 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 CORL311_LUNG NA CORL311_LUNG NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.11 159 19 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CORL311_LUNG NA CORL311_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.58 111 152 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes CORL311_LUNG NA CORL311_LUNG NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.80 3 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CORL311_LUNG NA CORL311_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 250 729 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CORL311_LUNG NA CORL311_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 123 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CORL47_LUNG NA CORL47_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 3 26 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 CORL47_LUNG NA CORL47_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.13 62 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CORL47_LUNG NA CORL47_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 86 116 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CORL47_LUNG NA CORL47_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 43 67 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CORL47_LUNG NA CORL47_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CORL47_LUNG NA CORL47_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.50 9 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CORL47_LUNG NA CORL47_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 30 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency CORL47_LUNG NA CORL47_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 808 92 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CORL47_LUNG NA CORL47_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 415 159 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CORL47_LUNG NA CORL47_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 20 233 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT CORL47_LUNG NA CORL47_LUNG NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.15 437 77 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 CORL47_LUNG NA CORL47_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.86 14 83 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CORL47_LUNG NA CORL47_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 115 439 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CORL47_LUNG NA CORL47_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 10 97 PATZ1 23598 broad.mit.edu 37 22 31741067 31741067 + Frame_Shift_Del DEL G - - rs714909 byFrequency;by1000genomes CORL47_LUNG NA CORL47_LUNG NA g.chr22:31741067delG uc003akq.2 - 1 1183 c.522delC c.(520-522)CTCfs p.L174fs PATZ1_uc003akp.2_Frame_Shift_Del_p.L174fs|PATZ1_uc003akr.2_Frame_Shift_Del_p.L174fs|PATZ1_uc003aks.2_Frame_Shift_Del_p.L174fs|uc003akt.2_5'Flank NM_014323 NP_055138 Q9HBE1 PATZ1_HUMAN POZ (BTB) and AT hook containing zinc finger 1 174 negative regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding EWSR1/PATZ1(2) soft_tissue(2) 2 GGGGGCGAAAGAGCATTATAT 0.587 0.47 63 57 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CORL88_LUNG NA CORL88_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 4 47 RHOC 389 broad.mit.edu 37 1 113245221 113245222 + Frame_Shift_Del DEL GT - - rs138595121 byFrequency;by1000genomes CORL88_LUNG NA CORL88_LUNG NA g.chr1:113245221_113245222delGT uc001ecp.1 - 5 671_672 c.371_372delAC c.(370-372)GACfs p.D124fs RHOC_uc001ecq.1_Frame_Shift_Del_p.D124fs|RHOC_uc001ecr.1_Frame_Shift_Del_p.D124fs|RHOC_uc009wgk.1_Frame_Shift_Del_p.D124fs NM_001042679 NP_001036144 P08134 RHOC_HUMAN ras homolog gene family, member C precursor 124 axon guidance|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction cytosol|plasma membrane GTP binding|GTPase activity|signal transducer activity ovary(1) 1 Lung SC(450;0.246) all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05) Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133) TGGTGTGCTCGTCTTGCCTCAG 0.584 0.38 53 33 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - CORL88_LUNG NA CORL88_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.31 212 94 TNN 63923 broad.mit.edu 37 1 175049402 175049402 + Frame_Shift_Del DEL C - - rs34902018 CORL88_LUNG NA CORL88_LUNG NA g.chr1:175049402delC uc001gkl.1 + 4 1001 c.888delC c.(886-888)TACfs p.Y296fs TNN_uc010pmx.1_Frame_Shift_Del_p.Y296fs NM_022093 NP_071376 Q9UQP3 TENN_HUMAN tenascin N precursor 296 Fibronectin type-III 1. cell growth|cell migration|signal transduction extracellular space|proteinaceous extracellular matrix large_intestine(5)|ovary(3)|central_nervous_system(1) 9 Breast(1374;0.000962) KIRC - Kidney renal clear cell carcinoma(1967;0.00198) TCAGCTACTACCCCCTGGGGA 0.572 0.32 71 33 CTLA4 1493 broad.mit.edu 37 2 204735492 204735492 + Frame_Shift_Del DEL T - - CORL88_LUNG NA CORL88_LUNG NA g.chr2:204735492delT uc002vak.1 + 2 450 c.293delT c.(292-294)CTAfs p.L98fs CTLA4_uc002val.1_Frame_Shift_Del_p.L98fs|CTLA4_uc010fty.1_Intron|CTLA4_uc010ftz.1_Intron NM_005214 NP_005205 P16410 CTLA4_HUMAN cytotoxic T-lymphocyte-associated protein 4 98 Ig-like V-type.|Extracellular (Potential). B cell receptor signaling pathway|immune response|negative regulation of B cell proliferation|negative regulation of regulatory T cell differentiation|positive regulation of apoptosis|response to DNA damage stimulus|T cell costimulation clathrin-coated endocytic vesicle|external side of plasma membrane|Golgi apparatus|integral to plasma membrane|perinuclear region of cytoplasm 0 Abatacept(DB01281) TTGACCTTCCTAGATGATTCC 0.547 0.44 49 39 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes CORL88_LUNG NA CORL88_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.60 4 6 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 CORL88_LUNG NA CORL88_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.22 39 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CORL88_LUNG NA CORL88_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 115 165 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CORL88_LUNG NA CORL88_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.54 12 14 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CORL88_LUNG NA CORL88_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CORL88_LUNG NA CORL88_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.99 1 74 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 CORL88_LUNG NA CORL88_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 945 322 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 CORL88_LUNG NA CORL88_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.34 45 23 VAV1 7409 broad.mit.edu 37 19 6825352 6825352 + Frame_Shift_Del DEL G - - CORL88_LUNG NA CORL88_LUNG NA g.chr19:6825352delG uc002mfu.1 + 8 859 c.762delG c.(760-762)ATGfs p.M254fs VAV1_uc010xjh.1_Frame_Shift_Del_p.M222fs|VAV1_uc010dva.1_Frame_Shift_Del_p.M254fs|VAV1_uc002mfv.1_Frame_Shift_Del_p.M199fs NM_005428 NP_005419 P15498 VAV_HUMAN vav 1 guanine nucleotide exchange factor 254 DH. apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation cytosol|plasma membrane metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1) 16 TAAAGGAGATGAAGGAAGCCC 0.587 0.53 33 37 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 CORL88_LUNG NA CORL88_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.52 27 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CORL88_LUNG NA CORL88_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 111 334 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CORL88_LUNG NA CORL88_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 59 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COV318_OVARY NA COV318_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 71 FAM132A 388581 broad.mit.edu 37 1 1178482 1178483 + In_Frame_Ins INS - CAC CAC rs78555129 byFrequency;by1000genomes COV318_OVARY NA COV318_OVARY NA g.chr1:1178482_1178483insCAC uc001adl.1 - 6 722_723 c.690_691insGTG c.(688-693)insGTG p.230_231insV NM_001014980 NP_001014980 Q5T7M4 F132A_HUMAN family with sequence similarity 132, member A 230_231 extracellular region 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217) Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.22e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199) 0.000 0.13 191 28 MSH6 2956 broad.mit.edu 37 2 48033791 48033792 + Splice_Site INS - TAAC TAAC COV318_OVARY NA COV318_OVARY NA g.chr2:48033791_48033792insTAAC uc002rwd.3 + 9 4153 c.4001_splice c.e9+1 p.R1334_splice MSH6_uc010fbj.2_Splice_Site_p.R1032_splice|MSH6_uc010yoi.1_Splice_Site_p.R1204_splice|MSH6_uc010yoj.1_Splice_Site_p.R1032_splice NM_000179 NP_000170 P52701 MSH6_HUMAN mutS homolog 6 determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes MutSalpha complex ATP binding|DNA-dependent ATPase activity|protein binding large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1) 168 Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) GATTATTTCGGTAACTAACTAA 0.337 0.32 21 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COV318_OVARY NA COV318_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.44 80 64 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 COV318_OVARY NA COV318_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 6 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 COV318_OVARY NA COV318_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 16 PDCD11 22984 broad.mit.edu 37 10 105203040 105203040 + Frame_Shift_Del DEL A - - COV318_OVARY NA COV318_OVARY NA g.chr10:105203040delA uc001kwy.1 + 33 5161 c.5074delA c.(5074-5076)AAAfs p.K1692fs NM_014976 NP_055791 Q14690 RRP5_HUMAN programmed cell death 11 1692 mRNA processing|rRNA processing nucleolus RNA binding|transcription factor binding ovary(2)|breast(2)|skin(2)|central_nervous_system(1) 7 Colorectal(252;0.0747)|Breast(234;0.128) Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208) CGAGCCTCTCAAAGTCTTTCT 0.557 0.23 33 10 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 COV318_OVARY NA COV318_OVARY NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.39 11 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 COV318_OVARY NA COV318_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 352 117 ALPK2 115701 broad.mit.edu 37 18 56196451 56196451 + Frame_Shift_Del DEL C - - rs7236563 byFrequency;by1000genomes COV318_OVARY NA COV318_OVARY NA g.chr18:56196451delC uc002lhj.3 - 6 5587 c.5373delG c.(5371-5373)AAGfs p.K1791fs ALPK2_uc002lhk.1_Frame_Shift_Del_p.K1122fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 1791 Ig-like 2. ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 CAGCTTGGATCTTTTTCAGTA 0.254 0.33 78 38 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COV318_OVARY NA COV318_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 106 370 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COV318_OVARY NA COV318_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 5 54 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COV434_OVARY NA COV434_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.86 7 42 DENND4B 9909 broad.mit.edu 37 1 153907279 153907281 + In_Frame_Del DEL CTG - - COV434_OVARY NA COV434_OVARY NA g.chr1:153907279_153907281delCTG uc001fdd.1 - 18 3129_3131 c.2728_2730delCAG c.(2728-2730)CAGdel p.Q910del uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) ACACctgctcctgctgctgctgc 0.463 0.12 68 9 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 COV434_OVARY NA COV434_OVARY NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.33 8 4 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 COV434_OVARY NA COV434_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.20 33 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COV434_OVARY NA COV434_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 128 141 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 COV434_OVARY NA COV434_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 11 24 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 COV434_OVARY NA COV434_OVARY NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.60 4 6 POU3F2 5454 broad.mit.edu 37 6 99283172 99283173 + In_Frame_Ins INS - CAG CAG COV434_OVARY NA COV434_OVARY NA g.chr6:99283172_99283173insCAG uc003ppe.2 + 1 593_594 c.423_424insCAG c.(421-426)insCAG p.149_150insQ NM_005604 NP_005595 P20265 PO3F2_HUMAN POU domain, class 3, transcription factor 2 149_150 positive regulation of cell proliferation identical protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197) BRCA - Breast invasive adenocarcinoma(108;0.0355) aacagcagcaacagcagcagca 0.465 0.31 88 39 ARID1B 57492 broad.mit.edu 37 6 157099402 157099403 + In_Frame_Ins INS - CAG CAG COV434_OVARY NA COV434_OVARY NA g.chr6:157099402_157099403insCAG uc003qqn.2 + 1 317_318 c.165_166insCAG c.(163-168)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) TAAACCAGTTCcagcagcagca 0.124 0.21 104 27 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes COV434_OVARY NA COV434_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 COV434_OVARY NA COV434_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 807 331 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 COV434_OVARY NA COV434_OVARY NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.31 9 4 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 COV434_OVARY NA COV434_OVARY NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.58 25 34 ATXN3 4287 broad.mit.edu 37 14 92537354 92537355 + In_Frame_Ins INS - CTGCTG CTGCTG rs12895357;rs67474612 byFrequency;by1000genomes COV434_OVARY NA COV434_OVARY NA g.chr14:92537354_92537355insCTGCTG uc001yac.3 - 10 984_985 c.915_916insCAGCAG c.(913-918)insCAGCAG p.305_306insQQ ATXN3_uc010aug.2_In_Frame_Ins_p.290_291insQQ|ATXN3_uc001yad.3_In_Frame_Ins_p.250_251insQQ|ATXN3_uc010auh.2_In_Frame_Ins_p.239_240insQQ|ATXN3_uc001yae.3_In_Frame_Ins_p.207_208insQQ NM_004993 NP_004984 P54252 ATX3_HUMAN ataxin 3 reference isoform 305_306 G -> QQQQQQQQQQQQR. cell death|nervous system development|nucleotide-excision repair|regulation of transcription, DNA-dependent|synaptic transmission|transcription, DNA-dependent cytoplasm|nuclear matrix|nucleoplasm cysteine-type peptidase activity|protein binding 0 all_cancers(154;0.0768) COAD - Colon adenocarcinoma(157;0.224) GATAGGTCCCCctgctgctgct 0.322 0.28 50 19 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 COV434_OVARY NA COV434_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 37 156 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COV434_OVARY NA COV434_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 133 429 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COV434_OVARY NA COV434_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 7 92 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COV504_OVARY NA COV504_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 54 BMPR2 659 broad.mit.edu 37 2 203329674 203329675 + Frame_Shift_Del DEL AA - - COV504_OVARY NA COV504_OVARY NA g.chr2:203329674_203329675delAA uc002uzf.3 + 2 1367_1368 c.219_220delAA c.(217-222)TCAAAAfs p.S73fs BMPR2_uc010ftr.2_Frame_Shift_Del_p.S73fs|BMPR2_uc002uze.2_Frame_Shift_Del_p.S73fs NM_001204 NP_001195 Q13873 BMPR2_HUMAN bone morphogenetic protein receptor type II 73_74 Extracellular (Potential). anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway integral to plasma membrane ATP binding|metal ion binding|transforming growth factor beta receptor activity ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1) 9 GGGAGAAATCAAAAGGGGACAT 0.381 0.23 55 16 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 COV504_OVARY NA COV504_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 27 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COV504_OVARY NA COV504_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 81 126 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 COV504_OVARY NA COV504_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 32 62 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes COV504_OVARY NA COV504_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 2 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 COV504_OVARY NA COV504_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 48 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes COV504_OVARY NA COV504_OVARY NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.12 50 7 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes COV504_OVARY NA COV504_OVARY NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.15 79 14 TP53 7157 broad.mit.edu 37 17 7576879 7576880 + Frame_Shift_Del DEL GT - - COV504_OVARY NA COV504_OVARY NA g.chr17:7576879_7576880delGT uc002gim.2 - 9 1160_1161 c.966_967delAC c.(964-969)CCACTGfs p.P322fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Frame_Shift_Del_p.P322fs|TP53_uc010cne.1_RNA|TP53_uc010cnf.1_Frame_Shift_Del_p.P190fs|TP53_uc010cng.1_Frame_Shift_Del_p.P190fs|TP53_uc002gii.1_Frame_Shift_Del_p.P190fs|TP53_uc010cnh.1_Frame_Shift_Del_p.P322fs|TP53_uc010cni.1_Frame_Shift_Del_p.P322fs|TP53_uc002gij.2_Frame_Shift_Del_p.P322fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 322_323 Interaction with HIPK1 (By similarity).|Interaction with CARM1.|Interaction with HIPK2. L -> P (in a sporadic cancer; somatic mutation).|L -> R (in a sporadic cancer; somatic mutation).|L -> M (in a sporadic cancer; somatic mutation).|L -> G (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|L -> V (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.P322L(2)|p.P322R(2)|p.L323V(1)|p.P318fs*21(1)|p.S315fs*22(1)|p.?(1)|p.P322fs*23(1)|p.L323G(1)|p.L323fs*22(1)|p.L323M(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) TCTCCATCCAGTGGTTTCTTCT 0.455 0.94 3 50 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 COV504_OVARY NA COV504_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 28 76 LMTK3 114783 broad.mit.edu 37 19 49001791 49001792 + Frame_Shift_Ins INS - G G COV504_OVARY NA COV504_OVARY NA g.chr19:49001791_49001792insG uc002pjk.2 - 12 2621_2622 c.2621_2622insC c.(2620-2622)CCGfs p.P874fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) CCCGGGGCCCCGGGAGTGGGAG 0.718 0.14 56 9 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COV504_OVARY NA COV504_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 23 212 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COV504_OVARY NA COV504_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 58 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 COV644_OVARY NA COV644_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 50 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - COV644_OVARY NA COV644_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.14 332 56 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 COV644_OVARY NA COV644_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.41 13 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 COV644_OVARY NA COV644_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 52 123 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 COV644_OVARY NA COV644_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 14 39 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 COV644_OVARY NA COV644_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.42 135 97 STK3 6788 broad.mit.edu 37 8 99560248 99560248 + Frame_Shift_Del DEL T - - COV644_OVARY NA COV644_OVARY NA g.chr8:99560248delT uc003yip.2 - 9 1231 c.1090delA c.(1090-1092)ACCfs p.T364fs STK3_uc003yio.2_Frame_Shift_Del_p.T392fs|STK3_uc010mbm.1_Frame_Shift_Del_p.T253fs NM_006281 NP_006272 Q13188 STK3_HUMAN serine/threonine kinase 3 364 apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis cytoplasm|nucleus ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity lung(3)|ovary(1) 4 Breast(36;2.4e-06) Breast(495;0.106) OV - Ovarian serous cystadenocarcinoma(57;0.0382) KIRC - Kidney renal clear cell carcinoma(542;9.44e-06) ATCACCATGGTCCCCAAGTCG 0.433 0.56 95 120 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 COV644_OVARY NA COV644_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 1 20 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency COV644_OVARY NA COV644_OVARY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 553 59 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 COV644_OVARY NA COV644_OVARY NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.69 16 35 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 COV644_OVARY NA COV644_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 442 213 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C COV644_OVARY NA COV644_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 17 141 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 COV644_OVARY NA COV644_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.53 43 48 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 COV644_OVARY NA COV644_OVARY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 54 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 COV644_OVARY NA COV644_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 162 527 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 COV644_OVARY NA COV644_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 2 27 FOXO4 4303 broad.mit.edu 37 X 70321277 70321277 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:70321277delG uc004dys.1 + 2 1550 c.1197delG c.(1195-1197)CTGfs p.L399fs FOXO4_uc010nkz.2_Intron|FOXO4_uc004dyt.1_Frame_Shift_Del_p.L344fs NM_005938 NP_005929 P98177 FOXO4_HUMAN forkhead box O4 399 cell cycle arrest|cell differentiation|embryo development|G1 phase of mitotic cell cycle|insulin receptor signaling pathway|mitotic cell cycle G2/M transition DNA damage checkpoint|muscle organ development|negative regulation of angiogenesis|negative regulation of cell proliferation|negative regulation of smooth muscle cell differentiation|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding central_nervous_system(2)|prostate(1) 3 Renal(35;0.156) TTCTGTTGCTGGGGGGGCTTC 0.632 0.85 13 71 KIAA2022 340533 broad.mit.edu 37 X 73962030 73962031 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:73962030_73962031insA uc004eby.2 - 3 2978_2979 c.2361_2362insT c.(2359-2364)TTTCTAfs p.F787fs NM_001008537 NP_001008537 Q5QGS0 K2022_HUMAN hypothetical protein LOC340533 787_788 base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle delta DNA polymerase complex 3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 GTCGTTGGTAGAAAAGTGGAAC 0.411 0.39 140 89 ATRX 546 broad.mit.edu 37 X 76845412 76845413 + Splice_Site INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:76845412_76845413insA uc004ecp.3 - 27 6343 c.6111_splice c.e27-1 p.V2037_splice ATRX_uc004ecq.3_Splice_Site_p.V1999_splice|ATRX_uc004eco.3_Splice_Site_p.V1822_splice NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) AAAACAAGGCTAAAAAAACAGA 0.203 0.38 33 20 TBX22 50945 broad.mit.edu 37 X 79277816 79277816 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:79277816delG uc010nmg.1 + 2 182 c.48delG c.(46-48)GTGfs p.V16fs TBX22_uc004edi.1_5'UTR|TBX22_uc004edj.1_Frame_Shift_Del_p.V16fs NM_001109878 NP_001103348 Q9Y458 TBX22_HUMAN T-box 22 isoform 1 16 V -> A (in a colorectal cancer sample; somatic mutation). multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter nucleus DNA binding|sequence-specific DNA binding transcription factor activity p.V16A(1) lung(7)|large_intestine(3)|central_nervous_system(2)|breast(1)|skin(1)|ovary(1) 15 0.000 0.39 1396 888 RPS6KA6 27330 broad.mit.edu 37 X 83371254 83371255 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:83371254_83371255insA uc004eej.1 - 12 1067_1068 c.990_991insT c.(988-993)TTTGCAfs p.F330fs RPS6KA6_uc011mqt.1_Frame_Shift_Ins_p.F330fs|RPS6KA6_uc011mqu.1_Frame_Shift_Ins_p.F227fs NM_014496 NP_055311 Q9UK32 KS6A6_HUMAN ribosomal protein S6 kinase polypeptide 6 330_331 AGC-kinase C-terminal. axon guidance|central nervous system development|intracellular protein kinase cascade|synaptic transmission cytosol|nucleoplasm ATP binding|magnesium ion binding|protein serine/threonine kinase activity lung(5)|stomach(1)|central_nervous_system(1)|skin(1) 8 TCAATATTTGCAAAAAACAGAT 0.257 0.51 42 44 HNRNPH2 3188 broad.mit.edu 37 X 100667564 100667565 + Frame_Shift_Ins INS - C C CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:100667564_100667565insC uc004ehm.2 + 2 758_759 c.588_589insC c.(586-591)GATCCCfs p.D196fs HNRNPH2_uc004ehn.2_Frame_Shift_Ins_p.D196fs NM_019597 NP_062543 P55795 HNRH2_HUMAN heterogeneous nuclear ribonucleoprotein H2 196_197 nuclear mRNA splicing, via spliceosome actin cytoskeleton|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm nucleotide binding|protein binding|RNA binding 0 CCCACTATGATCCCCCTCGAAA 0.510 0.48 58 54 HNRNPH2 3188 broad.mit.edu 37 X 100668111 100668112 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:100668111_100668112insT uc004ehm.2 + 2 1305_1306 c.1135_1136insT c.(1135-1137)CTTfs p.L379fs HNRNPH2_uc004ehn.2_Frame_Shift_Ins_p.L379fs NM_019597 NP_062543 P55795 HNRH2_HUMAN heterogeneous nuclear ribonucleoprotein H2 379 2 X 16 AA Gly-rich approximate repeats.|2 X 19 AA perfect repeats.|2-2. nuclear mRNA splicing, via spliceosome actin cytoskeleton|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm nucleotide binding|protein binding|RNA binding 0 CTATGTAGAACTTTTTTTGAAT 0.455 0.40 73 48 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 5 51 MST4 51765 broad.mit.edu 37 X 131207113 131207114 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:131207113_131207114insT uc004ewk.1 + 11 1519_1520 c.1218_1219insT c.(1216-1221)AAATTTfs p.K406fs MST4_uc004ewl.1_Frame_Shift_Ins_p.K329fs|MST4_uc011mux.1_Frame_Shift_Ins_p.K428fs|MST4_uc010nrj.1_Frame_Shift_Ins_p.K382fs|MST4_uc004ewm.1_Frame_Shift_Ins_p.K344fs NM_016542 NP_057626 Q9P289 MST4_HUMAN serine/threonine protein kinase MST4 isoform 1 406_407 cellular component disassembly involved in apoptosis|regulation of apoptosis cytosol|Golgi membrane ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity ovary(3)|lung(3)|stomach(2)|upper_aerodigestive_tract(1) 9 Acute lymphoblastic leukemia(192;0.000127) 0.000 0.10 777 89 GPR112 139378 broad.mit.edu 37 X 135404967 135404968 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:135404967_135404968insT uc004ezu.1 + 5 392_393 c.101_102insT c.(100-102)GATfs p.D34fs GPR112_uc010nsb.1_Intron NM_153834 NP_722576 Q8IZF6 GP112_HUMAN G-protein coupled receptor 112 34 Extracellular (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1) 12 Acute lymphoblastic leukemia(192;0.000127) AAAAAGCTGGATTTTTTTGGAA 0.356 0.51 65 68 GPR112 139378 broad.mit.edu 37 X 135405238 135405238 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:135405238delG uc004ezu.1 + 5 663 c.372delG c.(370-372)TTGfs p.L124fs GPR112_uc010nsb.1_Intron NM_153834 NP_722576 Q8IZF6 GP112_HUMAN G-protein coupled receptor 112 124 Extracellular (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1) 12 Acute lymphoblastic leukemia(192;0.000127) CAATATGCTTGATATGGGATG 0.438 0.50 114 115 SRPK3 26576 broad.mit.edu 37 X 153048689 153048690 + Frame_Shift_Ins INS - C C CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:153048689_153048690insC uc004fil.2 + 8 789_790 c.757_758insC c.(757-759)GCCfs p.A253fs SRPK3_uc004fik.2_Frame_Shift_Ins_p.A319fs|SRPK3_uc010nul.2_Frame_Shift_Ins_p.A211fs|SRPK3_uc004fin.2_Frame_Shift_Ins_p.A253fs|SRPK3_uc004fim.2_Frame_Shift_Ins_p.A253fs NM_014370 NP_055185 Q9UPE1 SRPK3_HUMAN serine arginine rich protein-specific kinase 3 253 Protein kinase. cell differentiation|muscle organ development|muscle tissue development ATP binding|protein serine/threonine kinase activity pancreas(2)|lung(1) 3 all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05) 0.000 0.22 1905 532 F8 2157 broad.mit.edu 37 X 154157686 154157686 + Frame_Shift_Del DEL T - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:154157686delT uc004fmt.2 - 14 4550 c.4379delA c.(4378-4380)AATfs p.N1460fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1460 B. N -> K (in HEMA). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AGAAAGGTTATTTTTTTTGGC 0.413 0.40 152 101 F8 2157 broad.mit.edu 37 X 154158427 154158428 + In_Frame_Ins INS - TTT TTT CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chrX:154158427_154158428insTTT uc004fmt.2 - 14 3808_3809 c.3637_3638insAAA c.(3637-3639)ATT>AAAATT p.1212_1213insK NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1212_1213 B. acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) TTCTTCCTGAATTTTTTTTTCT 0.327 0.33 80 40 DVL1 1855 broad.mit.edu 37 1 1271642 1271642 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:1271642delC uc001aer.3 - 15 1940 c.1893delG c.(1891-1893)GGGfs p.G631fs DVL1_uc002quu.2_Frame_Shift_Del_p.G373fs|DVL1_uc009vka.2_Frame_Shift_Del_p.G314fs|DVL1_uc001aeu.1_3'UTR NM_004421 NP_004412 O14640 DVL1_HUMAN dishevelled 1 656 canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome frizzled binding|identical protein binding|protein kinase binding|signal transducer activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145) 0.000 0.92 92 1123 SPEN 23013 broad.mit.edu 37 1 16256833 16256833 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:16256833delA uc001axk.1 + 11 4302 c.4098delA c.(4096-4098)CGAfs p.R1366fs SPEN_uc010obp.1_Frame_Shift_Del_p.R1325fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 1366 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) ATAGCCTTCGAAAAAGGTCTG 0.448 0.46 146 122 SPEN 23013 broad.mit.edu 37 1 16257321 16257322 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:16257321_16257322insT uc001axk.1 + 11 4790_4791 c.4586_4587insT c.(4585-4587)CGTfs p.R1529fs SPEN_uc010obp.1_Frame_Shift_Ins_p.R1488fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 1529 Potential. interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) TTTGCTTCTCGTTTTTTACACA 0.381 0.45 121 100 PTPRU 10076 broad.mit.edu 37 1 29639127 29639128 + Frame_Shift_Ins INS - C C CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:29639127_29639128insC uc001bru.2 + 23 3276_3277 c.3166_3167insC c.(3166-3168)GTCfs p.V1056fs PTPRU_uc001brv.2_Frame_Shift_Ins_p.V1052fs|PTPRU_uc001brw.2_Frame_Shift_Ins_p.V1046fs|PTPRU_uc009vtq.2_Frame_Shift_Ins_p.V1052fs|PTPRU_uc009vtr.2_Frame_Shift_Ins_p.V1043fs NM_005704 NP_005695 Q92729 PTPRU_HUMAN protein tyrosine phosphatase, receptor type, U 1056 Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential). canonical Wnt receptor signaling pathway|cell differentiation|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transmembrane receptor protein tyrosine phosphatase signaling pathway cell-cell junction|integral to plasma membrane beta-catenin binding|transmembrane receptor protein tyrosine phosphatase activity large_intestine(3)|ovary(1)|kidney(1)|central_nervous_system(1)|skin(1) 7 Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123) Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871) AGAGCATGGCGTCCCCTACCAT 0.634 0.36 9 5 MUTYH 4595 broad.mit.edu 37 1 45798844 45798845 + Splice_Site INS - G G CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:45798844_45798845insG uc001cnm.2 - 5 596 c.380_splice c.e5-1 p.V127_splice MUTYH_uc009vxn.2_Intron|MUTYH_uc001cnf.2_Splice_Site_p.V102_splice|MUTYH_uc009vxo.2_Splice_Site_p.V102_splice|MUTYH_uc001cng.2_Splice_Site_p.V113_splice|MUTYH_uc001cnj.2_Splice_Site_p.V10_splice|MUTYH_uc001cni.2_Splice_Site_p.V102_splice|MUTYH_uc001cnh.2_Splice_Site_p.V103_splice|MUTYH_uc001cno.2_Splice_Site_p.V10_splice|MUTYH_uc001cnk.2_Intron|MUTYH_uc010oll.1_Intron|MUTYH_uc001cnl.2_Splice_Site_p.V116_splice|MUTYH_uc009vxp.2_Splice_Site_p.V130_splice|MUTYH_uc001cnn.2_Splice_Site_p.V117_splice NM_012222 NP_036354 Q9UIF7 MUTYH_HUMAN mutY homolog isoform 1 depurination|mismatch repair nucleoplasm 4 iron, 4 sulfur cluster binding|DNA N-glycosylase activity|endonuclease activity|metal ion binding|MutSalpha complex binding 0 Acute lymphoblastic leukemia(166;0.155) AGACCCACACTGGGGGAAAGGG 0.614 0.43 39 29 PTGFR 5737 broad.mit.edu 37 1 78958518 78958519 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:78958518_78958519insT uc001din.2 + 2 356_357 c.90_91insT c.(88-93)GTATTTfs p.V30fs PTGFR_uc001dim.2_Frame_Shift_Ins_p.V30fs NM_000959 NP_000950 P43088 PF2R_HUMAN prostaglandin F receptor isoform a precursor 30_31 Extracellular (Potential). parturition extracellular region|integral to plasma membrane prostaglandin F receptor activity ovary(3)|breast(2)|skin(1) 6 Colorectal(170;0.248) Bimatoprost(DB00905)|Latanoprost(DB00654)|Travoprost(DB00287) 0.000 0.11 867 103 HSP90B3P 343477 broad.mit.edu 37 1 92109017 92109017 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:92109017delG uc010osx.1 + 3 1044 c.1044delG c.(1042-1044)AAGfs p.K348fs NR_003130 SubName: Full=cDNA FLJ58812, highly similar to Endoplasmin (Heat shock protein 90kDa beta member 1); 0 ATGTTGTCAAGGAAGGAATGA 0.408 0.48 128 119 PDE4DIP 9659 broad.mit.edu 37 1 144879085 144879086 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:144879085_144879086insT uc001elw.3 - 27 4655_4656 c.4364_4365insA c.(4363-4365)AATfs p.N1455fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Ins_p.N1411fs|PDE4DIP_uc001elv.3_Frame_Shift_Ins_p.N462fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 1455 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) CTTCTAGTCCATTTTTTGGGAG 0.520 0.25 115 39 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 262 85 MTMR11 10903 broad.mit.edu 37 1 149905828 149905828 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:149905828delG uc001etl.3 - 8 942 c.691delC c.(691-693)CGTfs p.R231fs MTMR11_uc001etm.1_Frame_Shift_Del_p.R159fs|MTMR11_uc010pbm.1_Frame_Shift_Del_p.R203fs|MTMR11_uc010pbn.1_Frame_Shift_Del_p.R73fs NM_001145862 NP_001139334 A4FU01 MTMRB_HUMAN myotubularin related protein 11 isoform a 231 Myotubularin phosphatase. phosphatase activity central_nervous_system(1) 1 Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171) LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247) CAGAAGTAACGGGGGAGGCTG 0.488 0.43 72 55 INSRR 3645 broad.mit.edu 37 1 156814053 156814053 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:156814053delC uc010pht.1 - 15 3011 c.2757delG c.(2755-2757)GGGfs p.G919fs NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron NM_014215 NP_055030 P14616 INSRR_HUMAN insulin receptor-related receptor precursor 919 Extracellular (Potential). protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity lung(11)|ovary(5)|skin(2)|kidney(1)|central_nervous_system(1) 20 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) GGACATGCAGCCCCCCAGCAT 0.562 0.45 17 14 RGL1 23179 broad.mit.edu 37 1 183881395 183881395 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:183881395delA uc001gqo.2 + 15 1899 c.1742delA c.(1741-1743)CAAfs p.Q581fs RGL1_uc010pof.1_Frame_Shift_Del_p.Q386fs|RGL1_uc001gqm.2_Frame_Shift_Del_p.Q616fs|RGL1_uc010pog.1_Frame_Shift_Del_p.Q579fs|RGL1_uc010poh.1_Frame_Shift_Del_p.Q579fs|RGL1_uc010poi.1_Frame_Shift_Del_p.Q552fs NM_015149 NP_055964 Q9NZL6 RGL1_HUMAN ral guanine nucleotide dissociation 581 Ser-rich. cellular lipid metabolic process|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction intracellular protein binding|Ral guanyl-nucleotide exchange factor activity breast(5)|ovary(4)|lung(2) 11 GATGAGCCTCAAAAAAAGGTA 0.488 0.43 31 23 TPR 7175 broad.mit.edu 37 1 186316497 186316498 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:186316497_186316498insT uc001grv.2 - 22 3166_3167 c.2869_2870insA c.(2869-2871)ACAfs p.T957fs NM_003292 NP_003283 P12270 TPR_HUMAN nuclear pore complex-associated protein TPR 957 Potential. carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm ATP binding|protein binding|serine-tRNA ligase activity ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1) 7 Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157) Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553) GCTCGTACTTGTTTTGAGTCTC 0.381 0.45 130 105 PTPRC 5788 broad.mit.edu 37 1 198682102 198682103 + Frame_Shift_Ins INS - T T rs145357582 byFrequency CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:198682102_198682103insT uc001gur.1 + 12 1366_1367 c.1186_1187insT c.(1186-1188)ATTfs p.I396fs PTPRC_uc001gus.1_Frame_Shift_Ins_p.I348fs|PTPRC_uc001gut.1_Frame_Shift_Ins_p.I235fs|PTPRC_uc009wzf.1_Frame_Shift_Ins_p.I284fs|PTPRC_uc010ppg.1_Frame_Shift_Ins_p.I332fs NM_002838 NP_002829 P08575 PTPRC_HUMAN protein tyrosine phosphatase, receptor type, C 396 Extracellular (Potential).|Fibronectin type-III 1. axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway focal adhesion|integral to plasma membrane|membrane raft protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1) 12 GCCTCAGATTATTTTTTGTAGA 0.327 0.35 57 31 DYRK3 8444 broad.mit.edu 37 1 206821440 206821441 + Frame_Shift_Ins INS - AA AA CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:206821440_206821441insAA uc001hej.2 + 3 1065_1066 c.897_898insAA c.(895-900)ATTAAAfs p.I299fs DYRK3_uc001hek.2_Intron|DYRK3_uc001hei.2_Frame_Shift_Ins_p.I279fs NM_003582 NP_003573 O43781 DYRK3_HUMAN dual-specificity tyrosine-(Y)-phosphorylation 299_300 Protein kinase. erythrocyte differentiation nucleus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity stomach(2)|central_nervous_system(1) 3 Breast(84;0.183) BRCA - Breast invasive adenocarcinoma(75;0.166) ATGAGCTGATTAAAAAAAATAA 0.406 0.32 174 81 OBSCN 84033 broad.mit.edu 37 1 228550390 228550391 + Frame_Shift_Ins INS - GG GG CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:228550390_228550391insGG uc009xez.1 + 80 18819_18820 c.18775_18776insGG c.(18775-18777)AGGfs p.R6259fs OBSCN_uc001hsr.1_Frame_Shift_Ins_p.R888fs NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 6259 apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) 0.000 0.25 1456 474 OBSCN 84033 broad.mit.edu 37 1 228562291 228562292 + Frame_Shift_Ins INS - CC CC rs138389654 by1000genomes CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr1:228562291_228562292insCC uc009xez.1 + 97 22545_22546 c.22501_22502insCC c.(22501-22503)GCCfs p.A7501fs OBSCN_uc001hsr.1_Frame_Shift_Ins_p.A2130fs NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 7501 Ig-like 55. apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) TGCAGACGGAGCCCCCCTGGAG 0.619 0.37 40 23 PXDN 7837 broad.mit.edu 37 2 1642734 1642734 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:1642734delC uc002qxa.2 - 21 4154 c.4090delG c.(4090-4092)GAAfs p.E1364fs NM_012293 NP_036425 Q92626 PXDN_HUMAN peroxidasin precursor 1364 extracellular matrix organization|hydrogen peroxide catabolic process|immune response endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity pancreas(6)|ovary(2) 8 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716) all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228) CTGAGATGTTCCCCCTGTCTC 0.522 0.42 164 119 BIRC6 57448 broad.mit.edu 37 2 32701335 32701336 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:32701335_32701336insA uc010ezu.2 + 34 6909_6910 c.6775_6776insA c.(6775-6777)GAAfs p.E2259fs NM_016252 NP_057336 Q9NR09 BIRC6_HUMAN baculoviral IAP repeat-containing 6 2259 anti-apoptosis|apoptosis intracellular acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1) 14 Acute lymphoblastic leukemia(172;0.155) 0.000 0.47 130 116 EML4 27436 broad.mit.edu 37 2 42488268 42488269 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:42488268_42488269insA uc002rsi.2 + 4 608_609 c.346_347insA c.(346-348)GAAfs p.E116fs EML4_uc002rsh.3_Frame_Shift_Ins_p.E116fs|EML4_uc010fap.2_Intron NM_019063 NP_061936 Q9HC35 EMAL4_HUMAN echinoderm microtubule associated protein like 4 116 microtubule-based process|mitosis cytoplasm|microtubule protein binding EML4/ALK(246) lung(246)|ovary(2)|central_nervous_system(1)|skin(1) 250 CAGTGGTACagaaaaaaagaaa 0.238 0.42 38 28 MAP4K4 9448 broad.mit.edu 37 2 102452431 102452432 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:102452431_102452432insA uc002tbg.2 + 9 819_820 c.764_765insA c.(763-765)TCAfs p.S255fs MAP4K4_uc002tbc.2_Frame_Shift_Ins_p.S255fs|MAP4K4_uc002tbd.2_Frame_Shift_Ins_p.S255fs|MAP4K4_uc002tbe.2_Frame_Shift_Ins_p.S255fs|MAP4K4_uc002tbf.2_Frame_Shift_Ins_p.S255fs|MAP4K4_uc010yvy.1_Frame_Shift_Ins_p.S255fs|MAP4K4_uc002tbh.2_Frame_Shift_Ins_p.S255fs|MAP4K4_uc002tbi.2_Intron|MAP4K4_uc010yvz.1_Frame_Shift_Ins_p.S235fs|MAP4K4_uc010fiw.1_Frame_Shift_Ins_p.S97fs|MAP4K4_uc002tbj.1_Frame_Shift_Ins_p.S151fs NM_145687 NP_663720 O95819 M4K4_HUMAN mitogen-activated protein kinase kinase kinase 255 Protein kinase. intracellular protein kinase cascade|regulation of JNK cascade|response to stress cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity stomach(1)|lung(1)|central_nervous_system(1)|skin(1) 4 CGGCTGAAGTCAAAAAAATGGT 0.416 0.49 39 38 MERTK 10461 broad.mit.edu 37 2 112786271 112786272 + Frame_Shift_Ins INS - C C CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:112786271_112786272insC uc002thk.1 + 19 2952_2953 c.2830_2831insC c.(2830-2832)GCCfs p.A944fs MERTK_uc002thl.1_Frame_Shift_Ins_p.A768fs NM_006343 NP_006334 Q12866 MERTK_HUMAN MER receptor tyrosine kinase precursor 944 Cytoplasmic (Potential). cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration integral to plasma membrane|soluble fraction ATP binding|transmembrane receptor protein tyrosine kinase activity lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1) 9 TCTGACTTCTGCCCCCTCTGCT 0.530 0.60 19 29 LRP1B 53353 broad.mit.edu 37 2 141143539 141143539 + Frame_Shift_Del DEL T - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:141143539delT uc002tvj.1 - 67 11426 c.10454delA c.(10453-10455)AACfs p.N3485fs NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 3485 Extracellular (Potential).|LDL-receptor class A 25. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) ACAGTTGTTGTTTTTACACTG 0.383 0.37 136 79 LRP1B 53353 broad.mit.edu 37 2 141474328 141474329 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:141474328_141474329insT uc002tvj.1 - 36 6787_6788 c.5815_5816insA c.(5815-5817)AGAfs p.R1939fs NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 1939 Extracellular (Potential).|LDL-receptor class B 19. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) AGTCTGATCTCTTTTAGCTCTG 0.371 0.45 119 99 RIF1 55183 broad.mit.edu 37 2 152316604 152316604 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:152316604delA uc002txm.2 + 26 3176 c.3046delA c.(3046-3048)AAAfs p.K1016fs RIF1_uc002txl.2_Frame_Shift_Del_p.K1016fs|RIF1_uc002txn.2_Frame_Shift_Del_p.K1016fs|RIF1_uc002txo.2_Frame_Shift_Del_p.K1016fs|RIF1_uc002txp.2_5'Flank NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1016 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) 0.000 0.40 267 181 RIF1 55183 broad.mit.edu 37 2 152320988 152320989 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:152320988_152320989insA uc002txm.2 + 30 5084_5085 c.4954_4955insA c.(4954-4956)GAAfs p.E1652fs RIF1_uc002txl.2_Frame_Shift_Ins_p.E1652fs|RIF1_uc002txn.2_Frame_Shift_Ins_p.E1652fs|RIF1_uc002txo.2_Frame_Shift_Ins_p.E1652fs|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1652 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) TGTGTGTGAGGAAAAAAATGAA 0.332 0.40 78 53 ACVR1 90 broad.mit.edu 37 2 158637068 158637069 + Frame_Shift_Del DEL CA - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:158637068_158637069delCA uc002tzm.3 - 5 450_451 c.111_112delTG c.(109-114)TGTGAAfs p.C37fs ACVR1_uc002tzn.3_Frame_Shift_Del_p.C37fs|ACVR1_uc010fog.2_Frame_Shift_Del_p.C37fs NM_001111067 NP_001104537 Q04771 ACVR1_HUMAN activin A receptor, type I precursor 37_38 Extracellular (Potential). BMP signaling pathway|G1/S transition of mitotic cell cycle|negative regulation of activin receptor signaling pathway|negative regulation of apoptosis|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway activin receptor complex activin binding|ATP binding|follistatin binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta binding ovary(2)|skin(1) 3 BRCA - Breast invasive adenocarcinoma(221;0.104) Adenosine triphosphate(DB00171) GAGAGACCTTCACACACACACA 0.475 0.43 115 86 LRP2 4036 broad.mit.edu 37 2 169997025 169997025 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:169997025delG uc002ues.2 - 72 13352 c.13139delC c.(13138-13140)CCAfs p.P4380fs NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 4380 EGF-like 17.|Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) 0.000 0.47 358 319 LRP2 4036 broad.mit.edu 37 2 170127593 170127594 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:170127593_170127594insA uc002ues.2 - 16 2353_2354 c.2140_2141insT c.(2140-2142)TCAfs p.S714fs LRP2_uc010zdf.1_Intron NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 714 Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) AACTTGGGATGAAAAAATGAGG 0.441 0.35 43 23 HOXD11 3237 broad.mit.edu 37 2 176972824 176972824 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:176972824delC uc002uki.2 + 1 741 c.741delC c.(739-741)GGCfs p.G247fs HOXD11_uc010fqx.2_Intron NM_021192 NP_067015 P31277 HXD11_HUMAN homeobox D11 247 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678) 0.000 0.23 47 14 NFE2L2 4780 broad.mit.edu 37 2 178095769 178095769 + Frame_Shift_Del DEL T - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:178095769delT uc002ulh.3 - 5 2117 c.1562delA c.(1561-1563)AATfs p.N521fs NFE2L2_uc002ulg.3_Frame_Shift_Del_p.N505fs|NFE2L2_uc010zfa.1_Frame_Shift_Del_p.N498fs|NFE2L2_uc002uli.3_Frame_Shift_Del_p.N505fs NM_006164 NP_006155 Q16236 NF2L2_HUMAN nuclear factor erythroid 2-like 2 isoform 1 521 Leucine-zipper. transcription from RNA polymerase II promoter centrosome|cytosol|nucleus|plasma membrane protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity central_nervous_system(1) 1 Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935) 0.000 0.31 655 290 TTN 7273 broad.mit.edu 37 2 179433954 179433955 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:179433954_179433955insT uc010zfg.1 - 275 69424_69425 c.69200_69201insA c.(69199-69201)AATfs p.N23067fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Ins_p.N16762fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.N16695fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.N16570fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 23994 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CAACAATGTAATTTTTTATTTT 0.391 0.49 96 92 TTN 7273 broad.mit.edu 37 2 179477254 179477255 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:179477254_179477255insT uc010zfg.1 - 215 42517_42518 c.42293_42294insA c.(42292-42294)AATfs p.N14098fs uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Ins_p.N7793fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.N7726fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.N7601fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 15025 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GGTCTGCTGTATTTTTTGTGAT 0.401 0.54 61 72 TTN 7273 broad.mit.edu 37 2 179616191 179616192 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:179616191_179616192insT uc002unb.2 - 46 11159_11160 c.10935_10936insA c.(10933-10938)AAACAAfs p.K3645fs TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron NM_133379 NP_596870 Q8WZ42 TITIN_HUMAN titin isoform novex-3 9490_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCCACATCTTGTTTTTTGTTAA 0.371 0.48 123 114 TTN 7273 broad.mit.edu 37 2 179616590 179616591 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:179616590_179616591insA uc002unb.2 - 46 10760_10761 c.10536_10537insT c.(10534-10539)TTTAAAfs p.F3512fs TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron NM_133379 NP_596870 Q8WZ42 TITIN_HUMAN titin isoform novex-3 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AAAACATATTTAAATGTAAGTT 0.381 0.43 60 46 TTN 7273 broad.mit.edu 37 2 179621155 179621155 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:179621155delA uc010zfh.1 - 44 10759 c.10535delT c.(10534-10536)TTAfs p.L3512fs TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc002unb.2_Intron NM_133437 NP_597681 Q8WZ42 TITIN_HUMAN titin isoform novex-2 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) ATCATCTTTTAAAACACAGAG 0.433 0.55 77 94 INPP5D 3635 broad.mit.edu 37 2 233990484 233990484 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:233990484delC uc010zmo.1 + 4 532 c.379delC c.(379-381)CCCfs p.P127fs INPP5D_uc010zmp.1_Frame_Shift_Del_p.P126fs NM_001017915 NP_001017915 Q92835 SHIP1_HUMAN SH2 containing inositol phosphatase isoform a 127 SH3-binding 1. apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway cytosol inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding ovary(1)|central_nervous_system(1) 2 Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843) Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185) ACCCGAGCTGCCCCCAAGAAA 0.607 0.43 40 30 PDCD1 5133 broad.mit.edu 37 2 242794439 242794440 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr2:242794439_242794440insT uc002wcq.3 - 3 570_571 c.502_503insA c.(502-504)ACCfs p.T168fs PDCD1_uc010fzs.2_Intron|PDCD1_uc010fzt.2_RNA NM_005018 NP_005009 Q15116 PDCD1_HUMAN programmed cell death 1 precursor 168 Extracellular (Potential). apoptosis|humoral immune response|multicellular organismal development|T cell costimulation integral to membrane protein tyrosine phosphatase activity|signal transducer activity ovary(1) 1 all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0219) 0.000 0.49 1135 1088 CNTN6 27255 broad.mit.edu 37 3 1427366 1427367 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr3:1427366_1427367insA uc003boz.2 + 20 2856_2857 c.2589_2590insA c.(2587-2592)ACCAAAfs p.T863fs CNTN6_uc011asj.1_Frame_Shift_Ins_p.T791fs|CNTN6_uc003bpa.2_Frame_Shift_Ins_p.T863fs NM_014461 NP_055276 Q9UQ52 CNTN6_HUMAN contactin 6 precursor 863_864 Fibronectin type-III 3. axon guidance|cell adhesion|central nervous system development|Notch signaling pathway anchored to membrane|plasma membrane skin(3)|lung(2)|breast(2)|pancreas(1) 8 all_cancers(2;0.000164)|all_epithelial(2;0.107) Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139) ATGTCACAACCAAAAACATCAC 0.421 0.39 40 26 MLH1 4292 broad.mit.edu 37 3 37048490 37048490 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr3:37048490delA uc003cgl.2 + 5 449 c.389delA c.(388-390)TACfs p.Y130fs MLH1_uc011aye.1_5'UTR|MLH1_uc011ayb.1_5'UTR|MLH1_uc010hge.2_Frame_Shift_Del_p.Y130fs|MLH1_uc003cgn.3_5'UTR|MLH1_uc011ayc.1_Frame_Shift_Del_p.Y32fs|MLH1_uc011ayd.1_5'UTR|MLH1_uc003cgo.2_5'UTR NM_000249 NP_000240 P40692 MLH1_HUMAN MutL protein homolog 1 130 mismatch repair|somatic hypermutation of immunoglobulin genes chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex ATP binding|ATPase activity|protein binding p.0?(1)|p.Y130fs*6(1) large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1) 77 AGAGCAAGTTACTCAGATGGA 0.373 0.98 2 88 ACVR2B 93 broad.mit.edu 37 3 38519759 38519760 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr3:38519759_38519760insA uc003cif.2 + 4 522_523 c.498_499insA c.(496-501)CCCTACfs p.P166fs ACVR2B_uc003cig.2_5'UTR NM_001106 NP_001097 Q13705 AVR2B_HUMAN activin A receptor, type IIB precursor 166_167 Cytoplasmic (Potential). activin receptor signaling pathway|anterior/posterior pattern formation|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|regulation of transcription, DNA-dependent cell surface|cytoplasm|integral to plasma membrane activin receptor activity|ATP binding|growth factor binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity lung(1) 1 Medulloblastoma(35;0.163) KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071) GCAAGCCCCCCTACGGTCATGT 0.614 0.42 56 40 ULK4 54986 broad.mit.edu 37 3 41938315 41938316 + Frame_Shift_Ins INS - G G CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr3:41938315_41938316insG uc003ckv.3 - 15 1729_1730 c.1528_1529insC c.(1528-1530)CTGfs p.L510fs ULK4_uc003ckw.2_Frame_Shift_Ins_p.L510fs|ULK4_uc003ckx.1_Frame_Shift_Ins_p.L510fs NM_017886 NP_060356 Q96C45 ULK4_HUMAN unc-51-like kinase 4 510 ATP binding|protein serine/threonine kinase activity 0 KIRC - Kidney renal clear cell carcinoma(284;0.214) CAGGCTTACCAGGGGGGAATGG 0.465 0.47 18 16 CCR3 1232 broad.mit.edu 37 3 46307370 46307371 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr3:46307370_46307371insT uc003cpg.1 + 4 1264_1265 c.721_722insT c.(721-723)ATTfs p.I241fs CCR3_uc003cpi.1_Frame_Shift_Ins_p.I241fs|CCR3_uc003cpj.1_Frame_Shift_Ins_p.I241fs|CCR3_uc003cpk.1_Frame_Shift_Ins_p.I262fs|CCR3_uc010hjb.1_Frame_Shift_Ins_p.I259fs|CCR3_uc003cpl.1_Frame_Shift_Ins_p.I274fs NM_178329 NP_847899 P51677 CCR3_HUMAN CC chemokine receptor 3 isoform 1 241 Helical; Name=6; (Potential). cell adhesion|cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cAMP nucleotide second messenger|inflammatory response|interspecies interaction between organisms|positive regulation of angiogenesis integral to plasma membrane ovary(3)|lung(3)|breast(1)|kidney(1) 8 BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216) 0.000 0.25 1014 333 PBRM1 55193 broad.mit.edu 37 3 52678784 52678784 + Frame_Shift_Del DEL T - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr3:52678784delT uc003des.2 - 8 847 c.835delA c.(835-837)ATAfs p.I279fs PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.I279fs|PBRM1_uc003der.2_Frame_Shift_Del_p.I279fs|PBRM1_uc003det.2_Frame_Shift_Del_p.I279fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.I279fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.I279fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.I279fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.I279fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.I279fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.I177fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 279 chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding p.I279fs*4(2) kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.29 526 215 FLNB 2317 broad.mit.edu 37 3 58089788 58089788 + Frame_Shift_Del DEL G - - rs145086495 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr3:58089788delG uc003djj.2 + 10 1751 c.1586delG c.(1585-1587)TGGfs p.W529fs FLNB_uc010hne.2_Frame_Shift_Del_p.W529fs|FLNB_uc003djk.2_Frame_Shift_Del_p.W529fs|FLNB_uc010hnf.2_Frame_Shift_Del_p.W529fs|FLNB_uc003djl.2_Frame_Shift_Del_p.W360fs|FLNB_uc003djm.2_Frame_Shift_Del_p.W360fs NM_001457 NP_001448 O75369 FLNB_HUMAN filamin B isoform 2 529 Filamin 3. actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction cell cortex|integral to membrane|nucleus|sarcomere actin binding breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1) 19 BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898) 0.000 0.62 774 1238 ROBO1 6091 broad.mit.edu 37 3 78710235 78710235 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr3:78710235delA uc003dqe.2 - 16 2473 c.2265delT c.(2263-2265)TTTfs p.F755fs ROBO1_uc003dqb.2_Frame_Shift_Del_p.F716fs|ROBO1_uc003dqc.2_Frame_Shift_Del_p.F719fs|ROBO1_uc003dqd.2_Frame_Shift_Del_p.F719fs|ROBO1_uc010hoh.2_5'UTR|ROBO1_uc011bgl.1_Frame_Shift_Del_p.F327fs|ROBO1_uc003dqf.1_Frame_Shift_Del_p.F434fs NM_002941 NP_002932 Q9Y6N7 ROBO1_HUMAN roundabout 1 isoform a 755 Extracellular (Potential).|Fibronectin type-III 2. activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway cell surface|cytoplasm|integral to plasma membrane axon guidance receptor activity|identical protein binding|LRR domain binding large_intestine(2) 2 Lung SC(41;0.0257)|Lung NSC(201;0.0439) LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274) GAAATTCATTAAAAAAAGGGC 0.398 0.51 87 92 CXCL9 4283 broad.mit.edu 37 4 76924805 76924806 + Frame_Shift_Ins INS - TT TT CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr4:76924805_76924806insTT uc003hjh.1 - 4 362_363 c.323_324insAA c.(322-324)AAGfs p.K108fs NM_002416 NP_002407 Q07325 CXCL9_HUMAN small inducible cytokine B9 precursor 108 cell-cell signaling|cellular defense response|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response extracellular space chemokine activity ovary(1) 1 Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934) TCAGAACTTTCTTTTTTTGATG 0.332 0.40 134 91 TBCK 93627 broad.mit.edu 37 4 107151546 107151548 + In_Frame_Del DEL AAG - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr4:107151546_107151548delAAG uc010ilv.2 - 19 2111_2113 c.1746_1748delCTT c.(1744-1749)TTCTTA>TTA p.F582del TBCK_uc003hyb.2_In_Frame_Del_p.F325del|TBCK_uc003hye.2_In_Frame_Del_p.F543del|TBCK_uc003hyc.2_In_Frame_Del_p.F519del|TBCK_uc003hyd.2_In_Frame_Del_p.F410del|TBCK_uc003hyf.2_In_Frame_Del_p.F582del NM_001163435 NP_001156907 Q8TEA7 TBCK_HUMAN TBC domain-containing protein kinase-like 582 Rab-GAP TBC. intracellular Rab GTPase activator activity large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1) 5 GTTGTCTTTTAAGAAGAAGTTAT 0.340 0.42 23 17 CFI 3426 broad.mit.edu 37 4 110687927 110687927 + Frame_Shift_Del DEL T - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr4:110687927delT uc003hzr.3 - 2 319 c.111delA c.(109-111)AAAfs p.K37fs CFI_uc011cft.1_Frame_Shift_Del_p.K37fs|CFI_uc003hzs.3_Frame_Shift_Del_p.K37fs NM_000204 NP_000195 P05156 CFAI_HUMAN complement factor I preproprotein 37 complement activation, classical pathway|innate immune response|proteolysis extracellular space|membrane scavenger receptor activity|serine-type endopeptidase activity 0 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.000331) GGTGAGTATATTTTTTTGCTA 0.398 0.39 67 42 EGF 1950 broad.mit.edu 37 4 110884434 110884434 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr4:110884434delA uc003hzy.3 + 9 1870 c.1418delA c.(1417-1419)GAAfs p.E473fs EGF_uc011cfu.1_Frame_Shift_Del_p.E431fs|EGF_uc011cfv.1_Frame_Shift_Del_p.E473fs NM_001963 NP_001954 P01133 EGF_HUMAN epidermal growth factor precursor 473 EGF-like 4.|Extracellular (Potential). angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface integral to membrane|plasma membrane|platelet alpha granule lumen calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity ovary(1)|breast(1)|central_nervous_system(1)|skin(1) 4 Hepatocellular(203;0.0893) OV - Ovarian serous cystadenocarcinoma(123;9.87e-06) Sulindac(DB00605) CAACTGGATGAAAAAAGCTGT 0.433 0.49 106 103 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.40 76 50 MAML3 55534 broad.mit.edu 37 4 140810639 140810641 + In_Frame_Del DEL GCT - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr4:140810639_140810641delGCT uc003ihz.1 - 3 2689_2691 c.1937_1939delAGC c.(1936-1941)CAGCCG>CCG p.Q646del MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 646 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) GGAGGTGGCGgctgctgctgctg 0.419 0.11 56 7 DCLK2 166614 broad.mit.edu 37 4 151023682 151023683 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr4:151023682_151023683insA uc003ilm.3 + 2 574_575 c.474_475insA c.(472-477)ACCAAAfs p.T158fs DCLK2_uc003iln.3_Frame_Shift_Ins_p.T158fs|DCLK2_uc003ilo.3_Frame_Shift_Ins_p.T158fs|DCLK2_uc003ilp.3_RNA NM_001040260 NP_001035350 Q8N568 DCLK2_HUMAN doublecortin-like kinase 2 isoform a 158_159 intracellular signal transduction cytoplasm|cytoskeleton ATP binding|protein serine/threonine kinase activity ovary(3) 3 all_hematologic(180;0.151) TCGATTACACCAAAAATATTAA 0.386 0.50 12 12 ING2 3622 broad.mit.edu 37 4 184432081 184432081 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr4:184432081delA uc003ivs.1 + 2 948 c.819delA c.(817-819)ACAfs p.T273fs ING2_uc011ckk.1_Frame_Shift_Del_p.T233fs NM_001564 NP_001555 Q9H160 ING2_HUMAN inhibitor of growth family, member 2 273 chromatin modification|positive regulation of transcription, DNA-dependent|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of growth|signal transduction|transcription, DNA-dependent CCAAT-binding factor complex|Sin3 complex chromatin binding|DNA binding|protein complex binding|zinc ion binding ovary(1) 1 all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|all_hematologic(60;0.0207)|Prostate(90;0.0235)|all_neural(102;0.202) all cancers(43;1.15e-26)|Epithelial(43;2.98e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|GBM - Glioblastoma multiforme(59;4.22e-06)|Colorectal(24;5.87e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155) 0.000 0.18 858 191 CASP3 836 broad.mit.edu 37 4 185552986 185552987 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr4:185552986_185552987insT uc003iwh.2 - 6 678_679 c.415_416insA c.(415-417)ATAfs p.I139fs CASP3_uc003iwg.2_Frame_Shift_Ins_p.I139fs|CASP3_uc003iwi.2_Frame_Shift_Ins_p.I139fs NM_004346 NP_004337 P42574 CASP3_HUMAN caspase 3 preproprotein 139 activation of caspase activity by cytochrome c|DNA fragmentation involved in apoptotic nuclear change|negative regulation of apoptosis|nerve growth factor receptor signaling pathway|nuclear fragmentation involved in apoptotic nuclear change|proteolysis|response to tumor necrosis factor cytosol|mitochondrion|nucleoplasm|plasma membrane cysteine-type endopeptidase activity|protein binding kidney(1) 1 all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.057)|all_hematologic(60;0.0592) all cancers(43;2.05e-27)|Epithelial(43;4.27e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.04e-11)|Colorectal(24;2e-05)|STAD - Stomach adenocarcinoma(60;2.35e-05)|GBM - Glioblastoma multiforme(59;4.94e-05)|COAD - Colon adenocarcinoma(29;0.00017)|BRCA - Breast invasive adenocarcinoma(30;0.000218)|LUSC - Lung squamous cell carcinoma(40;0.00904)|READ - Rectum adenocarcinoma(43;0.161) Melatonin(DB01065)|Minocycline(DB01017)|Simvastatin(DB00641) AAAGTTTGTTATTTTTTTCAGG 0.371 0.44 99 77 TRIO 7204 broad.mit.edu 37 5 14387627 14387627 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr5:14387627delA uc003jff.2 + 22 3657 c.3651delA c.(3649-3651)ATAfs p.I1217fs TRIO_uc003jfg.2_RNA|TRIO_uc011cna.1_Frame_Shift_Del_p.I1168fs|TRIO_uc003jfh.1_Frame_Shift_Del_p.I866fs NM_007118 NP_009049 O75962 TRIO_HUMAN triple functional domain (PTPRF interacting) 1217 apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway cytosol ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1) 18 Lung NSC(4;0.000742) CGGCAGAGATAAAAAAATGTG 0.443 0.43 91 70 TRIO 7204 broad.mit.edu 37 5 14477003 14477004 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr5:14477003_14477004insT uc003jff.2 + 41 6090_6091 c.6084_6085insT c.(6082-6087)GACTTTfs p.D2028fs TRIO_uc003jfg.2_RNA|TRIO_uc003jfh.1_Frame_Shift_Ins_p.D1677fs NM_007118 NP_009049 O75962 TRIO_HUMAN triple functional domain (PTPRF interacting) 2028_2029 DH 2. apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway cytosol ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1) 18 Lung NSC(4;0.000742) TTCTTTCCAGCTTTTTTTTAGG 0.292 0.42 46 33 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 21 63 PIK3R1 5295 broad.mit.edu 37 5 67589576 67589576 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr5:67589576delA uc003jva.2 + 11 1899 c.1339delA c.(1339-1341)AAAfs p.K447fs PIK3R1_uc003jvb.2_Frame_Shift_Del_p.K447fs|PIK3R1_uc003jvc.2_Frame_Shift_Del_p.K147fs|PIK3R1_uc003jvd.2_Frame_Shift_Del_p.K177fs|PIK3R1_uc003jve.2_Frame_Shift_Del_p.K126fs|PIK3R1_uc011crb.1_Frame_Shift_Del_p.K117fs NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 447 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.K448fs*32(2)|p.D434_Q475del(2)|p.G446_Y452>VI(1)|p.?(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) 0.000 0.29 818 336 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.35 426 230 CHD1 1105 broad.mit.edu 37 5 98195690 98195691 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr5:98195690_98195691insT uc003knf.2 - 32 4657_4658 c.4509_4510insA c.(4507-4512)AAACGGfs p.K1503fs CHD1_uc010jbn.2_Frame_Shift_Ins_p.K229fs NM_001270 NP_001261 O14646 CHD1_HUMAN chromodomain helicase DNA binding protein 1 1503_1504 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117) COAD - Colon adenocarcinoma(37;0.0717) Epirubicin(DB00445) GACTCCTGCCGTTTTTTAATAG 0.213 0.50 28 28 APC 324 broad.mit.edu 37 5 112175676 112175677 + Frame_Shift_Del DEL AG - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr5:112175676_112175677delAG uc010jby.2 + 16 4765_4766 c.4385_4386delAG c.(4384-4386)AAGfs p.K1462fs APC_uc011cvt.1_Frame_Shift_Del_p.K1444fs|APC_uc003kpz.3_Frame_Shift_Del_p.K1462fs|APC_uc003kpy.3_Frame_Shift_Del_p.K1462fs|APC_uc010jbz.2_Frame_Shift_Del_p.K1179fs|APC_uc010jca.2_Frame_Shift_Del_p.K762fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1462 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.S1465fs*3(20)|p.E1464fs*8(8)|p.K1462fs*6(3)|p.?(1)|p.K1454fs*3(1)|p.K1192fs*3(1)|p.K1462fs*5(1)|p.K1462fs*10(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) ACTGCTGAAAAGAGAGAGAGTG 0.450 0.43 76 58 FBN2 2201 broad.mit.edu 37 5 127610311 127610311 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr5:127610311delC uc003kuu.2 - 60 8098 c.7659delG c.(7657-7659)GGGfs p.G2553fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 2553 EGF-like 43; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) TACAGGTAAACCCCCCCAGGG 0.423 0.10 180 19 FBN2 2201 broad.mit.edu 37 5 127637081 127637082 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr5:127637081_127637082insT uc003kuu.2 - 47 6477_6478 c.6038_6039insA c.(6037-6039)AACfs p.N2013fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 2013 EGF-like 33; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) TACCTATACAGTTTTTGCCATC 0.337 0.46 69 58 ADAMTS19 171019 broad.mit.edu 37 5 128958022 128958023 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr5:128958022_128958023insT uc003kvb.1 + 10 1733_1734 c.1733_1734insT c.(1732-1734)TCTfs p.S578fs ADAMTS19_uc010jdh.1_RNA NM_133638 NP_598377 Q8TE59 ATS19_HUMAN ADAM metallopeptidase with thrombospondin type 1 578 Disintegrin. proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding ovary(5)|breast(2)|lung(1)|skin(1) 9 all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) OV - Ovarian serous cystadenocarcinoma(64;0.222) CCATTGGCTTCTTTTTGTCAGG 0.436 0.50 60 59 ARHGAP26 23092 broad.mit.edu 37 5 142434005 142434005 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr5:142434005delC uc011dbj.1 + 15 1322 c.1287delC c.(1285-1287)GACfs p.D429fs ARHGAP26_uc003lmt.2_Frame_Shift_Del_p.D429fs|ARHGAP26_uc003lmw.2_Frame_Shift_Del_p.D429fs NM_015071 NP_055886 Q9UNA1 RHG26_HUMAN GTPase regulator associated with the focal 429 Rho-GAP. actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction cytoskeleton|cytosol|focal adhesion cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding ovary(1) 1 all_hematologic(541;0.0416) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) TCATTTTAGACCCCAAGACTG 0.244 0.43 76 57 RANBP17 64901 broad.mit.edu 37 5 170610221 170610222 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr5:170610221_170610222insA uc003mba.2 + 17 1932_1933 c.1916_1917insA c.(1915-1917)CTAfs p.L639fs RANBP17_uc003mbb.2_Intron|RANBP17_uc003mbd.2_Frame_Shift_Ins_p.L2fs|RANBP17_uc010jjs.2_RNA|RANBP17_uc003mbc.2_Frame_Shift_Ins_p.L2fs NM_022897 NP_075048 Q9H2T7 RBP17_HUMAN RAN binding protein 17 639 mRNA transport|protein import into nucleus|transmembrane transport cytoplasm|nuclear pore GTP binding|protein transporter activity ovary(2)|central_nervous_system(1) 3 Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123) Medulloblastoma(196;0.0399)|all_neural(177;0.0966) Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516) AAATTCATGCTAAAAAACCACA 0.267 0.11 93 11 HNRNPH1 3187 broad.mit.edu 37 5 179044643 179044644 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr5:179044643_179044644insA uc003mkf.3 - 9 1034_1035 c.928_929insT c.(928-930)TCAfs p.S310fs HNRNPH1_uc011dgn.1_Frame_Shift_Ins_p.S40fs|HNRNPH1_uc003mkg.3_Frame_Shift_Ins_p.S218fs|HNRNPH1_uc003mke.3_Frame_Shift_Ins_p.S310fs|HNRNPH1_uc003mkh.3_Frame_Shift_Ins_p.S310fs NM_005520 NP_005511 P31943 HNRH1_HUMAN heterogeneous nuclear ribonucleoprotein H1 310 RRM 3.|2 X 16 AA Gly-rich approximate repeats. regulation of RNA splicing actin cytoskeleton|catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm nucleotide binding|poly(U) RNA binding|protein binding 0 GTTGAGCGGTGAAAAAAACTAC 0.381 0.43 95 72 PRPF4B 8899 broad.mit.edu 37 6 4031880 4031881 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:4031880_4031881insA uc003mvv.2 + 2 220_221 c.129_130insA c.(127-132)CACAAAfs p.H43fs PRPF4B_uc011dhv.1_RNA NM_003913 NP_003904 Q13523 PRP4B_HUMAN serine/threonine-protein kinase PRP4K 43_44 His-rich.|Arg/Lys-rich (basic). catalytic step 2 spliceosome ATP binding|protein binding|protein serine/threonine kinase activity breast(5) 5 Ovarian(93;0.0925) all_hematologic(90;0.0895) ACAGTCGTCACaaaaaaaagaa 0.168 0.30 55 24 PRPF4B 8899 broad.mit.edu 37 6 4052974 4052975 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:4052974_4052975insA uc003mvv.2 + 11 2424_2425 c.2333_2334insA c.(2332-2334)TTAfs p.L778fs PRPF4B_uc003mvw.2_RNA|C6orf146_uc010jnq.1_Intron|PRPF4B_uc011dhv.1_RNA NM_003913 NP_003904 Q13523 PRP4B_HUMAN serine/threonine-protein kinase PRP4K 778 Protein kinase. catalytic step 2 spliceosome ATP binding|protein binding|protein serine/threonine kinase activity breast(5) 5 Ovarian(93;0.0925) all_hematologic(90;0.0895) CGAGAGGTGTTAAAAAAATATG 0.302 0.45 68 55 MAK 4117 broad.mit.edu 37 6 10802238 10802238 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:10802238delG uc003mzl.2 - 7 947 c.718delC c.(718-720)CAGfs p.Q240fs SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jos.1_Intron|MAK_uc010jot.2_RNA|MAK_uc010jou.2_RNA|MAK_uc003mzm.2_Frame_Shift_Del_p.Q240fs|MAK_uc010jov.1_RNA NM_005906 NP_005897 P20794 MAK_HUMAN male germ cell-associated kinase 240 Protein kinase. cell differentiation|multicellular organismal development|spermatogenesis ATP binding|cyclin-dependent protein kinase activity breast(2)|skin(1) 3 Breast(50;0.107)|Ovarian(93;0.107) all_hematologic(90;0.117) GGAACACACTGGGGAAAACGG 0.428 0.43 85 65 DEK 7913 broad.mit.edu 37 6 18250048 18250049 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:18250048_18250049insT uc003ncr.1 - 7 788_789 c.595_596insA c.(595-597)ACTfs p.T199fs DEK_uc011djf.1_Frame_Shift_Ins_p.T165fs|DEK_uc011djg.1_RNA NM_003472 NP_003463 P35659 DEK_HUMAN DEK oncogene isoform 1 199 chromatin modification|regulation of transcription from RNA polymerase II promoter|signal transduction|transcription from RNA polymerase II promoter|viral genome replication nucleus DNA binding|histone binding kidney(1) 1 Ovarian(93;0.00769)|Breast(50;0.0495) all_hematologic(90;0.053) OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332) TTTGCTACAAGTTTTTTTAGAT 0.347 0.49 94 89 BAT3 7917 broad.mit.edu 37 6 31612922 31612923 + Frame_Shift_Ins INS - G G CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:31612922_31612923insG uc003nvg.3 - 10 1501_1502 c.1187_1188insC c.(1186-1188)CCAfs p.P396fs BAT3_uc003nvf.3_Frame_Shift_Ins_p.P390fs|BAT3_uc003nvh.3_Frame_Shift_Ins_p.P390fs|BAT3_uc003nvi.3_Frame_Shift_Ins_p.P390fs|BAT3_uc011dnw.1_Frame_Shift_Ins_p.P390fs|BAT3_uc011dnx.1_Frame_Shift_Ins_p.P390fs|BAT3_uc003nvj.1_Frame_Shift_Ins_p.P390fs NM_004639 NP_004630 P46379 BAG6_HUMAN HLA-B associated transcript-3 isoform a 396 Pro-rich.|4 X 29 AA approximate repeats. apoptosis in response to endoplasmic reticulum stress|brain development|cell differentiation|chromatin modification|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|embryo development|internal peptidyl-lysine acetylation|kidney development|lung development|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|protein stabilization|spermatogenesis|synaptonemal complex assembly|tail-anchored membrane protein insertion into ER membrane|transport|ubiquitin-dependent protein catabolic process BAT3 complex|nucleus polyubiquitin binding|proteasome binding|ribosome binding 0 CATTGGGAGTTGGGGGGGGCCG 0.579 0.40 18 12 FANCE 2178 broad.mit.edu 37 6 35425715 35425715 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:35425715delC uc003oko.1 + 4 1108 c.923delC c.(922-924)GCCfs p.A308fs FANCE_uc010jvw.1_Frame_Shift_Del_p.A308fs NM_021922 NP_068741 Q9HB96 FANCE_HUMAN Fanconi anemia, complementation group E 308 Interaction with FANCC. DNA repair nucleoplasm protein binding ovary(1)|lung(1)|skin(1) 3 TTGGAGGATGCCCCCCCAGTT 0.542 0.30 30 13 DNAH8 1769 broad.mit.edu 37 6 38816439 38816440 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:38816439_38816440insA uc003ooe.1 + 35 5010_5011 c.4410_4411insA c.(4408-4413)TTTAAAfs p.F1470fs NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 ATGCTCCATTTAAAAAAAATAT 0.342 0.45 67 54 PTK7 5754 broad.mit.edu 37 6 43100230 43100230 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:43100230delC uc003oub.1 + 7 1231 c.1033delC c.(1033-1035)CCCfs p.P345fs PTK7_uc003ouc.1_Frame_Shift_Del_p.P345fs|PTK7_uc003oud.1_Frame_Shift_Del_p.P345fs|PTK7_uc003oue.1_Frame_Shift_Del_p.P345fs|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Frame_Shift_Del_p.P353fs|PTK7_uc010jyj.1_Frame_Shift_Del_p.P21fs|PTK7_uc003oua.2_Frame_Shift_Del_p.P345fs NM_002821 NP_002812 Q13308 PTK7_HUMAN PTK7 protein tyrosine kinase 7 isoform a 345 Ig-like C2-type 4.|Extracellular (Potential). actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration cell-cell junction|integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ovary(2)|large_intestine(1) 3 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423) GACCTGCCTTCCCCCCAAGGG 0.617 0.32 54 25 PHF3 23469 broad.mit.edu 37 6 64395275 64395276 + Frame_Shift_Del DEL AA - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:64395275_64395276delAA uc003pep.1 + 3 1678_1679 c.1652_1653delAA c.(1651-1653)CAAfs p.Q551fs PHF3_uc010kaf.1_Frame_Shift_Del_p.Q551fs|PHF3_uc003pem.2_Frame_Shift_Del_p.Q504fs|PHF3_uc010kag.1_Frame_Shift_Del_p.Q463fs|PHF3_uc010kah.1_Frame_Shift_Del_p.Q365fs|PHF3_uc003pen.2_Frame_Shift_Del_p.Q463fs|PHF3_uc011dxs.1_Intron|PHF3_uc003peo.2_Frame_Shift_Del_p.Q551fs NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 551 multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) AGAAAAAAACAAATTGATAAGG 0.337 0.36 47 27 CYB5R4 51167 broad.mit.edu 37 6 84634230 84634231 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:84634230_84634231insA uc003pkf.2 + 10 865_866 c.733_734insA c.(733-735)CAAfs p.Q245fs NM_016230 NP_057314 Q7L1T6 NB5R4_HUMAN cytochrome b5 reductase 4 245 CS. cell development|detection of oxygen|generation of precursor metabolites and energy|glucose homeostasis|insulin secretion|response to antibiotic|superoxide metabolic process endoplasmic reticulum|perinuclear region of cytoplasm cytochrome-b5 reductase activity|heme binding|NAD(P)H oxidase activity breast(2) 2 all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128) BRCA - Breast invasive adenocarcinoma(397;0.0871) GATTGTTCTACAAAAAAAAGAG 0.337 0.35 99 53 AIM1 202 broad.mit.edu 37 6 106968043 106968044 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:106968043_106968044insA uc003prh.2 + 2 2223_2224 c.1736_1737insA c.(1735-1737)CCAfs p.P579fs NM_001624 NP_001615 Q9Y4K1 AIM1_HUMAN absent in melanoma 1 579 sugar binding breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1) 9 Breast(9;0.0138)|all_epithelial(6;0.169) all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473) Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305) all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858) GTGCAGTTGCCAACTTGTCACA 0.540 0.36 85 47 FRK 2444 broad.mit.edu 37 6 116265525 116265525 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:116265525delC uc003pwi.1 - 6 1469 c.1022delG c.(1021-1023)GGAfs p.G341fs NM_002031 NP_002022 P42685 FRK_HUMAN fyn-related kinase 341 Protein kinase. negative regulation of cell proliferation cytoplasm|nucleus ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding ovary(3)|lung(3) 6 all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465) all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625) ATAGGCCATTCCAGAGGCAAC 0.423 0.51 62 65 ESR1 2099 broad.mit.edu 37 6 152265516 152265517 + Frame_Shift_Ins INS - C C CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:152265516_152265517insC uc003qom.3 + 6 1339_1340 c.969_970insC c.(967-972)GAGCCCfs p.E323fs ESR1_uc010kin.2_Frame_Shift_Ins_p.E323fs|ESR1_uc010kio.2_Frame_Shift_Ins_p.E325fs|ESR1_uc010kip.2_Frame_Shift_Ins_p.E322fs|ESR1_uc003qon.3_Frame_Shift_Ins_p.E323fs|ESR1_uc003qoo.3_Frame_Shift_Ins_p.E323fs|ESR1_uc010kiq.2_Intron|ESR1_uc010kir.2_Intron|ESR1_uc011eet.1_Intron|ESR1_uc011eeu.1_Intron|ESR1_uc011eev.1_Intron|ESR1_uc011eew.1_Intron|ESR1_uc010kis.2_Intron|ESR1_uc011eex.1_Frame_Shift_Ins_p.E104fs|ESR1_uc010kit.1_Frame_Shift_Ins_p.E60fs|ESR1_uc011eey.1_Frame_Shift_Ins_p.E60fs NM_001122742 NP_001116214 P03372 ESR1_HUMAN estrogen receptor alpha isoform 4 323_324 Steroid-binding.|Interaction with AKAP13. positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus chromatin remodeling complex|cytoplasm|nucleoplasm beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding central_nervous_system(2)|ovary(1)|lung(1)|breast(1) 5 Ovarian(120;0.0448) BRCA - Breast invasive adenocarcinoma(37;0.0841) OV - Ovarian serous cystadenocarcinoma(155;4.55e-10) Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539) TGGATGCTGAGCCCCCGATACT 0.545 0.42 46 34 TBP 6908 broad.mit.edu 37 6 170871004 170871005 + In_Frame_Ins INS - CAA CAA CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr6:170871004_170871005insCAA uc003qxt.2 + 3 412_413 c.180_181insCAA c.(178-183)insCAA p.95_96insQ TBP_uc003qxu.2_In_Frame_Ins_p.95_96insQ|TBP_uc011ehf.1_In_Frame_Ins_p.75_76insQ|TBP_uc011ehg.1_In_Frame_Ins_p.95_96insQ NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 95_96 cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) Ggcagcagcagcaacaacaaca 0.198 0.33 26 13 GLI3 2737 broad.mit.edu 37 7 42005573 42005573 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:42005573delG uc011kbh.1 - 15 3189 c.3098delC c.(3097-3099)CCGfs p.P1033fs GLI3_uc011kbg.1_Frame_Shift_Del_p.P974fs NM_000168 NP_000159 P10071 GLI3_HUMAN GLI-Kruppel family member GLI3 1033 negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis cilium|cytosol|nucleolus beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1) 19 GGCCATCGCCGGGGGGTTGCA 0.701 0.38 8 5 EGFR 1956 broad.mit.edu 37 7 55229322 55229322 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:55229322delG uc003tqk.2 + 13 1875 c.1629delG c.(1627-1629)GAGfs p.E543fs EGFR_uc003tqi.2_Frame_Shift_Del_p.E543fs|EGFR_uc003tqj.2_Frame_Shift_Del_p.E543fs|EGFR_uc010kzg.1_Frame_Shift_Del_p.E498fs|EGFR_uc011kco.1_Frame_Shift_Del_p.E490fs|EGFR_uc011kcp.1_Intron|EGFR_uc011kcq.1_Intron NM_005228 NP_005219 P00533 EGFR_HUMAN epidermal growth factor receptor isoform a 543 Approximate.|Extracellular (Potential). activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1) 9571 all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318) GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607) Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072) ACCTTCTGGAGGGGTAGGAGG 0.532 0.44 9 7 PTPN12 5782 broad.mit.edu 37 7 77256104 77256104 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:77256104delC uc003ugh.2 + 13 1199 c.1108delC c.(1108-1110)CCCfs p.P370fs PTPN12_uc011kgp.1_Frame_Shift_Del_p.P251fs|PTPN12_uc011kgq.1_Frame_Shift_Del_p.P240fs|PTPN12_uc010lds.2_Frame_Shift_Del_p.P102fs NM_002835 NP_002826 Q05209 PTN12_HUMAN protein tyrosine phosphatase, non-receptor type 370 Interaction with TGFB1I1 (By similarity). soluble fraction non-membrane spanning protein tyrosine phosphatase activity|SH3 domain binding ovary(1)|breast(1)|pancreas(1) 3 0.000 0.14 1369 219 HGF 3082 broad.mit.edu 37 7 81334984 81334984 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:81334984delA uc003uhl.2 - 16 2008 c.1843delT c.(1843-1845)TATfs p.Y615fs HGF_uc003uhm.2_Frame_Shift_Del_p.Y610fs NM_000601 NP_000592 P14210 HGF_HUMAN hepatocyte growth factor isoform 1 615 Peptidase S1. epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling platelet alpha granule lumen growth factor activity|serine-type endopeptidase activity ovary(2)|central_nervous_system(2) 4 CCCCAGCCATAAACACTGCAA 0.348 0.43 69 53 AKAP9 10142 broad.mit.edu 37 7 91694626 91694626 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:91694626delA uc003ulg.2 + 25 6284 c.6059delA c.(6058-6060)CAAfs p.Q2020fs AKAP9_uc003ulf.2_Frame_Shift_Del_p.Q2020fs|AKAP9_uc003uli.2_Frame_Shift_Del_p.Q1643fs NM_005751 NP_005742 Q99996 AKAP9_HUMAN A-kinase anchor protein 9 isoform 2 2032 Potential.|Glu-rich. G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport centrosome|cytosol|Golgi apparatus receptor binding breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1) 26 all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) GATGACCTTCAAAAACAAGTG 0.313 0.44 32 25 AKAP9 10142 broad.mit.edu 37 7 91694694 91694695 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:91694694_91694695insA uc003ulg.2 + 25 6352_6353 c.6127_6128insA c.(6127-6129)GAAfs p.E2043fs AKAP9_uc003ulf.2_Frame_Shift_Ins_p.E2043fs|AKAP9_uc003uli.2_Frame_Shift_Ins_p.E1666fs NM_005751 NP_005742 Q99996 AKAP9_HUMAN A-kinase anchor protein 9 isoform 2 2055 Potential.|Glu-rich. G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport centrosome|cytosol|Golgi apparatus receptor binding breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1) 26 all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) GCTGGAACAAGAAAAAAATACT 0.327 0.26 64 23 STAG3 10734 broad.mit.edu 37 7 99778187 99778187 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:99778187delC uc003utx.1 + 2 163 c.8delC c.(7-9)TCCfs p.S3fs STAG3_uc010lgs.1_5'UTR|STAG3_uc011kjk.1_Frame_Shift_Del_p.S3fs NM_012447 NP_036579 Q9UJ98 STAG3_HUMAN stromal antigen 3 3 chromosome segregation|synaptonemal complex assembly chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex binding ovary(4)|skin(2)|lung(1)|kidney(1) 8 Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439) AGCATGTCTTCCCCGTTGCAA 0.532 0.43 39 29 PPP1R3A 5506 broad.mit.edu 37 7 113519428 113519428 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:113519428delG uc010ljy.1 - 4 1750 c.1719delC c.(1717-1719)CCCfs p.P573fs NM_002711 NP_002702 Q16821 PPR3A_HUMAN protein phosphatase 1, regulatory (inhibitor) 573 glycogen metabolic process integral to membrane lung(9)|ovary(9)|pancreas(7)|skin(6)|breast(2)|prostate(1) 34 TTGCCCGGGTGGGGATTGCGG 0.473 0.43 73 55 KIAA1549 57670 broad.mit.edu 37 7 138602055 138602056 + Frame_Shift_Ins INS - G G rs61746877 by1000genomes CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:138602055_138602056insG uc011kql.1 - 2 2365_2366 c.2316_2317insC c.(2314-2319)CCCGGCfs p.P772fs KIAA1549_uc003vuk.3_Frame_Shift_Ins_p.P722fs|KIAA1549_uc011kqj.1_Frame_Shift_Ins_p.P772fs NM_020910 NP_065961 Q9HCM3 K1549_HUMAN hypothetical protein LOC57670 isoform 1 772_773 integral to membrane KIAA1549/BRAF(229) central_nervous_system(229)|pancreas(1) 230 GACTCAGAGCCGGGGGGCACCA 0.460 0.37 39 23 EPHA1 2041 broad.mit.edu 37 7 143095951 143095951 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:143095951delC uc003wcz.2 - 6 1166 c.1079delG c.(1078-1080)GGAfs p.G360fs NM_005232 NP_005223 P21709 EPHA1_HUMAN ephrin receptor EphA1 precursor 360 Extracellular (Potential).|Fibronectin type-III 1. integral to plasma membrane ATP binding|ephrin receptor activity ovary(3)|lung(1)|breast(1) 5 Melanoma(164;0.205) Myeloproliferative disorder(862;0.0255) ATCCTGGCGTCCCCCCGTATC 0.657 0.45 18 15 EZH2 2146 broad.mit.edu 37 7 148506484 148506485 + Splice_Site INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:148506484_148506485insA uc003wfd.1 - 18 2181 c.2015_splice c.e18-1 p.D672_splice EZH2_uc011kug.1_Splice_Site_p.D621_splice|EZH2_uc003wfb.1_Splice_Site_p.D677_splice|EZH2_uc003wfc.1_Splice_Site_p.D633_splice|EZH2_uc011kuh.1_Splice_Site_p.D663_splice NM_004456 NP_004447 Q15910 EZH2_HUMAN enhancer of zeste 2 isoform a negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent ESC/E(Z) complex DNA binding|histone-lysine N-methyltransferase activity|protein binding haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1) 183 Melanoma(164;0.15) OV - Ovarian serous cystadenocarcinoma(82;0.00239) 0.000 0.56 229 286 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 12 MLL3 58508 broad.mit.edu 37 7 151845200 151845202 + In_Frame_Del DEL CTC - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:151845200_151845202delCTC uc003wla.2 - 52 14029_14031 c.13810_13812delGAG c.(13810-13812)GAGdel p.E4604del MLL3_uc003wkz.2_In_Frame_Del_p.E3722del|MLL3_uc003wkx.2_In_Frame_Del_p.E762del|MLL3_uc003wky.2_In_Frame_Del_p.E2168del NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 4604 FYR N-terminal. intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) GCCCATCCTTCTCCTCAATGGAG 0.537 0.46 64 55 PAXIP1 22976 broad.mit.edu 37 7 154782739 154782740 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:154782739_154782740insA uc003wlp.2 - 4 343_344 c.300_301insT c.(298-303)TTTGGAfs p.F100fs PAXIP1_uc003wlq.1_Frame_Shift_Ins_p.L12fs|PAXIP1_uc011kvs.1_Intron NM_007349 NP_031375 Q6ZW49 PAXI1_HUMAN PAX interacting protein 1 100_101 BRCT 2.|Interaction with PA1 (By similarity). DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent histone methyltransferase complex|nuclear matrix lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_neural(206;0.119) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.0296) UCEC - Uterine corpus endometrioid carcinoma (81;0.178) GCAGTGATTCCAAAAAAAATCT 0.332 0.40 85 56 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.31 18 8 MNX1 3110 broad.mit.edu 37 7 156802865 156802865 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr7:156802865delG uc003wnd.1 - 1 483 c.180delC c.(178-180)CCCfs p.P60fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.P60fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 60 humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.73 13 35 MCM4 4173 broad.mit.edu 37 8 48883979 48883979 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr8:48883979delA uc003xqk.1 + 13 1974 c.1879delA c.(1879-1881)AAAfs p.K627fs MCM4_uc003xql.1_Frame_Shift_Del_p.K627fs|MCM4_uc011ldi.1_Frame_Shift_Del_p.K614fs NM_182746 NP_877423 P33991 MCM4_HUMAN minichromosome maintenance complex component 4 627 MCM. cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle MCM complex ATP binding|DNA binding|helicase activity|protein binding ovary(2)|skin(2) 4 all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354) GTGGAATCCTAAAAAAACAAC 0.408 0.48 63 58 VCPIP1 80124 broad.mit.edu 37 8 67576521 67576521 + Frame_Shift_Del DEL T - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr8:67576521delT uc003xwn.2 - 1 2932 c.2673delA c.(2671-2673)AAAfs p.K891fs NM_025054 NP_079330 Q96JH7 VCIP1_HUMAN valosin containing protein (p97)/p47 complex 891 protein ubiquitination endoplasmic reticulum|Golgi stack ubiquitin-specific protease activity lung(2)|ovary(2)|central_nervous_system(1)|breast(1)|skin(1)|kidney(1) 8 Lung NSC(129;0.142)|all_lung(136;0.227) Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149) AGTACATTTCTTTTTCAGCTT 0.368 0.49 100 96 SGK3 23678 broad.mit.edu 37 8 67752239 67752239 + Frame_Shift_Del DEL T - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr8:67752239delT uc003xwr.2 + 11 1042 c.743delT c.(742-744)CTTfs p.L248fs SGK3_uc003xwp.2_Frame_Shift_Del_p.L242fs|SGK3_uc003xwt.2_Frame_Shift_Del_p.L248fs|SGK3_uc003xwu.2_Frame_Shift_Del_p.L248fs NM_001033578 NP_001028750 Q96BR1 SGK3_HUMAN serum/glucocorticoid regulated kinase 3 isoform 248 Protein kinase. cell communication|response to stress cytoplasmic membrane-bounded vesicle|early endosome ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity ovary(1)|large_intestine(1)|lung(1)|breast(1) 4 Breast(64;0.186) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206) ATTTGACAGCTTTTTTTCCAC 0.403 0.55 29 36 SGK3 23678 broad.mit.edu 37 8 67763086 67763086 + Frame_Shift_Del DEL T - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr8:67763086delT uc003xwr.2 + 16 1550 c.1251delT c.(1249-1251)CCTfs p.P417fs SGK3_uc003xwp.2_Frame_Shift_Del_p.P411fs|SGK3_uc003xwt.2_Frame_Shift_Del_p.P417fs|SGK3_uc003xwu.2_Frame_Shift_Del_p.P385fs NM_001033578 NP_001028750 Q96BR1 SGK3_HUMAN serum/glucocorticoid regulated kinase 3 isoform 417 Protein kinase. cell communication|response to stress cytoplasmic membrane-bounded vesicle|early endosome ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity ovary(1)|large_intestine(1)|lung(1)|breast(1) 4 Breast(64;0.186) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206) AGAATCATCCTTTTTTTGAAT 0.308 0.18 93 20 TRPS1 7227 broad.mit.edu 37 8 116430655 116430656 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr8:116430655_116430656insA uc003ynz.2 - 5 3145_3146 c.2686_2687insT c.(2686-2688)TGTfs p.C896fs TRPS1_uc011lhy.1_Frame_Shift_Ins_p.C900fs|TRPS1_uc003yny.2_Frame_Shift_Ins_p.C909fs|TRPS1_uc010mcy.2_Frame_Shift_Ins_p.C896fs NM_014112 NP_054831 Q9UHF7 TRPS1_HUMAN zinc finger transcription factor TRPS1 896 GATA-type. negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) GCAATTGGCACAAAAAACACCG 0.495 0.38 64 39 TRIB1 10221 broad.mit.edu 37 8 126443308 126443309 + Frame_Shift_Ins INS - C C CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr8:126443308_126443309insC uc003yrx.2 + 1 746_747 c.164_165insC c.(163-165)AGCfs p.S55fs TRIB1_uc011lis.1_5'Flank|TRIB1_uc010mdn.2_5'Flank NM_025195 NP_079471 Q96RU8 TRIB1_HUMAN G-protein-coupled receptor induced protein 55 Protein kinase. JNK cascade|negative regulation of lipopolysaccharide-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|regulation of MAP kinase activity|response to lipopolysaccharide cytoplasm|nucleus ATP binding|mitogen-activated protein kinase kinase binding|protein kinase activity|protein kinase inhibitor activity|transcription factor binding|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity lung(1) 1 all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108) STAD - Stomach adenocarcinoma(47;0.000918) 0.000 0.50 453 453 SCRIB 23513 broad.mit.edu 37 8 144886852 144886852 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr8:144886852delG uc003yzp.1 - 21 2902 c.2895delC c.(2893-2895)CCCfs p.P965fs SCRIB_uc003yzn.1_5'Flank|SCRIB_uc003yzo.1_Frame_Shift_Del_p.P965fs NM_015356 NP_056171 Q14160 SCRIB_HUMAN scribble isoform b 965 Interaction with ARHGEF7. activation of Rac GTPase activity|apoptosis involved in morphogenesis|cell migration|cell proliferation|cell-cell adhesion|establishment of apical/basal cell polarity|interspecies interaction between organisms|mammary gland duct morphogenesis|negative regulation of mitotic cell cycle|positive chemotaxis|positive regulation of apoptosis|positive regulation of receptor recycling|protein localization to adherens junction cell-cell adherens junction|Scrib-APC-beta-catenin complex protein binding urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)|pancreas(1) 5 all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18) CAGCAGCGGTGGGGGGTGAGG 0.706 0.47 8 7 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 12 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039782 + In_Frame_Del DEL CAGCAG - - rs113070757;rs62639301;rs139102413 byFrequency;byFrequency CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr9:2039777_2039782delCAGCAG uc003zhc.2 + 4 766_771 c.667_672delCAGCAG c.(667-672)CAGCAGdel p.QQ237del SMARCA2_uc003zhd.2_In_Frame_Del_p.QQ237del|SMARCA2_uc010mha.2_In_Frame_Del_p.QQ228del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 237_238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.25 1110 377 PAX5 5079 broad.mit.edu 37 9 36840626 36840626 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr9:36840626delG uc003zzo.1 - 10 1555 c.1107delC c.(1105-1107)CCCfs p.P369fs PAX5_uc011lpt.1_Frame_Shift_Del_p.P165fs|PAX5_uc011lpu.1_RNA|PAX5_uc011lpv.1_RNA|PAX5_uc011lpw.1_Frame_Shift_Del_p.P306fs|PAX5_uc011lpx.1_Frame_Shift_Del_p.P269fs|PAX5_uc011lpy.1_Frame_Shift_Del_p.P198fs|PAX5_uc010mls.1_Frame_Shift_Del_p.P263fs|PAX5_uc011lpz.1_Frame_Shift_Del_p.P326fs|PAX5_uc011lqa.1_Frame_Shift_Del_p.P261fs|PAX5_uc010mlq.1_RNA|PAX5_uc011lqb.1_RNA|PAX5_uc010mlo.1_Frame_Shift_Del_p.P335fs|PAX5_uc010mlp.1_Frame_Shift_Del_p.P340fs|PAX5_uc011lqc.1_Frame_Shift_Del_p.P297fs|PAX5_uc010mlr.1_Frame_Shift_Del_p.P292fs NM_016734 NP_057953 Q02548 PAX5_HUMAN paired box 5 369 cell differentiation|humoral immune response|nervous system development|organ morphogenesis|spermatogenesis|transcription from RNA polymerase II promoter nucleus DNA binding p.?(7) PAX5/JAK2(18) haematopoietic_and_lymphoid_tissue(142)|lung(3)|central_nervous_system(2) 147 all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44) GBM - Glioblastoma multiforme(29;0.0108) TATAATAGTAGGGGGAGCCTG 0.632 0.46 7 6 WNK2 65268 broad.mit.edu 37 9 96021610 96021610 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr9:96021610delC uc004ati.1 + 11 2780 c.2780delC c.(2779-2781)TCCfs p.S927fs WNK2_uc011lud.1_Frame_Shift_Del_p.S927fs|WNK2_uc004atj.2_Frame_Shift_Del_p.S927fs|WNK2_uc004atk.2_Frame_Shift_Del_p.S564fs|WNK2_uc010mrc.1_Frame_Shift_Del_p.S875fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 927 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 GTCCCTCCTTCCCCCCATCAC 0.662 0.33 28 14 PTCH1 5727 broad.mit.edu 37 9 98268792 98268793 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr9:98268792_98268793insT uc004avk.3 - 2 478_479 c.290_291insA c.(289-291)AACfs p.N97fs PTCH1_uc010mro.2_5'UTR|PTCH1_uc010mrp.2_5'UTR|PTCH1_uc010mrq.2_5'UTR|PTCH1_uc004avl.3_5'UTR|PTCH1_uc010mrr.2_Frame_Shift_Ins_p.N31fs|PTCH1_uc004avm.3_Frame_Shift_Ins_p.N96fs|PTCH1_uc010mrt.1_RNA|PTCH1_uc010mru.1_RNA|PTCH1_uc004avo.2_Frame_Shift_Ins_p.N31fs|PTCH1_uc010mrv.1_Intron|PTCH1_uc010mrw.1_Intron NM_000264 NP_000255 Q13635 PTC1_HUMAN patched isoform L 97 Cytoplasmic (Potential). embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway integral to plasma membrane hedgehog receptor activity p.C98fs*42(2)|p.N97fs*43(1) skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1) 379 Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136) ACTTGCCGCAGTTTTTTTGAAT 0.540 0.38 53 32 SMC2 10592 broad.mit.edu 37 9 106862449 106862450 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr9:106862449_106862450insA uc004bbv.2 + 6 844_845 c.556_557insA c.(556-558)GAAfs p.E186fs SMC2_uc004bbu.1_Frame_Shift_Ins_p.E186fs|SMC2_uc004bbw.2_Frame_Shift_Ins_p.E186fs|SMC2_uc011lvl.1_Frame_Shift_Ins_p.E186fs|SMC2_uc010mtg.1_Frame_Shift_Ins_p.E41fs|SMC2_uc010mth.1_Frame_Shift_Ins_p.E136fs|SMC2_uc004bbx.2_Frame_Shift_Ins_p.E186fs NM_001042551 NP_001036016 O95347 SMC2_HUMAN structural maintenance of chromosomes 2 186 Potential. cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism condensin complex|cytoplasm|nuclear chromosome ATP binding|protein heterodimerization activity p.E186K(1) ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1) 9 GAAAACTATAGAAAAAAAGGAG 0.297 0.43 40 30 SMC2 10592 broad.mit.edu 37 9 106864797 106864798 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr9:106864797_106864798insA uc004bbv.2 + 9 1251_1252 c.963_964insA c.(961-966)AAGAAAfs p.K321fs SMC2_uc004bbu.1_Frame_Shift_Ins_p.K321fs|SMC2_uc004bbw.2_Frame_Shift_Ins_p.K321fs|SMC2_uc011lvl.1_Frame_Shift_Ins_p.K321fs|SMC2_uc010mtg.1_Frame_Shift_Ins_p.K176fs|SMC2_uc010mth.1_Frame_Shift_Ins_p.K271fs|SMC2_uc004bbx.2_Frame_Shift_Ins_p.K321fs NM_001042551 NP_001036016 O95347 SMC2_HUMAN structural maintenance of chromosomes 2 321_322 Potential. cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism condensin complex|cytoplasm|nuclear chromosome ATP binding|protein heterodimerization activity ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1) 9 ATCTCAAGAAGAAAAATCTGGC 0.401 0.45 70 58 ABL1 25 broad.mit.edu 37 9 133755893 133755893 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr9:133755893delA uc004bzw.2 + 10 1523 c.1520delA c.(1519-1521)GAAfs p.E507fs ABL1_uc004bzv.2_Frame_Shift_Del_p.E526fs NM_005157 NP_005148 P00519 ABL1_HUMAN c-abl oncogene 1, receptor tyrosine kinase 507 actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1) 817 all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204) OV - Ovarian serous cystadenocarcinoma(145;5.4e-05) Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619) 0.000 0.49 452 426 TSC1 7248 broad.mit.edu 37 9 135781157 135781157 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr9:135781157delG uc004cca.2 - 15 2042 c.1808delC c.(1807-1809)CCGfs p.P603fs TSC1_uc004ccb.3_Frame_Shift_Del_p.P602fs|TSC1_uc011mcq.1_Frame_Shift_Del_p.P552fs|TSC1_uc011mcr.1_Intron NM_000368 NP_000359 Q92574 TSC1_HUMAN tuberous sclerosis 1 protein isoform 1 603 activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus cell cortex|lamellipodium|membrane|TSC1-TSC2 complex chaperone binding|protein N-terminus binding p.?(1) lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1) 14 OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06) ATGATCATACGGGGGAGGCTG 0.488 0.47 69 60 PRKCQ 5588 broad.mit.edu 37 10 6525427 6525428 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr10:6525427_6525428insT uc001ijj.1 - 11 1228_1229 c.1153_1154insA c.(1153-1155)ATGfs p.M385fs PRKCQ_uc009xim.1_Frame_Shift_Ins_p.M385fs|PRKCQ_uc001iji.1_Frame_Shift_Ins_p.M418fs|PRKCQ_uc009xin.1_Frame_Shift_Ins_p.M349fs|PRKCQ_uc010qax.1_Frame_Shift_Ins_p.M260fs NM_006257 NP_006248 Q04759 KPCT_HUMAN protein kinase C, theta 385 Protein kinase. axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|regulation of cell growth|T cell receptor signaling pathway cytosol ATP binding|metal ion binding|protein binding|protein kinase C activity ovary(3)|lung(2)|large_intestine(1) 6 TTTCCCCAACATTTTGTGCAAG 0.411 0.43 77 59 ERCC6 2074 broad.mit.edu 37 10 50682233 50682234 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr10:50682233_50682234insA uc001jhs.3 - 13 2591_2592 c.2437_2438insT c.(2437-2439)TCTfs p.S813fs ERCC6_uc009xod.2_5'UTR|ERCC6_uc010qgr.1_Frame_Shift_Ins_p.S183fs|ERCC6_uc001jhr.3_Frame_Shift_Ins_p.S181fs NM_000124 NP_000115 Q03468 ERCC6_HUMAN excision repair cross-complementing rodent 813 base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair nucleolus|soluble fraction|transcription elongation factor complex ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1) 16 GGGACCTCCAGAAAAGAGATCA 0.411 0.46 86 73 ERCC6 2074 broad.mit.edu 37 10 50690758 50690758 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr10:50690758delC uc001jhs.3 - 10 2298 c.2144delG c.(2143-2145)GGAfs p.G715fs ERCC6_uc010qgr.1_Frame_Shift_Del_p.G85fs|ERCC6_uc001jhr.3_Frame_Shift_Del_p.G115fs NM_000124 NP_000115 Q03468 ERCC6_HUMAN excision repair cross-complementing rodent 715 base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair nucleolus|soluble fraction|transcription elongation factor complex ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1) 16 ATTTGAATATCCCCCCATGGT 0.418 0.48 25 23 HBE1 3046 broad.mit.edu 37 11 5290740 5290741 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr11:5290740_5290741insA uc001mal.1 - 2 511_512 c.258_259insT c.(256-261)TTTGCTfs p.F86fs HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Frame_Shift_Ins_p.F86fs NM_005330 NP_005321 P02100 HBE_HUMAN epsilon globin 86_87 blood coagulation hemoglobin complex heme binding|oxygen binding|oxygen transporter activity 0 Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212) Epithelial(150;1.34e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135) CTCAGCTTAGCAAAGGCGGGCT 0.485 0.35 15 8 NR1H3 10062 broad.mit.edu 37 11 47282887 47282887 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr11:47282887delC uc009ylm.2 + 5 816 c.595delC c.(595-597)CCCfs p.P199fs NR1H3_uc009yll.1_Frame_Shift_Del_p.P205fs|NR1H3_uc010rhk.1_Frame_Shift_Del_p.P205fs|NR1H3_uc001nek.2_Frame_Shift_Del_p.P154fs|NR1H3_uc001nej.2_Frame_Shift_Del_p.P199fs|NR1H3_uc001nel.2_Frame_Shift_Del_p.P154fs|NR1H3_uc001nen.3_Frame_Shift_Del_p.P199fs|NR1H3_uc001nem.2_Frame_Shift_Del_p.P199fs|NR1H3_uc001nep.2_Frame_Shift_Del_p.P108fs NM_005693 NP_005684 Q13133 NR1H3_HUMAN nuclear receptor subfamily 1, group H, member 3 199 apoptotic cell clearance|cellular response to lipopolysaccharide|cholesterol homeostasis|negative regulation of cholesterol storage|negative regulation of inflammatory response|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of macrophage activation|negative regulation of pancreatic juice secretion|negative regulation of pinocytosis|negative regulation of secretion of lysosomal enzymes|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of cholesterol homeostasis|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of receptor biosynthetic process|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of circadian rhythm|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to progesterone stimulus|triglyceride homeostasis nuclear chromatin|nucleoplasm cholesterol binding|steroid hormone receptor activity|sterol response element binding|transcription coactivator activity|zinc ion binding ovary(2)|lung(1) 3 GGCTTCCTCACCCCCCCAAAT 0.592 0.53 38 43 MARK2 2011 broad.mit.edu 37 11 63667464 63667464 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr11:63667464delC uc001nxw.2 + 8 1229 c.650delC c.(649-651)GCCfs p.A217fs MARK2_uc001nxx.2_Frame_Shift_Del_p.A217fs|MARK2_uc001nxy.2_Frame_Shift_Del_p.A217fs|MARK2_uc001nxv.3_Frame_Shift_Del_p.A217fs|MARK2_uc001nxz.3_Frame_Shift_Del_p.A184fs|MARK2_uc009yoy.2_Frame_Shift_Del_p.A184fs NM_001039469 NP_001034558 Q7KZI7 MARK2_HUMAN MAP/microtubule affinity-regulating kinase 2 217 Protein kinase. cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress plasma membrane ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity stomach(1)|ovary(1)|lung(1) 3 CCTTATGCTGCCCCAGAACTC 0.493 0.42 142 103 MARK2 2011 broad.mit.edu 37 11 63668057 63668057 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr11:63668057delA uc001nxw.2 + 9 1374 c.795delA c.(793-795)GGAfs p.G265fs MARK2_uc001nxx.2_Frame_Shift_Del_p.G265fs|MARK2_uc001nxy.2_Frame_Shift_Del_p.G265fs|MARK2_uc001nxv.3_Frame_Shift_Del_p.G265fs|MARK2_uc001nxz.3_Frame_Shift_Del_p.G232fs|MARK2_uc009yoy.2_Frame_Shift_Del_p.G232fs NM_001039469 NP_001034558 Q7KZI7 MARK2_HUMAN MAP/microtubule affinity-regulating kinase 2 265 Protein kinase. cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress plasma membrane ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity stomach(1)|ovary(1)|lung(1) 3 TACTGAGGGGAAAATACCGTA 0.458 0.43 56 43 GUCY1A2 2977 broad.mit.edu 37 11 106810877 106810878 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr11:106810877_106810878insT uc001pjg.1 - 4 904_905 c.514_515insA c.(514-516)AGAfs p.R172fs GUCY1A2_uc010rvo.1_Frame_Shift_Ins_p.R172fs|GUCY1A2_uc009yxn.1_Frame_Shift_Ins_p.R172fs NM_000855 NP_000846 P33402 GCYA2_HUMAN guanylate cyclase 1, soluble, alpha 2 172 intracellular signal transduction|platelet activation cytoplasm GTP binding|guanylate cyclase activity|heme binding large_intestine(3)|lung(2)|pancreas(2)|ovary(1) 8 all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068) BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476) TTCACCAAATCTTTTTTGAATT 0.337 0.38 45 28 NPAT 4863 broad.mit.edu 37 11 108047079 108047080 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr11:108047079_108047080insT uc001pjz.3 - 12 1127_1128 c.1025_1026insA c.(1024-1026)AATfs p.N342fs NPAT_uc001pka.2_Frame_Shift_Ins_p.N137fs NM_002519 NP_002510 Q14207 NPAT_HUMAN nuclear protein, ataxia-telangiectasia locus 342 positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle Cajal body protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity ovary(2) 2 all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116) TTTGTGATATATTTTTATTATT 0.297 0.36 82 47 ATM 472 broad.mit.edu 37 11 108123615 108123616 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr11:108123615_108123616insT uc001pkb.1 + 12 2259_2260 c.1874_1875insT c.(1873-1875)AATfs p.N625fs ATM_uc009yxr.1_Frame_Shift_Ins_p.N625fs NM_000051 NP_000042 Q13315 ATM_HUMAN ataxia telangiectasia mutated isoform 1 625 cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence cytoplasmic membrane-bounded vesicle|nucleoplasm 1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1) 240 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147) GCTGCAATGAATTTTTTCCAAA 0.307 0.47 89 80 ATM 472 broad.mit.edu 37 11 108164163 108164164 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr11:108164163_108164164insA uc001pkb.1 + 31 5120_5121 c.4735_4736insA c.(4735-4737)CAAfs p.Q1579fs ATM_uc009yxr.1_Frame_Shift_Ins_p.Q1579fs|ATM_uc001pke.1_Frame_Shift_Ins_p.Q231fs|ATM_uc001pkf.2_Intron NM_000051 NP_000042 Q13315 ATM_HUMAN ataxia telangiectasia mutated isoform 1 1579 cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence cytoplasmic membrane-bounded vesicle|nucleoplasm 1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1) 240 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147) TATTACTCAGCAAAAAATCAAA 0.302 0.40 78 52 NCAM1 4684 broad.mit.edu 37 11 113076378 113076379 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr11:113076378_113076379insA uc009yyq.1 + 4 820_821 c.126_127insA c.(124-129)CTGAAAfs p.L42fs NCAM1_uc001pno.2_Frame_Shift_Ins_p.L42fs NM_001076682 NP_001070150 P13591 NCAM1_HUMAN neural cell adhesion molecule 1 isoform 3 160_161 Ig-like C2-type 2.|Extracellular (Potential). axon guidance|interferon-gamma-mediated signaling pathway anchored to membrane|extracellular region|Golgi membrane|integral to membrane ovary(1) 1 all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207) BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212) ATGTCATCCTGAAAAAAGATGG 0.515 0.42 93 66 ANKK1 255239 broad.mit.edu 37 11 113270238 113270239 + Frame_Shift_Ins INS - G G CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr11:113270238_113270239insG uc001pny.2 + 8 1641_1642 c.1547_1548insG c.(1546-1548)CAGfs p.Q516fs NM_178510 NP_848605 Q8NFD2 ANKK1_HUMAN ankyrin repeat and kinase domain containing 1 516 ANK 5. ATP binding|protein serine/threonine kinase activity lung(5)|stomach(1)|ovary(1)|breast(1) 8 all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194) BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238) CTGACCAGCCAGGGGGCTGAGT 0.604 0.43 30 23 SIK3 23387 broad.mit.edu 37 11 116729011 116729031 + In_Frame_Del DEL TGTTGCTGCTGCTGCTGCCGT - - rs78098996 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr11:116729011_116729031delTGTTGCTGCTGCTGCTGCCGT uc001ppy.2 - 20 2868_2888 c.2832_2852delACGGCAGCAGCAGCAGCAACA c.(2830-2853)CAACGGCAGCAGCAGCAGCAACAG>CAG p.944_951QRQQQQQQ>Q SIK3_uc001ppz.2_In_Frame_Del_p.783_790QRQQQQQQ>Q|SIK3_uc001pqa.2_In_Frame_Del_p.884_891QRQQQQQQ>Q|SIK3_uc001ppw.2_In_Frame_Del_p.301_308QRQQQQQQ>Q|SIK3_uc001ppx.2_In_Frame_Del_p.322_329QRQQQQQQ>Q|SIK3_uc001pqb.2_In_Frame_Del_p.247_254QRQQQQQQ>Q NM_025164 NP_079440 Q9Y2K2 SIK3_HUMAN serine/threonine-protein kinase QSK 944_951 Gln-rich. cytoplasm ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1) 12 ctgttgctgctgttgctgctgctgctgccgttgttgctgct 0.462 0.24 55 17 MLL 4297 broad.mit.edu 37 11 118344954 118344955 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr11:118344954_118344955insA uc001pta.2 + 3 3103_3104 c.3080_3081insA c.(3079-3081)CTAfs p.L1027fs MLL_uc001ptb.2_Frame_Shift_Ins_p.L1027fs|MLL_uc001psz.1_Frame_Shift_Ins_p.L1060fs|MLL_uc001ptd.1_Frame_Shift_Ins_p.L19fs NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 1027 apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) GCCAGCCTCCTAAAAAAGGCCA 0.470 0.39 41 26 NCAPD3 23310 broad.mit.edu 37 11 134048586 134048586 + Frame_Shift_Del DEL G - - rs138442478 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr11:134048586delG uc001qhd.1 - 22 3331 c.2725delC c.(2725-2727)CAGfs p.Q909fs NCAPD3_uc010scm.1_RNA|NCAPD3_uc009zda.1_RNA NM_015261 NP_056076 P42695 CNDD3_HUMAN non-SMC condensin II complex, subunit D3 909 cell division|mitotic chromosome condensation nuclear centromeric heterochromatin|nuclear condensin complex methylated histone residue binding ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1) 5 all_hematologic(175;0.127) all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227) CCTCTGACCTGGGGGGGTGGC 0.522 0.53 8 9 PIK3C2G 5288 broad.mit.edu 37 12 18641399 18641400 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr12:18641399_18641400insA uc001rdt.2 + 18 2514_2515 c.2398_2399insA c.(2398-2400)GAAfs p.E800fs PIK3C2G_uc010sia.1_RNA|PIK3C2G_uc010sib.1_Frame_Shift_Ins_p.E841fs|PIK3C2G_uc010sic.1_Frame_Shift_Ins_p.E619fs NM_004570 NP_004561 O75747 P3C2G_HUMAN phosphoinositide-3-kinase, class 2 gamma 800 cell communication|phosphatidylinositol-mediated signaling membrane|phosphatidylinositol 3-kinase complex 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2) 21 Hepatocellular(102;0.194) AAAAAATGCAGAAAATGAAGCT 0.371 0.37 63 37 PLEKHA5 54477 broad.mit.edu 37 12 19410381 19410381 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr12:19410381delA uc001reb.2 + 6 533 c.447delA c.(445-447)TCAfs p.S149fs PLEKHA5_uc010sie.1_Frame_Shift_Del_p.S149fs|PLEKHA5_uc001rea.2_Frame_Shift_Del_p.S149fs|PLEKHA5_uc009zin.2_5'UTR|PLEKHA5_uc010sif.1_Frame_Shift_Del_p.S41fs|PLEKHA5_uc010sig.1_Frame_Shift_Del_p.S41fs|PLEKHA5_uc010sih.1_Frame_Shift_Del_p.S41fs NM_019012 NP_061885 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A 149 1-phosphatidylinositol binding|protein binding ovary(1)|kidney(1)|skin(1) 3 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) CACGAGCTTCAAAAAAAGTTC 0.318 0.45 40 33 ITPR2 3709 broad.mit.edu 37 12 26848542 26848543 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr12:26848542_26848543insT uc001rhg.2 - 10 1409_1410 c.992_993insA c.(991-993)AATfs p.N331fs NM_002223 NP_002214 Q14571 ITPR2_HUMAN inositol 1,4,5-triphosphate receptor, type 2 331 Cytoplasmic (Potential).|MIR 4. activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 14 Colorectal(261;0.0847) TACTCACCACATTTTTTCCTTC 0.322 0.47 62 54 LRRK2 120892 broad.mit.edu 37 12 40671946 40671946 + Frame_Shift_Del DEL A - - rs141585121 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr12:40671946delA uc001rmg.3 + 18 2245 c.2124delA c.(2122-2124)TTAfs p.L708fs LRRK2_uc001rmh.1_Frame_Shift_Del_p.L330fs NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 708 activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) ATGATTACTTAAAAAATGTGA 0.368 0.44 106 84 PDZRN4 29951 broad.mit.edu 37 12 41966167 41966168 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr12:41966167_41966168insA uc010skn.1 + 10 1057_1058 c.989_990insA c.(988-990)CCAfs p.P330fs PDZRN4_uc001rmq.3_Frame_Shift_Ins_p.P271fs|PDZRN4_uc009zjz.2_Frame_Shift_Ins_p.P269fs|PDZRN4_uc001rmr.2_Frame_Shift_Ins_p.P156fs NM_013377 NP_037509 Q6ZMN7 PZRN4_HUMAN PDZ domain containing RING finger 4 isoform 2 529 ubiquitin-protein ligase activity|zinc ion binding lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1) 11 all_cancers(12;0.000673) Lung NSC(34;0.0205)|all_lung(34;0.0264) TTTTCTTAGCCAAAAAAGCAAG 0.361 0.44 47 37 VDR 7421 broad.mit.edu 37 12 48250939 48250941 + In_Frame_Del DEL AGG - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr12:48250939_48250941delAGG uc001rqm.2 - 7 836_838 c.554_556delCCT c.(553-558)TCCTGC>TGC p.S185del VDR_uc001rql.2_In_Frame_Del_p.S235del|VDR_uc001rqn.2_In_Frame_Del_p.S185del|VDR_uc010slq.1_In_Frame_Del_p.S153del NM_001017535 NP_001017535 P11473 VDR_HUMAN vitamin D (1,25-dihydroxyvitamin D3) receptor 185 Hinge. decidualization|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D 24-hydroxylase activity|regulation of calcidiol 1-monooxygenase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor nucleoplasm retinoid X receptor binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|vitamin D3 receptor activity|zinc ion binding ovary(1)|central_nervous_system(1)|skin(1) 3 Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214) GBM - Glioblastoma multiforme(48;0.17) Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910) TGATCTGAGCAGGAGGAGGAGGA 0.601 0.35 44 24 HOXC9 3225 broad.mit.edu 37 12 54396298 54396300 + In_Frame_Del DEL AGA - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr12:54396298_54396300delAGA uc001sep.2 + 3 721_723 c.623_625delAGA c.(622-627)GAGAAG>GAG p.K209del HOXC9_uc001seq.2_In_Frame_Del_p.K209del NM_006897 NP_008828 P31274 HXC9_HUMAN homeobox C9 209 Homeobox. multicellular organismal development nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity large_intestine(1)|pancreas(1)|skin(1) 3 CTGGAACTGGAGAAGGAGTTTCT 0.557 0.42 7 5 LRP1 4035 broad.mit.edu 37 12 57567696 57567697 + Frame_Shift_Ins INS - C C CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr12:57567696_57567697insC uc001snd.2 + 22 3946_3947 c.3480_3481insC c.(3478-3483)CTGCCCfs p.L1160fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 1160_1161 LDL-receptor class A 10.|Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CAGTCTGCCTGCCCCCTGACAA 0.629 0.41 85 60 LRP1 4035 broad.mit.edu 37 12 57603940 57603940 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr12:57603940delC uc001snd.2 + 81 13034 c.12568delC c.(12568-12570)CCCfs p.P4190fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 4190 Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CTCTCCAACGCCCCCCCCAGA 0.637 0.39 14 9 LGR5 8549 broad.mit.edu 37 12 71978362 71978363 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr12:71978362_71978363insA uc001swl.2 + 18 2620_2621 c.2572_2573insA c.(2572-2574)GAAfs p.E858fs LGR5_uc001swm.2_Frame_Shift_Ins_p.E834fs|LGR5_uc001swn.1_RNA NM_003667 NP_003658 O75473 LGR5_HUMAN leucine-rich repeat-containing G protein-coupled 858 Cytoplasmic (Potential). integral to plasma membrane protein-hormone receptor activity lung(4)|skin(3)|ovary(1)|pancreas(1) 9 TGATGATGTCGAAAAACAGTCC 0.470 0.40 194 129 UBE3B 89910 broad.mit.edu 37 12 109926469 109926469 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr12:109926469delA uc001top.2 + 7 1143 c.540delA c.(538-540)GGAfs p.G180fs UBE3B_uc001toq.2_Frame_Shift_Del_p.G180fs|UBE3B_uc001tol.1_Frame_Shift_Del_p.G180fs|UBE3B_uc001tom.2_Frame_Shift_Del_p.G180fs|UBE3B_uc001ton.2_Frame_Shift_Del_p.G180fs|UBE3B_uc001too.1_RNA|UBE3B_uc009zvj.1_Frame_Shift_Del_p.G180fs|UBE3B_uc001tor.2_Frame_Shift_Del_p.G180fs NM_130466 NP_569733 Q7Z3V4 UBE3B_HUMAN ubiquitin protein ligase E3B 180 protein ubiquitination involved in ubiquitin-dependent protein catabolic process intracellular ubiquitin-protein ligase activity ovary(2)|lung(2) 4 TTCTTCGGGGAAAAGGTCTGT 0.463 0.42 106 78 KSR2 283455 broad.mit.edu 37 12 118298146 118298146 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr12:118298146delG uc001two.2 - 2 239 c.184delC c.(184-186)CAGfs p.Q62fs NM_173598 NP_775869 Q6VAB6 KSR2_HUMAN kinase suppressor of ras 2 91 intracellular signal transduction cytoplasm|membrane ATP binding|metal ion binding|protein serine/threonine kinase activity lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1) 15 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) TGCCGTAGCTGGGGGAAGCCG 0.627 0.45 104 85 POLE 5426 broad.mit.edu 37 12 133245024 133245024 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr12:133245024delG uc001uks.1 - 19 2135 c.2091delC c.(2089-2091)CCCfs p.P697fs POLE_uc010tbq.1_RNA|POLE_uc009zyu.1_Frame_Shift_Del_p.P670fs NM_006231 NP_006222 Q07864 DPOE1_HUMAN DNA-directed DNA polymerase epsilon 697 base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair nucleoplasm chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding ovary(3)|skin(3)|lung(1)|central_nervous_system(1) 8 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.0416) OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05) 0.000 0.46 884 756 ZMYM5 9205 broad.mit.edu 37 13 20426143 20426145 + In_Frame_Del DEL CAT - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr13:20426143_20426145delCAT uc010tcn.1 - 3 441_443 c.176_178delATG c.(175-180)GATGTT>GTT p.D59del ZMYM5_uc001umm.1_5'UTR|ZMYM5_uc001umn.2_In_Frame_Del_p.D59del|ZMYM5_uc001umo.2_In_Frame_Del_p.D59del NM_001142684 NP_001136156 Q9UJ78 ZMYM5_HUMAN zinc finger protein 237 isoform 3 59 Poly-Asp. nucleus zinc ion binding 0 all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431) ATAAACACAAcatcatcatcatc 0.340 0.32 17 8 SACS 26278 broad.mit.edu 37 13 23904280 23904281 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr13:23904280_23904281insT uc001uon.2 - 10 14323_14324 c.13734_13735insA c.(13732-13737)AAAGTGfs p.K4578fs SACS_uc001uoo.2_Frame_Shift_Ins_p.K4431fs|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 4578_4579 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) TATCTTCACACTTTTTGTTGCA 0.347 0.11 85 11 FLT1 2321 broad.mit.edu 37 13 28903817 28903818 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr13:28903817_28903818insT uc001usb.3 - 19 2926_2927 c.2641_2642insA c.(2641-2643)ATCfs p.I881fs FLT1_uc010aaq.2_Frame_Shift_Ins_p.I6fs|FLT1_uc001usa.3_Frame_Shift_Ins_p.I99fs NM_002019 NP_002010 P17948 VGFR1_HUMAN fms-related tyrosine kinase 1 isoform 1 881 Cytoplasmic (Potential).|Protein kinase. cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway extracellular space|Golgi apparatus|integral to plasma membrane|nucleus ATP binding|growth factor binding|vascular endothelial growth factor receptor activity lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1) 24 Acute lymphoblastic leukemia(6;0.04) Lung SC(185;0.0262)|Breast(139;0.188) Colorectal(13;0.000674) all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207) Sunitinib(DB01268) GTGGGTCAAGATTTTTAGCTCA 0.584 0.41 45 31 BRCA2 675 broad.mit.edu 37 13 32912346 32912346 + Frame_Shift_Del DEL A - - rs80359406 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr13:32912346delA uc001uub.1 + 11 4081 c.3854delA c.(3853-3855)GAAfs p.E1285fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 1285 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) ACTGTAAGTGAAAAAAATAAT 0.264 0.42 64 47 CCNA1 8900 broad.mit.edu 37 13 37011855 37011856 + Frame_Shift_Ins INS - C C CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr13:37011855_37011856insC uc001uvr.3 + 3 737_738 c.387_388insC c.(385-390)GAGCCCfs p.E129fs CCNA1_uc010teo.1_Frame_Shift_Ins_p.E85fs|CCNA1_uc010abq.2_Frame_Shift_Ins_p.E85fs|CCNA1_uc010abp.2_Frame_Shift_Ins_p.E85fs|CCNA1_uc001uvs.3_Frame_Shift_Ins_p.E128fs|CCNA1_uc010abr.2_RNA NM_003914 NP_003905 P78396 CCNA1_HUMAN cyclin A1 isoform a 129_130 cell division|G2/M transition of mitotic cell cycle|male meiosis I|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|spermatogenesis cytosol|microtubule cytoskeleton|nucleoplasm protein kinase binding lung(2)|skin(2)|ovary(1) 5 Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242) GGGTCCAAGAGCCCCCCAAGCA 0.505 0.39 101 65 CSNK1A1L 122011 broad.mit.edu 37 13 37678703 37678704 + Frame_Shift_Ins INS - T T rs56252523 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr13:37678703_37678704insT uc001uwm.1 - 1 1098_1099 c.690_691insA c.(688-693)AAACAAfs p.K230fs NM_145203 NP_660204 Q8N752 KC1AL_HUMAN casein kinase 1, alpha 1-like 230_231 Protein kinase. Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity large_intestine(1) 1 Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109) all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407) TCATATTTTTGTTTTTTTGTCA 0.426 0.37 127 76 AKAP6 9472 broad.mit.edu 37 14 33293161 33293162 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr14:33293161_33293162insA uc001wrq.2 + 13 6312_6313 c.6142_6143insA c.(6142-6144)CAAfs p.Q2048fs NM_004274 NP_004265 Q13023 AKAP6_HUMAN A-kinase anchor protein 6 2048 protein targeting calcium channel complex|nuclear membrane|sarcoplasmic reticulum protein kinase A binding|receptor binding breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1) 21 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) GBM - Glioblastoma multiforme(265;0.019) TGTTTTCCATCAAAAAGATGCC 0.411 0.44 148 115 FANCM 57697 broad.mit.edu 37 14 45645954 45645955 + Frame_Shift_Ins INS - A A rs143681767 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr14:45645954_45645955insA uc001wwd.3 + 14 4096_4097 c.3997_3998insA c.(3997-3999)CAAfs p.Q1333fs FANCM_uc010anf.2_Frame_Shift_Ins_p.Q1307fs|FANCM_uc001wwe.3_Frame_Shift_Ins_p.Q869fs|FANCM_uc010ang.2_Frame_Shift_Ins_p.Q547fs NM_020937 NP_065988 Q8IYD8 FANCM_HUMAN Fanconi anemia, complementation group M 1333 DNA repair Fanconi anaemia nuclear complex ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding ovary(3)|lung(2)|breast(2) 7 TTTACCAGTGCAAAAAAAAGTT 0.327 0.41 111 78 BMP4 652 broad.mit.edu 37 14 54416870 54416870 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr14:54416870delG uc001xal.3 - 3 1294 c.1107delC c.(1105-1107)CCCfs p.P369fs BMP4_uc010aoh.2_Frame_Shift_Del_p.P369fs|BMP4_uc001xao.3_Frame_Shift_Del_p.P369fs|BMP4_uc001xan.3_Frame_Shift_Del_p.P369fs NM_130851 NP_570912 P12644 BMP4_HUMAN bone morphogenetic protein 4 preproprotein 369 activation of MAPKK activity|blood vessel endothelial cell proliferation involved in sprouting angiogenesis|BMP signaling pathway involved in heart induction|BMP signaling pathway involved in nephric duct formation|branching involved in ureteric bud morphogenesis|bronchus development|bud dilation involved in lung branching|cardiac septum development|cartilage development|endocardial cushion development|epithelial cell proliferation involved in lung morphogenesis|intermediate mesodermal cell differentiation|lung alveolus development|lymphoid progenitor cell differentiation|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway|negative regulation of branching involved in ureteric bud morphogenesis|negative regulation of cell proliferation involved in heart morphogenesis|negative regulation of glomerular mesangial cell proliferation|negative regulation of glomerulus development|negative regulation of immature T cell proliferation in thymus|negative regulation of MAP kinase activity|negative regulation of metanephric comma-shaped body morphogenesis|negative regulation of metanephric S-shaped body morphogenesis|negative regulation of mitosis|negative regulation of myoblast differentiation|negative regulation of phosphorylation|negative regulation of striated muscle tissue development|negative regulation of thymocyte apoptosis|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of apoptosis|positive regulation of bone mineralization|positive regulation of cardiac muscle fiber development|positive regulation of cartilage development|positive regulation of collagen biosynthetic process|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of kidney development|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|protein localization to nucleus|pulmonary artery endothelial tube morphogenesis|secondary heart field specification|SMAD protein signal transduction|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway|steroid hormone mediated signaling pathway extracellular space|proteinaceous extracellular matrix BMP receptor binding|chemoattractant activity|cytokine activity|growth factor activity 0 AACAGGCTTTGGGGATACTGG 0.498 0.45 184 153 FBLN5 10516 broad.mit.edu 37 14 92349371 92349372 + Frame_Shift_Del DEL CA - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr14:92349371_92349372delCA uc001xzx.3 - 8 1261_1262 c.788_789delTG c.(787-789)GTGfs p.V263fs FBLN5_uc010aud.2_Frame_Shift_Del_p.V268fs|FBLN5_uc010aue.2_Frame_Shift_Del_p.V304fs NM_006329 NP_006320 Q9UBX5 FBLN5_HUMAN fibulin 5 precursor 263 EGF-like 5; calcium-binding (Potential). cell-matrix adhesion|elastic fiber assembly|protein localization at cell surface|regulation of removal of superoxide radicals extracellular space|proteinaceous extracellular matrix|soluble fraction calcium ion binding|integrin binding|protein C-terminus binding ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1) 6 all_cancers(154;0.0722) CGGGCTGGTTCACACACTCATG 0.550 0.39 69 44 KIAA1409 57578 broad.mit.edu 37 14 94121740 94121740 + Frame_Shift_Del DEL T - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr14:94121740delT uc001ybv.1 + 37 6178 c.6095delT c.(6094-6096)GTTfs p.V2032fs KIAA1409_uc001ybs.1_Frame_Shift_Del_p.V2010fs NM_020818 NP_065869 Q9P2D8 UNC79_HUMAN hypothetical protein LOC57578 2187 integral to membrane ovary(10)|skin(4)|large_intestine(3) 17 all_cancers(154;0.0354)|all_epithelial(191;0.216) Epithelial(152;0.188) CTGCCTTGTGTTTTACCTCTG 0.408 0.48 86 80 EIF2AK4 440275 broad.mit.edu 37 15 40257981 40257982 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr15:40257981_40257982insA uc001zkm.1 + 8 1004_1005 c.954_955insA c.(952-957)CAGAAAfs p.Q318fs EIF2AK4_uc001zkl.2_Frame_Shift_Ins_p.Q318fs|EIF2AK4_uc010bbj.1_Frame_Shift_Ins_p.Q47fs NM_001013703 NP_001013725 Q9P2K8 E2AK4_HUMAN eukaryotic translation initiation factor 2 alpha 318_319 Protein kinase 1. translation cytosolic ribosome aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity lung(2)|stomach(1)|skin(1) 4 all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119) GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616) TTCAGTGGCAGAAAAAAATGGG 0.436 0.43 87 66 EIF2AK4 440275 broad.mit.edu 37 15 40282507 40282508 + Frame_Shift_Ins INS - T T rs35250897 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr15:40282507_40282508insT uc001zkm.1 + 16 2610_2611 c.2560_2561insT c.(2560-2562)ATTfs p.I854fs EIF2AK4_uc010bbj.1_Frame_Shift_Ins_p.I555fs|EIF2AK4_uc001zkn.1_5'Flank NM_001013703 NP_001013725 Q9P2K8 E2AK4_HUMAN eukaryotic translation initiation factor 2 alpha 854 Protein kinase 2. translation cytosolic ribosome aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity lung(2)|stomach(1)|skin(1) 4 all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119) GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616) GCCTGTCAACATTTTTTTGGAT 0.356 0.45 128 103 CASC5 57082 broad.mit.edu 37 15 40916444 40916445 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr15:40916444_40916445insA uc010bbs.1 + 11 4221_4222 c.4060_4061insA c.(4060-4062)GAAfs p.E1354fs CASC5_uc010ucq.1_Frame_Shift_Ins_p.E1178fs|CASC5_uc001zme.2_Frame_Shift_Ins_p.E1328fs|CASC5_uc010bbt.1_Frame_Shift_Ins_p.E1328fs NM_170589 NP_733468 Q8NG31 CASC5_HUMAN cancer susceptibility candidate 5 isoform 1 1354 acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm protein binding breast(3)|central_nervous_system(1)|skin(1) 5 all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946) GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211) TAAAGATGAGGAAAAAGCCAAT 0.386 0.46 155 131 MGA 23269 broad.mit.edu 37 15 42019595 42019596 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr15:42019595_42019596insA uc010ucy.1 + 10 3829_3830 c.3648_3649insA c.(3646-3651)CCCAATfs p.P1216fs MGA_uc010ucz.1_Frame_Shift_Ins_p.P1216fs NM_001164273 NP_001157745 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 1 1216_1217 MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) CTCCCAAACCCAATCCTGTGGT 0.376 0.38 99 60 TP53BP1 7158 broad.mit.edu 37 15 43748661 43748661 + Frame_Shift_Del DEL T - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr15:43748661delT uc001zrs.2 - 12 2278 c.2130delA c.(2128-2130)AAAfs p.K710fs TP53BP1_uc010udp.1_Frame_Shift_Del_p.K710fs|TP53BP1_uc001zrq.3_Frame_Shift_Del_p.K715fs|TP53BP1_uc001zrr.3_Frame_Shift_Del_p.K715fs|TP53BP1_uc010udq.1_Frame_Shift_Del_p.K715fs NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 710 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) CTGAGCATTCTTTTTTTGGCA 0.403 0.45 88 71 FBN1 2200 broad.mit.edu 37 15 48784719 48784719 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr15:48784719delC uc001zwx.1 - 24 3121 c.2793delG c.(2791-2793)GGGfs p.G931fs NM_000138 NP_000129 P35555 FBN1_HUMAN fibrillin 1 precursor 931 EGF-like 14; calcium-binding. heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development basement membrane|extracellular space|microfibril calcium ion binding|extracellular matrix structural constituent|protein binding ovary(2)|large_intestine(1) 3 all_lung(180;0.00279) all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05) ACTTGAATGACCCCCTAGTGT 0.343 0.35 91 49 IDH2 3418 broad.mit.edu 37 15 90631918 90631918 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr15:90631918delC uc002box.2 - 4 521 c.435delG c.(433-435)GGGfs p.G145fs IDH2_uc010uqb.1_Frame_Shift_Del_p.G93fs|IDH2_uc010uqc.1_Frame_Shift_Del_p.G15fs|IDH2_uc010bnu.2_Intron NM_002168 NP_002159 P48735 IDHP_HUMAN isocitrate dehydrogenase 2 (NADP+), 145 2-oxoglutarate metabolic process|glyoxylate cycle|isocitrate metabolic process|tricarboxylic acid cycle mitochondrial matrix isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding haematopoietic_and_lymphoid_tissue(621)|central_nervous_system(80)|bone(7)|skin(3) 711 Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04) BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106) 0.000 0.50 832 828 BLM 641 broad.mit.edu 37 15 91306293 91306294 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr15:91306293_91306294insA uc002bpr.2 + 8 2077_2078 c.1980_1981insA c.(1978-1983)CATAAAfs p.H660fs BLM_uc010uqh.1_Frame_Shift_Ins_p.H660fs|BLM_uc010uqi.1_Frame_Shift_Ins_p.H285fs|BLM_uc010bnx.2_Frame_Shift_Ins_p.H660fs|BLM_uc002bps.1_Frame_Shift_Ins_p.H222fs NM_000057 NP_000048 P54132 BLM_HUMAN Bloom syndrome protein 660_661 double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray cytoplasm|lateral element|nuclear matrix|nucleolus|PML body ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding p.H660Y(1) ovary(3)|skin(2)|breast(1) 6 Lung NSC(78;0.0875)|all_lung(78;0.109) Lung(145;0.189) AGATTTTTCATAAAAAATTTGG 0.371 0.44 98 76 AXIN1 8312 broad.mit.edu 37 16 396916 396916 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr16:396916delG uc002cgp.1 - 2 287 c.110delC c.(109-111)CCGfs p.P37fs AXIN1_uc002cgq.1_Frame_Shift_Del_p.P37fs NM_003502 NP_003493 O15169 AXIN1_HUMAN axin 1 isoform a 37 activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding breast(1)|liver(1) 2 all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187) GGCGGGCCTCGGGTCTGTGGA 0.607 0.53 42 48 TSC2 7249 broad.mit.edu 37 16 2108787 2108788 + Frame_Shift_Ins INS - T T rs137853976 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr16:2108787_2108788insT uc002con.2 + 10 994_995 c.888_889insT c.(886-891)GTGTTTfs p.V296fs TSC2_uc010bsd.2_Frame_Shift_Ins_p.V296fs|TSC2_uc002coo.2_Frame_Shift_Ins_p.V296fs|TSC2_uc010uvv.1_Frame_Shift_Ins_p.V259fs|TSC2_uc010uvw.1_Frame_Shift_Ins_p.V247fs|TSC2_uc002cop.2_Frame_Shift_Ins_p.V96fs NM_000548 NP_000539 P49815 TSC2_HUMAN tuberous sclerosis 2 isoform 1 296_297 Required for interaction with TSC1. cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex GTPase activator activity|protein homodimerization activity central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1) 10 Hepatocellular(780;0.0202) GAGGAGCCGTGTTTTTTGTGGG 0.579 0.60 4 6 CREBBP 1387 broad.mit.edu 37 16 3929877 3929878 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr16:3929877_3929878insT uc002cvv.2 - 1 244_245 c.40_41insA c.(40-42)AGAfs p.R14fs CREBBP_uc002cvw.2_Frame_Shift_Ins_p.R14fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 14 cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) GAGTTTGGCTCTTTTGGGGTTG 0.436 0.67 6 12 ERCC4 2072 broad.mit.edu 37 16 14042196 14042196 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr16:14042196delA uc002dce.2 + 11 2752 c.2743delA c.(2743-2745)AAAfs p.K915fs ERCC4_uc010uyz.1_Frame_Shift_Del_p.K465fs NM_005236 NP_005227 Q92889 XPF_HUMAN excision repair cross-complementing rodent 915 Interaction with EME1 and ERCC1. double-strand break repair via homologous recombination|meiotic mismatch repair|negative regulation of telomere maintenance|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|nucleotide-excision repair, DNA incision, 5'-to lesion|resolution of meiotic recombination intermediates|telomere maintenance via telomere shortening|transcription-coupled nucleotide-excision repair nuclear chromosome, telomeric region|nucleoplasm|nucleotide-excision repair factor 1 complex damaged DNA binding|protein C-terminus binding|protein N-terminus binding|single-stranded DNA binding|single-stranded DNA specific endodeoxyribonuclease activity lung(4)|ovary(3)|skin(2)|pancreas(1) 10 AGGAAAAGGGAAAAAGTGAAC 0.408 0.52 57 61 CHD9 80205 broad.mit.edu 37 16 53262999 53263000 + Frame_Shift_Ins INS - T T CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr16:53262999_53263000insT uc002ehb.2 + 7 2437_2438 c.2273_2274insT c.(2272-2274)CATfs p.H758fs CHD9_uc002egy.2_Frame_Shift_Ins_p.H758fs|CHD9_uc002eha.1_Frame_Shift_Ins_p.H758fs|CHD9_uc002ehc.2_Frame_Shift_Ins_p.H758fs|CHD9_uc002ehd.2_Frame_Shift_Ins_p.H284fs NM_025134 NP_079410 Q3L8U1 CHD9_HUMAN chromodomain helicase DNA binding protein 9 758 Chromo 1. cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleoplasm ATP binding|DNA binding|helicase activity|protein binding lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1) 7 all_cancers(37;0.0212) CAAAGAGCACATTTTTTTGCAG 0.317 0.39 30 19 ADAMTS18 170692 broad.mit.edu 37 16 77356310 77356311 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr16:77356310_77356311insA uc002ffc.3 - 14 2504_2505 c.2085_2086insT c.(2083-2088)TTTGCAfs p.F695fs ADAMTS18_uc010chc.1_Frame_Shift_Ins_p.F283fs|ADAMTS18_uc002ffe.1_Frame_Shift_Ins_p.F391fs NM_199355 NP_955387 Q8TE60 ATS18_HUMAN ADAM metallopeptidase with thrombospondin type 1 695_696 Cys-rich. proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding p.A696fs*18(2) large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1) 18 CCGGACATTGCAAAAAAAAATT 0.406 0.29 112 46 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 42 518 ULK2 9706 broad.mit.edu 37 17 19687070 19687070 + Frame_Shift_Del DEL G - - rs147422998 byFrequency;by1000genomes CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr17:19687070delG uc002gwm.3 - 22 2909 c.2400delC c.(2398-2400)CCCfs p.P800fs ULK2_uc002gwn.2_Frame_Shift_Del_p.P800fs NM_001142610 NP_001136082 Q8IYT8 ULK2_HUMAN unc-51-like kinase 2 800 signal transduction ATP binding|protein binding|protein serine/threonine kinase activity skin(2)|large_intestine(1)|stomach(1) 4 all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186) CCTCTAGGCTGGGGGGTGAAG 0.587 0.58 19 26 NF1 4763 broad.mit.edu 37 17 29557945 29557946 + Splice_Site INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr17:29557945_29557946insA uc002hgg.2 + 24 3530 c.3197_splice c.e24+2 p.R1066_splice NF1_uc002hgh.2_Splice_Site_p.R1066_splice|NF1_uc010csn.1_Splice_Site_p.R926_splice|NF1_uc002hgi.1_Splice_Site_p.R99_splice NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) TCTTACAAGGTAAAAAAAGAAT 0.332 0.31 74 33 NF1 4763 broad.mit.edu 37 17 29683558 29683558 + Frame_Shift_Del DEL C - - rs66883224 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr17:29683558delC uc002hgg.2 + 52 8029 c.7696delC c.(7696-7698)CCCfs p.P2566fs NF1_uc002hgh.2_Frame_Shift_Del_p.P2545fs|NF1_uc010cso.2_Frame_Shift_Del_p.P754fs|NF1_uc010wbt.1_Frame_Shift_Del_p.P44fs|NF1_uc010wbu.1_RNA NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 2566 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) GATCACAACACCCCCCAAAAT 0.368 0.21 33 9 ORMDL3 94103 broad.mit.edu 37 17 38078820 38078821 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr17:38078820_38078821insA uc002htj.1 - 4 584_585 c.444_445insT c.(442-447)TTTGGAfs p.F148fs ORMDL3_uc002hti.1_RNA|ORMDL3_uc002htk.1_Frame_Shift_Ins_p.F148fs NM_139280 NP_644809 Q8N138 ORML3_HUMAN ORM1-like 3 148_149 Cytoplasmic (Potential). ceramide metabolic process integral to membrane|SPOTS complex protein binding 0 Colorectal(19;0.000442) Lung(15;0.0234) 0.000 0.51 108 112 WNK4 65266 broad.mit.edu 37 17 40939870 40939870 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr17:40939870delG uc002ibj.2 + 8 1837 c.1816delG c.(1816-1818)GGGfs p.G606fs WNK4_uc010wgx.1_Frame_Shift_Del_p.G270fs|WNK4_uc002ibk.1_Frame_Shift_Del_p.G378fs|WNK4_uc010wgy.1_Intron NM_032387 NP_115763 Q96J92 WNK4_HUMAN WNK lysine deficient protein kinase 4 606 intracellular protein kinase cascade tight junction ATP binding|protein serine/threonine kinase activity ovary(3)|skin(3)|stomach(1) 7 Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.0749) TCAGCCCCCTGGGGGGGTGCC 0.637 0.44 29 23 PPM1D 8493 broad.mit.edu 37 17 58725429 58725429 + Frame_Shift_Del DEL A - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr17:58725429delA uc002iyt.1 + 4 1225 c.1003delA c.(1003-1005)AAAfs p.K335fs PPM1D_uc010ddm.1_RNA NM_003620 NP_003611 O15297 PPM1D_HUMAN protein phosphatase 1D 335 PP2C-like. negative regulation of cell proliferation|protein dephosphorylation|response to radiation nucleus|protein serine/threonine phosphatase complex metal ion binding|protein binding|protein serine/threonine phosphatase activity upper_aerodigestive_tract(1) 1 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) Epithelial(12;6.75e-12)|all cancers(12;1.96e-10) 0.000 0.58 694 955 P4HB 5034 broad.mit.edu 37 17 79803088 79803088 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr17:79803088delC uc002kbn.1 - 10 1575 c.1378delG c.(1378-1380)GAAfs p.E460fs P4HB_uc002kbl.1_Frame_Shift_Del_p.E137fs|P4HB_uc002kbm.1_Frame_Shift_Del_p.E137fs NM_000918 NP_000909 P07237 PDIA1_HUMAN prolyl 4-hydroxylase, beta subunit precursor 460 Thioredoxin 2. E -> Q (in Ref. 15; CAA30112). cell redox homeostasis|glycerol ether metabolic process|lipid metabolic process|lipoprotein metabolic process|peptidyl-proline hydroxylation to 4-hydroxy-L-proline cell surface|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|extracellular region|melanosome|plasma membrane electron carrier activity|procollagen-proline 4-dioxygenase activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity 0 all_neural(118;0.0878)|Ovarian(332;0.12) BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509) AGCGTGCGTTCCCCGTTGTAA 0.587 0.45 43 35 ROCK1 6093 broad.mit.edu 37 18 18629104 18629105 + Frame_Shift_Ins INS - A A rs35810558 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr18:18629104_18629105insA uc002kte.2 - 4 1303_1304 c.362_363insT c.(361-363)TTCfs p.F121fs NM_005406 NP_005397 Q13464 ROCK1_HUMAN Rho-associated, coiled-coil containing protein 121 Protein kinase. actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction centriole|cytosol|Golgi membrane ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity lung(2)|breast(2)|central_nervous_system(1) 5 Melanoma(1;0.165) TTTCTTCCCAGAAAAAAGCAGA 0.361 0.41 110 78 NOTCH3 4854 broad.mit.edu 37 19 15308383 15308383 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr19:15308383delG uc002nan.2 - 2 201 c.125delC c.(124-126)CCTfs p.P42fs NOTCH3_uc002nao.1_Frame_Shift_Del_p.P42fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 42 Extracellular (Potential).|EGF-like 1. Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.49 627 607 CPAMD8 27151 broad.mit.edu 37 19 17039884 17039884 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr19:17039884delC uc002nfb.2 - 24 3185 c.3153delG c.(3151-3153)GGGfs p.G1051fs NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 1004 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 TGTTCTGATGCCCCCCCAGGA 0.587 0.42 38 27 CPAMD8 27151 broad.mit.edu 37 19 17081703 17081703 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr19:17081703delG uc002nfb.2 - 18 2384 c.2352delC c.(2350-2352)CCCfs p.P784fs NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 737 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 0.000 0.49 458 441 CRTC1 23373 broad.mit.edu 37 19 18887992 18887993 + Frame_Shift_Ins INS - C C CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr19:18887992_18887993insC uc002nkb.3 + 14 1793_1794 c.1705_1706insC c.(1705-1707)TCCfs p.S569fs CRTC1_uc010ebv.2_Frame_Shift_Ins_p.S585fs|CRTC1_uc010ebw.2_Frame_Shift_Ins_p.S405fs|CRTC1_uc002nkc.3_Frame_Shift_Ins_p.S267fs NM_015321 NP_056136 Q6UUV9 CRTC1_HUMAN mucoepidermoid carcinoma translocated 1 isoform 569 interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus|plasma membrane cAMP response element binding protein binding|protein binding CRTC1/MAML2(516) salivary_gland(474)|lung(35)|thyroid(4)|breast(3)|skin(2)|ovary(1) 519 GACAGGAGAGTCCCCCCCCAGC 0.614 0.39 20 13 MAP3K10 4294 broad.mit.edu 37 19 40719462 40719462 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr19:40719462delC uc002ona.2 + 9 2164 c.1876delC c.(1876-1878)CCCfs p.P626fs MAP3K10_uc002onb.2_Frame_Shift_Del_p.P15fs NM_002446 NP_002437 Q02779 M3K10_HUMAN mitogen-activated protein kinase kinase kinase 626 activation of JUN kinase activity|induction of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of JNK cascade|protein autophosphorylation|smoothened signaling pathway cytoplasm ATP binding|bHLH transcription factor binding|JUN kinase kinase kinase activity|protein homodimerization activity|transcription corepressor activity ovary(2)|lung(2)|skin(1)|pancreas(1) 6 0.000 0.38 269 167 CIC 23152 broad.mit.edu 37 19 42795609 42795609 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr19:42795609delC uc002otf.1 + 10 2729 c.2689delC c.(2689-2691)CCCfs p.P897fs NM_015125 NP_055940 Q96RK0 CIC_HUMAN capicua homolog 897 Pro-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1) 11 Prostate(69;0.00682) CTCCGCCCCACCCCCCAAAGG 0.607 0.39 17 11 CIC 23152 broad.mit.edu 37 19 42798427 42798428 + Frame_Shift_Ins INS - G G CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr19:42798427_42798428insG uc002otf.1 + 18 4338_4339 c.4298_4299insG c.(4297-4299)GAGfs p.E1433fs NM_015125 NP_055940 Q96RK0 CIC_HUMAN capicua homolog 1433 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1) 11 Prostate(69;0.00682) GCCAAGTGCGAGGGGGACATCT 0.624 0.41 10 7 DMPK 1760 broad.mit.edu 37 19 46283130 46283130 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr19:46283130delG uc002pdd.1 - 1 732 c.188delC c.(187-189)CCAfs p.P63fs DMPK_uc010xxs.1_5'Flank|DMPK_uc002pde.1_Frame_Shift_Del_p.P63fs|DMPK_uc002pdf.1_Intron|DMPK_uc002pdg.1_Intron|DMPK_uc002pdh.1_Intron|DMPK_uc002pdi.1_Intron|DMPK_uc010xxt.1_Intron|DMPK_uc010xxu.1_Frame_Shift_Del_p.P63fs NM_001081563 NP_001075032 Q09013 DMPK_HUMAN myotonic dystrophy protein kinase isoform 1 63 regulation of heart contraction ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity lung(3) 3 Ovarian(192;0.0308)|all_neural(266;0.112) OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24) GGGCTCCGCTGGGGGGGTGGT 0.617 0.39 30 19 LMTK3 114783 broad.mit.edu 37 19 49001851 49001851 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr19:49001851delG uc002pjk.2 - 12 2562 c.2562delC c.(2560-2562)CCCfs p.P854fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.39 926 583 LMTK3 114783 broad.mit.edu 37 19 49001891 49001892 + Frame_Shift_Ins INS - C C CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr19:49001891_49001892insC uc002pjk.2 - 12 2521_2522 c.2521_2522insG c.(2521-2523)GCGfs p.A841fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.48 749 703 DNMT3B 1789 broad.mit.edu 37 20 31384650 31384651 + Frame_Shift_Ins INS - GG GG CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr20:31384650_31384651insGG uc002wyc.2 + 13 1673_1674 c.1352_1353insGG c.(1351-1353)GAGfs p.E451fs DNMT3B_uc010ztx.1_RNA|DNMT3B_uc010zty.1_RNA|DNMT3B_uc002wyd.2_Frame_Shift_Ins_p.E431fs|DNMT3B_uc002wye.2_Frame_Shift_Ins_p.E431fs|DNMT3B_uc010gee.2_RNA|DNMT3B_uc010gef.2_RNA|DNMT3B_uc010ztz.1_Frame_Shift_Ins_p.E389fs|DNMT3B_uc010zua.1_Frame_Shift_Ins_p.E355fs|DNMT3B_uc002wyf.2_Frame_Shift_Ins_p.E443fs|DNMT3B_uc002wyg.2_Frame_Shift_Ins_p.E150fs NM_006892 NP_008823 Q9UBC3 DNM3B_HUMAN DNA cytosine-5 methyltransferase 3 beta isoform 451 GATA-type; atypical.|ADD.|Interaction with the PRC2/EED-EZH2 complex (By similarity). negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation metal ion binding|protein binding|transcription corepressor activity lung(3)|ovary(2) 5 CCTCTCTTTGAGGGGGGGCTCT 0.559 0.33 12 6 SULF2 55959 broad.mit.edu 37 20 46386097 46386097 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr20:46386097delG uc002xto.2 - 2 341 c.11delC c.(10-12)CCGfs p.P4fs SULF2_uc002xtr.2_Frame_Shift_Del_p.P4fs|SULF2_uc002xtq.2_Frame_Shift_Del_p.P4fs|SULF2_uc010ghv.1_Frame_Shift_Del_p.P4fs NM_018837 NP_061325 Q8IWU5 SULF2_HUMAN sulfatase 2 isoform a precursor 4 bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway cell surface|endoplasmic reticulum|extracellular space|Golgi stack arylsulfatase activity|calcium ion binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 CACGAGGCTCGGGGGGCCCAT 0.567 0.50 13 13 GNAS 2778 broad.mit.edu 37 20 57429035 57429035 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr20:57429035delC uc002xzw.2 + 1 1000 c.715delC c.(715-717)CCCfs p.P239fs GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_RNA NM_080425 NP_536350 P63092 GNAS2_HUMAN GNAS complex locus XLas Error:Variant_position_missing_in_P63092_after_alignment activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1) 292 all_lung(29;0.0104) BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109) CGACAGCCCACCCCCGGGGCT 0.652 0.59 7 10 GNAS 2778 broad.mit.edu 37 20 57484580 57484580 + Frame_Shift_Del DEL T - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr20:57484580delT uc002xzw.2 + 9 2878 c.2593delT c.(2593-2595)TTTfs p.F865fs GNAS_uc002xzt.2_3'UTR|GNAS_uc010gjq.2_Frame_Shift_Del_p.F163fs|GNAS_uc002xzx.2_Frame_Shift_Del_p.F163fs|GNAS_uc010gjr.2_Frame_Shift_Del_p.F113fs|GNAS_uc002xzy.2_Frame_Shift_Del_p.F148fs|GNAS_uc002yaa.2_Frame_Shift_Del_p.F208fs|GNAS_uc010zzt.1_Frame_Shift_Del_p.F223fs|GNAS_uc002yab.2_Intron|GNAS_uc002yad.2_Frame_Shift_Del_p.F113fs|GNAS_uc002yae.2_Frame_Shift_Del_p.F147fs NM_080425 NP_536350 P63092 GNAS2_HUMAN GNAS complex locus XLas 222 activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1) 292 all_lung(29;0.0104) BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109) CACCAGCATGTTTGACGTGGG 0.507 0.58 14 19 TIAM1 7074 broad.mit.edu 37 21 32639025 32639025 + Frame_Shift_Del DEL G - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr21:32639025delG uc002yow.1 - 5 736 c.264delC c.(262-264)CCCfs p.P88fs TIAM1_uc011adk.1_Frame_Shift_Del_p.P88fs|TIAM1_uc011adl.1_Frame_Shift_Del_p.P88fs|TIAM1_uc002yox.1_Intron NM_003253 NP_003244 Q13009 TIAM1_HUMAN T-cell lymphoma invasion and metastasis 1 88 apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cell-cell junction|cytosol receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity lung(3)|breast(3)|ovary(2)|large_intestine(2) 10 CCACCCAGATGGGGCTCCCGA 0.597 0.55 29 35 HUNK 30811 broad.mit.edu 37 21 33368251 33368251 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr21:33368251delC uc002yph.2 + 10 1836 c.1476delC c.(1474-1476)TTCfs p.F492fs NM_014586 NP_055401 P57058 HUNK_HUMAN hormonally upregulated Neu-associated kinase 492 multicellular organismal development|signal transduction ATP binding|protein serine/threonine kinase activity stomach(1)|skin(1) 2 AGTCCAGCTTCCCCGACAAAG 0.597 0.49 33 32 HUNK 30811 broad.mit.edu 37 21 33371238 33371239 + Frame_Shift_Ins INS - C C CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr21:33371238_33371239insC uc002yph.2 + 11 2246_2247 c.1886_1887insC c.(1885-1887)AGCfs p.S629fs NM_014586 NP_055401 P57058 HUNK_HUMAN hormonally upregulated Neu-associated kinase 629 multicellular organismal development|signal transduction ATP binding|protein serine/threonine kinase activity stomach(1)|skin(1) 2 GATAAGAACAGCCCCCCAAAAG 0.594 0.46 22 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 212 497 CLTCL1 8218 broad.mit.edu 37 22 19167753 19167754 + Splice_Site INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr22:19167753_19167754insA uc002zpb.2 - 33 4979 c.4904_splice c.e33-1 p.D1635_splice CLTCL1_uc011agv.1_Splice_Site_p.D1578_splice|SLC25A1_uc002zoy.2_5'Flank|SLC25A1_uc002zoz.2_5'Flank|SLC25A1_uc002zpa.2_5'Flank|CLTCL1_uc011agt.1_Splice_Site_p.D426_splice|CLTCL1_uc011agu.1_Splice_Site_p.D332_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) CATCAAAATCTAAAAAAACCAG 0.525 0.41 60 42 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 5 71 RGL4 266747 broad.mit.edu 37 22 24034550 24034550 + Frame_Shift_Del DEL C - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr22:24034550delC uc002zxn.2 + 2 1378 c.208delC c.(208-210)CCCfs p.P70fs LOC91316_uc002zxh.3_RNA|LOC91316_uc002zxi.3_RNA|LOC91316_uc002zxk.3_Intron|LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_Intron|LOC91316_uc002zxm.3_Intron|RGL4_uc002zxo.2_Frame_Shift_Del_p.P70fs|RGL4_uc002zxp.1_5'UTR|RGL4_uc002zxq.2_5'UTR NM_153615 NP_705843 Q8IZJ4 RGDSR_HUMAN ral guanine nucleotide dissociation 70 small GTPase mediated signal transduction cytoplasmic membrane-bounded vesicle guanyl-nucleotide exchange factor activity ovary(1) 1 GTTCAACTGGCCCCCCGAAAA 0.572 0.42 81 59 MYH9 4627 broad.mit.edu 37 22 36708256 36708257 + Frame_Shift_Ins INS - G G rs145517108 byFrequency CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr22:36708256_36708257insG uc003apg.2 - 14 1796_1797 c.1565_1566insC c.(1564-1566)CCGfs p.P522fs MYH9_uc003aph.1_Frame_Shift_Ins_p.P386fs NM_002473 NP_002464 P35579 MYH9_HUMAN myosin, heavy polypeptide 9, non-muscle 522 Myosin head-like. actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1) 11 CCAGAATGCCCGGGGGGCCTGC 0.639 0.44 47 37 DDX17 10521 broad.mit.edu 37 22 38897211 38897211 + Frame_Shift_Del DEL T - - CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr22:38897211delT uc003avy.3 - 2 465 c.362delA c.(361-363)AAGfs p.K121fs DDX17_uc003avx.3_Frame_Shift_Del_p.K121fs|DDX17_uc011anu.1_Frame_Shift_Del_p.K34fs NM_001098504 NP_001091974 Q92841 DDX17_HUMAN DEAD box polypeptide 17 isoform 3 42 RNA processing nucleus ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity skin(3)|upper_aerodigestive_tract(1) 4 Melanoma(58;0.0286) 0.000 0.54 547 630 EP300 2033 broad.mit.edu 37 22 41558756 41558757 + Frame_Shift_Ins INS - A A CW2_LARGE_INTESTINE NA CW2_LARGE_INTESTINE NA g.chr22:41558756_41558757insA uc003azl.3 + 21 4096_4097 c.3701_3702insA c.(3700-3702)AGAfs p.R1234fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1234 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding p.Y1198_L1243del(1) haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 TTTTCCAAGAGAAAAAATGACA 0.366 0.11 107 13 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.83 11 52 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.27 610 230 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.38 16 10 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.60 22 33 HTT 3064 broad.mit.edu 37 4 3076604 3076609 + In_Frame_Del DEL CAGCAG - - rs10618869 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr4:3076604_3076609delCAGCAG uc011bvq.1 + 2 203_208 c.58_63delCAGCAG c.(58-63)CAGCAGdel p.QQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagc 0.330 0.20 70 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.19 71 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 149 350 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.80 31 125 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.33 8 4 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.28 59 23 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.12 315 44 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 14 PRKDC 5591 broad.mit.edu 37 8 48815248 48815250 + In_Frame_Del DEL CTC - - D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr8:48815248_48815250delCTC uc003xqi.2 - 27 3205_3207 c.3148_3150delGAG c.(3148-3150)GAGdel p.E1050del PRKDC_uc003xqj.2_In_Frame_Del_p.E1050del|PRKDC_uc011ldh.1_In_Frame_Del_p.E1050del NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic 1050 cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) CTGGACTCTTCTCCTGCTGCTGT 0.429 0.46 212 184 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.14 70 11 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 47 KIAA1462 57608 broad.mit.edu 37 10 30316500 30316501 + In_Frame_Ins INS - CTGCTG CTGCTG D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr10:30316500_30316501insCTGCTG uc001iux.2 - 2 2635_2636 c.2576_2577insCAGCAG c.(2575-2577)AGT>AGCAGCAGT p.859_859S>SSS KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_In_Frame_Ins_p.721_721S>SSS|KIAA1462_uc009xle.1_In_Frame_Ins_p.859_859S>SSS NM_020848 NP_065899 Q9P266 K1462_HUMAN hypothetical protein LOC57608 859 Ser-rich. ovary(4) 4 CACTCTCCTCActgctgctgct 0.460 0.28 31 12 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 1.00 0 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.51 688 718 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 2 21 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 44 192 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.94 65 992 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 D283MED_CENTRAL_NERVOUS_SYSTEM NA D283MED_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 8 141 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 34 DENND4B 9909 broad.mit.edu 37 1 153907279 153907281 + In_Frame_Del DEL CTG - - D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr1:153907279_153907281delCTG uc001fdd.1 - 18 3129_3131 c.2728_2730delCAG c.(2728-2730)CAGdel p.Q910del uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) ACACctgctcctgctgctgctgc 0.463 0.10 70 8 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.38 15 9 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.24 26 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 92 123 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 19 32 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 14 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.93 1 14 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.11 89 11 PPP3R2 5535 broad.mit.edu 37 9 104357003 104357004 + Frame_Shift_Ins INS - AGGTT AGGTT D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr9:104357003_104357004insAGGTT uc004bbr.2 - 1 280_281 c.209_210insAACCT c.(208-210)GATfs p.D70fs GRIN3A_uc004bbp.1_Intron|GRIN3A_uc004bbq.1_Intron|PPP3R2_uc010mtf.1_Intron NM_147180 NP_671709 Q96LZ3 CANB2_HUMAN protein phosphatase 3 regulatory subunit B, beta 67 EF-hand 2.|2. calcium ion binding ovary(1)|skin(1) 2 Acute lymphoblastic leukemia(62;0.0527) Cyclosporine(DB00091) CCACTTCTCCATCACCGTCGGT 0.569 0.37 43 25 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 626 250 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.25 80 26 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.59 19 27 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.75 27 83 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 91 429 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 D341MED_CENTRAL_NERVOUS_SYSTEM NA D341MED_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 3 84 ATRX 546 broad.mit.edu 37 X 76907782 76907784 + In_Frame_Del DEL TCC - - DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chrX:76907782_76907784delTCC uc004ecp.3 - 15 4609_4611 c.4377_4379delGGA c.(4375-4380)GAGGAA>GAA p.1459_1460EE>E ATRX_uc004ecq.3_In_Frame_Del_p.1421_1422EE>E|ATRX_uc004eco.3_In_Frame_Del_p.1244_1245EE>E NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 1459_1460 Poly-Glu. DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) ctcctcctcttcctcctcctcct 0.212 0.74 35 98 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 4 60 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 95 21 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.53 9 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 82 141 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 29 68 PIK3R1 5295 broad.mit.edu 37 5 67589149 67589151 + In_Frame_Del DEL ATT - - DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chr5:67589149_67589151delATT uc003jva.2 + 10 1697_1699 c.1137_1139delATT c.(1135-1140)AAATTA>AAA p.L380del PIK3R1_uc003jvb.2_In_Frame_Del_p.L380del|PIK3R1_uc003jvc.2_In_Frame_Del_p.L80del|PIK3R1_uc003jvd.2_In_Frame_Del_p.L110del|PIK3R1_uc003jve.2_In_Frame_Del_p.L59del|PIK3R1_uc011crb.1_In_Frame_Del_p.L50del NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 380 SH2 1. epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.L380del(1)|p.?(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) GAAATAACAAATTAATCAAAATA 0.305 0.55 32 39 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.50 7 7 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.65 35 65 THAP11 57215 broad.mit.edu 37 16 67876823 67876824 + In_Frame_Ins INS - CAG CAG rs28647874;rs34213159 byFrequency DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chr16:67876823_67876824insCAG uc002euo.2 + 1 611_612 c.366_367insCAG c.(364-369)insCAG p.132_133insQ CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 132_133 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) agcagcagcaacagcagcagca 0.302 0.32 198 95 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 8 73 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.41 452 309 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 4 135 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes DAOY_CENTRAL_NERVOUS_SYSTEM NA DAOY_CENTRAL_NERVOUS_SYSTEM NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.19 338 80 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.85 6 34 LOC642587 642587 broad.mit.edu 37 1 209605636 209605637 + In_Frame_Ins INS - AGC AGC rs146499758;rs3842530 by1000genomes DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:209605636_209605637insAGC uc009xcn.2 + 4 634_635 c.251_252insAGC c.(250-252)GTA>GTAGCA p.97_98insA NM_001104548 NP_001098018 hypothetical protein LOC642587 0 OV - Ovarian serous cystadenocarcinoma(81;0.0422) gccaccaccgTagcagcagcag 0.272 0.36 7 4 MAGI1 9223 broad.mit.edu 37 3 65425586 65425591 + In_Frame_Del DEL TGCTGT - - rs62637700;rs139785185;rs35698502;rs79701778 byFrequency DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:65425586_65425591delTGCTGT uc003dmn.2 - 9 1759_1764 c.1233_1238delACAGCA c.(1231-1239)CAACAGCAG>CAG p.411_413QQQ>Q MAGI1_uc003dmm.2_In_Frame_Del_p.411_413QQQ>Q|MAGI1_uc003dmo.2_In_Frame_Del_p.411_413QQQ>Q|MAGI1_uc003dmp.2_In_Frame_Del_p.411_413QQQ>Q|MAGI1_uc010hny.2_In_Frame_Del_p.296_298QQQ>Q NM_001033057 NP_001028229 Q96QZ7 MAGI1_HUMAN membrane associated guanylate kinase, WW and PDZ 411_413 Poly-Gln. cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly tight junction ATP binding|protein C-terminus binding lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1) 6 Lung NSC(201;0.0016) BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133) ctgctgctgctgctgttgctgctgct 0.354 0.16 48 9 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.25 122 40 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 95 134 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.26 94 33 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.37 17 10 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 1 13 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.35 60 33 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 15 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.80 3 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 475 74 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.22 43 12 NFKBIA 4792 broad.mit.edu 37 14 35871610 35871618 + In_Frame_Del DEL GTGAACTCC - - rs139180460 DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:35871610_35871618delGTGAACTCC uc001wtf.3 - 5 998_1006 c.888_896delGGAGTTCAC c.(886-897)ACGGAGTTCACA>ACA p.296_299TEFT>T NFKBIA_uc001wte.3_In_Frame_Del_p.206_209TEFT>T|NFKBIA_uc001wtg.3_In_Frame_Del_p.253_256TEFT>T|NFKBIA_uc010amo.2_RNA NM_020529 NP_065390 P25963 IKBA_HUMAN nuclear factor of kappa light polypeptide gene 296_299 anti-apoptosis|apoptosis|cellular response to cold|cytoplasmic sequestering of NF-kappaB|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of DNA binding|negative regulation of lipid storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of NF-kappaB transcription factor activity|nerve growth factor receptor signaling pathway|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|I-kappaB/NF-kappaB complex|nucleus|plasma membrane identical protein binding|NF-kappaB binding|nuclear localization sequence binding|ubiquitin protein ligase binding breast(2) 2 Breast(36;0.0484)|Hepatocellular(127;0.158) Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891) GBM - Glioblastoma multiforme(112;0.0222) CTCGTCCTCTGTGAACTCCGTGAACTCTG 0.555 0.34 160 84 ADAMTSL3 57188 broad.mit.edu 37 15 84568398 84568399 + Splice_Site INS - A A DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:84568398_84568399insA uc002bjz.3 + 15 1840 c.1616_splice c.e15-1 p.E539_splice ADAMTSL3_uc010bmt.1_Splice_Site_p.E539_splice|ADAMTSL3_uc010bmu.1_Splice_Site_p.E539_splice NM_207517 NP_997400 P82987 ATL3_HUMAN ADAMTS-like 3 precursor proteinaceous extracellular matrix metallopeptidase activity|zinc ion binding ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1) 27 BRCA - Breast invasive adenocarcinoma(143;0.211) CTTTTTCTTAGAAAAAAGTCCA 0.371 0.33 12 6 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 30 277 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 20 79 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.14 107 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 94 336 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 7 93 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 9 77 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.58 11 15 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.38 21 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 85 144 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 26 41 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.83 2 10 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 4 32 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.45 11 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 3 49 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.26 975 342 TSC1 7248 broad.mit.edu 37 9 135771987 135771988 + In_Frame_Ins INS - GCT GCT rs118203743 DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr9:135771987_135771988insGCT uc004cca.2 - 23 3363_3364 c.3129_3130insAGC c.(3127-3132)insAGC p.1043_1044insS TSC1_uc004ccb.3_In_Frame_Ins_p.1042_1043insS|TSC1_uc011mcq.1_In_Frame_Ins_p.992_993insS|TSC1_uc011mcr.1_In_Frame_Ins_p.236_236A>AA NM_000368 NP_000359 Q92574 TSC1_HUMAN tuberous sclerosis 1 protein isoform 1 1043_1044 activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus cell cortex|lamellipodium|membrane|TSC1-TSC2 complex chaperone binding|protein N-terminus binding p.S1043N(1)|p.?(1) lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1) 14 OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06) GTAGAAAGCTCgctgctgctgc 0.574 0.31 111 51 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 686 346 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.83 10 48 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.31 38 17 ATP8B1 5205 broad.mit.edu 37 18 55365040 55365040 + Frame_Shift_Del DEL T - - DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr18:55365040delT uc002lgw.2 - 6 614 c.614delA c.(613-615)AATfs p.N205fs uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 205 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) 0.000 0.13 65 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 43 142 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 214 933 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA DBTRG05MG_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 110 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 38 IRS1 3667 broad.mit.edu 37 2 227661396 227661398 + In_Frame_Del DEL TGC - - DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:227661396_227661398delTGC uc002voh.3 - 1 2109_2111 c.2057_2059delGCA c.(2056-2061)AGCAAC>AAC p.S686del NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 686 Poly-Ser. fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) GGGACGGCGTtgctgctgctgct 0.547 0.30 167 72 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.29 25 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 86 129 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.56 21 27 SBDS 51119 broad.mit.edu 37 7 66456200 66456200 + Frame_Shift_Del DEL C - - DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:66456200delC uc003tvm.1 - 4 732 c.548delG c.(547-549)GGCfs p.G183fs NM_016038 NP_057122 Q9Y3A5 SBDS_HUMAN Shwachman-Bodian-Diamond syndrome protein 183 bone marrow development|bone mineralization|leukocyte chemotaxis|mature ribosome assembly|mitotic spindle stabilization|positive regulation of translation|ribosomal large subunit biogenesis|rRNA processing cytoplasm|nucleolus|nucleoplasm|spindle pole microtubule binding|ribosome binding|rRNA binding ovary(1) 1 CAGCTTCTTGCCTTCATTGAC 0.393 0.18 248 55 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 29 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.45 6 5 SPRY2 10253 broad.mit.edu 37 13 80910957 80910957 + Frame_Shift_Del DEL T - - DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:80910957delT uc001vli.2 - 2 1862 c.884delA c.(883-885)AACfs p.N295fs SPRY2_uc001vlj.2_Frame_Shift_Del_p.N295fs NM_005842 NP_005833 O43597 SPY2_HUMAN sprouty 2 295 Cys-rich. epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of ERK1 and ERK2 cascade|positive regulation of gene expression|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein kinase B signaling cascade cytosol|microtubule|ruffle membrane protein serine/threonine kinase activator activity ovary(1)|lung(1) 2 Medulloblastoma(90;0.18) Acute lymphoblastic leukemia(28;0.218)|Breast(118;0.244) GBM - Glioblastoma multiforme(99;0.0318) TGTGTTTGAGTTTTTACAGCG 0.433 0.20 246 63 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.69 25 55 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.14 56 9 JAK3 3718 broad.mit.edu 37 19 17953309 17953310 + Frame_Shift_Del DEL GC - - DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:17953309_17953310delGC uc002nhn.3 - 6 776_777 c.676_677delGC c.(676-678)GCCfs p.A226fs JAK3_uc010ebh.2_RNA|JAK3_uc002nho.2_Frame_Shift_Del_p.A226fs|JAK3_uc010xpx.1_Frame_Shift_Del_p.A226fs|JAK3_uc010xpy.1_3'UTR NM_000215 NP_000206 P52333 JAK3_HUMAN Janus kinase 3 226 FERM. B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis cytoskeleton|cytosol|endomembrane system|membrane ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1) 56 0.000 0.27 1004 380 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.82 49 225 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 200 456 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 5 67 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 58 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.13 674 101 LEMD1 93273 broad.mit.edu 37 1 205388453 205388453 + Frame_Shift_Del DEL T - - DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:205388453delT uc001hcj.1 - 3 212 c.110delA c.(109-111)AAGfs p.K37fs LEMD1_uc001hci.1_Frame_Shift_Del_p.K37fs|LEMD1_uc001hck.1_RNA|LEMD1_uc001hcl.1_Intron|LEMD1_uc001hcm.1_Intron|LEMD1_uc001hcn.1_Intron Q68G75 LEMD1_HUMAN RecName: Full=LEM domain-containing protein 1; Short=LEMP-1; AltName: Full=Cancer/testis antigen 50; Short=CT50; 37 LEM. integral to membrane|nuclear envelope 0 Breast(84;0.247) BRCA - Breast invasive adenocarcinoma(75;0.0938) CTGTACTAACTTTTTTTCATA 0.433 0.65 230 427 TNS1 7145 broad.mit.edu 37 2 218712886 218712887 + In_Frame_Ins INS - GCT GCT rs61747065 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:218712886_218712887insGCT uc002vgt.2 - 17 2376_2377 c.1978_1979insAGC c.(1978-1980)CCT>CAGCCT p.659_660insQ TNS1_uc002vgr.2_In_Frame_Ins_p.659_660insQ|TNS1_uc002vgs.2_In_Frame_Ins_p.659_660insQ|TNS1_uc010zjv.1_In_Frame_Ins_p.659_660insQ|TNS1_uc010fvj.1_In_Frame_Ins_p.727_728insQ|TNS1_uc010fvk.1_In_Frame_Ins_p.784_785insQ|TNS1_uc010fvi.1_In_Frame_Ins_p.346_347insQ NM_022648 NP_072174 Q9HBL0 TENS1_HUMAN tensin 659_660 Gln-rich. cytoplasm|cytoskeleton|focal adhesion actin binding ovary(3)|breast(1) 4 Renal(207;0.0483)|Lung NSC(271;0.213) Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013) AGGTGGGCGAGgctgctgctgc 0.564 0.44 20 16 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.30 19 8 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.25 44 15 HTT 3064 broad.mit.edu 37 4 3076604 3076609 + In_Frame_Del DEL CAGCAG - - rs10618869 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:3076604_3076609delCAGCAG uc011bvq.1 + 2 203_208 c.58_63delCAGCAG c.(58-63)CAGCAGdel p.QQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagc 0.330 0.26 52 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.12 69 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.75 96 284 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 59 168 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.56 7 9 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.27 61 22 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 2 23 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 36 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.51 515 545 ATN1 1822 broad.mit.edu 37 12 7045892 7045894 + In_Frame_Del DEL CAG - - rs66756893;rs67074116 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:7045892_7045894delCAG uc001qrw.1 + 5 1699_1701 c.1462_1464delCAG c.(1462-1464)CAGdel p.Q502del ATN1_uc001qrx.1_In_Frame_Del_p.Q502del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagc 0.458 0.28 83 33 CREBBP 1387 broad.mit.edu 37 16 3781773 3781784 + Splice_Site DEL CTACCTCCTTGT - - DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:3781773_3781784delCTACCTCCTTGT uc002cvv.2 - 29 5094 c.4890_splice c.e29+1 p.E1630_splice CREBBP_uc002cvw.2_Splice_Site_p.E1592_splice NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) CAGCCCACGCCTACCTCCTTGTGCTTCTCCAT 0.538 0.59 173 244 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.80 6 24 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.78 40 139 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 59 798 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 6 136 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 28 TTN 7273 broad.mit.edu 37 2 179433954 179433955 + Frame_Shift_Ins INS - T T DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chr2:179433954_179433955insT uc010zfg.1 - 275 69424_69425 c.69200_69201insA c.(69199-69201)AATfs p.N23067fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Ins_p.N16762fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.N16695fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.N16570fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 23994 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CAACAATGTAATTTTTTATTTT 0.391 0.33 138 67 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.17 48 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.32 13 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 59 88 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 20 41 NOTCH4 4855 broad.mit.edu 37 6 32191658 32191659 + In_Frame_Ins INS - AGCAGCAGC AGCAGCAGC rs148290402;rs150280230;rs144295198 by1000genomes DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chr6:32191658_32191659insAGCAGCAGC uc003obb.2 - 1 186_187 c.47_48insGCTGCTGCT c.(46-48)CTA>CTGCTGCTGCTA p.16_16L>LLLL NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Ins_p.16_16L>LLLL NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 CTGAGACACATagcagcagcag 0.535 0.18 60 13 MYST3 7994 broad.mit.edu 37 8 41790713 41790714 + In_Frame_Ins INS - GGT GGT DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chr8:41790713_41790714insGGT uc010lxb.2 - 18 5568_5569 c.5024_5025insACC c.(5023-5025)CCC>CCACCC p.1675_1675P>PP MYST3_uc010lxc.2_In_Frame_Ins_p.1675_1675P>PP|MYST3_uc003xon.3_In_Frame_Ins_p.1675_1675P>PP NM_001099412 NP_001092882 Q92794 MYST3_HUMAN MYST histone acetyltransferase (monocytic 1675 Gln/Pro-rich. histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1) 7 all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211) all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983) Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171) gctgctgctggggtggtggagg 0.119 0.29 45 18 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.58 13 18 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.64 4 7 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.54 26 31 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 4 83 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 38 371 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DETROIT562_UPPER_AERODIGESTIVE_TRACT NA DETROIT562_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 13 153 FAM48B1 100130302 broad.mit.edu 37 X 24382374 24382388 + In_Frame_Del DEL TGCTGCTGCTGCTGC - - rs10560780 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chrX:24382374_24382388delTGCTGCTGCTGCTGC uc011mjx.1 + 1 1497_1511 c.1497_1511delTGCTGCTGCTGCTGC c.(1495-1512)ATTGCTGCTGCTGCTGCT>ATT p.AAAAA510del NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 ctgctgctattgctgctgctgctgctgctgctgct 0.191 0.17 35 7 NUDT11 55190 broad.mit.edu 37 X 51238942 51238943 + Frame_Shift_Ins INS - CT CT DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chrX:51238942_51238943insCT uc010njt.2 - 1 517_518 c.354_355insAG c.(352-357)GAGTGGfs p.E118fs NM_018159 NP_060629 Q96G61 NUD11_HUMAN nudix-type motif 11 118_119 Nudix hydrolase. cytoplasm diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding 0 Ovarian(276;0.236) ACTTTGAACCACTCTCGCTTCC 0.530 0.45 62 50 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 6 64 EPHA10 284656 broad.mit.edu 37 1 38184441 38184443 + In_Frame_Del DEL AAG - - DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr1:38184441_38184443delAAG uc009vvi.2 - 16 2888_2890 c.2802_2804delCTT c.(2800-2805)TCCTTT>TCT p.F935del EPHA10_uc001cbt.2_RNA|EPHA10_uc009vvh.1_RNA|EPHA10_uc001cbu.2_RNA|EPHA10_uc001cbv.1_RNA NM_001099439 NP_001092909 Q5JZY3 EPHAA_HUMAN EPH receptor A10 isofom 3 935 Cytoplasmic (Potential).|SAM. extracellular region|integral to membrane|integral to plasma membrane ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity breast(4)|stomach(3)|lung(1) 8 Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197) Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) CACAGAGCCAAAGGAGGGGAAGG 0.675 0.50 6 6 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 264 75 MSH2 4436 broad.mit.edu 37 2 47641559 47641559 + Splice_Site DEL T - - rs11309117 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr2:47641559delT uc002rvy.1 + 5 1010 c.942_splice c.e5+2 p.Q314_splice MSH2_uc010yoh.1_Splice_Site_p.Q248_splice|MSH2_uc002rvz.2_Splice_Site_p.Q314_splice|MSH2_uc010fbg.2_Intron NM_000251 NP_000242 P43246 MSH2_HUMAN mutS homolog 2 B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes MutSalpha complex|MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1) 55 all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) CTTTTTCAGGTaaaaaaaaaa 0.299 0.16 37 7 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.24 48 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 89 165 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.39 31 20 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.24 42 13 PKHD1 5314 broad.mit.edu 37 6 51484251 51484251 + Frame_Shift_Del DEL G - - DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr6:51484251delG uc003pah.1 - 67 12129 c.11853delC c.(11851-11853)TCCfs p.S3951fs NM_138694 NP_619639 P08F94 PKHD1_HUMAN fibrocystin isoform 1 3951 Cytoplasmic (Potential). cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body protein binding|receptor activity lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1) 44 Lung NSC(77;0.0605) CTTTCCTTCTGGACACTCCAT 0.527 0.42 117 85 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 4 25 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.88 5 37 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 737 363 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.44 10 8 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.43 35 26 MEF2A 4205 broad.mit.edu 37 15 100252710 100252712 + In_Frame_Del DEL CAG - - DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr15:100252710_100252712delCAG uc010urw.1 + 11 1617_1619 c.1258_1260delCAG c.(1258-1260)CAGdel p.Q430del MEF2A_uc010urv.1_In_Frame_Del_p.Q360del|MEF2A_uc010bos.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvf.2_In_Frame_Del_p.Q422del|MEF2A_uc002bve.2_In_Frame_Del_p.Q428del|MEF2A_uc002bvg.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvi.2_In_Frame_Del_p.Q420del|MEF2A_uc010bot.2_In_Frame_Del_p.Q352del NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 430 Gln/Pro-rich. Missing (in Ref. 4; AAB17195/AAB17196). apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) ATCGGGCTTCcagcagcagcagc 0.493 0.25 21 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.75 50 151 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 80 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 32 427 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DKMG_CENTRAL_NERVOUS_SYSTEM NA DKMG_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 101 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DMS114_LUNG NA DMS114_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 34 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT DMS114_LUNG NA DMS114_LUNG NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.53 80 92 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes DMS114_LUNG NA DMS114_LUNG NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.50 8 8 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 DMS114_LUNG NA DMS114_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 20 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DMS114_LUNG NA DMS114_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.51 109 113 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DMS114_LUNG NA DMS114_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.21 95 25 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 DMS114_LUNG NA DMS114_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.24 42 13 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes DMS114_LUNG NA DMS114_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DMS114_LUNG NA DMS114_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 573 111 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 DMS114_LUNG NA DMS114_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.52 16 17 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DMS114_LUNG NA DMS114_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 104 67 AXL 558 broad.mit.edu 37 19 41737179 41737179 + Frame_Shift_Del DEL C - - DMS114_LUNG NA DMS114_LUNG NA g.chr19:41737179delC uc010ehj.2 + 6 949 c.759delC c.(757-759)TACfs p.Y253fs CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Frame_Shift_Del_p.Y253fs|AXL_uc010ehk.2_Frame_Shift_Del_p.Y253fs NM_021913 NP_068713 P30530 UFO_HUMAN AXL receptor tyrosine kinase isoform 1 253 Extracellular (Potential).|Fibronectin type-III 1. integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1) 13 GCGGCATCTACCCCCTGACCC 0.627 0.41 128 89 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DMS114_LUNG NA DMS114_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.94 23 366 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DMS114_LUNG NA DMS114_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 103 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DMS153_LUNG NA DMS153_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.81 10 44 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - DMS153_LUNG NA DMS153_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.16 162 31 HOXD13 3239 broad.mit.edu 37 2 176957624 176957624 + Frame_Shift_Del DEL C - - DMS153_LUNG NA DMS153_LUNG NA g.chr2:176957624delC uc002ukf.1 + 1 93 c.6delC c.(4-6)AGCfs p.S2fs NM_000523 NP_000514 P35453 HXD13_HUMAN homeobox D13 2 skeletal system development|transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding lung(1) 1 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0526)|READ - Rectum adenocarcinoma(9;0.0678) 0.000 0.65 146 272 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DMS153_LUNG NA DMS153_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.34 51 26 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DMS153_LUNG NA DMS153_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.44 10 8 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 DMS153_LUNG NA DMS153_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.61 44 69 ADHFE1 137872 broad.mit.edu 37 8 67356940 67356940 + Frame_Shift_Del DEL T - - DMS153_LUNG NA DMS153_LUNG NA g.chr8:67356940delT uc003xwb.3 + 5 344 c.310delT c.(310-312)TTTfs p.F104fs ADHFE1_uc003xwd.3_RNA|ADHFE1_uc003xwc.3_Frame_Shift_Del_p.F56fs|ADHFE1_uc003xwe.3_RNA|ADHFE1_uc003xwf.3_RNA|ADHFE1_uc011les.1_Frame_Shift_Del_p.F34fs|ADHFE1_uc011leq.1_RNA|ADHFE1_uc011ler.1_RNA NM_144650 NP_653251 Q8IWW8 HOT_HUMAN alcohol dehydrogenase, iron containing, 1 104 2-oxoglutarate metabolic process|molecular hydrogen transport mitochondrial matrix hydroxyacid-oxoacid transhydrogenase activity|metal ion binding ovary(1)|lung(1)|breast(1)|skin(1) 4 Lung NSC(129;0.197) Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226) TGGCATCCCCTTTACGGTTTA 0.408 0.35 32 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 DMS153_LUNG NA DMS153_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 35 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency DMS153_LUNG NA DMS153_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.23 23 7 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 DMS153_LUNG NA DMS153_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 1.00 0 19 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DMS153_LUNG NA DMS153_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 162 63 PLEKHA5 54477 broad.mit.edu 37 12 19496335 19496335 + Frame_Shift_Del DEL A - - DMS153_LUNG NA DMS153_LUNG NA g.chr12:19496335delA uc001reb.2 + 17 2406 c.2320delA c.(2320-2322)AAAfs p.K774fs PLEKHA5_uc010sie.1_Frame_Shift_Del_p.K877fs|PLEKHA5_uc001rea.2_Frame_Shift_Del_p.K832fs|PLEKHA5_uc009zin.2_Frame_Shift_Del_p.K532fs|PLEKHA5_uc010sif.1_Frame_Shift_Del_p.K705fs|PLEKHA5_uc010sig.1_Frame_Shift_Del_p.K693fs|PLEKHA5_uc010sih.1_Frame_Shift_Del_p.K666fs|PLEKHA5_uc001rec.1_Frame_Shift_Del_p.K520fs|PLEKHA5_uc009zio.2_Frame_Shift_Del_p.K96fs NM_019012 NP_061885 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A 774 1-phosphatidylinositol binding|protein binding ovary(1)|kidney(1)|skin(1) 3 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) AGGGCTGAGTAAACATAAGCA 0.343 0.53 7 8 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency DMS153_LUNG NA DMS153_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.43 8 6 RB1 5925 broad.mit.edu 37 13 49027149 49027150 + Frame_Shift_Ins INS - A A DMS153_LUNG NA DMS153_LUNG NA g.chr13:49027149_49027150insA uc001vcb.2 + 18 1882_1883 c.1716_1717insA c.(1714-1719)CTTATTfs p.L572fs NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 572_573 Domain A.|Pocket; binds T and E1A. androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.?(6)|p.L572fs*2(1) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) TATTTGATCTTATTAAACAATC 0.342 1.00 0 28 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DMS153_LUNG NA DMS153_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 13 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DMS153_LUNG NA DMS153_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 101 443 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DMS153_LUNG NA DMS153_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 3 24 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DMS273_LUNG NA DMS273_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 8 89 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - DMS273_LUNG NA DMS273_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.29 485 199 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes DMS273_LUNG NA DMS273_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.69 4 9 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 DMS273_LUNG NA DMS273_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 35 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DMS273_LUNG NA DMS273_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 63 85 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DMS273_LUNG NA DMS273_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 43 75 NPM1 4869 broad.mit.edu 37 5 170819969 170819971 + In_Frame_Del DEL GAT - - DMS273_LUNG NA DMS273_LUNG NA g.chr5:170819969_170819971delGAT uc011dex.1 + 7 646_648 c.511_513delGAT c.(511-513)GATdel p.D173del NPM1_uc003mbh.2_In_Frame_Del_p.D173del|NPM1_uc003mbi.2_In_Frame_Del_p.D173del|NPM1_uc003mbj.2_In_Frame_Del_p.D173del NM_002520 NP_002511 P06748 NPM_HUMAN nucleophosmin 1 isoform 1 173 Asp/Glu-rich (highly acidic).|Required for interaction with SENP3. anti-apoptosis|cell aging|CenH3-containing nucleosome assembly at centromere|centrosome cycle|DNA repair|interspecies interaction between organisms|intracellular protein transport|negative regulation of cell proliferation|negative regulation of centrosome duplication|nucleocytoplasmic transport|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|regulation of endodeoxyribonuclease activity|regulation of endoribonuclease activity|ribosome assembly|signal transduction nucleolus|nucleoplasm|ribonucleoprotein complex|spindle pole centrosome histone binding|NF-kappaB binding|protein binding|protein heterodimerization activity|protein homodimerization activity|ribosomal large subunit binding|ribosomal small subunit binding|RNA binding|Tat protein binding|transcription coactivator activity|unfolded protein binding NPM1/ALK(632) haematopoietic_and_lymphoid_tissue(3109)|skin(1) 3110 Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963) Medulloblastoma(196;0.0208)|all_neural(177;0.0416) Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516) tgatgaagaggatgatgatgaAG 0.241 0.54 94 110 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 DMS273_LUNG NA DMS273_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.53 16 18 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes DMS273_LUNG NA DMS273_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 21 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 DMS273_LUNG NA DMS273_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 12 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency DMS273_LUNG NA DMS273_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.27 38 14 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 DMS273_LUNG NA DMS273_LUNG NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.45 11 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DMS273_LUNG NA DMS273_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 265 133 C14orf4 64207 broad.mit.edu 37 14 77493762 77493770 + In_Frame_Del DEL TGCTGCTGC - - DMS273_LUNG NA DMS273_LUNG NA g.chr14:77493762_77493770delTGCTGCTGC uc001xsy.2 - 1 1265_1273 c.366_374delGCAGCAGCA c.(364-375)CAGCAGCAGCAA>CAA p.122_125QQQQ>Q NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 122_125 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) GAgctgttgttgctgctgctgctgctgct 0.230 0.49 19 18 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DMS273_LUNG NA DMS273_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 23 100 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DMS273_LUNG NA DMS273_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 167 641 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DMS273_LUNG NA DMS273_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 80 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DMS454_LUNG NA DMS454_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 1 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DMS454_LUNG NA DMS454_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.39 66 42 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DMS454_LUNG NA DMS454_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 32 52 MAS1L 116511 broad.mit.edu 37 6 29454551 29454551 + Frame_Shift_Del DEL C - - DMS454_LUNG NA DMS454_LUNG NA g.chr6:29454551delC uc011dlq.1 - 1 1129 c.1129delG c.(1129-1131)GAAfs p.E377fs NM_052967 NP_443199 P35410 MAS1L_HUMAN MAS1 oncogene-like 377 Cytoplasmic (Potential). cytoplasm|integral to membrane|nucleus|plasma membrane G-protein coupled receptor activity ovary(7)|lung(2) 9 0.000 0.31 647 286 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes DMS454_LUNG NA DMS454_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.73 3 8 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - DMS454_LUNG NA DMS454_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 10 MYST3 7994 broad.mit.edu 37 8 41834562 41834563 + In_Frame_Ins INS - CCT CCT rs143853582 DMS454_LUNG NA DMS454_LUNG NA g.chr8:41834562_41834563insCCT uc010lxb.2 - 8 1870_1871 c.1326_1327insAGG c.(1324-1329)insAGG p.442_443insR MYST3_uc010lxc.2_In_Frame_Ins_p.442_443insR|MYST3_uc003xon.3_In_Frame_Ins_p.442_443insR|MYST3_uc010lxd.2_In_Frame_Ins_p.442_443insR NM_001099412 NP_001092882 Q92794 MYST3_HUMAN MYST histone acetyltransferase (monocytic 442_443 Interaction with RUNX1-1. histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1) 7 all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211) all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983) Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171) TTCCTGTTGCCCCTCTTTCTGA 0.441 0.11 253 30 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 DMS454_LUNG NA DMS454_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DMS454_LUNG NA DMS454_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 214 57 ATN1 1822 broad.mit.edu 37 12 7045892 7045897 + In_Frame_Del DEL CAGCAG - - rs66756893;rs67074116;rs145352906 byFrequency DMS454_LUNG NA DMS454_LUNG NA g.chr12:7045892_7045897delCAGCAG uc001qrw.1 + 5 1699_1704 c.1462_1467delCAGCAG c.(1462-1467)CAGCAGdel p.QQ500del ATN1_uc001qrx.1_In_Frame_Del_p.QQ500del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 500_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagc 0.456 0.26 20 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DMS454_LUNG NA DMS454_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.26 32 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DMS454_LUNG NA DMS454_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 99 421 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DMS454_LUNG NA DMS454_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.87 5 34 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DMS53_LUNG NA DMS53_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 6 62 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - DMS53_LUNG NA DMS53_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 247 73 TTN 7273 broad.mit.edu 37 2 179643830 179643830 + Frame_Shift_Del DEL C - - DMS53_LUNG NA DMS53_LUNG NA g.chr2:179643830delC uc010zfg.1 - 24 4203 c.3979delG c.(3979-3981)GATfs p.D1327fs TTN_uc010zfh.1_Frame_Shift_Del_p.D1281fs|TTN_uc010zfi.1_Frame_Shift_Del_p.D1281fs|TTN_uc010zfj.1_Frame_Shift_Del_p.D1281fs|TTN_uc002unb.2_Frame_Shift_Del_p.D1327fs|uc002unc.1_Intron NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 1327 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CGCTTGCCATCTTTGTACCAA 0.368 0.26 108 37 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes DMS53_LUNG NA DMS53_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.50 5 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DMS53_LUNG NA DMS53_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 103 91 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DMS53_LUNG NA DMS53_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.60 33 50 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 DMS53_LUNG NA DMS53_LUNG NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.43 8 6 MET 4233 broad.mit.edu 37 7 116409775 116409777 + In_Frame_Del DEL TAC - - rs115574135 by1000genomes DMS53_LUNG NA DMS53_LUNG NA g.chr7:116409775_116409777delTAC uc003vij.2 + 12 2847_2849 c.2660_2662delTAC c.(2659-2664)TTACAT>TAT p.887_888LH>Y MET_uc010lkh.2_In_Frame_Del_p.905_906LH>Y|MET_uc011knj.1_In_Frame_Del_p.457_458LH>Y NM_000245 NP_000236 P08581 MET_HUMAN met proto-oncogene isoform b precursor 887_888 Extracellular (Potential). axon guidance|cell proliferation basal plasma membrane|integral to plasma membrane ATP binding|hepatocyte growth factor receptor activity|protein binding upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1) 159 all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125) Ovarian(593;0.133) GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512) AATATACACTTACATTCTGAAGC 0.379 0.22 138 40 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes DMS53_LUNG NA DMS53_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 2 35 PREX2 80243 broad.mit.edu 37 8 68995532 68995532 + Frame_Shift_Del DEL A - - DMS53_LUNG NA DMS53_LUNG NA g.chr8:68995532delA uc003xxv.1 + 18 1963 c.1936delA c.(1936-1938)ATGfs p.M646fs PREX2_uc003xxu.1_Frame_Shift_Del_p.M646fs|PREX2_uc011lez.1_Frame_Shift_Del_p.M581fs NM_024870 NP_079146 Q70Z35 PREX2_HUMAN DEP domain containing 2 isoform a 646 PDZ 1. G-protein coupled receptor protein signaling pathway|intracellular signal transduction intracellular protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1) 17 CCTAGTTTTTATGAGACCTTT 0.348 0.24 121 39 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 DMS53_LUNG NA DMS53_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 50 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DMS53_LUNG NA DMS53_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 986 235 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 DMS53_LUNG NA DMS53_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.52 15 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C DMS53_LUNG NA DMS53_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 6 94 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DMS53_LUNG NA DMS53_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.42 125 92 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DMS53_LUNG NA DMS53_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 108 1014 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DMS53_LUNG NA DMS53_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 48 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DMS79_LUNG NA DMS79_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 2 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DMS79_LUNG NA DMS79_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 56 94 ADAM29 11086 broad.mit.edu 37 4 175898930 175898983 + In_Frame_Del DEL CCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAA - - rs111721161;rs139608576;rs149749808;rs146283611;rs139492823 byFrequency;byFrequency;byFrequency DMS79_LUNG NA DMS79_LUNG NA g.chr4:175898930_175898983delCCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAA uc003iuc.2 + 5 2924_2977 c.2254_2307delCCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAA c.(2254-2307)CCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAAdel p.PQVMPSQSQPPVTPSQSQ752del ADAM29_uc003iud.2_In_Frame_Del_p.PQVMPSQSQPPVTPSQSQ752del|ADAM29_uc010irr.2_In_Frame_Del_p.PQVMPSQSQPPVTPSQSQ752del|ADAM29_uc011cki.1_In_Frame_Del_p.PQVMPSQSQPPVTPSQSQ752del NM_014269 NP_055084 Q9UKF5 ADA29_HUMAN ADAM metallopeptidase domain 29 preproprotein 752_769 Cytoplasmic (Potential).|4.|9 X 9 AA approximate repeats. QPRVM -> HPQLT (in Ref. 1; AAF03777). proteolysis|spermatogenesis integral to plasma membrane metalloendopeptidase activity|zinc ion binding skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1) 16 Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164) all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286) CCAGAGTCATCCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAACCTCGGGTGA 0.559 0.88 21 148 LIFR 3977 broad.mit.edu 37 5 38506008 38506008 + Frame_Shift_Del DEL T - - DMS79_LUNG NA DMS79_LUNG NA g.chr5:38506008delT uc010ive.1 - 9 1622 c.1290delA c.(1288-1290)AAAfs p.K430fs LIFR_uc003jli.2_Frame_Shift_Del_p.K430fs NM_001127671 NP_001121143 P42702 LIFR_HUMAN leukemia inhibitory factor receptor precursor 430 Extracellular (Potential). positive regulation of cell proliferation extracellular region|integral to plasma membrane ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity ovary(3)|large_intestine(1) 4 all_lung(31;0.00021) ACAGCTTACCTTTTTCAGTTA 0.274 0.49 23 22 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes DMS79_LUNG NA DMS79_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 16 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 DMS79_LUNG NA DMS79_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.35 13 7 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency DMS79_LUNG NA DMS79_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.17 87 18 GLYATL2 219970 broad.mit.edu 37 11 58604624 58604624 + Frame_Shift_Del DEL T - - DMS79_LUNG NA DMS79_LUNG NA g.chr11:58604624delT uc001nnd.3 - 5 471 c.340delA c.(340-342)ATAfs p.I114fs GLYATL2_uc009ymq.2_Frame_Shift_Del_p.I114fs NM_145016 NP_659453 Q8WU03 GLYL2_HUMAN glycine-N-acyltransferase-like 2 114 mitochondrion glycine N-acyltransferase activity ovary(1)|skin(1) 2 Breast(21;0.0044)|all_epithelial(135;0.0216) Glycine(DB00145) ACCTTTCTTATTGCTTCATCC 0.398 0.51 91 96 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DMS79_LUNG NA DMS79_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 786 443 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency DMS79_LUNG NA DMS79_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.14 110 18 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 DMS79_LUNG NA DMS79_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.51 47 49 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C DMS79_LUNG NA DMS79_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 2 12 TP53 7157 broad.mit.edu 37 17 7577101 7577101 + Frame_Shift_Del DEL C - - DMS79_LUNG NA DMS79_LUNG NA g.chr17:7577101delC uc002gim.2 - 8 1031 c.837delG c.(835-837)GGGfs p.G279fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Frame_Shift_Del_p.G279fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.G147fs|TP53_uc010cng.1_Frame_Shift_Del_p.G147fs|TP53_uc002gii.1_Frame_Shift_Del_p.G147fs|TP53_uc010cnh.1_Frame_Shift_Del_p.G279fs|TP53_uc010cni.1_Frame_Shift_Del_p.G279fs|TP53_uc002gij.2_Frame_Shift_Del_p.G279fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 279 Interaction with DNA.||Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). G -> E (in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation).|G -> W (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.G279E(31)|p.G279R(7)|p.0?(7)|p.G279V(4)|p.G279G(3)|p.G279W(2)|p.?(2)|p.G279fs*65(2)|p.G279fs*27(2)|p.A276_R283delACPGRDRR(1)|p.A276fs*64(1)|p.G279_R280delGR(1)|p.R280fs*62(1)|p.G279fs*59(1)|p.F270_D281del12(1)|p.P278_G279insXXXXX(1)|p.C275_R283delCACPGRDRR(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.V272_K292del21(1)|p.C275fs*20(1)|p.G279fs*26(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GCCGGTCTCTCCCAGGACAGG 0.547 0.89 2 16 CPAMD8 27151 broad.mit.edu 37 19 17025516 17025517 + Frame_Shift_Ins INS - C C DMS79_LUNG NA DMS79_LUNG NA g.chr19:17025516_17025517insC uc002nfb.2 - 28 3909_3910 c.3877_3878insG c.(3877-3879)GCCfs p.A1293fs NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 1246 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 GGAGCCATCGGCCTGCTGCTGC 0.644 0.40 33 22 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DMS79_LUNG NA DMS79_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.75 35 103 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DMS79_LUNG NA DMS79_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 16 43 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DMS79_LUNG NA DMS79_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 47 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.74 5 14 TAL1 6886 broad.mit.edu 37 1 47691376 47691376 + Frame_Shift_Del DEL C - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:47691376delC uc001cqx.2 - 2 762 c.185delG c.(184-186)GGCfs p.G62fs TAL1_uc009vyq.2_5'Flank|TAL1_uc001cqy.2_Frame_Shift_Del_p.G62fs|TAL1_uc001cra.1_Intron|TAL1_uc001cqz.1_Intron NM_003189 NP_003180 P17542 TAL1_HUMAN T-cell acute lymphocytic leukemia 1 62 basophil differentiation|cell fate commitment|cell proliferation|embryonic hemopoiesis|erythrocyte differentiation|megakaryocyte differentiation|positive regulation of cell division|positive regulation of chromatin assembly or disassembly|positive regulation of erythrocyte differentiation|positive regulation of mitotic cell cycle|positive regulation of protein complex assembly|positive regulation of transcription from RNA polymerase II promoter nuclear chromatin E-box binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity lung(1) 1 0.000 0.36 158 89 NFE2L2 4780 broad.mit.edu 37 2 178096095 178096095 + Frame_Shift_Del DEL C - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:178096095delC uc002ulh.3 - 5 1791 c.1236delG c.(1234-1236)GGGfs p.G412fs NFE2L2_uc002ulg.3_Frame_Shift_Del_p.G396fs|NFE2L2_uc010zfa.1_Frame_Shift_Del_p.G389fs|NFE2L2_uc002uli.3_Frame_Shift_Del_p.G396fs NM_006164 NP_006155 Q16236 NF2L2_HUMAN nuclear factor erythroid 2-like 2 isoform 1 412 transcription from RNA polymerase II promoter centrosome|cytosol|nucleus|plasma membrane protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity central_nervous_system(1) 1 Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935) 0.000 0.18 1024 232 NFE2L2 4780 broad.mit.edu 37 2 178098846 178098847 + Frame_Shift_Ins INS - T T DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:178098846_178098847insT uc002ulh.3 - 2 753_754 c.198_199insA c.(196-201)CAAGAGfs p.Q66fs NFE2L2_uc002ulg.3_Frame_Shift_Ins_p.Q50fs|NFE2L2_uc010zfa.1_Frame_Shift_Ins_p.Q50fs|NFE2L2_uc002uli.3_Frame_Shift_Ins_p.Q50fs|NFE2L2_uc010fra.2_Frame_Shift_Ins_p.Q50fs|NFE2L2_uc010frb.2_Frame_Shift_Ins_p.Q50fs NM_006164 NP_006155 Q16236 NF2L2_HUMAN nuclear factor erythroid 2-like 2 isoform 1 66_67 transcription from RNA polymerase II promoter centrosome|cytosol|nucleus|plasma membrane protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity central_nervous_system(1) 1 Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935) 0.000 0.41 472 331 TTN 7273 broad.mit.edu 37 2 179424205 179424205 + Frame_Shift_Del DEL C - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179424205delC uc010zfg.1 - 275 79174 c.78950delG c.(78949-78951)CGTfs p.R26317fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.R20012fs|TTN_uc010zfi.1_Frame_Shift_Del_p.R19945fs|TTN_uc010zfj.1_Frame_Shift_Del_p.R19820fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 27244 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GCTGGCCTCACGTTTTTCTAT 0.433 0.42 89 64 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 32 51 NIPBL 25836 broad.mit.edu 37 5 37007447 37007447 + Frame_Shift_Del DEL A - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:37007447delA uc003jkl.3 + 18 4609 c.4110delA c.(4108-4110)GCAfs p.A1370fs NIPBL_uc003jkk.3_Frame_Shift_Del_p.A1370fs NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 1370 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) GTTCAAAAGCAAAACGGGCTA 0.294 0.17 54 11 RICTOR 253260 broad.mit.edu 37 5 38945793 38945793 + Frame_Shift_Del DEL T - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:38945793delT uc003jlp.2 - 34 4457 c.4433delA c.(4432-4434)AATfs p.N1478fs RICTOR_uc003jlo.2_Frame_Shift_Del_p.N1502fs|RICTOR_uc010ivf.2_Intron NM_152756 NP_689969 Q6R327 RICTR_HUMAN rapamycin-insensitive companion of mTOR 1478 actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation cytosol|TORC2 complex protein binding ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1) 10 all_lung(31;0.000396) GTGAAAAGAATTTTTTACAAG 0.338 0.41 44 31 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.85 5 28 PLAT 5327 broad.mit.edu 37 8 42037509 42037509 + Frame_Shift_Del DEL G - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:42037509delG uc003xos.2 - 12 1507 c.1298delC c.(1297-1299)CCGfs p.P433fs PLAT_uc010lxf.1_Frame_Shift_Del_p.P350fs|PLAT_uc010lxg.1_Frame_Shift_Del_p.P258fs|PLAT_uc003xot.2_Frame_Shift_Del_p.P387fs|PLAT_uc011lcm.1_Frame_Shift_Del_p.P344fs|PLAT_uc011lcn.1_Frame_Shift_Del_p.P307fs NM_000930 NP_000921 P00750 TPA_HUMAN plasminogen activator, tissue isoform 1 433 Peptidase S1. blood coagulation|fibrinolysis|negative regulation of proteolysis|protein modification process|proteolysis cell surface|cytoplasm|extracellular space protein binding|serine-type endopeptidase activity breast(1)|skin(1) 2 all_cancers(6;3.84e-26)|all_epithelial(6;9.61e-28)|all_lung(13;7.2e-13)|Lung NSC(13;1.18e-11)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211) all_lung(54;0.000378)|Lung NSC(58;0.00145)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954) BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00135)|Colorectal(10;0.00165)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024) Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Iloprost(DB01088)|Reteplase(DB00015)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013) CAGGTCCGCCGGGGGAAGGCA 0.642 0.39 22 14 PLAG1 5324 broad.mit.edu 37 8 57079754 57079754 + Frame_Shift_Del DEL T - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:57079754delT uc003xsq.3 - 3 1002 c.551delA c.(550-552)AAGfs p.K184fs PLAG1_uc003xsr.3_Frame_Shift_Del_p.K184fs|PLAG1_uc010lyi.2_Frame_Shift_Del_p.K184fs|PLAG1_uc010lyj.2_Frame_Shift_Del_p.K102fs NM_001114635 NP_001108107 Q6DJT9 PLAG1_HUMAN pleiomorphic adenoma gene 1 isoform b 184 Decreased nuclear import with localization in the nucleus but also in the cytoplasm. nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding CTNNB1/PLAG1(60)|FGFR1_ENST00000447712/PLAG1(28)|CHCHD7/PLAG1(12)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|COL1A2/PLAG1(3)|TCEA1_ENST00000521604/PLAG1(3) salivary_gland(113)|soft_tissue(13)|lung(1)|central_nervous_system(1)|breast(1) 129 all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125) Epithelial(17;0.00179)|all cancers(17;0.0125) GCACTGGTGCTTTTTTTCTTT 0.483 0.17 76 16 NBN 4683 broad.mit.edu 37 8 90967512 90967512 + Frame_Shift_Del DEL T - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:90967512delT uc003yej.1 - 10 1506 c.1396delA c.(1396-1398)AGGfs p.R466fs NBN_uc003yei.1_Frame_Shift_Del_p.R384fs|NBN_uc011lgb.1_Frame_Shift_Del_p.R466fs NM_002485 NP_002476 O60934 NBN_HUMAN nibrin 466 Nuclear localization signal. KR->AA: Blocks the association with KPNA2, and reduces nuclear foci formation in response to ionizing radiation. cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm protein N-terminus binding|transcription factor binding central_nervous_system(3)|kidney(3)|lung(1) 7 BRCA - Breast invasive adenocarcinoma(11;0.0344) AAAACAGACCTTTTTTTGGTA 0.338 0.27 68 25 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 16 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.49 334 320 CDK9 1025 broad.mit.edu 37 9 130550838 130550839 + Frame_Shift_Ins INS - C C DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:130550838_130550839insC uc004bse.2 + 6 743_744 c.620_621insC c.(619-621)GGCfs p.G207fs NM_001261 NP_001252 P50750 CDK9_HUMAN cyclin-dependent kinase 9 207 Protein kinase. cell proliferation|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction transcription elongation factor complex ATP binding|cyclin-dependent protein kinase activity|DNA binding|protein binding|RNA polymerase II carboxy-terminal domain kinase activity lung(1) 1 0.000 0.29 407 167 MAMDC4 158056 broad.mit.edu 37 9 139748663 139748663 + Frame_Shift_Del DEL C - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:139748663delC uc004cjs.2 + 7 721 c.671delC c.(670-672)ACCfs p.T224fs MAMDC4_uc011mej.1_5'UTR NM_206920 NP_996803 Q6UXC1 AEGP_HUMAN apical early endosomal glycoprotein precursor 224 Extracellular (Potential). protein transport integral to membrane breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1) 7 all_cancers(76;0.0763)|all_epithelial(76;0.198) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171) 0.000 0.28 237 90 MYO3A 53904 broad.mit.edu 37 10 26462760 26462760 + Frame_Shift_Del DEL A - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:26462760delA uc001isn.2 + 30 3927 c.3567delA c.(3565-3567)CCAfs p.P1189fs MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron NM_017433 NP_059129 Q8NEV4 MYO3A_HUMAN myosin IIIA 1189 protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception cytoplasm|filamentous actin|filopodium|myosin complex actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 18 ATCAGACTCCAAAAAAAATGA 0.403 0.17 52 11 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.37 12 7 SLC3A2 6520 broad.mit.edu 37 11 62649528 62649529 + Frame_Shift_Ins INS - A A DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62649528_62649529insA uc001nwd.2 + 5 1115_1116 c.891_892insA c.(889-894)GCTAAAfs p.A297fs SLC3A2_uc001nwb.2_Frame_Shift_Ins_p.A328fs|SLC3A2_uc001nwc.2_Frame_Shift_Ins_p.A298fs|SLC3A2_uc001nwe.2_Frame_Shift_Ins_p.A266fs|SLC3A2_uc001nwf.2_Frame_Shift_Ins_p.A235fs|SLC3A2_uc001nwg.2_Frame_Shift_Ins_p.A196fs|SLC3A2_uc010rml.1_5'Flank NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c 297_298 Extracellular (Potential). blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.11 143 17 CDC42BPG 55561 broad.mit.edu 37 11 64606323 64606324 + Frame_Shift_Ins INS - T T DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:64606323_64606324insT uc001obs.3 - 8 927_928 c.927_928insA c.(925-930)CAAGACfs p.Q309fs NM_017525 NP_059995 Q6DT37 MRCKG_HUMAN CDC42 binding protein kinase gamma (DMPK-like) 309_310 Protein kinase. actin cytoskeleton reorganization|intracellular signal transduction cell leading edge|centrosome ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity lung(3)|central_nervous_system(1) 4 CGGATCAGGTCTTGGGCGCTGG 0.663 0.22 101 29 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 183 101 MLL 4297 broad.mit.edu 37 11 118367017 118367017 + Frame_Shift_Del DEL C - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:118367017delC uc001pta.2 + 20 5613 c.5590delC c.(5590-5592)CCCfs p.P1864fs MLL_uc001ptb.2_Frame_Shift_Del_p.P1867fs NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 1864 apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) GCTGAACCCACCCCCAGGCAT 0.428 0.37 79 47 NCAPD3 23310 broad.mit.edu 37 11 134062752 134062752 + Frame_Shift_Del DEL G - - rs147739086 DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:134062752delG uc001qhd.1 - 16 2483 c.1877delC c.(1876-1878)CCGfs p.P626fs NCAPD3_uc010scm.1_RNA|NCAPD3_uc009zda.1_RNA NM_015261 NP_056076 P42695 CNDD3_HUMAN non-SMC condensin II complex, subunit D3 626 cell division|mitotic chromosome condensation nuclear centromeric heterochromatin|nuclear condensin complex methylated histone residue binding ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1) 5 all_hematologic(175;0.127) all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227) CATCACCACCGGGACCACCCC 0.542 0.38 64 40 KRAS 3845 broad.mit.edu 37 12 25368390 25368390 + Frame_Shift_Del DEL T - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:25368390delT uc001rgp.1 - 5 736 c.555delA c.(553-555)AAAfs p.K185fs KRAS_uc001rgq.1_Intron NM_033360 NP_203524 P01116 RASK_HUMAN c-K-ras2 protein isoform a precursor 185 Hypervariable region. activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction plasma membrane GTP binding|GTPase activity|protein binding large_intestine(12391)|pancreas(3285)|lung(2847)|biliary_tract(521)|ovary(443)|endometrium(339)|haematopoietic_and_lymphoid_tissue(318)|stomach(203)|thyroid(149)|prostate(85)|soft_tissue(77)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|liver(31)|breast(28)|testis(17)|oesophagus(15)|central_nervous_system(9)|peritoneum(6)|salivary_gland(6)|kidney(5)|gastrointestinal_tract_(site_indeterminate)(5)|thymus(5)|eye(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1) 21052 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) TTATAATGCATTTTTTAATTT 0.348 0.40 29 19 ERBB3 2065 broad.mit.edu 37 12 56486818 56486818 + Frame_Shift_Del DEL T - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:56486818delT uc001sjh.2 + 11 1425 c.1232delT c.(1231-1233)GTTfs p.V411fs ERBB3_uc009zoj.2_Intron|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_Frame_Shift_Del_p.V352fs|ERBB3_uc009zok.2_5'Flank|ERBB3_uc001sjk.2_5'Flank|ERBB3_uc001sjj.1_5'Flank NM_001982 NP_001973 P21860 ERBB3_HUMAN erbB-3 isoform 1 precursor 411 Extracellular (Potential). cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1) 8 OV - Ovarian serous cystadenocarcinoma(18;0.112) AACTTCAGTGTTTTTTCCAAT 0.502 0.44 79 62 LRP1 4035 broad.mit.edu 37 12 57560722 57560723 + Frame_Shift_Ins INS - C C DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:57560722_57560723insC uc001snd.2 + 18 3273_3274 c.2807_2808insC c.(2806-2808)TGCfs p.C936fs LRP1_uc009zph.1_5'Flank|LRP1_uc009zpi.1_5'Flank NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 936 LDL-receptor class A 5.|Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) GCCCGCACCTGCCCCCCCAACC 0.589 0.20 37 9 DDIT3 1649 broad.mit.edu 37 12 57911083 57911083 + Frame_Shift_Del DEL C - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:57911083delC uc001soi.2 - 3 287 c.107delG c.(106-108)GGTfs p.G36fs MARS_uc001sof.1_RNA|DDIT3_uc009zps.2_Frame_Shift_Del_p.G59fs|DDIT3_uc009zpt.2_Frame_Shift_Del_p.G59fs NM_004083 NP_004074 P35638 DDIT3_HUMAN DNA-damage-inducible transcript 3 36 cell cycle arrest|cell redox homeostasis|mRNA transcription from RNA polymerase II promoter|negative regulation of determination of dorsal identity|regulation of DNA-dependent transcription in response to stress|response to DNA damage stimulus nucleus protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription factor binding FUS/DDIT3(623)|EWSR1/DDIT3(43) soft_tissue(666)|large_intestine(1)|central_nervous_system(1)|lung(1)|skin(1)|ovary(1) 671 AACATAGGTACCCCCATTTTC 0.483 0.22 83 24 ABCC4 10257 broad.mit.edu 37 13 95696015 95696016 + Frame_Shift_Ins INS - T T DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:95696015_95696016insT uc001vmd.3 - 29 3774_3775 c.3655_3656insA c.(3655-3657)ATCfs p.I1219fs ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_Frame_Shift_Ins_p.I1172fs NM_005845 NP_005836 O15439 MRP4_HUMAN ATP-binding cassette, sub-family C, member 4 1219 ABC transporter 2. platelet activation|platelet degranulation integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane 15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity central_nervous_system(3)|skin(1) 4 all_neural(89;0.0878)|Medulloblastoma(90;0.163) Cefazolin(DB01327) TTTCTCCCGGATTTTTTTTTGT 0.376 0.13 47 7 TFDP1 7027 broad.mit.edu 37 13 114290967 114290967 + Frame_Shift_Del DEL A - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:114290967delA uc001vtw.2 + 10 1170 c.958delA c.(958-960)AAAfs p.K320fs TFDP1_uc010tkd.1_Frame_Shift_Del_p.K225fs|TFDP1_uc010tke.1_Frame_Shift_Del_p.K225fs|TFDP1_uc001vty.3_Frame_Shift_Del_p.K320fs|TFDP1_uc001vtx.2_Frame_Shift_Del_p.K200fs NM_007111 NP_009042 Q14186 TFDP1_HUMAN transcription factor Dp-1 320 Enhances binding of RB protein to E2F. cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|regulation of transcription from RNA polymerase II promoter transcription factor complex DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding lung(4)|ovary(2)|skin(1) 7 Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218) all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153) all cancers(43;0.0576) CGAAGACCTTAAAATGGCCAG 0.562 0.39 52 33 TNFRSF12A 51330 broad.mit.edu 37 16 3071772 3071772 + Frame_Shift_Del DEL C - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:3071772delC uc002csv.3 + 4 421 c.335delC c.(334-336)ACCfs p.T112fs TNFRSF12A_uc002csw.3_Frame_Shift_Del_p.T77fs|THOC6_uc002ctb.2_5'Flank|THOC6_uc002ctd.2_5'Flank|THOC6_uc002ctc.2_5'Flank|THOC6_uc002cta.2_5'Flank NM_016639 NP_057723 Q9NP84 TNR12_HUMAN tumor necrosis factor receptor superfamily, 112 Cytoplasmic (Potential). angiogenesis|apoptosis integral to membrane receptor activity 0 TATCTTGCAGCCCCCATAGAG 0.612 0.38 59 36 PALB2 79728 broad.mit.edu 37 16 23647309 23647310 + Frame_Shift_Ins INS - T T DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:23647309_23647310insT uc002dlx.1 - 4 757_758 c.557_558insA c.(556-558)AATfs p.N186fs NM_024675 NP_078951 Q86YC2 PALB2_HUMAN partner and localizer of BRCA2 186 Interaction with RAD51.|Interaction with BRCA1. double-strand break repair via homologous recombination nucleoplasm DNA binding|protein binding lung(3)|breast(3)|ovary(2)|skin(1)|kidney(1)|pancreas(1) 11 GBM - Glioblastoma multiforme(48;0.0167) ATCTAGCAGGATTTTTGCTACT 0.376 0.20 118 29 EDC4 23644 broad.mit.edu 37 16 67913786 67913788 + In_Frame_Del DEL AGC - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:67913786_67913788delAGC uc002eur.2 + 16 2021_2023 c.1855_1857delAGC c.(1855-1857)AGCdel p.S629del EDC4_uc010cer.2_In_Frame_Del_p.S248del|EDC4_uc010vkg.1_In_Frame_Del_p.S561del|EDC4_uc002eus.2_In_Frame_Del_p.S359del|EDC4_uc002eut.1_5'Flank NM_014329 NP_055144 Q6P2E9 EDC4_HUMAN autoantigen RCD8 629 Ser-rich. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay cytoplasmic mRNA processing body|cytosol|nucleus protein binding ovary(2)|central_nervous_system(2) 4 Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121) cagcagcggtagcagcagcagca 0.458 0.52 10 11 PSKH1 5681 broad.mit.edu 37 16 67942845 67942845 + Frame_Shift_Del DEL C - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:67942845delC uc002euv.2 + 2 363 c.193delC c.(193-195)CCCfs p.P65fs PSKH1_uc010cet.2_Frame_Shift_Del_p.P65fs NM_006742 NP_006733 P11801 KPSH1_HUMAN protein serine kinase H1 65 endoplasmic reticulum membrane|Golgi apparatus|microtubule organizing center|nuclear speck|plasma membrane ATP binding|protein serine/threonine kinase activity 0 Ovarian(137;0.192) OV - Ovarian serous cystadenocarcinoma(108;0.0044)|Epithelial(162;0.0197)|all cancers(182;0.128) 0.000 0.10 959 109 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 27 308 TP53 7157 broad.mit.edu 37 17 7577036 7577036 + Frame_Shift_Del DEL G - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:7577036delG uc002gim.2 - 8 1096 c.902delC c.(901-903)CCAfs p.P301fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Frame_Shift_Del_p.P301fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.P169fs|TP53_uc010cng.1_Frame_Shift_Del_p.P169fs|TP53_uc002gii.1_Frame_Shift_Del_p.P169fs|TP53_uc010cnh.1_Frame_Shift_Del_p.P301fs|TP53_uc010cni.1_Frame_Shift_Del_p.P301fs|TP53_uc002gij.2_Frame_Shift_Del_p.P301fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 301 Interaction with HIPK1 (By similarity).|Interaction with CARM1. P -> T (in a sporadic cancer; somatic mutation).|P -> A (in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.P301fs*44(9)|p.0?(7)|p.G302fs*4(4)|p.?(3)|p.P301fs*5(3)|p.P301S(3)|p.P301_S303delPGS(1)|p.L299fs*2(1)|p.P301P(1)|p.L265_K305del41(1)|p.P301Q(1)|p.P301fs*45(1)|p.P301T(1)|p.G293fs*1(1)|p.P301L(1)|p.P301A(1)|p.E298_P301delELPP(1)|p.H296_S303delHHELPPGS(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.57 127 171 C17orf37 84299 broad.mit.edu 37 17 37885956 37885957 + Frame_Shift_Ins INS - C C DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:37885956_37885957insC uc002hsq.2 - 3 285_286 c.245_246insG c.(244-246)GGCfs p.G82fs NM_032339 NP_115715 Q9BRT3 CQ037_HUMAN hypothetical protein LOC84299 82 cell redox homeostasis cytosol|membrane selenium binding 0 all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052) UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;3.72e-63)|all cancers(3;1.87e-56)|BRCA - Breast invasive adenocarcinoma(8;6.8e-45)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171) CATAGGGAAAGCCCCCATTCTC 0.470 0.51 51 53 COL1A1 1277 broad.mit.edu 37 17 48267689 48267689 + Frame_Shift_Del DEL G - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:48267689delG uc002iqm.2 - 35 2576 c.2450delC c.(2449-2451)CCTfs p.P817fs NM_000088 NP_000079 P02452 CO1A1_HUMAN alpha 1 type I collagen preproprotein 817 Triple-helical region. axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception collagen type I|extracellular space|plasma membrane identical protein binding|platelet-derived growth factor binding COL1A1/PDGFB(372) soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1) 382 Collagenase(DB00048)|Palifermin(DB00039) 0.000 0.54 227 266 CPAMD8 27151 broad.mit.edu 37 19 17081703 17081703 + Frame_Shift_Del DEL G - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:17081703delG uc002nfb.2 - 18 2384 c.2352delC c.(2350-2352)CCCfs p.P784fs NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 737 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 0.000 0.20 216 53 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.45 33 27 DNMT3B 1789 broad.mit.edu 37 20 31390266 31390266 + Frame_Shift_Del DEL G - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:31390266delG uc002wyc.2 + 20 2542 c.2221delG c.(2221-2223)GGGfs p.G741fs DNMT3B_uc002wyd.2_Frame_Shift_Del_p.G721fs|DNMT3B_uc002wye.2_Frame_Shift_Del_p.G721fs|DNMT3B_uc010gee.2_RNA|DNMT3B_uc010gef.2_RNA|DNMT3B_uc010ztz.1_Frame_Shift_Del_p.G679fs|DNMT3B_uc010zua.1_Frame_Shift_Del_p.G645fs|DNMT3B_uc002wyf.2_Frame_Shift_Del_p.G733fs|DNMT3B_uc002wyg.2_Frame_Shift_Del_p.G440fs|DNMT3B_uc010geg.2_Frame_Shift_Del_p.G40fs|DNMT3B_uc010geh.2_RNA NM_006892 NP_008823 Q9UBC3 DNM3B_HUMAN DNA cytosine-5 methyltransferase 3 beta isoform 741 negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation metal ion binding|protein binding|transcription corepressor activity lung(3)|ovary(2) 5 CAACCTACCCGGGATGAACAG 0.473 0.11 77 10 RBL1 5933 broad.mit.edu 37 20 35696591 35696592 + Splice_Site INS - A A DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:35696591_35696592insA uc002xgi.2 - 3 370 c.291_splice c.e3-1 p.S97_splice RBL1_uc010zvt.1_Splice_Site|RBL1_uc002xgj.1_Splice_Site_p.S97_splice|RBL1_uc010gfv.1_Splice_Site NM_002895 NP_002886 P28749 RBL1_HUMAN retinoblastoma-like protein 1 isoform a cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent transcription factor binding lung(5)|skin(3)|ovary(2) 10 Myeloproliferative disorder(115;0.00878) TGTATTAAACTAAAAAAAAAAA 0.272 0.29 17 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 157 463 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 2 21 TNRC6B 23112 broad.mit.edu 37 22 40706848 40706848 + Frame_Shift_Del DEL G - - DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:40706848delG uc011aor.1 + 17 4497 c.4286delG c.(4285-4287)CGGfs p.R1429fs TNRC6B_uc003aym.2_Frame_Shift_Del_p.R625fs|TNRC6B_uc003ayn.3_Frame_Shift_Del_p.R1319fs|TNRC6B_uc003ayo.2_Frame_Shift_Del_p.R1176fs NM_001162501 NP_001155973 Q9UPQ9 TNR6B_HUMAN trinucleotide repeat containing 6B isoform 1 1429 gene silencing by RNA|regulation of translation cytoplasmic mRNA processing body nucleotide binding|RNA binding 0 GGTAAAACCCGGGGAGGGTCA 0.473 0.50 13 13 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 4 40 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.20 394 101 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 104 131 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 32 69 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.18 193 43 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 19 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 24 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.24 28 9 COBRA1 25920 broad.mit.edu 37 9 140158792 140158793 + Frame_Shift_Ins INS - T T DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:140158792_140158793insT uc004cmm.3 + 6 1082_1083 c.879_880insT c.(877-882)GGCCAGfs p.G293fs NM_015456 NP_056271 Q8WX92 NELFB_HUMAN cofactor of BRCA1 293_294 negative regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction cytoplasm|nucleoplasm protein binding 0 all_cancers(76;0.0926) STAD - Stomach adenocarcinoma(284;0.137) OV - Ovarian serous cystadenocarcinoma(145;9.42e-05)|Epithelial(140;0.000766) 0.000 1.00 0 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 342 162 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.60 8 12 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 59 707 NLK 51701 broad.mit.edu 37 17 26370014 26370016 + In_Frame_Del DEL CCT - - DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:26370014_26370016delCCT uc010crj.2 + 1 327_329 c.115_117delCCT c.(115-117)CCTdel p.P41del NLK_uc010cri.1_RNA NM_016231 NP_057315 Q9UBE8 NLK_HUMAN nemo like kinase 41 intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway cytoplasm|nucleus ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding ovary(1)|lung(1)|central_nervous_system(1) 3 all_lung(13;0.000343)|Lung NSC(42;0.00184) UCEC - Uterine corpus endometrioid carcinoma (53;0.168) TCCACACCTCCCTCCTCCTCACC 0.488 0.39 115 74 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.82 16 73 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 39 259 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 9 107 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 DOV13_OVARY NA DOV13_OVARY NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.42 69 49 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DOV13_OVARY NA DOV13_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 6 61 F8 2157 broad.mit.edu 37 X 154157686 154157686 + Frame_Shift_Del DEL T - - DOV13_OVARY NA DOV13_OVARY NA g.chrX:154157686delT uc004fmt.2 - 14 4550 c.4379delA c.(4378-4380)AATfs p.N1460fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1460 B. N -> K (in HEMA). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AGAAAGGTTATTTTTTTTGGC 0.413 0.20 198 48 ZNF643 65243 broad.mit.edu 37 1 40923072 40923072 + Frame_Shift_Del DEL T - - DOV13_OVARY NA DOV13_OVARY NA g.chr1:40923072delT uc001cfn.1 + 4 694 c.397delT c.(397-399)TGGfs p.W133fs ZNF643_uc001cfl.1_Frame_Shift_Del_p.W31fs|ZNF643_uc001cfm.1_5'UTR NM_023070 NP_075558 Q9UJL9 ZN643_HUMAN zinc finger protein 643 133 KRAB. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(2) 2 Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0393) OV - Ovarian serous cystadenocarcinoma(33;5.25e-18) 0.000 0.27 698 257 TTN 7273 broad.mit.edu 37 2 179606355 179606356 + Frame_Shift_Ins INS - A A DOV13_OVARY NA DOV13_OVARY NA g.chr2:179606355_179606356insA uc010zfh.1 - 46 11315_11316 c.11091_11092insT c.(11089-11094)TTTGTTfs p.F3697fs TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Frame_Shift_Ins_p.F3630fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.F3505fs|TTN_uc002umz.1_Intron NM_133437 NP_597681 Q8WZ42 TITIN_HUMAN titin isoform novex-2 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CCGTCAAAAACAAATTTGTAGT 0.406 0.32 92 44 GPR87 53836 broad.mit.edu 37 3 151012814 151012814 + Frame_Shift_Del DEL T - - DOV13_OVARY NA DOV13_OVARY NA g.chr3:151012814delT uc003eyt.2 - 3 581 c.220delA c.(220-222)ACCfs p.T74fs MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron NM_023915 NP_076404 Q9BY21 GPR87_HUMAN G protein-coupled receptor 87 74 Cytoplasmic (Potential). integral to membrane|plasma membrane purinergic nucleotide receptor activity, G-protein coupled large_intestine(1) 1 LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517) ATGAAGCTGGTTTTATTCCTA 0.398 0.30 78 33 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DOV13_OVARY NA DOV13_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 54 67 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DOV13_OVARY NA DOV13_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 21 37 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes DOV13_OVARY NA DOV13_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 2 14 PTK2B 2185 broad.mit.edu 37 8 27296841 27296842 + Frame_Shift_Ins INS - C C DOV13_OVARY NA DOV13_OVARY NA g.chr8:27296841_27296842insC uc003xfn.1 + 25 2568_2569 c.1760_1761insC c.(1759-1761)CTCfs p.L587fs PTK2B_uc003xfo.1_Frame_Shift_Ins_p.L587fs|PTK2B_uc003xfp.1_Frame_Shift_Ins_p.L587fs|PTK2B_uc003xfq.1_Frame_Shift_Ins_p.L587fs|PTK2B_uc003xfr.1_Frame_Shift_Ins_p.L333fs NM_173174 NP_775266 Q14289 FAK2_HUMAN PTK2B protein tyrosine kinase 2 beta isoform a 587 Protein kinase. apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly cytosol ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity lung(3)|ovary(1)|skin(1) 5 Ovarian(32;2.72e-05) UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229) GTGACTCGTCTCCCCATCAAAT 0.480 0.33 62 31 WHSC1L1 54904 broad.mit.edu 37 8 38205092 38205092 + Frame_Shift_Del DEL T - - DOV13_OVARY NA DOV13_OVARY NA g.chr8:38205092delT uc003xli.2 - 2 1116 c.598delA c.(598-600)AGCfs p.S200fs WHSC1L1_uc011lbm.1_Frame_Shift_Del_p.S200fs|WHSC1L1_uc010lwe.2_Frame_Shift_Del_p.S200fs|WHSC1L1_uc003xlj.2_Frame_Shift_Del_p.S200fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 200 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TGCTTGTTGCTTTTTTTCCTC 0.378 0.32 113 54 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency DOV13_OVARY NA DOV13_OVARY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.70 150 344 PAX5 5079 broad.mit.edu 37 9 36882049 36882050 + Frame_Shift_Ins INS - G G rs34810717 byFrequency;by1000genomes DOV13_OVARY NA DOV13_OVARY NA g.chr9:36882049_36882050insG uc003zzo.1 - 8 1411_1412 c.963_964insC c.(961-966)CCCGCTfs p.P321fs PAX5_uc011lpt.1_Frame_Shift_Ins_p.P117fs|PAX5_uc011lpu.1_Intron|PAX5_uc011lpv.1_Intron|PAX5_uc011lpw.1_Intron|PAX5_uc011lpx.1_Intron|PAX5_uc011lpy.1_Intron|PAX5_uc010mls.1_Intron|PAX5_uc011lpz.1_Frame_Shift_Ins_p.P278fs|PAX5_uc011lqa.1_Frame_Shift_Ins_p.P213fs|PAX5_uc010mlq.1_RNA|PAX5_uc011lqb.1_RNA|PAX5_uc010mlo.1_Intron|PAX5_uc010mlp.1_Frame_Shift_Ins_p.P321fs|PAX5_uc011lqc.1_Frame_Shift_Ins_p.P278fs|PAX5_uc010mlr.1_Intron NM_016734 NP_057953 Q02548 PAX5_HUMAN paired box 5 321_322 cell differentiation|humoral immune response|nervous system development|organ morphogenesis|spermatogenesis|transcription from RNA polymerase II promoter nucleus DNA binding p.?(22)|p.A322fs*19(3) PAX5/JAK2(18) haematopoietic_and_lymphoid_tissue(142)|lung(3)|central_nervous_system(2) 147 all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44) GBM - Glioblastoma multiforme(29;0.0108) CCCTGTCCAGCGGGGGGGACGT 0.639 0.55 22 27 PRKACG 5568 broad.mit.edu 37 9 71628914 71628914 + Frame_Shift_Del DEL C - - DOV13_OVARY NA DOV13_OVARY NA g.chr9:71628914delC uc004agy.2 - 1 126 c.95delG c.(94-96)GGAfs p.G32fs NM_002732 NP_002723 P22612 KAPCG_HUMAN protein kinase, cAMP-dependent, catalytic, 32 activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|gluconeogenesis|intracellular protein kinase cascade|male gonad development|nerve growth factor receptor signaling pathway|regulation of insulin secretion|spermatogenesis|transmembrane transport|triglyceride catabolic process|water transport cytosol|nucleoplasm ATP binding|cAMP-dependent protein kinase activity ovary(1)|pancreas(1)|skin(1) 3 AGCGGGGTTTCCCCATCTGTA 0.597 0.49 142 136 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DOV13_OVARY NA DOV13_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 189 64 ATN1 1822 broad.mit.edu 37 12 7045893 7045894 + In_Frame_Ins INS - GCA GCA rs67074116 DOV13_OVARY NA DOV13_OVARY NA g.chr12:7045893_7045894insGCA uc001qrw.1 + 5 1700_1701 c.1463_1464insGCA c.(1462-1464)CAG>CAGCAG p.488_488Q>QQ ATN1_uc001qrx.1_In_Frame_Ins_p.488_488Q>QQ NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 488 Poly-Gln. Missing. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 caacagcaacagcagcagcagc 0.455 0.14 44 7 BCL11B 64919 broad.mit.edu 37 14 99642282 99642282 + Frame_Shift_Del DEL G - - DOV13_OVARY NA DOV13_OVARY NA g.chr14:99642282delG uc001yga.2 - 4 1158 c.891delC c.(889-891)CCCfs p.P297fs BCL11B_uc001ygb.2_Frame_Shift_Del_p.P226fs NM_138576 NP_612808 Q9C0K0 BC11B_HUMAN B-cell CLL/lymphoma 11B isoform 1 297 nucleus zinc ion binding central_nervous_system(8)|large_intestine(1)|lung(1) 10 Melanoma(154;0.0866)|all_epithelial(191;0.241) COAD - Colon adenocarcinoma(157;0.103) 0.000 0.39 237 152 FURIN 5045 broad.mit.edu 37 15 91424579 91424579 + Frame_Shift_Del DEL C - - DOV13_OVARY NA DOV13_OVARY NA g.chr15:91424579delC uc002bpu.1 + 16 2072 c.1856delC c.(1855-1857)GCCfs p.A619fs NM_002569 NP_002560 P09958 FURIN_HUMAN furin preproprotein 619 Cys-rich. cell proliferation|negative regulation of low-density lipoprotein particle receptor catabolic process|negative regulation of transforming growth factor-beta1 production|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|Notch signaling pathway|peptide biosynthetic process|peptidyl-glutamic acid carboxylation|post-translational protein modification|secretion by cell|signal peptide processing|transforming growth factor beta receptor signaling pathway|viral assembly, maturation, egress, and release cell surface|Golgi lumen|Golgi membrane|integral to membrane|membrane raft|plasma membrane|trans-Golgi network|trans-Golgi network transport vesicle metal ion binding|nerve growth factor binding|peptide binding|protease binding|serine-type endopeptidase activity|serine-type endopeptidase inhibitor activity central_nervous_system(4)|lung(2)|breast(1) 7 Lung NSC(78;0.0771)|all_lung(78;0.137) Lung(145;0.189) CCAGGGTTCGCCCCCCAAGTC 0.637 0.19 161 37 FURIN 5045 broad.mit.edu 37 15 91424648 91424648 + Frame_Shift_Del DEL C - - DOV13_OVARY NA DOV13_OVARY NA g.chr15:91424648delC uc002bpu.1 + 16 2141 c.1925delC c.(1924-1926)GCCfs p.A642fs NM_002569 NP_002560 P09958 FURIN_HUMAN furin preproprotein 642 Cys-rich. cell proliferation|negative regulation of low-density lipoprotein particle receptor catabolic process|negative regulation of transforming growth factor-beta1 production|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|Notch signaling pathway|peptide biosynthetic process|peptidyl-glutamic acid carboxylation|post-translational protein modification|secretion by cell|signal peptide processing|transforming growth factor beta receptor signaling pathway|viral assembly, maturation, egress, and release cell surface|Golgi lumen|Golgi membrane|integral to membrane|membrane raft|plasma membrane|trans-Golgi network|trans-Golgi network transport vesicle metal ion binding|nerve growth factor binding|peptide binding|protease binding|serine-type endopeptidase activity|serine-type endopeptidase inhibitor activity central_nervous_system(4)|lung(2)|breast(1) 7 Lung NSC(78;0.0771)|all_lung(78;0.137) Lung(145;0.189) AGCGTCTGCGCCCCCTGCCAC 0.662 0.23 143 43 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C DOV13_OVARY NA DOV13_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 9 108 MYH3 4621 broad.mit.edu 37 17 10554894 10554894 + Frame_Shift_Del DEL T - - DOV13_OVARY NA DOV13_OVARY NA g.chr17:10554894delT uc002gmq.1 - 4 517 c.440delA c.(439-441)AAGfs p.K147fs NM_002470 NP_002461 P11055 MYH3_HUMAN myosin, heavy chain 3, skeletal muscle, 147 Myosin head-like. muscle filament sliding|muscle organ development cytosol|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|microfilament motor activity ovary(4)|central_nervous_system(2)|pancreas(1) 7 CTCCTGGCGCTTTTTGCCTCG 0.577 0.24 66 21 LDLR 3949 broad.mit.edu 37 19 11240334 11240336 + In_Frame_Del DEL CAG - - rs139796500 DOV13_OVARY NA DOV13_OVARY NA g.chr19:11240334_11240336delCAG uc002mqk.3 + 17 2703_2705 c.2535_2537delCAG c.(2533-2538)TACAGC>TAC p.S846del LDLR_uc010xlk.1_In_Frame_Del_p.S846del|LDLR_uc010xll.1_In_Frame_Del_p.S805del|LDLR_uc010xlm.1_In_Frame_Del_p.S699del|LDLR_uc010xln.1_In_Frame_Del_p.S668del|LDLR_uc010xlo.1_In_Frame_Del_p.S678del|LDLR_uc010dxu.2_In_Frame_Del_p.A13del NM_000527 NP_000518 P01130 LDLR_HUMAN low density lipoprotein receptor precursor 846 Required for MYLIP-triggered down- regulation of LDLR.|Cytoplasmic (Potential). cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity ovary(2)|skin(2) 4 Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524) GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197) Methyl aminolevulinate(DB00992)|Porfimer(DB00707) AGGACGGCTACAGCTACCCCTCG 0.571 0.96 3 78 PRKACA 5566 broad.mit.edu 37 19 14218178 14218178 + Frame_Shift_Del DEL T - - DOV13_OVARY NA DOV13_OVARY NA g.chr19:14218178delT uc002myc.2 - 2 290 c.90delA c.(88-90)AAAfs p.K30fs PRKACA_uc002myb.2_Frame_Shift_Del_p.K22fs|PRKACA_uc010xnm.1_Translation_Start_Site|PRKACA_uc002myd.2_Translation_Start_Site NM_002730 NP_002721 P17612 KAPCA_HUMAN cAMP-dependent protein kinase catalytic subunit 30 activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|G2/M transition of mitotic cell cycle|gluconeogenesis|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|regulation of insulin secretion|transmembrane transport|triglyceride catabolic process|water transport cAMP-dependent protein kinase complex|centrosome|cytosol|nucleoplasm|plasma membrane ATP binding|cAMP-dependent protein kinase activity|cAMP-dependent protein kinase inhibitor activity|protein kinase binding lung(1) 1 GACTTTCCCATTTTTTAAGAA 0.552 0.33 31 15 BRD4 23476 broad.mit.edu 37 19 15376247 15376248 + Frame_Shift_Ins INS - G G DOV13_OVARY NA DOV13_OVARY NA g.chr19:15376247_15376248insG uc002nar.2 - 5 988_989 c.766_767insC c.(766-768)CAGfs p.Q256fs BRD4_uc002nas.2_Frame_Shift_Ins_p.Q256fs|BRD4_uc002nat.3_Frame_Shift_Ins_p.Q256fs|BRD4_uc002nau.3_Frame_Shift_Ins_p.Q256fs NM_058243 NP_490597 O60885 BRD4_HUMAN bromodomain-containing protein 4 isoform long 256 interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle condensed nuclear chromosome|cytoplasm protein binding ovary(2) 2 OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18) 0.000 0.20 369 91 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DOV13_OVARY NA DOV13_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.72 14 36 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DOV13_OVARY NA DOV13_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.55 388 465 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DOV13_OVARY NA DOV13_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 94 MED15 51586 broad.mit.edu 37 22 20918916 20918918 + In_Frame_Del DEL CAG - - DOV13_OVARY NA DOV13_OVARY NA g.chr22:20918916_20918918delCAG uc002zsp.2 + 6 711_713 c.631_633delCAG c.(631-633)CAGdel p.Q218del MED15_uc002zsn.1_In_Frame_Del_p.Q137del|MED15_uc002zso.2_In_Frame_Del_p.Q147del|MED15_uc002zsq.2_In_Frame_Del_p.Q218del|MED15_uc010gso.2_In_Frame_Del_p.Q218del|MED15_uc002zsr.2_In_Frame_Del_p.Q192del|MED15_uc011ahs.1_In_Frame_Del_p.Q192del|MED15_uc011aht.1_In_Frame_Del_p.Q192del|MED15_uc002zss.2_In_Frame_Del_p.Q137del|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 218 Poly-Gln. Missing (in Ref. 4; CAG30423). regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) gcagcagctccagcagcagcagc 0.187 0.20 28 7 DDX17 10521 broad.mit.edu 37 22 38881964 38881965 + In_Frame_Ins INS - GGA GGA DOV13_OVARY NA DOV13_OVARY NA g.chr22:38881964_38881965insGGA uc003avy.3 - 13 2274_2275 c.2171_2172insTCC c.(2170-2172)CCC>CCTCCC p.724_724P>PP DDX17_uc003avw.3_In_Frame_Ins_p.176_176P>PP|DDX17_uc010gxp.2_In_Frame_Ins_p.174_174P>PP|DDX17_uc003avx.3_In_Frame_Ins_p.722_722P>PP NM_001098504 NP_001091974 Q92841 DDX17_HUMAN DEAD box polypeptide 17 isoform 3 643 Poly-Pro. RNA processing nucleus ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity skin(3)|upper_aerodigestive_tract(1) 4 Melanoma(58;0.0286) 0.000 0.22 583 160 SSX3 10214 broad.mit.edu 37 X 48209463 48209463 + Frame_Shift_Del DEL G - - DU145_PROSTATE NA DU145_PROSTATE NA g.chrX:48209463delG uc004djd.1 - 6 519 c.425delC c.(424-426)CCGfs p.P142fs SSX3_uc004dje.2_Frame_Shift_Del_p.P142fs NM_021014 NP_066294 Q99909 SSX3_HUMAN synovial sarcoma, X breakpoint 3 isoform a 142 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus nucleic acid binding 0 TGGTTTTCCCGGGGGGCACAG 0.493 0.88 14 105 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DU145_PROSTATE NA DU145_PROSTATE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 31 NOTCH2 4853 broad.mit.edu 37 1 120480570 120480571 + Frame_Shift_Ins INS - T T DU145_PROSTATE NA DU145_PROSTATE NA g.chr1:120480570_120480571insT uc001eik.2 - 20 3502_3503 c.3246_3247insA c.(3244-3249)AAAGCAfs p.K1082fs NOTCH2_uc001eil.2_Frame_Shift_Ins_p.K1082fs NM_024408 NP_077719 Q04721 NOTC2_HUMAN notch 2 preproprotein 1082_1083 EGF-like 28.|Extracellular (Potential). anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1) 27 all_neural(166;0.153) all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809) Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133) TGGGACTCTGCTTTTTTCTGAA 0.485 0.27 217 81 BCL9 607 broad.mit.edu 37 1 147090982 147090982 + Frame_Shift_Del DEL C - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr1:147090982delC uc001epq.2 + 8 1761 c.1021delC c.(1021-1023)CCCfs p.P341fs BCL9_uc010ozr.1_Frame_Shift_Del_p.P267fs NM_004326 NP_004317 O00512 BCL9_HUMAN B-cell CLL/lymphoma 9 341 Pro-rich. Wnt receptor signaling pathway nucleus protein binding ovary(2)|large_intestine(2)|breast(1)|skin(1) 6 all_hematologic(923;0.115) CAGTGGCGAGCCCCCCACACT 0.587 0.16 328 62 MTMR11 10903 broad.mit.edu 37 1 149901148 149901150 + In_Frame_Del DEL AAC - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr1:149901148_149901150delAAC uc001etl.3 - 17 2252_2254 c.2001_2003delGTT c.(1999-2004)GAGTTA>GAA p.L669del SF3B4_uc001etj.1_5'Flank|SF3B4_uc001etk.1_5'Flank|SF3B4_uc009wll.1_5'Flank|MTMR11_uc001etm.1_In_Frame_Del_p.L597del NM_001145862 NP_001139334 A4FU01 MTMRB_HUMAN myotubularin related protein 11 isoform a 669 phosphatase activity central_nervous_system(1) 1 Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171) LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247) TTTCCGTAATAACTCCTGAAGAT 0.468 0.17 374 76 PRRX1 5396 broad.mit.edu 37 1 170695520 170695521 + Frame_Shift_Ins INS - G G DU145_PROSTATE NA DU145_PROSTATE NA g.chr1:170695520_170695521insG uc001ghf.2 + 3 624_625 c.577_578insG c.(577-579)TGGfs p.W193fs PRRX1_uc001ghe.2_Frame_Shift_Ins_p.W193fs NM_022716 NP_073207 P54821 PRRX1_HUMAN paired mesoderm homeobox 1 isoform pmx-1b 193 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity ovary(1) 1 all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181) TTATCTCTCCTGGGGGACAGCG 0.554 0.27 219 83 PIK3C2B 5287 broad.mit.edu 37 1 204438447 204438447 + Frame_Shift_Del DEL G - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr1:204438447delG uc001haw.2 - 3 963 c.484delC c.(484-486)CGAfs p.R162fs PIK3C2B_uc010pqv.1_Frame_Shift_Del_p.R162fs|PIK3C2B_uc001hax.1_Frame_Shift_Del_p.R162fs|PIK3C2B_uc009xbd.1_RNA NM_002646 NP_002637 O00750 P3C2B_HUMAN phosphoinositide-3-kinase, class 2 beta 162 Pro-rich.|Interaction with GRB2. cell communication|phosphatidylinositol-mediated signaling endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1) 7 all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227) GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193) ATAGAAGCTCGGGGAGGCAGA 0.557 0.25 86 29 ROCK2 9475 broad.mit.edu 37 2 11355499 11355500 + Frame_Shift_Ins INS - T T DU145_PROSTATE NA DU145_PROSTATE NA g.chr2:11355499_11355500insT uc002rbd.1 - 15 2085_2086 c.1636_1637insA c.(1636-1638)AGAfs p.R546fs NM_004850 NP_004841 O75116 ROCK2_HUMAN Rho-associated, coiled-coil containing protein 546 REM.|Potential.|Interaction with PPP1R12A. axon guidance|cytokinesis|intracellular signal transduction cytosol|plasma membrane ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity stomach(2)|skin(2) 4 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162) GTTTTGATTTCTTTTTTTCAAA 0.312 0.24 335 103 BCL11A 53335 broad.mit.edu 37 2 60688969 60688969 + Frame_Shift_Del DEL G - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr2:60688969delG uc002sae.1 - 4 1306 c.1078delC c.(1078-1080)CTCfs p.L360fs BCL11A_uc002sab.2_Frame_Shift_Del_p.L360fs|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Frame_Shift_Del_p.L326fs|BCL11A_uc002sad.1_Frame_Shift_Del_p.L208fs|BCL11A_uc002saf.1_Frame_Shift_Del_p.L326fs NM_022893 NP_075044 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A isoform 1 360 Pro-rich. negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|cytoplasm|nucleus|nucleus nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding central_nervous_system(6)|breast(3)|ovary(2)|skin(2) 13 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) 0.000 0.30 570 248 BCL2L11 10018 broad.mit.edu 37 2 111921728 111921729 + Frame_Shift_Ins INS - A A DU145_PROSTATE NA DU145_PROSTATE NA g.chr2:111921728_111921729insA uc002tgv.1 + 4 805_806 c.517_518insA c.(517-519)CAAfs p.Q173fs BCL2L11_uc002tgu.1_Frame_Shift_Ins_p.Q113fs|BCL2L11_uc002tgw.1_RNA|BCL2L11_uc002tgx.1_RNA|BCL2L11_uc010fkd.1_RNA|BCL2L11_uc002tgy.1_RNA|BCL2L11_uc002tgz.1_Frame_Shift_Ins_p.Q83fs|BCL2L11_uc010fke.1_RNA|BCL2L11_uc002tha.1_3'UTR|BCL2L11_uc002thb.1_RNA|BCL2L11_uc002thc.1_RNA|BCL2L11_uc002thd.1_3'UTR NM_138621 NP_619527 O43521 B2L11_HUMAN BCL2-like 11 isoform 1 173 activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|nerve growth factor receptor signaling pathway|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria cytosol|endomembrane system|mitochondrial outer membrane|plasma membrane protein binding|protein binding 0 GAATAATTACCAAGCAGCCGAA 0.460 0.46 79 68 TTN 7273 broad.mit.edu 37 2 179435978 179435978 + Frame_Shift_Del DEL T - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr2:179435978delT uc010zfg.1 - 275 67401 c.67177delA c.(67177-67179)ACAfs p.T22393fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.T16088fs|TTN_uc010zfi.1_Frame_Shift_Del_p.T16021fs|TTN_uc010zfj.1_Frame_Shift_Del_p.T15896fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 23320 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GGAATAGGTGTTTTATTCAAC 0.418 0.47 55 49 TTN 7273 broad.mit.edu 37 2 179474290 179474290 + Frame_Shift_Del DEL G - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr2:179474290delG uc010zfg.1 - 222 44267 c.44043delC c.(44041-44043)CCCfs p.P14681fs uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.P8376fs|TTN_uc010zfi.1_Frame_Shift_Del_p.P8309fs|TTN_uc010zfj.1_Frame_Shift_Del_p.P8184fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 15608 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GAATGACTTTGGGGGCATCTA 0.338 0.42 234 169 COL3A1 1281 broad.mit.edu 37 2 189859023 189859023 + Frame_Shift_Del DEL G - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr2:189859023delG uc002uqj.1 + 18 1375 c.1258delG c.(1258-1260)GGTfs p.G420fs COL3A1_uc010frw.1_RNA NM_000090 NP_000081 P02461 CO3A1_HUMAN collagen type III alpha 1 preproprotein 420 Triple-helical region. G -> S (in a colorectal cancer sample; somatic mutation). axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway collagen type III|extracellular space extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding p.G420S(1) central_nervous_system(7)|ovary(4)|large_intestine(2) 13 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141) Collagenase(DB00048)|Palifermin(DB00039) AGGACCAGCCGGTGCTAATGG 0.488 0.46 111 95 ALS2 57679 broad.mit.edu 37 2 202611413 202611413 + Frame_Shift_Del DEL A - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr2:202611413delA uc002uyo.2 - 9 2230 c.1874delT c.(1873-1875)TTAfs p.L625fs ALS2_uc002uyp.3_Frame_Shift_Del_p.L625fs|ALS2_uc002uyq.2_Frame_Shift_Del_p.L625fs|ALS2_uc010ftl.2_5'Flank NM_020919 NP_065970 Q96Q42 ALS2_HUMAN alsin isoform 1 625 RCC1 5. cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity skin(5)|lung(1)|breast(1) 7 TGTATCCACTAAAAACAGGGA 0.458 0.45 154 124 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes DU145_PROSTATE NA DU145_PROSTATE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.56 7 9 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 DU145_PROSTATE NA DU145_PROSTATE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.48 12 11 MECOM 2122 broad.mit.edu 37 3 168807891 168807891 + Frame_Shift_Del DEL T - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr3:168807891delT uc003ffi.3 - 14 3003 c.2734delA c.(2734-2736)ACAfs p.T912fs MECOM_uc010hwk.1_Frame_Shift_Del_p.T926fs|MECOM_uc003ffj.3_Frame_Shift_Del_p.T977fs|MECOM_uc011bpi.1_Frame_Shift_Del_p.T904fs|MECOM_uc003ffn.3_Frame_Shift_Del_p.T912fs|MECOM_uc003ffk.2_Frame_Shift_Del_p.T903fs|MECOM_uc003ffl.2_Frame_Shift_Del_p.T1063fs|MECOM_uc011bpj.1_Frame_Shift_Del_p.T1100fs|MECOM_uc011bpk.1_Frame_Shift_Del_p.T902fs NM_005241 NP_005232 Q03112 EVI1_HUMAN MDS1 and EVI1 complex locus isoform b 912 Asp/Glu-rich (acidic). apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle nuclear speck DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1) 14 TCCTTTCCTGTTTTTCCAGTA 0.418 0.56 307 394 HTT 3064 broad.mit.edu 37 4 3076604 3076612 + In_Frame_Del DEL CAGCAGCAG - - rs10618869 DU145_PROSTATE NA DU145_PROSTATE NA g.chr4:3076604_3076612delCAGCAGCAG uc011bvq.1 + 2 203_211 c.58_66delCAGCAGCAG c.(58-66)CAGCAGCAGdel p.QQQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagcagc 0.325 0.13 78 12 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 DU145_PROSTATE NA DU145_PROSTATE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.15 39 7 TET2 54790 broad.mit.edu 37 4 106155778 106155779 + Frame_Shift_Ins INS - A A DU145_PROSTATE NA DU145_PROSTATE NA g.chr4:106155778_106155779insA uc003hxk.2 + 3 1065_1066 c.679_680insA c.(679-681)GAAfs p.E227fs TET2_uc011cez.1_Frame_Shift_Ins_p.E248fs|TET2_uc003hxj.2_RNA|TET2_uc010ilp.1_Frame_Shift_Ins_p.E227fs|TET2_uc003hxi.1_Frame_Shift_Ins_p.E227fs NM_001127208 NP_001120680 Q6N021 TET2_HUMAN tet oncogene family member 2 isoform a 227 cell cycle|myeloid cell differentiation metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen haematopoietic_and_lymphoid_tissue(732)|pancreas(1) 733 Myeloproliferative disorder(5;0.0393) OV - Ovarian serous cystadenocarcinoma(123;7.18e-08) TGAACTCCTGGAAAAAACACTG 0.406 0.41 241 165 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DU145_PROSTATE NA DU145_PROSTATE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.73 65 173 MAML3 55534 broad.mit.edu 37 4 140811064 140811066 + Splice_Site DEL TGC - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr4:140811064_140811066delTGC uc003ihz.1 - 3 2265 c.1513_splice c.e3-1 p.Q505_splice MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) TGAGtgctgttgctgctgctgct 0.251 0.15 190 34 GAB1 2549 broad.mit.edu 37 4 144361499 144361499 + Frame_Shift_Del DEL C - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr4:144361499delC uc003ije.2 + 6 1908 c.1549delC c.(1549-1551)CCCfs p.P517fs GAB1_uc003ijd.2_Frame_Shift_Del_p.P517fs|GAB1_uc011chq.1_Frame_Shift_Del_p.P414fs NM_002039 NP_002030 Q13480 GAB1_HUMAN GRB2-associated binding protein 1 isoform b 517 Pro-rich. cell proliferation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway cytosol SH3/SH2 adaptor activity breast(2)|lung(1)|skin(1) 4 all_hematologic(180;0.158) CTGTGAACCACCCCCCGTGGA 0.512 0.23 309 90 NKD2 85409 broad.mit.edu 37 5 1038446 1038447 + In_Frame_Ins INS - CAC CAC rs3840989 DU145_PROSTATE NA DU145_PROSTATE NA g.chr5:1038446_1038447insCAC uc003jbt.1 + 10 1319_1320 c.1314_1315insCAC c.(1312-1317)insCAC p.447_448insH NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 447_448 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.14 469 79 CLPTM1L 81037 broad.mit.edu 37 5 1325891 1325892 + Frame_Shift_Ins INS - A A DU145_PROSTATE NA DU145_PROSTATE NA g.chr5:1325891_1325892insA uc003jch.2 - 10 1166_1167 c.1120_1121insT c.(1120-1122)TGGfs p.W374fs CLPTM1L_uc003jcg.2_Frame_Shift_Ins_p.W205fs NM_030782 NP_110409 Q96KA5 CLP1L_HUMAN CLPTM1-like 374 Cytoplasmic (Potential). apoptosis integral to membrane breast(1)|central_nervous_system(1) 2 Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09) Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181) KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208) CAGGCCTCTCCAAAAAATAGTC 0.450 0.44 161 127 SKP2 6502 broad.mit.edu 37 5 36170454 36170455 + Frame_Shift_Ins INS - A A rs142374565 byFrequency DU145_PROSTATE NA DU145_PROSTATE NA g.chr5:36170454_36170455insA uc003jkc.1 + 6 862_863 c.680_681insA c.(679-681)GCAfs p.A227fs SKP2_uc011cou.1_Frame_Shift_Ins_p.A13fs|SKP2_uc003jkd.2_Frame_Shift_Ins_p.A227fs NM_005983 NP_005974 Q13309 SKP2_HUMAN S-phase kinase-associated protein 2 isoform 1 227 LRR 4. anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G1/S transition of mitotic cell cycle|S phase of mitotic cell cycle nucleoplasm|SCF ubiquitin ligase complex protein binding central_nervous_system(2)|ovary(1)|breast(1) 4 all_lung(31;5.63e-05) Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202) AGTACTCTCGCAAAAAACTCAA 0.396 0.15 612 111 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 DU145_PROSTATE NA DU145_PROSTATE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.18 125 27 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes DU145_PROSTATE NA DU145_PROSTATE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.50 5 5 MAS1L 116511 broad.mit.edu 37 6 29454867 29454867 + Frame_Shift_Del DEL G - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr6:29454867delG uc011dlq.1 - 1 813 c.813delC c.(811-813)CCCfs p.P271fs NM_052967 NP_443199 P35410 MAS1L_HUMAN MAS1 oncogene-like 271 Helical; Name=6; (Potential). cytoplasm|integral to membrane|nucleus|plasma membrane G-protein coupled receptor activity ovary(7)|lung(2) 9 0.000 0.71 79 189 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 DU145_PROSTATE NA DU145_PROSTATE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.23 36 11 PHF3 23469 broad.mit.edu 37 6 64415953 64415953 + Frame_Shift_Del DEL A - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr6:64415953delA uc003pep.1 + 11 3428 c.3402delA c.(3400-3402)CCAfs p.P1134fs PHF3_uc010kah.1_Frame_Shift_Del_p.P948fs|PHF3_uc003pen.2_Frame_Shift_Del_p.P1046fs|PHF3_uc011dxs.1_Frame_Shift_Del_p.P403fs NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 1134 multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) ATCTTTCTCCAAAAAAAGTAA 0.358 0.88 22 169 AKAP12 9590 broad.mit.edu 37 6 151672999 151673000 + Frame_Shift_Ins INS - C C DU145_PROSTATE NA DU145_PROSTATE NA g.chr6:151672999_151673000insC uc011eep.1 + 4 3713_3714 c.3473_3474insC c.(3472-3474)ATCfs p.I1158fs AKAP12_uc003qoe.2_Frame_Shift_Ins_p.I1158fs|AKAP12_uc003qof.2_Frame_Shift_Ins_p.I1060fs|AKAP12_uc010kim.2_Intron|AKAP12_uc003qog.2_Frame_Shift_Ins_p.I1053fs NM_005100 NP_005091 Q02952 AKA12_HUMAN A kinase (PRKA) anchor protein 12 isoform 1 1158 G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting cell cortex|cytoskeleton|plasma membrane adenylate cyclase binding|protein kinase A binding large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1) 8 Ovarian(120;0.125) BRCA - Breast invasive adenocarcinoma(37;0.175) OV - Ovarian serous cystadenocarcinoma(155;2.98e-11) GAACAGGCTATCCCCCCTGACT 0.530 0.10 152 17 C6orf97 80129 broad.mit.edu 37 6 151936775 151936775 + Frame_Shift_Del DEL A - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr6:151936775delA uc003qol.2 + 10 1997 c.1908delA c.(1906-1908)CTAfs p.L636fs NM_025059 NP_079335 Q8IYT3 CF097_HUMAN hypothetical protein LOC80129 636 Potential. 0 Ovarian(120;0.126) BRCA - Breast invasive adenocarcinoma(37;0.111) OV - Ovarian serous cystadenocarcinoma(155;1.48e-10) TGAAGACACTAAAAAAATCTC 0.403 0.43 8 6 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 DU145_PROSTATE NA DU145_PROSTATE NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.20 129 32 GLI3 2737 broad.mit.edu 37 7 42005573 42005573 + Frame_Shift_Del DEL G - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr7:42005573delG uc011kbh.1 - 15 3189 c.3098delC c.(3097-3099)CCGfs p.P1033fs GLI3_uc011kbg.1_Frame_Shift_Del_p.P974fs NM_000168 NP_000159 P10071 GLI3_HUMAN GLI-Kruppel family member GLI3 1033 negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis cilium|cytosol|nucleolus beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1) 19 0.000 0.24 1523 479 AKAP9 10142 broad.mit.edu 37 7 91671391 91671392 + Frame_Shift_Ins INS - AG AG DU145_PROSTATE NA DU145_PROSTATE NA g.chr7:91671391_91671392insAG uc003ulg.2 + 19 5174_5175 c.4949_4950insAG c.(4948-4950)TCAfs p.S1650fs AKAP9_uc003ulf.2_Frame_Shift_Ins_p.S1650fs|AKAP9_uc003uli.2_Frame_Shift_Ins_p.S1275fs NM_005751 NP_005742 Q99996 AKAP9_HUMAN A-kinase anchor protein 9 isoform 2 1662 G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport centrosome|cytosol|Golgi apparatus receptor binding breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1) 26 all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) AACCTGGTTTCAGAGAGAGAGA 0.416 0.47 159 141 AKAP9 10142 broad.mit.edu 37 7 91732039 91732039 + Frame_Shift_Del DEL G - - rs143306820 DU145_PROSTATE NA DU145_PROSTATE NA g.chr7:91732039delG uc003ulg.2 + 46 11454 c.11229delG c.(11227-11229)ATGfs p.M3743fs AKAP9_uc003ulf.2_Frame_Shift_Del_p.M3735fs|AKAP9_uc003uli.2_Frame_Shift_Del_p.M3366fs|AKAP9_uc003ulj.2_Frame_Shift_Del_p.M1513fs|AKAP9_uc003ull.2_Frame_Shift_Del_p.M639fs NM_005751 NP_005742 Q99996 AKAP9_HUMAN A-kinase anchor protein 9 isoform 2 3747 G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport centrosome|cytosol|Golgi apparatus receptor binding breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1) 26 all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) TTGCCCGGATGGGGGGGCAGC 0.537 0.16 260 48 TRRAP 8295 broad.mit.edu 37 7 98528336 98528336 + Frame_Shift_Del DEL G - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr7:98528336delG uc003upp.2 + 25 3683 c.3474delG c.(3472-3474)CTGfs p.L1158fs TRRAP_uc011kis.1_Frame_Shift_Del_p.L1158fs|TRRAP_uc003upr.2_Frame_Shift_Del_p.L850fs NM_003496 NP_003487 Q9Y4A5 TRRAP_HUMAN transformation/transcription domain-associated 1158 histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1) 37 all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274) STAD - Stomach adenocarcinoma(171;0.215) ATGCAAAGCTGGGGGGTGTGG 0.507 0.17 337 71 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT DU145_PROSTATE NA DU145_PROSTATE NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.17 695 141 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes DU145_PROSTATE NA DU145_PROSTATE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 21 FASTK 10922 broad.mit.edu 37 7 150774992 150774993 + Frame_Shift_Ins INS - A A DU145_PROSTATE NA DU145_PROSTATE NA g.chr7:150774992_150774993insA uc003wix.1 - 5 1110_1111 c.1012_1013insT c.(1012-1014)TCCfs p.S338fs uc011kvf.1_5'Flank|FASTK_uc003wiw.1_Frame_Shift_Ins_p.S99fs|FASTK_uc003wiy.1_Frame_Shift_Ins_p.S197fs|FASTK_uc003wiz.1_Frame_Shift_Ins_p.S311fs|FASTK_uc003wja.1_3'UTR NM_006712 NP_006703 Q14296 FASTK_HUMAN Fas-activated serine/threonine kinase isoform 1 338 apoptosis|induction of apoptosis by extracellular signals|regulation of RNA splicing ATP binding|Fas-activated serine/threonine kinase activity|protein binding lung(2)|stomach(2) 4 OV - Ovarian serous cystadenocarcinoma(82;0.00989) UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138) GAAGCCAGGGGAAAAAACAAAG 0.619 0.22 154 43 MLL3 58508 broad.mit.edu 37 7 151845524 151845524 + Frame_Shift_Del DEL A - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr7:151845524delA uc003wla.2 - 52 13707 c.13488delT c.(13486-13488)TTTfs p.F4496fs MLL3_uc003wkz.2_Frame_Shift_Del_p.F3614fs|MLL3_uc003wkx.2_Frame_Shift_Del_p.F654fs|MLL3_uc003wky.2_Frame_Shift_Del_p.F2060fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 4496 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTTTGTCCTTAAAAAACATGC 0.433 0.36 358 202 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.69 4 9 SGK223 157285 broad.mit.edu 37 8 8234287 8234287 + Frame_Shift_Del DEL G - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr8:8234287delG uc003wsh.3 - 2 1632 c.1632delC c.(1630-1632)CCCfs p.P544fs NM_001080826 NP_001074295 Q86YV5 SG223_HUMAN pragmin 544 ATP binding|non-membrane spanning protein tyrosine kinase activity 0 TGGACAACTTGGGGGGAATGG 0.642 0.13 174 25 BAG4 9530 broad.mit.edu 37 8 38067842 38067843 + Frame_Shift_Ins INS - A A DU145_PROSTATE NA DU145_PROSTATE NA g.chr8:38067842_38067843insA uc003xky.1 + 5 1487_1488 c.1205_1206insA c.(1204-1206)GGAfs p.G402fs BAG4_uc003xkz.1_Frame_Shift_Ins_p.G366fs NM_004874 NP_004865 O95429 BAG4_HUMAN BCL2-associated athanogene 4 402 BAG. anti-apoptosis|apoptosis|protein folding cytoplasm|nucleus receptor signaling protein activity ovary(1) 1 Colorectal(12;0.000442) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121) GAATTTGTAGGAAAAAAGACAG 0.416 0.24 194 61 PRKDC 5591 broad.mit.edu 37 8 48701554 48701555 + Frame_Shift_Ins INS - T T DU145_PROSTATE NA DU145_PROSTATE NA g.chr8:48701554_48701555insT uc003xqi.2 - 77 10871_10872 c.10814_10815insA c.(10813-10815)AACfs p.N3605fs PRKDC_uc003xqj.2_Frame_Shift_Ins_p.N3605fs|PRKDC_uc011ldh.1_Intron NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic 3605 cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) TTTTTTCAATGTTTTTTTTATT 0.401 0.36 345 190 SULF1 23213 broad.mit.edu 37 8 70488249 70488249 + Frame_Shift_Del DEL G - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr8:70488249delG uc010lza.1 + 6 934 c.217delG c.(217-219)GGGfs p.G73fs SULF1_uc003xyd.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xye.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xyf.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xyg.2_Frame_Shift_Del_p.G73fs NM_015170 NP_055985 Q8IWU6 SULF1_HUMAN sulfatase 1 precursor 73 apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway cell surface|endoplasmic reticulum|extracellular space|Golgi stack arylsulfatase activity|calcium ion binding central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1) 7 Breast(64;0.0654) Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534) TATGGAACATGGGGGGGCCAC 0.493 0.18 122 26 SULF1 23213 broad.mit.edu 37 8 70515459 70515459 + Frame_Shift_Del DEL C - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr8:70515459delC uc010lza.1 + 11 1811 c.1094delC c.(1093-1095)GCCfs p.A365fs SULF1_uc003xyd.2_Frame_Shift_Del_p.A365fs|SULF1_uc003xye.2_Frame_Shift_Del_p.A365fs|SULF1_uc003xyf.2_Frame_Shift_Del_p.A365fs|SULF1_uc003xyg.2_Frame_Shift_Del_p.A365fs|SULF1_uc003xyh.1_RNA NM_015170 NP_055985 Q8IWU6 SULF1_HUMAN sulfatase 1 precursor 365 apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway cell surface|endoplasmic reticulum|extracellular space|Golgi stack arylsulfatase activity|calcium ion binding central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1) 7 Breast(64;0.0654) Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534) ATTGACTTGGCCCCCACGATC 0.542 0.21 264 69 FBXO43 286151 broad.mit.edu 37 8 101153916 101153916 + Frame_Shift_Del DEL T - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr8:101153916delT uc003yjd.2 - 2 1279 c.566delA c.(565-567)AATfs p.N189fs FBXO43_uc003yje.2_Frame_Shift_Del_p.N155fs|FBXO43_uc010mbp.1_Frame_Shift_Del_p.N189fs NM_001029860 NP_001025031 Q4G163 FBX43_HUMAN F-box protein 43 isoform b 189 meiosis zinc ion binding kidney(1)|skin(1) 2 all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798) Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957) GCTTGGAATATTTTTTTCTAA 0.333 0.28 494 193 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 DU145_PROSTATE NA DU145_PROSTATE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 33 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency DU145_PROSTATE NA DU145_PROSTATE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.28 51 20 TEK 7010 broad.mit.edu 37 9 27158026 27158026 + Frame_Shift_Del DEL A - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr9:27158026delA uc003zqi.3 + 2 692 c.250delA c.(250-252)AAAfs p.K84fs TEK_uc010mjc.1_Intron|TEK_uc011lnn.1_Frame_Shift_Del_p.K84fs|TEK_uc011lno.1_Frame_Shift_Del_p.K84fs|TEK_uc011lnp.1_Intron|TEK_uc003zqj.1_Frame_Shift_Del_p.K61fs NM_000459 NP_000450 Q02763 TIE2_HUMAN TEK tyrosine kinase, endothelial precursor 84 Extracellular (Potential).|Ig-like C2-type 1. angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1) 12 all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255) Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027) AGAATGGGCTAAAAAAGTTGT 0.468 0.47 113 99 XPA 7507 broad.mit.edu 37 9 100449473 100449474 + Frame_Shift_Del DEL CA - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr9:100449473_100449474delCA uc004axr.3 - 4 576_577 c.459_460delTG c.(457-462)TGTGATfs p.C153fs XPA_uc004axs.3_RNA NM_000380 NP_000371 P23025 XPA_HUMAN xeroderma pigmentosum, complementation group A 153_154 nucleotide-excision repair, DNA damage removal nucleoplasm damaged DNA binding|metal ion binding|nucleotide binding|protein domain specific binding|protein homodimerization activity breast(1) 1 Acute lymphoblastic leukemia(62;0.158) TTTTCTAAATCACAGTCTTTCA 0.327 0.24 370 116 MUSK 4593 broad.mit.edu 37 9 113509997 113509998 + Frame_Shift_Ins INS - A A DU145_PROSTATE NA DU145_PROSTATE NA g.chr9:113509997_113509998insA uc004bey.2 + 7 928_929 c.830_831insA c.(829-831)CCAfs p.P277fs MUSK_uc004bex.2_Frame_Shift_Ins_p.P287fs NM_005592 NP_005583 O15146 MUSK_HUMAN skeletal muscle receptor tyrosine kinase 277 Ig-like 3.|Extracellular (Potential). transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(3)|ovary(2)|central_nervous_system(1) 6 ATCACCAAGCCAGGACTCTACA 0.470 0.29 242 99 NLRP6 171389 broad.mit.edu 37 11 280794 280796 + In_Frame_Del DEL AAG - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr11:280794_280796delAAG uc010qvs.1 + 4 1060_1062 c.1060_1062delAAG c.(1060-1062)AAGdel p.K356del NLRP6_uc010qvt.1_In_Frame_Del_p.K356del NM_138329 NP_612202 P59044 NALP6_HUMAN NLR family, pyrin domain containing 6 356 NACHT. cytoplasm ATP binding upper_aerodigestive_tract(1)|skin(1) 2 all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122) CGACAAGGACAAGAAGAAGTATT 0.655 0.41 45 31 NLRP10 338322 broad.mit.edu 37 11 7981739 7981740 + Frame_Shift_Ins INS - A A DU145_PROSTATE NA DU145_PROSTATE NA g.chr11:7981739_7981740insA uc001mfv.1 - 2 1436_1437 c.1419_1420insT c.(1417-1422)TTTCATfs p.F473fs NM_176821 NP_789791 Q86W26 NAL10_HUMAN NLR family, pyrin domain containing 10 473_474 NACHT. ATP binding lung(4)|ovary(2)|pancreas(1)|kidney(1)|skin(1) 9 Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189) GACATGGCATGAAAAAAGTCCT 0.535 0.45 235 193 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 DU145_PROSTATE NA DU145_PROSTATE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.31 9 4 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DU145_PROSTATE NA DU145_PROSTATE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.42 566 415 FLT1 2321 broad.mit.edu 37 13 28964154 28964154 + Frame_Shift_Del DEL A - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr13:28964154delA uc001usb.3 - 13 2033 c.1748delT c.(1747-1749)TTAfs p.L583fs FLT1_uc010aar.1_Frame_Shift_Del_p.L583fs|FLT1_uc001usc.3_Frame_Shift_Del_p.L583fs|FLT1_uc010aas.1_RNA|FLT1_uc010aat.1_Frame_Shift_Del_p.L66fs NM_002019 NP_002010 P17948 VGFR1_HUMAN fms-related tyrosine kinase 1 isoform 1 583 Ig-like C2-type 6.|Extracellular (Potential). cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway extracellular space|Golgi apparatus|integral to plasma membrane|nucleus ATP binding|growth factor binding|vascular endothelial growth factor receptor activity lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1) 24 Acute lymphoblastic leukemia(6;0.04) Lung SC(185;0.0262)|Breast(139;0.188) Colorectal(13;0.000674) all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207) Sunitinib(DB01268) GTCTCTGTATAAGAACTTGTT 0.393 0.96 18 389 OR4E2 26686 broad.mit.edu 37 14 22133806 22133806 + Frame_Shift_Del DEL C - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr14:22133806delC uc010tmd.1 + 1 510 c.510delC c.(508-510)GGCfs p.G170fs NM_001001912 NP_001001912 Q8NGC2 OR4E2_HUMAN olfactory receptor, family 4, subfamily E, 170 Extracellular (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(2)|pancreas(1)|skin(1) 4 all_cancers(95;0.00113) Acute lymphoblastic leukemia(2;0.0279) GBM - Glioblastoma multiforme(265;0.0137) CTTACTGTGGCCCCAACATTA 0.463 0.42 699 506 KTN1 3895 broad.mit.edu 37 14 56083367 56083367 + Frame_Shift_Del DEL A - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr14:56083367delA uc001xcb.2 + 4 958 c.656delA c.(655-657)GAAfs p.E219fs KTN1_uc001xce.2_Frame_Shift_Del_p.E219fs|KTN1_uc001xcc.2_Frame_Shift_Del_p.E219fs|KTN1_uc001xcd.2_Frame_Shift_Del_p.E219fs|KTN1_uc010trb.1_Frame_Shift_Del_p.E219fs|KTN1_uc001xcf.1_Frame_Shift_Del_p.E219fs NM_182926 NP_891556 Q86UP2 KTN1_HUMAN kinectin 1 isoform a 219 Lumenal (Potential). microtubule-based movement endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction breast(3)|ovary(2)|lung(1)|central_nervous_system(1) 7 CAAAAGACAGAAAATGGTGAG 0.403 0.42 146 106 UNC13C 440279 broad.mit.edu 37 15 54305757 54305757 + Frame_Shift_Del DEL A - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr15:54305757delA uc002ack.2 + 1 657 c.657delA c.(655-657)CGAfs p.R219fs NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 219 exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) GAACTGTCCGAAACCCAAAGA 0.433 0.40 101 67 UNC13C 440279 broad.mit.edu 37 15 54557651 54557652 + Frame_Shift_Ins INS - T T DU145_PROSTATE NA DU145_PROSTATE NA g.chr15:54557651_54557652insT uc002ack.2 + 8 3775_3776 c.3775_3776insT c.(3775-3777)ATTfs p.I1259fs UNC13C_uc002acl.2_Frame_Shift_Ins_p.I89fs NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 1259 C2 1. exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) AACAAAAACCATTTTTGGAAAT 0.307 0.29 75 30 CSPG4 1464 broad.mit.edu 37 15 75970186 75970186 + Frame_Shift_Del DEL G - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr15:75970186delG uc002baw.2 - 9 5085 c.4992delC c.(4990-4992)CCCfs p.P1664fs NM_001897 NP_001888 Q6UVK1 CSPG4_HUMAN chondroitin sulfate proteoglycan 4 precursor 1664 Extracellular (Potential).|Cysteine-containing.|Neurite growth inhibition (By similarity).|CSPG 11. angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane protein kinase binding|signal transducer activity ovary(2)|pancreas(1) 3 0.000 0.11 1256 149 NTRK3 4916 broad.mit.edu 37 15 88679254 88679254 + Frame_Shift_Del DEL G - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr15:88679254delG uc002bme.1 - 8 945 c.783delC c.(781-783)ACCfs p.T261fs NTRK3_uc002bmh.2_Frame_Shift_Del_p.T261fs|NTRK3_uc002bmf.1_Frame_Shift_Del_p.T261fs|NTRK3_uc010upl.1_Frame_Shift_Del_p.T163fs|NTRK3_uc010bnh.1_Frame_Shift_Del_p.T261fs|NTRK3_uc002bmg.2_Frame_Shift_Del_p.T261fs NM_001012338 NP_001012338 Q16288 NTRK3_HUMAN neurotrophic tyrosine kinase, receptor, type 3 261 Ig-like C2-type 1.|Extracellular (Potential). transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ETV6/NTRK3(234) soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1) 281 BRCA - Breast invasive adenocarcinoma(143;0.211) CATGAACATTGGTCCAGTTCA 0.458 0.45 179 149 FANCI 55215 broad.mit.edu 37 15 89858530 89858530 + Frame_Shift_Del DEL C - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr15:89858530delC uc010bnp.1 + 37 3924 c.3834delC c.(3832-3834)CACfs p.H1278fs FANCI_uc002bnm.1_Frame_Shift_Del_p.H1218fs|FANCI_uc002bnn.1_RNA|FANCI_uc002bnp.1_Frame_Shift_Del_p.H1038fs|FANCI_uc002bnq.1_Frame_Shift_Del_p.H691fs NM_001113378 NP_001106849 Q9NVI1 FANCI_HUMAN Fanconi anemia, complementation group I isoform 1278 cell cycle|DNA repair nucleoplasm protein binding ovary(2) 2 Lung NSC(78;0.0472)|all_lung(78;0.089) TGATGCAGCACATGAAGCTCA 0.458 0.27 30 11 CREBBP 1387 broad.mit.edu 37 16 3779755 3779755 + Frame_Shift_Del DEL G - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr16:3779755delG uc002cvv.2 - 31 5497 c.5293delC c.(5293-5295)CAGfs p.Q1765fs CREBBP_uc002cvw.2_Frame_Shift_Del_p.Q1727fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1765 TAZ-type 2.|Interaction with TRERF1. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) CGTGACTCCTGGGGGCTCTTT 0.632 0.44 78 61 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C DU145_PROSTATE NA DU145_PROSTATE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 61 700 RAI1 10743 broad.mit.edu 37 17 17697093 17697094 + In_Frame_Ins INS - CAG CAG DU145_PROSTATE NA DU145_PROSTATE NA g.chr17:17697093_17697094insCAG uc002grm.2 + 3 1300_1301 c.831_832insCAG c.(829-834)insCAG p.291_292insQ RAI1_uc002grn.1_In_Frame_Ins_p.291_292insQ NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291_292 Gln-rich. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) TCAGCTATGACcagcagcagca 0.510 0.45 21 17 STK11 6794 broad.mit.edu 37 19 1220438 1220442 + Frame_Shift_Del DEL CAAGC - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr19:1220438_1220442delCAAGC uc002lrl.1 + 4 1646_1650 c.531_535delCAAGC c.(529-537)ATCAAGCCGfs p.I177fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 177_179 Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.Y156fs*87(4)|p.?(4)|p.G52_P179del(1)|p.K178fs*86(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.95 76 1350 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DU145_PROSTATE NA DU145_PROSTATE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 29 145 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DU145_PROSTATE NA DU145_PROSTATE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 173 560 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DU145_PROSTATE NA DU145_PROSTATE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 11 140 NF2 4771 broad.mit.edu 37 22 30069309 30069311 + In_Frame_Del DEL GAG - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr22:30069309_30069311delGAG uc003age.3 + 12 1617_1619 c.1174_1176delGAG c.(1174-1176)GAGdel p.E394del NF2_uc003afy.3_In_Frame_Del_p.E394del|NF2_uc003afz.3_In_Frame_Del_p.E311del|NF2_uc003agf.3_In_Frame_Del_p.E394del|NF2_uc003agb.3_In_Frame_Del_p.E317del|NF2_uc003agc.3_In_Frame_Del_p.E356del|NF2_uc003agd.3_Intron|NF2_uc003agg.3_In_Frame_Del_p.E394del|NF2_uc003aga.3_In_Frame_Del_p.E352del|NF2_uc003agh.3_In_Frame_Del_p.E353del|NF2_uc003agi.3_In_Frame_Del_p.E311del|NF2_uc003agj.3_Intron|NF2_uc003agk.3_In_Frame_Del_p.E356del|NF2_uc010gvp.2_In_Frame_Del_p.E58del|NF2_uc011akq.1_In_Frame_Del_p.E20del NM_000268 NP_000259 P35240 MERL_HUMAN neurofibromin 2 isoform 1 394 Glu-rich. actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane cytoskeletal protein binding|protein binding p.L383fs*12(1)|p.M375fs*20(1)|p.E392*(1)|p.?(1) meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1) 728 CCAGATCACCGAGGAGGAGGCAA 0.586 0.87 4 27 MAPK12 6300 broad.mit.edu 37 22 50694549 50694549 + Frame_Shift_Del DEL T - - DU145_PROSTATE NA DU145_PROSTATE NA g.chr22:50694549delT uc003bkm.1 - 7 735 c.584delA c.(583-585)GAGfs p.E195fs MAPK12_uc003bkn.2_Frame_Shift_Del_p.E14fs|MAPK12_uc003bko.2_Frame_Shift_Del_p.E105fs|MAPK12_uc003bkl.1_Frame_Shift_Del_p.E185fs|MAPK12_uc003bkp.2_5'UTR|MAPK12_uc003bkq.2_Frame_Shift_Del_p.E14fs NM_002969 NP_002960 P53778 MK12_HUMAN mitogen-activated protein kinase 12 195 Protein kinase. cell cycle arrest|DNA damage induced protein phosphorylation|muscle organ development|myoblast differentiation|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|Ras protein signal transduction mitochondrion|nucleoplasm ATP binding|magnesium ion binding|MAP kinase activity|protein binding 0 all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247) CAAGATGACCTCGGGAGCCCG 0.602 0.50 8 8 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 DU4475_BREAST NA DU4475_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 5 57 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - DU4475_BREAST NA DU4475_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.16 305 56 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 DU4475_BREAST NA DU4475_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 112 160 GRM8 2918 broad.mit.edu 37 7 126882932 126882933 + Frame_Shift_Ins INS - TCCC TCCC DU4475_BREAST NA DU4475_BREAST NA g.chr7:126882932_126882933insTCCC uc003vlr.2 - 1 637_638 c.326_327insGGGA c.(325-327)GACfs p.D109fs GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Frame_Shift_Ins_p.D109fs|GRM8_uc010lkz.1_RNA NM_000845 NP_000836 O00222 GRM8_HUMAN glutamate receptor, metabotropic 8 isoform a 109 Extracellular (Potential). negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception integral to plasma membrane lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1) 23 Prostate(267;0.186) L-Glutamic Acid(DB00142) 0.000 0.13 843 127 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes DU4475_BREAST NA DU4475_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 12 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 DU4475_BREAST NA DU4475_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.40 9 6 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 DU4475_BREAST NA DU4475_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 3 46 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency DU4475_BREAST NA DU4475_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.29 469 192 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 DU4475_BREAST NA DU4475_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 758 334 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes DU4475_BREAST NA DU4475_BREAST NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.23 99 30 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 DU4475_BREAST NA DU4475_BREAST NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.29 54 22 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 DU4475_BREAST NA DU4475_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 55 150 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 DU4475_BREAST NA DU4475_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 127 386 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 DU4475_BREAST NA DU4475_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 5 52 ZNRF3 84133 broad.mit.edu 37 22 29445818 29445819 + In_Frame_Ins INS - CAG CAG DU4475_BREAST NA DU4475_BREAST NA g.chr22:29445818_29445819insCAG uc003aeg.2 + 8 1514_1515 c.1349_1350insCAG c.(1348-1350)GAC>GACAGC p.457_458insS ZNRF3_uc003aeh.1_In_Frame_Ins_p.457_458insS NM_032173 NP_115549 Q9ULT6 ZNRF3_HUMAN zinc and ring finger 3 557_558 Cytoplasmic (Potential). integral to membrane zinc ion binding ovary(1) 1 0.000 0.23 478 140 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 6 131 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 532 163 LOC642587 642587 broad.mit.edu 37 1 209605636 209605637 + In_Frame_Ins INS - AGC AGC rs146499758;rs3842530 by1000genomes EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:209605636_209605637insAGC uc009xcn.2 + 4 634_635 c.251_252insAGC c.(250-252)GTA>GTAGCA p.97_98insA NM_001104548 NP_001098018 hypothetical protein LOC642587 0 OV - Ovarian serous cystadenocarcinoma(81;0.0422) gccaccaccgTagcagcagcag 0.272 0.27 43 16 HTT 3064 broad.mit.edu 37 4 3076672 3076673 + In_Frame_Ins INS - CCGCCG CCGCCG rs76533208 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:3076672_3076673insCCGCCG uc011bvq.1 + 2 271_272 c.126_127insCCGCCG c.(124-129)insCCGCCG p.50_51insPP NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 48_49 Poly-Pro. establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) aacagccgccaccgccgccgcc 0.084 0.12 103 14 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.29 210 86 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.28 60 23 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.76 95 296 ATXN1 6310 broad.mit.edu 37 6 16327907 16327909 + In_Frame_Del DEL TGA - - rs59310777 by1000genomes EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:16327907_16327909delTGA uc003nbt.2 - 8 1604_1606 c.633_635delTCA c.(631-636)CATCAG>CAG p.H211del ATXN1_uc010jpi.2_In_Frame_Del_p.H211del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 211 Poly-Gln. H -> HQ (in Ref. 1; CAA55793). cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgctgatgctgatgct 0.384 0.68 55 117 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.23 47 14 ARID1B 57492 broad.mit.edu 37 6 157099402 157099403 + In_Frame_Ins INS - CAGCAG CAGCAG EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:157099402_157099403insCAGCAG uc003qqn.2 + 1 317_318 c.165_166insCAGCAG c.(163-168)insCAGCAG p.73_74insQQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) TAAACCAGTTCcagcagcagca 0.124 0.27 112 42 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 21 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.33 49 24 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 31 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.44 60 47 MLLT3 4300 broad.mit.edu 37 9 20414311 20414313 + In_Frame_Del DEL CTG - - EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:20414311_20414313delCTG uc003zoe.2 - 5 790_792 c.531_533delCAG c.(529-534)AGCAGT>AGT p.177_178SS>S MLLT3_uc011lne.1_In_Frame_Del_p.145_146SS>S|MLLT3_uc011lnf.1_In_Frame_Del_p.174_175SS>S|MLLT3_uc003zof.2_5'UTR NM_004529 NP_004520 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia 177_178 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding lung(2)|ovary(1) 3 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) gctgctgctactgctgctgctgc 0.143 0.21 456 120 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 1394 282 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.40 21 14 SIX4 51804 broad.mit.edu 37 14 61190562 61190563 + In_Frame_Ins INS - GCC GCC EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:61190562_61190563insGCC uc001xfc.2 - 1 230_231 c.230_231insGGC c.(229-231)GCC>GCGGCC p.77_77A>AA SIX4_uc010app.1_In_Frame_Ins_p.69_69A>AA NM_017420 NP_059116 Q9UIU6 SIX4_HUMAN sine oculis homeobox homolog 4 77 Ala-rich. nucleus breast(3)|ovary(1) 4 OV - Ovarian serous cystadenocarcinoma(108;0.0275) 0.000 0.20 341 87 SALL1 6299 broad.mit.edu 37 16 51175655 51175656 + In_Frame_Ins INS - GCT GCT rs113614842 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:51175655_51175656insGCT uc010vgs.1 - 2 508_509 c.477_478insAGC c.(475-480)insAGC p.159_160insS SALL1_uc010vgr.1_In_Frame_Ins_p.62_63insS|SALL1_uc010cbv.2_Intron NM_002968 NP_002959 Q9NSC2 SALL1_HUMAN sal-like 1 isoform a 159_160 Poly-Gly. adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development chromocenter|cytoplasm|heterochromatin|nucleus beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding skin(5)|ovary(3) 8 all_cancers(37;0.0322) COAD - Colon adenocarcinoma(2;0.24) ccgccgccgccgctgctgctgc 0.460 0.38 8 5 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.49 27 26 SERPINB4 6318 broad.mit.edu 37 18 61308109 61308110 + Frame_Shift_Ins INS - T T EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr18:61308109_61308110insT uc002ljf.2 - 5 553_554 c.467_468insA c.(466-468)AATfs p.N156fs SERPINB4_uc002lje.2_Frame_Shift_Ins_p.N156fs|SERPINB4_uc002ljg.2_Intron NM_002974 NP_002965 P48594 SPB4_HUMAN serine (or cysteine) proteinase inhibitor, clade 156 immune response|regulation of proteolysis cytoplasm|extracellular region protein binding|serine-type endopeptidase inhibitor activity ovary(2)|lung(1) 3 CTCTCCTACCATTCGTTTGACT 0.446 0.46 169 143 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 33 136 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.20 252 64 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 140 316 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 7 111 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 EBC1_LUNG NA EBC1_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.50 25 25 CDKL4 344387 broad.mit.edu 37 2 39414801 39414802 + Frame_Shift_Ins INS - AA AA EBC1_LUNG NA EBC1_LUNG NA g.chr2:39414801_39414802insAA uc002rrm.2 - 6 701_702 c.701_702insTT c.(700-702)TTCfs p.F234fs CDKL4_uc010fal.1_Frame_Shift_Ins_p.F234fs NM_001009565 NP_001009565 Q5MAI5 CDKL4_HUMAN cyclin-dependent kinase-like 4 234 Protein kinase. cytoplasm ATP binding|cyclin-dependent protein kinase activity ovary(1) 1 all_hematologic(82;0.248) TGATGCCATGGAAAAACCCGTT 0.327 0.29 141 58 TP63 8626 broad.mit.edu 37 3 189582134 189582135 + Frame_Shift_Ins INS - A A EBC1_LUNG NA EBC1_LUNG NA g.chr3:189582134_189582135insA uc003fry.2 + 5 782_783 c.693_694insA c.(691-696)TACAAAfs p.Y231fs TP63_uc003frx.2_Frame_Shift_Ins_p.Y231fs|TP63_uc003frz.2_Frame_Shift_Ins_p.Y231fs|TP63_uc010hzc.1_Frame_Shift_Ins_p.Y231fs|TP63_uc003fsa.2_Frame_Shift_Ins_p.Y137fs|TP63_uc003fsb.2_Frame_Shift_Ins_p.Y137fs|TP63_uc003fsc.2_Frame_Shift_Ins_p.Y137fs|TP63_uc003fsd.2_Frame_Shift_Ins_p.Y137fs|TP63_uc010hzd.1_Frame_Shift_Ins_p.Y52fs|TP63_uc003fse.1_Frame_Shift_Ins_p.Y112fs NM_003722 NP_003713 Q9H3D4 P63_HUMAN tumor protein p63 isoform 1 231_232 K -> E (in SHFM4). anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1) 12 all_cancers(143;3.35e-10)|Ovarian(172;0.0925) Lung(62;3.33e-05) GBM - Glioblastoma multiforme(93;0.0227) TGCCTGTCTACAAAAAAGCTGA 0.510 0.48 93 86 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 EBC1_LUNG NA EBC1_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.66 72 137 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes EBC1_LUNG NA EBC1_LUNG NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.97 25 785 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 EBC1_LUNG NA EBC1_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.85 17 93 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 EBC1_LUNG NA EBC1_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.68 36 76 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - EBC1_LUNG NA EBC1_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.75 3 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 EBC1_LUNG NA EBC1_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 31 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 EBC1_LUNG NA EBC1_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 250 84 WNK1 65125 broad.mit.edu 37 12 936329 936353 + Frame_Shift_Del DEL TGTGACAACATCTTTATCACCGGCC - - rs72648621 byFrequency;by1000genomes EBC1_LUNG NA EBC1_LUNG NA g.chr12:936329_936353delTGTGACAACATCTTTATCACCGGCC uc001qio.3 + 3 1561_1585 c.1054_1078delTGTGACAACATCTTTATCACCGGCC c.(1054-1080)TGTGACAACATCTTTATCACCGGCCCTfs p.C352fs WNK1_uc001qin.2_Frame_Shift_Del_p.C352fs|WNK1_uc001qip.3_Frame_Shift_Del_p.C352fs NM_018979 NP_061852 Q9H4A3 WNK1_HUMAN WNK lysine deficient protein kinase 1 352_360 Protein kinase. intracellular protein kinase cascade|ion transport|neuron development cytoplasm ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1) 23 all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632) Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197) CGATCTTAAATGTGACAACATCTTTATCACCGGCCCTACTGGCTC 0.471 0.25 264 89 NCOR2 9612 broad.mit.edu 37 12 124887059 124887061 + In_Frame_Del DEL GCT - - rs67031864 EBC1_LUNG NA EBC1_LUNG NA g.chr12:124887059_124887061delGCT uc010tba.1 - 14 1646_1648 c.1529_1531delAGC c.(1528-1533)CAGCCC>CCC p.Q510del NCOR2_uc010tay.1_In_Frame_Del_p.Q510del|NCOR2_uc010taz.1_In_Frame_Del_p.Q510del|NCOR2_uc010tbb.1_In_Frame_Del_p.Q510del|NCOR2_uc010tbc.1_In_Frame_Del_p.Q509del|NCOR2_uc001ugj.1_In_Frame_Del_p.Q510del NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 510 Poly-Gln. cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) CGGGGCATGGgctgctgctgctg 0.305 0.25 36 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 EBC1_LUNG NA EBC1_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 114 293 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 EBC1_LUNG NA EBC1_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.87 2 13 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ECC10_STOMACH NA ECC10_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 29 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - ECC10_STOMACH NA ECC10_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.43 142 107 FGF2 2247 broad.mit.edu 37 4 123748258 123748259 + Frame_Shift_Ins INS - G G ECC10_STOMACH NA ECC10_STOMACH NA g.chr4:123748258_123748259insG uc003iev.1 + 1 396_397 c.328_329insG c.(328-330)CGGfs p.R110fs NM_002006 NP_001997 P09038 FGF2_HUMAN fibroblast growth factor 2 110 activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing extracellular space fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity ovary(1)|lung(1)|central_nervous_system(1) 3 Pentosan Polysulfate(DB00686) 0.000 0.20 28 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ECC10_STOMACH NA ECC10_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.23 69 21 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes ECC10_STOMACH NA ECC10_STOMACH NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.57 157 207 APC 324 broad.mit.edu 37 5 112175951 112175952 + Frame_Shift_Ins INS - A A ECC10_STOMACH NA ECC10_STOMACH NA g.chr5:112175951_112175952insA uc010jby.2 + 16 5040_5041 c.4660_4661insA c.(4660-4662)GAAfs p.E1554fs APC_uc011cvt.1_Frame_Shift_Ins_p.E1536fs|APC_uc003kpz.3_Frame_Shift_Ins_p.E1554fs|APC_uc003kpy.3_Frame_Shift_Ins_p.E1554fs|APC_uc010jbz.2_Frame_Shift_Ins_p.E1271fs|APC_uc010jca.2_Frame_Shift_Ins_p.E854fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1554 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.T1556fs*3(35)|p.E1554fs*5(2)|p.E1554*(2)|p.?(1)|p.T1556fs*9(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1554fs*11(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GAAAGAGGCAGAAAAAACTATT 0.342 0.73 4 11 SFRS3 6428 broad.mit.edu 37 6 36564724 36564725 + Frame_Shift_Ins INS - A A ECC10_STOMACH NA ECC10_STOMACH NA g.chr6:36564724_36564725insA uc003omj.2 + 2 356_357 c.185_186insA c.(184-186)GCAfs p.A62fs SFRS3_uc003omk.2_RNA|SFRS3_uc011dtp.1_Frame_Shift_Ins_p.A62fs NM_003017 NP_003008 P84103 SRSF3_HUMAN splicing factor, arginine/serine-rich 3 62 RRM. mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription nucleoplasm nucleotide binding|protein binding|RNA binding 0 GCAGCTGATGCAGTCCGAGAGC 0.426 0.20 158 40 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes ECC10_STOMACH NA ECC10_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 12 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - ECC10_STOMACH NA ECC10_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.94 1 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 ECC10_STOMACH NA ECC10_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 93 17 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 ECC10_STOMACH NA ECC10_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.48 22 20 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 ECC10_STOMACH NA ECC10_STOMACH NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.10 126 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ECC10_STOMACH NA ECC10_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 91 342 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ECC10_STOMACH NA ECC10_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 2 37 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ECC12_STOMACH NA ECC12_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 25 XIAP 331 broad.mit.edu 37 X 123025155 123025157 + In_Frame_Del DEL GAG - - ECC12_STOMACH NA ECC12_STOMACH NA g.chrX:123025155_123025157delGAG uc010nqu.2 + 4 1171_1173 c.1045_1047delGAG c.(1045-1047)GAGdel p.E350del XIAP_uc004etx.2_In_Frame_Del_p.E350del|XIAP_uc010nqv.2_5'UTR NM_001167 NP_001158 P98170 XIAP_HUMAN baculoviral IAP repeat-containing protein 4 350 anti-apoptosis|apoptosis|induction of apoptosis by intracellular signals|response to DNA damage stimulus cytosol caspase inhibitor activity|ligase activity|protein binding|zinc ion binding ovary(1)|lung(1) 2 TCATTCACTTGAGGAGTGTCTGG 0.197 0.92 1 11 FGF2 2247 broad.mit.edu 37 4 123748258 123748259 + Frame_Shift_Ins INS - G G ECC12_STOMACH NA ECC12_STOMACH NA g.chr4:123748258_123748259insG uc003iev.1 + 1 396_397 c.328_329insG c.(328-330)CGGfs p.R110fs NM_002006 NP_001997 P09038 FGF2_HUMAN fibroblast growth factor 2 110 activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing extracellular space fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity ovary(1)|lung(1)|central_nervous_system(1) 3 Pentosan Polysulfate(DB00686) 0.000 0.13 146 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ECC12_STOMACH NA ECC12_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.29 53 22 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 ECC12_STOMACH NA ECC12_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 19 34 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes ECC12_STOMACH NA ECC12_STOMACH NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.40 49 32 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - ECC12_STOMACH NA ECC12_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.87 2 13 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 ECC12_STOMACH NA ECC12_STOMACH NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.27 36 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 ECC12_STOMACH NA ECC12_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 10 CEP110 11064 broad.mit.edu 37 9 123935748 123935748 + Frame_Shift_Del DEL T - - ECC12_STOMACH NA ECC12_STOMACH NA g.chr9:123935748delT uc004bkx.1 + 39 6676 c.6645delT c.(6643-6645)CCTfs p.P2215fs CEP110_uc004blb.1_Frame_Shift_Del_p.P884fs|CEP110_uc010mvp.1_Frame_Shift_Del_p.P165fs NM_007018 NP_008949 Q7Z7A1 CNTRL_HUMAN centrosomal protein 110kDa 2215 Sufficient for interaction with HOOK2.|Potential. cell division|G2/M transition of mitotic cell cycle centrosome|cytosol protein binding 0 ATGAGGGACCTTTTGAAGAAA 0.413 0.91 7 72 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 ECC12_STOMACH NA ECC12_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 163 23 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 ECC12_STOMACH NA ECC12_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.22 47 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ECC12_STOMACH NA ECC12_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 46 121 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ECC12_STOMACH NA ECC12_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 6 49 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.78 6 21 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 265 75 CDKL2 8999 broad.mit.edu 37 4 76539607 76539610 + Frame_Shift_Del DEL ATTC - - ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr4:76539607_76539610delATTC uc003hiq.2 - 3 717_720 c.192_195delGAAT c.(190-195)GTGAATfs p.V64fs CDKL2_uc011cbp.1_Frame_Shift_Del_p.V64fs|CDKL2_uc010iix.1_Intron NM_003948 NP_003939 Q92772 CDKL2_HUMAN cyclin-dependent kinase-like 2 64_65 Protein kinase. sex differentiation|signal transduction cytoplasm|nucleus ATP binding|cyclin-dependent protein kinase activity ovary(2)|stomach(2)|breast(2)|skin(1) 7 Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122) CTTCCAAGAGATTCACCAAGTTTT 0.309 0.18 68 15 CCNA2 890 broad.mit.edu 37 4 122743803 122743804 + Splice_Site INS - A A ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr4:122743803_122743804insA uc003iec.3 - 2 519 c.214_splice c.e2-1 p.V72_splice NM_001237 NP_001228 P20248 CCNA2_HUMAN cyclin A cell division|mitosis|mitotic cell cycle G2/M transition DNA damage checkpoint|Ras protein signal transduction|regulation of cyclin-dependent protein kinase activity cytoplasm|nucleoplasm protein kinase binding ovary(1) 1 GGGTGCAACCTAAAAAAAAATT 0.406 0.13 65 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.28 55 21 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.36 56 32 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.60 4 6 NUP153 9972 broad.mit.edu 37 6 17633077 17633078 + Splice_Site INS - G G rs36027788;rs147103527 ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr6:17633077_17633078insG uc003ncd.1 - 17 2665 c.2465_splice c.e17-1 p.G822_splice NUP153_uc011dje.1_Splice_Site_p.G853_splice|NUP153_uc010jpl.1_Splice_Site_p.G780_splice NM_005124 NP_005115 P49790 NU153_HUMAN nucleoporin 153kDa carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm DNA binding|protein binding|transporter activity|zinc ion binding lung(4)|ovary(2)|breast(2)|skin(1) 9 Breast(50;0.0259)|Ovarian(93;0.0584) all_hematologic(90;0.125) all cancers(50;0.0981)|Epithelial(50;0.112) CTGAACTTCCTAAAAAAAAAAA 0.406 0.55 22 27 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.80 2 8 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.95 1 19 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 55 8 RARG 5916 broad.mit.edu 37 12 53621292 53621293 + Frame_Shift_Ins INS - C C ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr12:53621292_53621293insC uc001sce.2 - 3 522_523 c.37_38insG c.(37-39)GCCfs p.A13fs RARG_uc001scf.2_Frame_Shift_Ins_p.A13fs|RARG_uc001scg.2_Intron|RARG_uc010soc.1_Intron NM_000966 NP_000957 P13631 RARG_HUMAN retinoic acid receptor, gamma isoform 1 13 Modulating. canonical Wnt receptor signaling pathway|embryonic eye morphogenesis|embryonic hindlimb morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|regulation of cell size|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid integral to membrane|transcription factor complex retinoic acid receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding breast(2)|ovary(1)|lung(1) 4 Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tazarotene(DB00799)|Tretinoin(DB00755) AGGCCCCAGGGCACCAGCCGCA 0.658 0.40 6 4 JUB 84962 broad.mit.edu 37 14 23450905 23450905 + Frame_Shift_Del DEL C - - ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr14:23450905delC uc001whz.2 - 1 947 c.571delG c.(571-573)GCAfs p.A191fs NM_032876 NP_116265 Q96IF1 JUB_HUMAN ajuba isoform 1 191 PreLIM. cell cycle|gene silencing by miRNA|positive regulation of protein complex assembly cell-cell junction|cytoplasmic mRNA processing body|microtubule organizing center alpha-catenin binding|zinc ion binding 0 all_cancers(95;4.6e-05) GBM - Glioblastoma multiforme(265;0.0122) CCTGCCGGTGCTCCGGCCAGG 0.721 1.00 0 11 MAPK6 5597 broad.mit.edu 37 15 52338753 52338754 + Frame_Shift_Ins INS - T T ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr15:52338753_52338754insT uc002abp.2 + 2 890_891 c.96_97insT c.(94-99)GGCTTGfs p.G32fs NM_002748 NP_002739 Q16659 MK06_HUMAN mitogen-activated protein kinase 6 32_33 ATP (By similarity).|Protein kinase. cell cycle ATP binding|MAP kinase activity lung(3)|ovary(1) 4 all cancers(107;0.0028) GAGGCAATGGCTTGGTTTTTTC 0.396 0.15 45 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 60 270 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ECGI10_OESOPHAGUS NA ECGI10_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 58 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.85 7 41 LRP1B 53353 broad.mit.edu 37 2 142567922 142567922 + Frame_Shift_Del DEL G - - EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr2:142567922delG uc002tvj.1 - 2 1103 c.131delC c.(130-132)ACTfs p.T44fs LRP1B_uc010fnl.1_Frame_Shift_Del_p.T81fs NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 44 Extracellular (Potential).|LDL-receptor class A 1. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) GGAGACACAAGTCACGTGATC 0.443 0.40 53 36 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.28 28 11 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376116 + In_Frame_Del DEL TGCTGC - - rs143860374;rs62265537 EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr3:113376111_113376116delTGCTGC uc003eam.2 - 7 4824_4829 c.4413_4418delGCAGCA c.(4411-4419)CAGCAGCAA>CAA p.1471_1473QQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1415_1417QQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1471_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgct 0.359 0.38 13 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 58 76 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 19 27 ADAMTS19 171019 broad.mit.edu 37 5 129037216 129037232 + Frame_Shift_Del DEL GCCCGCCTCTGCCCAGC - - EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr5:129037216_129037232delGCCCGCCTCTGCCCAGC uc003kvb.1 + 20 3072_3088 c.3072_3088delGCCCGCCTCTGCCCAGC c.(3070-3090)AAGCCCGCCTCTGCCCAGCGCfs p.K1024fs ADAMTS19_uc010jdh.1_RNA NM_133638 NP_598377 Q8TE59 ATS19_HUMAN ADAM metallopeptidase with thrombospondin type 1 1024_1030 TSP type-1 3. proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding ovary(5)|breast(2)|lung(1)|skin(1) 9 all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) OV - Ovarian serous cystadenocarcinoma(64;0.222) TTGGGCCCAAGCCCGCCTCTGCCCAGCGCTGTGAGGG 0.576 0.16 108 20 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.33 10 5 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 3 24 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.53 7 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 22 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 706 129 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.27 99 37 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.28 115 44 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 9 91 AKT2 208 broad.mit.edu 37 19 40741837 40741837 + Frame_Shift_Del DEL A - - EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr19:40741837delA uc002onf.2 - 11 1397 c.1135delT c.(1135-1137)TCCfs p.S379fs AKT2_uc010egs.2_Frame_Shift_Del_p.S336fs|AKT2_uc010egt.2_Frame_Shift_Del_p.S317fs|AKT2_uc010xvj.1_Frame_Shift_Del_p.S317fs|AKT2_uc010egu.1_Frame_Shift_Del_p.S317fs|AKT2_uc002one.2_Frame_Shift_Del_p.S275fs NM_001626 NP_001617 P31751 AKT2_HUMAN AKT2 kinase 379 Protein kinase. insulin receptor signaling pathway|negative regulation of plasma membrane long-chain fatty acid transport|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process cytosol|nucleus ATP binding|protein binding|protein serine/threonine kinase activity lung(2) 2 Lung(22;0.000499) GCAAGCAGGGACTTGGCCTCG 0.677 0.18 53 12 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.75 56 170 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.20 51 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 72 543 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 EFE184_ENDOMETRIUM NA EFE184_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 67 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 EFM192A_BREAST NA EFM192A_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.96 3 71 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - EFM192A_BREAST NA EFM192A_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.51 187 196 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 EFM192A_BREAST NA EFM192A_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 70 121 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 EFM192A_BREAST NA EFM192A_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.32 70 33 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 EFM192A_BREAST NA EFM192A_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1 0 19 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 EFM192A_BREAST NA EFM192A_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 217 122 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C EFM192A_BREAST NA EFM192A_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 8 57 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 EFM192A_BREAST NA EFM192A_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 25 73 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 EFM192A_BREAST NA EFM192A_BREAST NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 "B melanoma antigen family, member 2 precursor" 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.13 103 16 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 EFM192A_BREAST NA EFM192A_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 13 107 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 EFM192A_BREAST NA EFM192A_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.94 2 33 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 EFM19_BREAST NA EFM19_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.98 3 133 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - EFM19_BREAST NA EFM19_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.12 1504 200 SOX11 6664 broad.mit.edu 37 2 5833526 5833534 + In_Frame_Del DEL GACGACGAC - - EFM19_BREAST NA EFM19_BREAST NA g.chr2:5833526_5833534delGACGACGAC uc002qyj.2 + 1 728_736 c.673_681delGACGACGAC c.(673-681)GACGACGACdel p.DDD231del NM_003108 NP_003099 P35716 SOX11_HUMAN SRY-box 11 231_233 Poly-Asp. cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis cytoplasm|nucleolus enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding central_nervous_system(3) 3 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) OV - Ovarian serous cystadenocarcinoma(76;0.132) 0.000 0.68 233 499 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 EFM19_BREAST NA EFM19_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. "regulation of transcription, DNA-dependent" membrane|nucleus "calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity" skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.36 0.33 97 48 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 EFM19_BREAST NA EFM19_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs "SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA;" GAAGAAGTCGATTAGGAGTTCA 0.545 0.2 150 38 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 EFM19_BREAST NA EFM19_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.6 140 213 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 EFM19_BREAST NA EFM19_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 38 97 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - EFM19_BREAST NA EFM19_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.33 10 5 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 EFM19_BREAST NA EFM19_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.3 251 109 ATN1 1822 broad.mit.edu 37 12 7045892 7045894 + In_Frame_Del DEL CAG - - rs66756893;rs67074116 EFM19_BREAST NA EFM19_BREAST NA g.chr12:7045892_7045894delCAG uc001qrw.1 + 5 1699_1701 c.1462_1464delCAG c.(1462-1464)CAGdel p.Q502del ATN1_uc001qrx.1_In_Frame_Del_p.Q502del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagc 0.458 0.11 56 7 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 EFM19_BREAST NA EFM19_BREAST NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.55 17 21 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 EFM19_BREAST NA EFM19_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.35 91 49 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 EFM19_BREAST NA EFM19_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 41 355 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 EFM19_BREAST NA EFM19_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.94 18 267 LRP1B 53353 broad.mit.edu 37 2 141130676 141130684 + In_Frame_Del DEL GATCTTTGG - - EFO21_OVARY NA EFO21_OVARY NA g.chr2:141130676_141130684delGATCTTTGG uc002tvj.1 - 69 11633_11641 c.10661_10669delCCAAAGATC c.(10660-10671)TCCAAAGATCAG>TAG p.3554_3557SKDQ>* NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 3554_3557 Extracellular (Potential).|LDL-receptor class A 27. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) CACCGGAACTGATCTTTGGAACAACTTGT 0.364 0.17 661 135 KALRN 8997 broad.mit.edu 37 3 124436112 124436121 + Frame_Shift_Del DEL CTTAGACTAC - - EFO21_OVARY NA EFO21_OVARY NA g.chr3:124436112_124436121delCTTAGACTAC uc003ehg.2 + 59 8422_8431 c.8295_8304delCTTAGACTAC c.(8293-8304)CTCTTAGACTACfs p.L2765fs KALRN_uc003ehk.2_Frame_Shift_Del_p.L1068fs NM_001024660 NP_001019831 O60229 KALRN_HUMAN kalirin, RhoGEF kinase isoform 1 2764_2767 Protein kinase. apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport actin cytoskeleton|cytosol ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1) 6 ATGGCCGGCTCTTAGACTACCTTATGAATC 0.400 0.12 392 53 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 EFO21_OVARY NA EFO21_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.31 86 38 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 EFO21_OVARY NA EFO21_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.53 60 69 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 EFO21_OVARY NA EFO21_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.78 29 105 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT EFO21_OVARY NA EFO21_OVARY NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.31 632 285 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 EFO21_OVARY NA EFO21_OVARY NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.63 14 24 NUMA1 4926 broad.mit.edu 37 11 71723446 71723448 + Splice_Site DEL CCT - - EFO21_OVARY NA EFO21_OVARY NA g.chr11:71723446_71723448delCCT uc001orl.1 - 16 4822 c.4650_splice c.e16+1 p.Q1550_splice NUMA1_uc009ysw.1_Intron|NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Intron|NUMA1_uc001orn.2_Splice_Site_p.Q1113_splice NM_006185 NP_006176 Q14980 NUMA1_HUMAN nuclear mitotic apparatus protein 1 G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole protein binding|structural molecule activity ovary(3)|lung(2)|skin(2)|central_nervous_system(1) 8 TCAGGCATTACCTGCTTAGTTTG 0.552 0.40 475 319 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C EFO21_OVARY NA EFO21_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 20 189 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 EFO21_OVARY NA EFO21_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 139 738 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 EFO21_OVARY NA EFO21_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.87 22 146 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 3 51 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 301 85 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.49 99 96 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.52 30 33 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 15 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.47 18 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 280 65 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 9 58 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.55 19 23 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 135 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 50 425 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 84 BTK 695 broad.mit.edu 37 X 100608923 100608924 + Frame_Shift_Ins INS - G G rs104894770;rs128621204 EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:100608923_100608924insG uc004ehg.2 - 17 1877_1878 c.1684_1685insC c.(1684-1686)CGGfs p.R562fs BTK_uc004ehf.2_Frame_Shift_Ins_p.R62fs|BTK_uc010nnh.2_Intron|BTK_uc010nni.2_Intron|BTK_uc004ehe.2_RNA|BTK_uc010nnj.2_RNA|BTK_uc010nnk.2_RNA|BTK_uc010nnl.2_Frame_Shift_Ins_p.R38fs|BTK_uc010nnm.2_Frame_Shift_Ins_p.R132fs|BTK_uc010nnn.2_Frame_Shift_Ins_p.R386fs|BTK_uc010nno.2_Frame_Shift_Ins_p.R596fs|BTK_uc004ehh.1_RNA NM_000061 NP_000052 Q06187 BTK_HUMAN Bruton agammaglobulinemia tyrosine kinase 562 Protein kinase. R -> W (in XLA). calcium-mediated signaling|induction of apoptosis by extracellular signals|mesoderm development cytosol|membrane raft|nucleus|plasma membrane ATP binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol-3,4,5-trisphosphate binding lung(3)|central_nervous_system(2)|ovary(1) 6 TGGGGACCACCGGACTGGAAAT 0.446 0.10 69 8 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 3 34 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 281 109 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.45 12 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 78 86 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.60 19 29 ATXN1 6310 broad.mit.edu 37 6 16327907 16327909 + In_Frame_Del DEL TGA - - rs59310777 by1000genomes EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:16327907_16327909delTGA uc003nbt.2 - 8 1604_1606 c.633_635delTCA c.(631-636)CATCAG>CAG p.H211del ATXN1_uc010jpi.2_In_Frame_Del_p.H211del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 211 Poly-Gln. H -> HQ (in Ref. 1; CAA55793). cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgctgatgctgatgct 0.384 0.12 101 14 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 3 19 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.30 86 37 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.75 4 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 1045 228 PLEKHA5 54477 broad.mit.edu 37 12 19427887 19427888 + Frame_Shift_Ins INS - G G EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:19427887_19427888insG uc001reb.2 + 10 1351_1352 c.1265_1266insG c.(1264-1266)AAGfs p.K422fs PLEKHA5_uc010sie.1_Frame_Shift_Ins_p.K428fs|PLEKHA5_uc001rea.2_Frame_Shift_Ins_p.K422fs|PLEKHA5_uc009zin.2_Frame_Shift_Ins_p.K180fs|PLEKHA5_uc010sif.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc010sig.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc010sih.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc001rec.1_Frame_Shift_Ins_p.K110fs NM_019012 NP_061885 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A 422 1-phosphatidylinositol binding|protein binding ovary(1)|kidney(1)|skin(1) 3 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) AAAATCCAGAAGGGGAGGGGTC 0.470 0.14 43 7 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.20 51 13 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.71 6 15 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.20 39 10 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 0.73 14 37 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.35 114 62 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 106 320 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 8 139 SPEN 23013 broad.mit.edu 37 1 16258933 16258934 + Frame_Shift_Ins INS - C C EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:16258933_16258934insC uc001axk.1 + 11 6402_6403 c.6198_6199insC c.(6196-6201)AAACCGfs p.K2066fs SPEN_uc010obp.1_Frame_Shift_Ins_p.K2025fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2066_2067 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) TAGAGAAAAAACCGGCCCCTGA 0.475 0.10 83 9 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 224 48 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.31 9 4 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.31 22 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 68 126 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.22 35 10 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 42 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 363 87 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.85 4 23 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.32 90 42 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.21 75 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 70 376 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 106 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.18 134 29 SSX3 10214 broad.mit.edu 37 X 48209462 48209463 + Frame_Shift_Ins INS - G G rs6651589 byFrequency;by1000genomes EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:48209462_48209463insG uc004djd.1 - 6 519_520 c.425_426insC c.(424-426)CCGfs p.P142fs SSX3_uc004dje.2_Frame_Shift_Ins_p.P142fs NM_021014 NP_066294 Q99909 SSX3_HUMAN synovial sarcoma, X breakpoint 3 isoform a 142 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus nucleic acid binding 0 TTGGTTTTCCCGGGGGGCACAG 0.495 0.47 113 100 FAM123B 139285 broad.mit.edu 37 X 63410654 63410654 + Frame_Shift_Del DEL A - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:63410654delA uc004dvo.2 - 2 2786 c.2513delT c.(2512-2514)TTGfs p.L838fs NM_152424 NP_689637 Q5JTC6 F123B_HUMAN family with sequence similarity 123B 838 Wnt receptor signaling pathway cytoplasm|nucleus|plasma membrane p.0?(40) kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1) 112 0.000 0.12 722 99 FAM123B 139285 broad.mit.edu 37 X 63410656 63410656 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:63410656delG uc004dvo.2 - 2 2784 c.2511delC c.(2509-2511)TCCfs p.S837fs NM_152424 NP_689637 Q5JTC6 F123B_HUMAN family with sequence similarity 123B 837 Wnt receptor signaling pathway cytoplasm|nucleus|plasma membrane p.0?(40) kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1) 112 AGGCTTCCAAGGAGGCTGCAA 0.522 0.52 49 54 FOXO4 4303 broad.mit.edu 37 X 70321276 70321277 + Frame_Shift_Ins INS - G G EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:70321276_70321277insG uc004dys.1 + 2 1549_1550 c.1196_1197insG c.(1195-1197)CTGfs p.L399fs FOXO4_uc010nkz.2_Intron|FOXO4_uc004dyt.1_Frame_Shift_Ins_p.L344fs NM_005938 NP_005929 P98177 FOXO4_HUMAN forkhead box O4 399 cell cycle arrest|cell differentiation|embryo development|G1 phase of mitotic cell cycle|insulin receptor signaling pathway|mitotic cell cycle G2/M transition DNA damage checkpoint|muscle organ development|negative regulation of angiogenesis|negative regulation of cell proliferation|negative regulation of smooth muscle cell differentiation|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding central_nervous_system(2)|prostate(1) 3 Renal(35;0.156) CTTCTGTTGCTGGGGGGGCTTC 0.634 0.36 52 29 ATRX 546 broad.mit.edu 37 X 76874315 76874316 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:76874315_76874316insT uc004ecp.3 - 21 5638_5639 c.5406_5407insA c.(5404-5409)AAACGTfs p.K1802fs ATRX_uc004ecq.3_Frame_Shift_Ins_p.K1764fs|ATRX_uc004eco.3_Frame_Shift_Ins_p.K1587fs NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 1802_1803 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) ATGTGAGCACGTTTTTTCATCA 0.332 0.51 117 122 ATRX 546 broad.mit.edu 37 X 76918920 76918921 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:76918920_76918921insT uc004ecp.3 - 12 4302_4303 c.4070_4071insA c.(4069-4071)AAGfs p.K1357fs ATRX_uc004ecq.3_Frame_Shift_Ins_p.K1319fs|ATRX_uc004eco.3_Frame_Shift_Ins_p.K1142fs|ATRX_uc004ecr.2_Frame_Shift_Ins_p.K1289fs NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 1357 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) TAGGCTTTGTCTTTTTTTCTTC 0.361 0.47 203 178 HNRNPH2 3188 broad.mit.edu 37 X 100668111 100668112 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:100668111_100668112insT uc004ehm.2 + 2 1305_1306 c.1135_1136insT c.(1135-1137)CTTfs p.L379fs HNRNPH2_uc004ehn.2_Frame_Shift_Ins_p.L379fs NM_019597 NP_062543 P55795 HNRH2_HUMAN heterogeneous nuclear ribonucleoprotein H2 379 2 X 16 AA Gly-rich approximate repeats.|2 X 19 AA perfect repeats.|2-2. nuclear mRNA splicing, via spliceosome actin cytoskeleton|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm nucleotide binding|protein binding|RNA binding 0 CTATGTAGAACTTTTTTTGAAT 0.455 0.27 84 31 NRK 203447 broad.mit.edu 37 X 105150508 105150509 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:105150508_105150509insA uc004emd.2 + 11 1250_1251 c.947_948insA c.(946-948)ATAfs p.I316fs NRK_uc010npc.1_5'UTR NM_198465 NP_940867 Q7Z2Y5 NRK_HUMAN Nik related kinase 316 ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1) 14 GTTCGGGATATAAAAAATGAAC 0.332 0.50 162 164 NRK 203447 broad.mit.edu 37 X 105150575 105150576 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:105150575_105150576insA uc004emd.2 + 11 1317_1318 c.1014_1015insA c.(1012-1017)CAGAAAfs p.Q338fs NRK_uc010npc.1_5'UTR NM_198465 NP_940867 Q7Z2Y5 NRK_HUMAN Nik related kinase 338_339 ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1) 14 AAAAAAGACAGAAAAAAGGTAG 0.292 0.15 105 19 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.38 34 21 XIAP 331 broad.mit.edu 37 X 123025155 123025157 + In_Frame_Del DEL GAG - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:123025155_123025157delGAG uc010nqu.2 + 4 1171_1173 c.1045_1047delGAG c.(1045-1047)GAGdel p.E350del XIAP_uc004etx.2_In_Frame_Del_p.E350del|XIAP_uc010nqv.2_5'UTR NM_001167 NP_001158 P98170 XIAP_HUMAN baculoviral IAP repeat-containing protein 4 350 anti-apoptosis|apoptosis|induction of apoptosis by intracellular signals|response to DNA damage stimulus cytosol caspase inhibitor activity|ligase activity|protein binding|zinc ion binding ovary(1)|lung(1) 2 TCATTCACTTGAGGAGTGTCTGG 0.197 0.32 108 50 ELF4 2000 broad.mit.edu 37 X 129208563 129208564 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:129208563_129208564insA uc004evd.3 - 3 624_625 c.239_240insT c.(238-240)TTGfs p.L80fs ELF4_uc004eve.3_Frame_Shift_Ins_p.L80fs NM_001421 NP_001412 Q99607 ELF4_HUMAN E74-like factor 4 80 natural killer cell proliferation|NK T cell proliferation|positive regulation of transcription from RNA polymerase II promoter PML body protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity ovary(1) 1 GACCTGTCAGCAAAAAACTGCC 0.530 0.50 57 58 GPR112 139378 broad.mit.edu 37 X 135426885 135426886 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:135426885_135426886insA uc004ezu.1 + 6 1311_1312 c.1020_1021insA c.(1018-1023)ATGAAAfs p.M340fs GPR112_uc010nsb.1_Frame_Shift_Ins_p.M135fs|GPR112_uc010nsc.1_Frame_Shift_Ins_p.M107fs NM_153834 NP_722576 Q8IZF6 GP112_HUMAN G-protein coupled receptor 112 340_341 Extracellular (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1) 12 Acute lymphoblastic leukemia(192;0.000127) CCAATTCCATGAAAAAAACGAA 0.386 0.39 142 90 GPR112 139378 broad.mit.edu 37 X 135443713 135443714 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:135443713_135443714insA uc004ezu.1 + 12 7535_7536 c.7244_7245insA c.(7243-7245)ATAfs p.I2415fs GPR112_uc010nsb.1_Frame_Shift_Ins_p.I2210fs|GPR112_uc010nsc.1_Frame_Shift_Ins_p.I2043fs NM_153834 NP_722576 Q8IZF6 GP112_HUMAN G-protein coupled receptor 112 2415 Extracellular (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1) 12 Acute lymphoblastic leukemia(192;0.000127) ACCAGATGCATAAAAAATGAGG 0.411 0.45 41 33 PNCK 139728 broad.mit.edu 37 X 152938062 152938063 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:152938062_152938063insC uc011myu.1 - 3 593_594 c.407_408insG c.(406-408)GGCfs p.G136fs PNCK_uc011myt.1_Frame_Shift_Ins_p.G70fs|PNCK_uc004fia.2_Frame_Shift_Ins_p.G65fs|PNCK_uc004fhz.3_5'UTR|PNCK_uc010nuh.2_Frame_Shift_Ins_p.G136fs|PNCK_uc011myv.1_Frame_Shift_Ins_p.G80fs|PNCK_uc011myw.1_Frame_Shift_Ins_p.G80fs NM_001039582 NP_001034671 Q6P2M8 KCC1B_HUMAN pregnancy upregulated non-ubiquitously expressed 53 Protein kinase. cytoplasm|nucleus ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity breast(1) 1 all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) GGGCCTCCTTGCCCCGGAGGGC 0.653 0.54 6 7 F8 2157 broad.mit.edu 37 X 154158599 154158600 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chrX:154158599_154158600insT uc004fmt.2 - 14 3636_3637 c.3465_3466insA c.(3463-3468)AAATCTfs p.K1155fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1155_1156 B. acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) CCTTCCACAGATTTTTCTGGTC 0.426 0.47 218 191 B3GALT6 126792 broad.mit.edu 37 1 1168239 1168240 + Frame_Shift_Ins INS - G G EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:1168239_1168240insG uc001adk.2 + 1 611_612 c.581_582insG c.(580-582)CCGfs p.P194fs SDF4_uc001adh.3_5'Flank|SDF4_uc001adi.3_5'Flank|SDF4_uc009vjv.2_5'Flank|SDF4_uc009vjw.2_5'Flank NM_080605 NP_542172 Q96L58 B3GT6_HUMAN beta-1,3-galactosyltransferase 6 194 Lumenal (Potential). glycosaminoglycan biosynthetic process|protein glycosylation Golgi cisterna membrane|Golgi medial cisterna|integral to membrane galactosylxylosylprotein 3-beta-galactosyltransferase activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.22e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199) 0.000 0.15 293 50 DVL1 1855 broad.mit.edu 37 1 1271681 1271682 + Frame_Shift_Ins INS - G G EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:1271681_1271682insG uc001aer.3 - 15 1900_1901 c.1853_1854insC c.(1852-1854)CCGfs p.P618fs DVL1_uc002quu.2_Frame_Shift_Ins_p.P360fs|DVL1_uc009vka.2_Frame_Shift_Ins_p.P301fs|DVL1_uc001aeu.1_3'UTR NM_004421 NP_004412 O14640 DVL1_HUMAN dishevelled 1 643 canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome frizzled binding|identical protein binding|protein kinase binding|signal transducer activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145) 0.000 0.28 619 246 EPHA2 1969 broad.mit.edu 37 1 16462199 16462199 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:16462199delG uc001aya.1 - 6 1516 c.1379delC c.(1378-1380)CCGfs p.P460fs EPHA2_uc010oca.1_Frame_Shift_Del_p.P460fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 460 Extracellular (Potential).|Fibronectin type-III 2. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) 0.000 0.35 483 265 EPHA8 2046 broad.mit.edu 37 1 22923835 22923836 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:22923835_22923836insC uc001bfx.1 + 10 1921_1922 c.1796_1797insC c.(1795-1797)CACfs p.H599fs NM_020526 NP_065387 P29322 EPHA8_HUMAN ephrin receptor EphA8 isoform 1 precursor 599 Cytoplasmic (Potential). integral to plasma membrane ATP binding|ephrin receptor activity central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1) 13 Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199) CCTCTGCATCACCCCCCGGGAA 0.653 0.31 24 11 ARID1A 8289 broad.mit.edu 37 1 27097688 27097688 + Frame_Shift_Del DEL A - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:27097688delA uc001bmv.1 + 12 3650 c.3277delA c.(3277-3279)AAAfs p.K1093fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.K1093fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.K1093fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.K710fs|ARID1A_uc001bmx.1_5'UTR|ARID1A_uc009vsm.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1093 ARID. androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CAGCTCCTTGAAAAAGCAGTA 0.473 0.34 65 33 THRAP3 9967 broad.mit.edu 37 1 36755074 36755075 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:36755074_36755075insA uc001cae.3 + 5 1678_1679 c.1454_1455insA c.(1453-1455)AGAfs p.R485fs THRAP3_uc001caf.3_Frame_Shift_Ins_p.R485fs|THRAP3_uc001cag.1_Frame_Shift_Ins_p.R485fs NM_005119 NP_005110 Q9Y2W1 TR150_HUMAN thyroid hormone receptor associated protein 3 485 androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter mediator complex ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding ovary(5)|lung(3)|breast(1) 9 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) GAAAAGCAGAGAAAAACAGAGG 0.505 0.40 81 55 CDKN2C 1031 broad.mit.edu 37 1 51436083 51436084 + Frame_Shift_Ins INS - G G rs66765738 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:51436083_51436084insG uc001csf.2 + 2 1259_1260 c.43_44insG c.(43-45)AGGfs p.R15fs CDKN2C_uc001csg.2_Frame_Shift_Ins_p.R15fs NM_001262 NP_001253 P42773 CDN2C_HUMAN cyclin-dependent kinase inhibitor 2C 15 ANK 1. cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|regulation of cyclin-dependent protein kinase activity cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|protein kinase binding p.0?(4)|p.R15fs*4(1) central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(5)|ovary(2)|thyroid(1)|lung(1)|kidney(1) 17 GBM - Glioblastoma multiforme(3;3.61e-13)|all cancers(3;0.00151) CGCAGCTGCCAGGGGGGACCTA 0.465 0.45 76 63 JAK1 3716 broad.mit.edu 37 1 65339110 65339111 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:65339110_65339111insT uc001dbu.1 - 5 674_675 c.425_426insA c.(424-426)AAGfs p.K142fs JAK1_uc009wam.1_Frame_Shift_Ins_p.K130fs|JAK1_uc001dbv.2_RNA NM_002227 NP_002218 P23458 JAK1_HUMAN janus kinase 1 142 FERM. interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway cytoskeleton|cytosol|endomembrane system|membrane|nucleus ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity p.K142fs*26(3) haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1) 61 BRCA - Breast invasive adenocarcinoma(111;0.0485) CATCTGGAATCTTTTTTTTCTC 0.480 0.36 226 128 BCL10 8915 broad.mit.edu 37 1 85736510 85736511 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:85736510_85736511insT uc001dkz.2 - 3 841_842 c.136_137insA c.(136-138)ATAfs p.I46fs NM_003921 NP_003912 O95999 BCL10_HUMAN B-cell CLL/lymphoma 10 46 CARD. I->A: Abolishes cell death-inducing capability. apoptosis|cellular response to mechanical stimulus|innate immune response|interleukin-6 biosynthetic process|lymphotoxin A biosynthetic process|negative regulation of mature B cell apoptosis|neural tube closure|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 biosynthetic process|positive regulation of mast cell cytokine production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of transcription, DNA-dependent|protein homooligomerization|response to molecule of bacterial origin|T cell receptor signaling pathway CBM complex|cytosol|lysosome|membrane raft|nucleus|perinuclear region of cytoplasm NF-kappaB binding|protease binding|protein C-terminus binding|protein kinase B binding|protein self-association|transcription coactivator activity|ubiquitin binding|ubiquitin protein ligase binding lung(2) 2 all cancers(265;0.0114)|Epithelial(280;0.0311) TCTACTGAGTATTTTTTTTGCA 0.347 0.50 50 51 TRIM33 51592 broad.mit.edu 37 1 115053622 115053622 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:115053622delC uc001eew.2 - 1 160 c.76delG c.(76-78)GCCfs p.A26fs TRIM33_uc001eex.2_Frame_Shift_Del_p.A26fs NM_015906 NP_056990 Q9UPN9 TRI33_HUMAN tripartite motif-containing 33 protein isoform 26 Necessary for E3 ubiquitin-protein ligase activity and repression of SMAD4 signaling and transcriptional repression. negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent nucleus co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 11 all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184) all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05) Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133) 0.000 0.49 312 302 PDE4DIP 9659 broad.mit.edu 37 1 144911965 144911966 + Splice_Site INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:144911965_144911966insA uc001elw.3 - 16 2437 c.2146_splice c.e16-1 p.G716_splice NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Splice_Site_p.G782_splice|PDE4DIP_uc001emc.1_Splice_Site_p.G716_splice|PDE4DIP_uc001emd.1_Splice_Site_p.G716_splice|PDE4DIP_uc001emb.1_Splice_Site_p.G879_splice|PDE4DIP_uc001eme.1_Splice_Site_p.G245_splice|PDE4DIP_uc001emf.1_Splice_Site_p.G501_splice NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) CATTGAACCCTAAAAAATTGCA 0.371 0.24 282 90 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 440 93 NTRK1 4914 broad.mit.edu 37 1 156838011 156838011 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:156838011delC uc001fqh.1 + 5 600 c.544delC c.(544-546)CCCfs p.P182fs NTRK1_uc001fqf.1_Frame_Shift_Del_p.P152fs|NTRK1_uc009wsi.1_5'UTR|NTRK1_uc001fqi.1_Frame_Shift_Del_p.P182fs|NTRK1_uc009wsk.1_Frame_Shift_Del_p.P182fs NM_002529 NP_002520 P04629 NTRK1_HUMAN neurotrophic tyrosine kinase, receptor, type 1 182 LRRCT.|Extracellular (Potential). activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction endosome|integral to plasma membrane ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity lung(9)|ovary(6)|stomach(1)|central_nervous_system(1) 17 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) Imatinib(DB00619) TGGGCAAGGGCCCCTGGCCCA 0.652 0.36 7 4 RNASEL 6041 broad.mit.edu 37 1 182545526 182545527 + Splice_Site INS - AAA AAA EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:182545526_182545527insAAA uc001gpj.1 - 5 2073 c.1906_splice c.e5-1 p.I636_splice RNASEL_uc009wxz.1_Splice_Site_p.I636_splice NM_021133 NP_066956 Q05823 RN5A_HUMAN ribonuclease L mRNA processing|response to virus|type I interferon-mediated signaling pathway mitochondrion ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding ovary(4)|stomach(1) 5 TTCATTAATCTAAAAAAACAAA 0.267 0.24 77 24 TPR 7175 broad.mit.edu 37 1 186291529 186291530 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:186291529_186291530insA uc001grv.2 - 45 6678_6679 c.6381_6382insT c.(6379-6384)TTTGATfs p.F2127fs NM_003292 NP_003283 P12270 TPR_HUMAN nuclear pore complex-associated protein TPR 2127_2128 carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm ATP binding|protein binding|serine-tRNA ligase activity ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1) 7 Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157) Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553) TCTTCATCATCAAAAAAATGCT 0.342 0.27 236 86 PIK3C2B 5287 broad.mit.edu 37 1 204438537 204438538 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:204438537_204438538insA uc001haw.2 - 3 872_873 c.393_394insT c.(391-396)TTTGATfs p.F131fs PIK3C2B_uc010pqv.1_Frame_Shift_Ins_p.F131fs|PIK3C2B_uc001hax.1_Frame_Shift_Ins_p.F131fs|PIK3C2B_uc009xbd.1_RNA NM_002646 NP_002637 O00750 P3C2B_HUMAN phosphoinositide-3-kinase, class 2 beta 131_132 Interaction with GRB2. cell communication|phosphatidylinositol-mediated signaling endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1) 7 all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227) GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193) TCTGAACCATCAAAAATGTAGA 0.579 0.25 151 50 IKBKE 9641 broad.mit.edu 37 1 206652329 206652330 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:206652329_206652330insC uc001hdz.1 + 10 1404_1405 c.1036_1037insC c.(1036-1038)GCCfs p.A346fs IKBKE_uc009xbv.1_Frame_Shift_Ins_p.A346fs|IKBKE_uc001hea.1_Frame_Shift_Ins_p.A261fs NM_014002 NP_054721 Q14164 IKKE_HUMAN IKK-related kinase epsilon 346 DNA damage response, signal transduction resulting in induction of apoptosis|innate immune response|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|endosome membrane|plasma membrane|PML body ATP binding|IkappaB kinase activity|NF-kappaB-inducing kinase activity|protein binding ovary(3)|lung(3)|central_nervous_system(1)|skin(1) 8 Breast(84;0.137) GACCAGTGTGGCCCCCCGACAC 0.639 0.28 34 13 DYRK3 8444 broad.mit.edu 37 1 206821440 206821441 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:206821440_206821441insA uc001hej.2 + 3 1065_1066 c.897_898insA c.(895-900)ATTAAAfs p.I299fs DYRK3_uc001hek.2_Intron|DYRK3_uc001hei.2_Frame_Shift_Ins_p.I279fs NM_003582 NP_003573 O43781 DYRK3_HUMAN dual-specificity tyrosine-(Y)-phosphorylation 299_300 Protein kinase. erythrocyte differentiation nucleus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity stomach(2)|central_nervous_system(1) 3 Breast(84;0.183) BRCA - Breast invasive adenocarcinoma(75;0.166) ATGAGCTGATTAAAAAAAATAA 0.406 0.30 340 149 TGFB2 7042 broad.mit.edu 37 1 218609370 218609371 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:218609370_218609371insA uc001hlm.2 + 5 1466_1467 c.813_814insA c.(811-816)AGGAAAfs p.R271fs TGFB2_uc001hln.2_Frame_Shift_Ins_p.R299fs|TGFB2_uc010pue.1_Intron|TGFB2_uc001hlo.2_Intron NM_003238 NP_003229 P61812 TGFB2_HUMAN transforming growth factor, beta 2 isoform 2 271_272 activation of protein kinase activity|angiogenesis|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cardioblast differentiation|catagen|cell cycle arrest|cell death|cell growth|cell-cell junction organization|cell-cell signaling|collagen fibril organization|dopamine biosynthetic process|embryonic digestive tract development|eye development|glial cell migration|hair follicle morphogenesis|hemopoiesis|menstrual cycle phase|negative regulation of alkaline phosphatase activity|negative regulation of cell growth|negative regulation of epithelial cell proliferation|negative regulation of immune response|negative regulation of macrophage cytokine production|neuron development|neutrophil chemotaxis|odontogenesis|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of cardioblast differentiation|positive regulation of catagen|positive regulation of cell adhesion mediated by integrin|positive regulation of cell cycle|positive regulation of cell division|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of epithelial cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of heart contraction|positive regulation of immune response|positive regulation of integrin biosynthetic process|positive regulation of neuron apoptosis|positive regulation of ossification|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein secretion|positive regulation of stress-activated MAPK cascade|regulation of transforming growth factor-beta2 production|response to hypoxia|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein import into nucleus|somatic stem cell division|transforming growth factor beta receptor signaling pathway axon|extracellular matrix|extracellular space|neuronal cell body|platelet alpha granule lumen beta-amyloid binding|cytokine activity|growth factor activity|protein heterodimerization activity|protein homodimerization activity|receptor signaling protein serine/threonine kinase activity|type II transforming growth factor beta receptor binding 0 all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776) AGTCCACTAGGAAAAAAAACAG 0.431 0.25 159 54 PARP1 142 broad.mit.edu 37 1 226564829 226564829 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:226564829delG uc001hqd.3 - 13 2092 c.1921delC c.(1921-1923)CTGfs p.L641fs NM_001618 NP_001609 P09874 PARP1_HUMAN poly (ADP-ribose) polymerase family, member 1 641 cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter nuclear envelope|nucleolus|transcription factor complex DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding lung(3)|ovary(2)|breast(2)|skin(2)|upper_aerodigestive_tract(1) 10 Breast(184;0.133) GBM - Glioblastoma multiforme(131;0.0531) TCAATCTCCAGGGGGTAGAAC 0.393 0.52 48 53 CDC42BPA 8476 broad.mit.edu 37 1 227235660 227235661 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:227235660_227235661insT uc001hqr.2 - 22 3898_3899 c.2955_2956insA c.(2953-2958)AAAGGAfs p.K985fs CDC42BPA_uc001hqq.2_Frame_Shift_Ins_p.K284fs|CDC42BPA_uc001hqs.2_Frame_Shift_Ins_p.K904fs|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Frame_Shift_Ins_p.K965fs|CDC42BPA_uc001hqp.2_Frame_Shift_Ins_p.K141fs|CDC42BPA_uc001hqu.1_Frame_Shift_Ins_p.K192fs NM_003607 NP_003598 Q5VT25 MRCKA_HUMAN CDC42-binding protein kinase alpha isoform B 998_999 actin cytoskeleton reorganization|intracellular signal transduction cell leading edge|cell-cell junction|cytoplasm ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1) 11 all_cancers(173;0.156)|Prostate(94;0.0792) CCAGGACATCCTTTTTTCCTTA 0.381 0.31 254 114 OBSCN 84033 broad.mit.edu 37 1 228550390 228550391 + Frame_Shift_Ins INS - G G EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:228550390_228550391insG uc009xez.1 + 80 18819_18820 c.18775_18776insG c.(18775-18777)AGGfs p.R6259fs OBSCN_uc001hsr.1_Frame_Shift_Ins_p.R888fs NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 6259 apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) 0.000 0.19 871 198 NUP133 55746 broad.mit.edu 37 1 229625705 229625705 + Frame_Shift_Del DEL A - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr1:229625705delA uc001htn.2 - 9 1283 c.1191delT c.(1189-1191)TTTfs p.F397fs NM_018230 NP_060700 Q8WUM0 NU133_HUMAN nucleoporin 133kDa 397 carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction condensed chromosome kinetochore|cytosol|Nup107-160 complex nucleocytoplasmic transporter activity|protein binding breast(4)|skin(2)|ovary(1) 7 Breast(184;0.104)|Ovarian(103;0.249) Prostate(94;0.167) ATCTTACCTGAAAAGGTGGAT 0.274 0.31 170 78 PXDN 7837 broad.mit.edu 37 2 1652983 1652984 + Frame_Shift_Ins INS - G G EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:1652983_1652984insG uc002qxa.2 - 17 2632_2633 c.2568_2569insC c.(2566-2571)CCCTGCfs p.P856fs NM_012293 NP_036425 Q92626 PXDN_HUMAN peroxidasin precursor 856_857 extracellular matrix organization|hydrogen peroxide catabolic process|immune response endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity pancreas(6)|ovary(2) 8 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716) all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228) 0.000 0.44 548 428 MYCN 4613 broad.mit.edu 37 2 16082314 16082314 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:16082314delC uc002rci.2 + 2 428 c.128delC c.(127-129)ACCfs p.T43fs MYCNOS_uc002rch.1_5'Flank|MYCN_uc010yjr.1_Frame_Shift_Del_p.T35fs NM_005378 NP_005369 P04198 MYCN_HUMAN v-myc myelocytomatosis viral related oncogene, 43 regulation of transcription from RNA polymerase II promoter chromatin|nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity central_nervous_system(2)|ovary(1)|lung(1)|skin(1) 5 all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197) GBM - Glioblastoma multiforme(3;0.000332) 0.000 0.47 166 146 BIRC6 57448 broad.mit.edu 37 2 32749990 32749991 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:32749990_32749991insA uc010ezu.2 + 58 11793_11794 c.11659_11660insA c.(11659-11661)CAAfs p.Q3887fs NM_016252 NP_057336 Q9NR09 BIRC6_HUMAN baculoviral IAP repeat-containing 6 3887 anti-apoptosis|apoptosis intracellular acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1) 14 Acute lymphoblastic leukemia(172;0.155) AATTAGTGAACAAAAAGATGAC 0.302 0.46 37 31 BCL11A 53335 broad.mit.edu 37 2 60689253 60689254 + Frame_Shift_Ins INS - G G EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:60689253_60689254insG uc002sae.1 - 4 1021_1022 c.793_794insC c.(793-795)CTGfs p.L265fs BCL11A_uc002sab.2_Frame_Shift_Ins_p.L265fs|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Frame_Shift_Ins_p.L231fs|BCL11A_uc002sad.1_Frame_Shift_Ins_p.L113fs|BCL11A_uc002saf.1_Frame_Shift_Ins_p.L231fs NM_022893 NP_075044 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A isoform 1 265 Pro-rich. negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|cytoplasm|nucleus|nucleus nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding central_nervous_system(6)|breast(3)|ovary(2)|skin(2) 13 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) 0.000 0.36 578 329 IL1R2 7850 broad.mit.edu 37 2 102638649 102638649 + Frame_Shift_Del DEL A - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:102638649delA uc002tbm.2 + 6 918 c.689delA c.(688-690)AAAfs p.K230fs IL1R2_uc002tbn.2_Frame_Shift_Del_p.K230fs|IL1R2_uc002tbo.1_Frame_Shift_Del_p.K230fs NM_004633 NP_004624 P27930 IL1R2_HUMAN interleukin 1 receptor, type II precursor 230 Extracellular (Potential). immune response integral to membrane|plasma membrane interleukin-1, Type II, blocking receptor activity ovary(1)|breast(1) 2 Anakinra(DB00026) TCTTTCTCAGAAAAAAAAGAA 0.438 0.50 90 90 LRP1B 53353 broad.mit.edu 37 2 141243011 141243012 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:141243011_141243012insT uc002tvj.1 - 59 10297_10298 c.9325_9326insA c.(9325-9327)AGAfs p.R3109fs NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 3109 Extracellular (Potential).|LDL-receptor class B 29. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) TTCAATGATTCTTTTTTCTGTG 0.406 0.47 140 123 LRP1B 53353 broad.mit.edu 37 2 141773283 141773284 + Frame_Shift_Ins INS - A A rs138993428 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:141773283_141773284insA uc002tvj.1 - 13 3143_3144 c.2171_2172insT c.(2170-2172)TTGfs p.L724fs LRP1B_uc010fnl.1_Intron NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 724 Extracellular (Potential).|LDL-receptor class B 8. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) GAGTCCCATTCAAAAATACTTT 0.376 0.48 151 137 HOXD11 3237 broad.mit.edu 37 2 176972823 176972824 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:176972823_176972824insC uc002uki.2 + 1 740_741 c.740_741insC c.(739-741)GGCfs p.G247fs HOXD11_uc010fqx.2_Intron NM_021192 NP_067015 P31277 HXD11_HUMAN homeobox D11 247 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678) 0.000 0.38 111 69 TTN 7273 broad.mit.edu 37 2 179437956 179437957 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:179437956_179437957insT uc010zfg.1 - 275 65422_65423 c.65198_65199insA c.(65197-65199)AATfs p.N21733fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Ins_p.N15428fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.N15361fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.N15236fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 22660 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTCCAGCAGCATTTTCAGCCAT 0.411 0.49 293 282 TTN 7273 broad.mit.edu 37 2 179485562 179485563 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:179485562_179485563insT uc010zfg.1 - 196 38294_38295 c.38070_38071insA c.(38068-38073)AAAGACfs p.K12690fs TTN_uc010zfh.1_Frame_Shift_Ins_p.K6385fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.K6318fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.K6193fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 13617_13618 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TAGACTAGGTCTTTTTGGAGAA 0.371 0.46 236 201 TTN 7273 broad.mit.edu 37 2 179514565 179514566 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:179514565_179514566insT uc010zfg.1 - 165 32795_32796 c.32571_32572insA c.(32569-32574)AAACCAfs p.K10857fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc010fre.1_Intron|TTN_uc002umw.1_RNA|TTN_uc002umx.1_5'UTR NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 11784_11785 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GGTGCTTCTGGTTTTTTGATGA 0.351 0.46 112 96 TTN 7273 broad.mit.edu 37 2 179528183 179528183 + Frame_Shift_Del DEL T - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:179528183delT uc010zfk.1 - 17 1579 c.1031delA c.(1030-1032)AAGfs p.K344fs TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron Q8WZ42 TITIN_HUMAN SubName: Full=Titin; Flags: Fragment; 11556 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CACTTCAGGCTTTTTAGGAGG 0.373 0.35 42 23 STAT1 6772 broad.mit.edu 37 2 191859804 191859805 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:191859804_191859805insA uc002usj.2 - 10 1314_1315 c.926_927insT c.(925-927)TTCfs p.F309fs STAT1_uc010fse.1_Frame_Shift_Ins_p.F309fs|STAT1_uc002usk.2_Frame_Shift_Ins_p.F309fs|STAT1_uc002usl.2_Frame_Shift_Ins_p.F311fs|STAT1_uc010fsf.1_Frame_Shift_Ins_p.F121fs NM_007315 NP_009330 P42224 STAT1_HUMAN signal transducer and activator of transcription 309 activation of caspase activity|I-kappaB kinase/NF-kappaB cascade|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway|tyrosine phosphorylation of STAT protein cytosol|nucleolus|nucleoplasm calcium ion binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity|signal transducer activity lung(3)|breast(3)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1) 10 OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141) Fludarabine(DB01073) TGAGCTGCTGGAAAAGACTGAA 0.386 0.44 136 105 STK17B 9262 broad.mit.edu 37 2 197004350 197004350 + Frame_Shift_Del DEL T - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:197004350delT uc002utk.2 - 7 1154 c.830delA c.(829-831)AATfs p.N277fs STK17B_uc010fsh.2_Frame_Shift_Del_p.N277fs NM_004226 NP_004217 O94768 ST17B_HUMAN serine/threonine kinase 17B 277 Protein kinase. apoptosis|induction of apoptosis|intracellular protein kinase cascade nucleus ATP binding|protein serine/threonine kinase activity lung(2) 2 OV - Ovarian serous cystadenocarcinoma(117;0.141) TTACTCTGGATTTTTTACTAA 0.249 0.42 107 76 IDH1 3417 broad.mit.edu 37 2 209116180 209116180 + Frame_Shift_Del DEL A - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:209116180delA uc002vcs.2 - 3 342 c.96delT c.(94-96)TTTfs p.F32fs IDH1_uc002vct.2_Frame_Shift_Del_p.F32fs|IDH1_uc002vcu.2_Frame_Shift_Del_p.F32fs NM_005896 NP_005887 O75874 IDHC_HUMAN isocitrate dehydrogenase 1 (NADP+), soluble 32 F -> I (in Ref. 3; CAB66637). 2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle cytosol|peroxisomal matrix isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1) 2868 Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136) CCACGTAGGGAAAAATGAGTT 0.338 0.50 152 153 IGFBP5 3488 broad.mit.edu 37 2 217542949 217542949 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:217542949delG uc002vgj.3 - 3 1347 c.573delC c.(571-573)CCCfs p.P191fs NM_000599 NP_000590 P24593 IBP5_HUMAN insulin-like growth factor binding protein 5 191 Thyroglobulin type-1. negative regulation of insulin-like growth factor receptor signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|negative regulation of translation|signal transduction insulin-like growth factor I binding 0 Renal(323;0.0822) Epithelial(149;2.1e-06)|all cancers(144;0.000165)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942) 0.000 0.56 151 191 EPHA4 2043 broad.mit.edu 37 2 222429082 222429083 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr2:222429082_222429083insT uc002vmq.2 - 3 233_234 c.191_192insA c.(190-192)AATfs p.N64fs EPHA4_uc002vmr.2_Frame_Shift_Ins_p.N64fs|EPHA4_uc010zlm.1_Frame_Shift_Ins_p.N5fs|EPHA4_uc010zln.1_Frame_Shift_Ins_p.N64fs NM_004438 NP_004429 P54764 EPHA4_HUMAN ephrin receptor EphA4 precursor 64 Extracellular (Potential). integral to plasma membrane ATP binding|ephrin receptor activity lung(6)|large_intestine(2)|central_nervous_system(2)|urinary_tract(1)|skin(1) 12 Renal(207;0.0183) Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154) GGATTGGTGTATTTTTTTCATC 0.441 0.50 161 164 CNTN6 27255 broad.mit.edu 37 3 1445067 1445068 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr3:1445067_1445068insT uc003boz.2 + 23 3319_3320 c.3052_3053insT c.(3052-3054)ATTfs p.I1018fs CNTN6_uc011asj.1_Frame_Shift_Ins_p.I946fs|CNTN6_uc003bpa.2_Frame_Shift_Ins_p.I1018fs NM_014461 NP_055276 Q9UQ52 CNTN6_HUMAN contactin 6 precursor 1018 axon guidance|cell adhesion|central nervous system development|Notch signaling pathway anchored to membrane|plasma membrane skin(3)|lung(2)|breast(2)|pancreas(1) 8 all_cancers(2;0.000164)|all_epithelial(2;0.107) Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139) TGTCATTGTGATTTTTCACTGT 0.312 0.43 65 50 ITPR1 3708 broad.mit.edu 37 3 4738955 4738955 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr3:4738955delG uc003bqa.2 + 34 4727 c.4379delG c.(4378-4380)AGGfs p.R1460fs ITPR1_uc010hca.1_Frame_Shift_Del_p.R1445fs|ITPR1_uc011asu.1_Intron|ITPR1_uc003bqc.2_Frame_Shift_Del_p.R391fs NM_001099952 NP_001093422 Q14643 ITPR1_HUMAN inositol 1,4,5-triphosphate receptor, type 1 1469 Cytoplasmic (Potential). activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1) 21 Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982) GACATCTGCAGGGTAAGGCTT 0.353 0.46 52 44 PPARG 5468 broad.mit.edu 37 3 12458270 12458270 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr3:12458270delC uc003bwx.2 + 6 978 c.887delC c.(886-888)ACCfs p.T296fs PPARG_uc003bwr.2_Frame_Shift_Del_p.T268fs|PPARG_uc003bws.2_Frame_Shift_Del_p.T268fs|PPARG_uc003bwu.2_Frame_Shift_Del_p.T268fs|PPARG_uc003bwv.2_Intron|PPARG_uc010hea.1_RNA NM_015869 NP_056953 P37231 PPARG_HUMAN peroxisome proliferative activated receptor 296 activation of caspase activity|cell fate commitment|cell maturation|cellular response to insulin stimulus|epithelial cell differentiation|glucose homeostasis|induction of apoptosis|innate immune response|lipid homeostasis|lipoprotein transport|long-chain fatty acid transport|low-density lipoprotein particle receptor biosynthetic process|monocyte differentiation|negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|placenta development|positive regulation of fat cell differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to lipid|response to low-density lipoprotein particle stimulus|white fat cell differentiation cytosol|nucleoplasm activating transcription factor binding|arachidonic acid binding|drug binding|enzyme binding|prostaglandin receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding ovary(1)|kidney(1) 2 Atorvastatin(DB01076)|Icosapent(DB00159)|Pioglitazone(DB01132)|Rosiglitazone(DB00412)|Troglitazone(DB00197) AAACACATCACCCCCCTGCAG 0.473 0.32 80 38 TGFBR2 7048 broad.mit.edu 37 3 30691871 30691872 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr3:30691871_30691872insA uc003ceo.2 + 3 755_756 c.373_374insA c.(373-375)GAAfs p.E125fs TGFBR2_uc003cen.2_Frame_Shift_Ins_p.E150fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 125 Extracellular (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 CATTATGAAGGAAAAAAAAAAG 0.421 0.34 161 84 OXSR1 9943 broad.mit.edu 37 3 38284237 38284237 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr3:38284237delC uc003chy.2 + 12 1420 c.1078delC c.(1078-1080)CCCfs p.P360fs OXSR1_uc010hhb.2_Frame_Shift_Del_p.P294fs NM_005109 NP_005100 O95747 OXSR1_HUMAN oxidative-stress responsive 1 360 intracellular protein kinase cascade|response to oxidative stress ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity skin(1) 1 KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738) CGTTTAGTCTCCCCGAGTGAA 0.338 0.49 112 106 SMARCC1 6599 broad.mit.edu 37 3 47677567 47677568 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr3:47677567_47677568insT uc003crq.2 - 23 2553_2554 c.2435_2436insA c.(2434-2436)AATfs p.N812fs SMARCC1_uc011bbc.1_RNA|SMARCC1_uc011bbd.1_Frame_Shift_Ins_p.N703fs NM_003074 NP_003065 Q92922 SMRC1_HUMAN SWI/SNF-related matrix-associated 812 Glu-rich. chromatin remodeling|nervous system development|transcription, DNA-dependent nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex DNA binding|protein N-terminus binding|transcription coactivator activity skin(2)|lung(1) 3 BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01) 0.000 0.44 160 124 PBRM1 55193 broad.mit.edu 37 3 52621519 52621519 + Frame_Shift_Del DEL T - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr3:52621519delT uc003des.2 - 19 2985 c.2973delA c.(2971-2973)AAAfs p.K991fs PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.K991fs|PBRM1_uc003der.2_Frame_Shift_Del_p.K959fs|PBRM1_uc003det.2_Frame_Shift_Del_p.K1006fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.K1006fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.K991fs|PBRM1_uc010hmk.1_Intron|PBRM1_uc003dey.2_Intron|PBRM1_uc003dez.1_Frame_Shift_Del_p.K990fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.K903fs|PBRM1_uc003dfa.1_Frame_Shift_Del_p.K337fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 991 BAH 1. chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.48 199 186 FLNB 2317 broad.mit.edu 37 3 58107009 58107010 + Frame_Shift_Ins INS - G G EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr3:58107009_58107010insG uc003djj.2 + 20 3070_3071 c.2905_2906insG c.(2905-2907)AGGfs p.R969fs FLNB_uc010hne.2_Frame_Shift_Ins_p.R969fs|FLNB_uc003djk.2_Frame_Shift_Ins_p.R969fs|FLNB_uc010hnf.2_Frame_Shift_Ins_p.R969fs|FLNB_uc003djl.2_Frame_Shift_Ins_p.R800fs|FLNB_uc003djm.2_Frame_Shift_Ins_p.R800fs NM_001457 NP_001448 O75369 FLNB_HUMAN filamin B isoform 2 969 Filamin 8. actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction cell cortex|integral to membrane|nucleus|sarcomere actin binding breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1) 19 BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898) 0.000 0.93 38 496 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.50 15 15 FAM157A 728262 broad.mit.edu 37 3 197880183 197880184 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr3:197880183_197880184insT uc011bup.1 + 2 262_263 c.262_263insT c.(262-264)CTTfs p.L88fs NM_001145248 NP_001138720 C9JC47 F157A_HUMAN family with sequence similarity 157, member A 88 Gln-rich. 0 ACTGGATTTGCTTTTTCACCAG 0.361 0.36 7 4 GAK 2580 broad.mit.edu 37 4 861065 861066 + Frame_Shift_Ins INS - G G EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr4:861065_861066insG uc003gbm.3 - 21 2749_2750 c.2550_2551insC c.(2548-2553)CCCGGCfs p.P850fs GAK_uc003gbn.3_Frame_Shift_Ins_p.P771fs|GAK_uc010ibk.1_Frame_Shift_Ins_p.P744fs|GAK_uc010ibi.2_Frame_Shift_Ins_p.P31fs|GAK_uc010ibj.2_RNA|GAK_uc003gbl.3_Frame_Shift_Ins_p.P714fs NM_005255 NP_005246 O14976 GAK_HUMAN cyclin G associated kinase 850_851 cell cycle focal adhesion|Golgi apparatus|perinuclear region of cytoplasm ATP binding|heat shock protein binding|protein serine/threonine kinase activity lung(2)|central_nervous_system(1)|skin(1) 4 Colorectal(103;0.219) GCTGCCAGGCCGGGGGGCTCTG 0.653 0.42 7 5 FGFR3 2261 broad.mit.edu 37 4 1806180 1806181 + Frame_Shift_Ins INS - CC CC EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr4:1806180_1806181insCC uc003gdr.3 + 9 1455_1456 c.1199_1200insCC c.(1198-1200)AGCfs p.S400fs FGFR3_uc003gdu.2_Frame_Shift_Ins_p.S402fs|FGFR3_uc003gds.3_Intron|FGFR3_uc003gdq.3_Frame_Shift_Ins_p.S400fs NM_000142 NP_000133 P22607 FGFR3_HUMAN fibroblast growth factor receptor 3 isoform 1 400 Cytoplasmic (Potential). bone maturation|cell growth|insulin receptor signaling pathway|JAK-STAT cascade|MAPKKK cascade|negative regulation of developmental growth|positive regulation of cell proliferation integral to plasma membrane ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|identical protein binding urinary_tract(2177)|skin(314)|upper_aerodigestive_tract(57)|haematopoietic_and_lymphoid_tissue(24)|prostate(9)|cervix(6)|central_nervous_system(4)|large_intestine(3)|lung(3)|testis(2)|pancreas(1) 2600 Breast(71;0.212)|all_epithelial(65;0.241) all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234) Palifermin(DB00039) CGCCTGCGCAGCCCCCCCAAGA 0.629 0.19 48 11 TXK 7294 broad.mit.edu 37 4 48073655 48073656 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr4:48073655_48073656insT uc003gxx.3 - 14 1479_1480 c.1393_1394insA c.(1393-1395)ATGfs p.M465fs TXK_uc010igj.2_RNA|TXK_uc011bzj.1_Frame_Shift_Ins_p.M152fs NM_003328 NP_003319 P42681 TXK_HUMAN TXK tyrosine kinase 465 Protein kinase. cytoplasm ATP binding|non-membrane spanning protein tyrosine kinase activity 0 TTCAAAAGGCATTTTTCCTTCT 0.396 0.57 55 72 EPHA5 2044 broad.mit.edu 37 4 66280007 66280007 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr4:66280007delG uc003hcy.2 - 7 1875 c.1682delC c.(1681-1683)CCAfs p.P561fs EPHA5_uc003hcx.2_Frame_Shift_Del_p.P492fs|EPHA5_uc003hcz.2_Frame_Shift_Del_p.P561fs|EPHA5_uc011cah.1_Frame_Shift_Del_p.P561fs|EPHA5_uc011cai.1_Frame_Shift_Del_p.P561fs|EPHA5_uc003hda.2_Frame_Shift_Del_p.P561fs NM_004439 NP_004430 P54756 EPHA5_HUMAN ephrin receptor EphA5 isoform a precursor 561 Extracellular (Potential). cAMP-mediated signaling|neuron development dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum ATP binding|transmembrane-ephrin receptor activity lung(19)|stomach(2)|ovary(2)|central_nervous_system(1) 24 CTTACACACTGGGGTGGTTTC 0.453 0.35 60 32 CXCL9 4283 broad.mit.edu 37 4 76924805 76924806 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr4:76924805_76924806insT uc003hjh.1 - 4 362_363 c.323_324insA c.(322-324)AAGfs p.K108fs NM_002416 NP_002407 Q07325 CXCL9_HUMAN small inducible cytokine B9 precursor 108 cell-cell signaling|cellular defense response|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response extracellular space chemokine activity ovary(1) 1 Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934) TCAGAACTTTCTTTTTTTGATG 0.332 0.27 272 103 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.24 32 10 PPP3CA 5530 broad.mit.edu 37 4 102117101 102117102 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr4:102117101_102117102insT uc011cen.1 - 2 905_906 c.230_231insA c.(229-231)AATfs p.N77fs PPP3CA_uc003hvu.2_Frame_Shift_Ins_p.N77fs|PPP3CA_uc010ilj.2_Frame_Shift_Ins_p.N77fs|PPP3CA_uc003hvt.2_Frame_Shift_Ins_p.N64fs|PPP3CA_uc003hvs.2_Intron|PPP3CA_uc010ilk.2_Frame_Shift_Ins_p.N77fs NM_000944 NP_000935 Q08209 PP2BA_HUMAN protein phosphatase 3, catalytic subunit, alpha 77 Catalytic. protein dephosphorylation calcineurin complex|cytosol|nucleus calcium ion binding|calmodulin binding ovary(1)|skin(1) 2 OV - Ovarian serous cystadenocarcinoma(123;6.79e-08) TATCCAGCAAATTTTTTTCCTG 0.416 0.31 108 48 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.43 57 43 FBXW7 55294 broad.mit.edu 37 4 153249360 153249361 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr4:153249360_153249361insT uc003ims.2 - 9 1566_1567 c.1417_1418insA c.(1417-1419)AGAfs p.R473fs FBXW7_uc011cii.1_Frame_Shift_Ins_p.R473fs|FBXW7_uc003imt.2_Frame_Shift_Ins_p.R473fs|FBXW7_uc011cih.1_Frame_Shift_Ins_p.R297fs|FBXW7_uc003imq.2_Frame_Shift_Ins_p.R393fs|FBXW7_uc003imr.2_Frame_Shift_Ins_p.R355fs NM_033632 NP_361014 Q969H0 FBXW7_HUMAN F-box and WD repeat domain containing 7 isoform 473 WD 3. interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex protein binding|protein binding p.R473fs*4(3)|p.R473fs*25(2) haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1) 308 all_hematologic(180;0.093) Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067) TTTCCCTTACCTTTTTTCATGA 0.416 0.31 290 128 NIPBL 25836 broad.mit.edu 37 5 37000935 37000936 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr5:37000935_37000936insA uc003jkl.3 + 13 4018_4019 c.3519_3520insA c.(3517-3522)AAGAAAfs p.K1173fs NIPBL_uc003jkk.3_Frame_Shift_Ins_p.K1173fs NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 1173_1174 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) 0.000 0.34 131 66 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.44 50 39 CCNB1 891 broad.mit.edu 37 5 68464035 68464036 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr5:68464035_68464036insA uc003jvm.2 + 3 405_406 c.228_229insA c.(226-231)GATAAAfs p.D76fs CCNB1_uc011crd.1_Frame_Shift_Ins_p.D76fs|CCNB1_uc010ixb.2_Frame_Shift_Ins_p.D76fs NM_031966 NP_114172 P14635 CCNB1_HUMAN cyclin B1 76_77 Lys-rich. anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitotic cell cycle spindle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|mitotic spindle stabilization|positive regulation of attachment of spindle microtubules to kinetochore|positive regulation of mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of cyclin-dependent protein kinase activity condensed nuclear chromosome outer kinetochore|cytosol|microtubule organizing center|nucleoplasm|spindle pole 0 Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198) OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177) AAGTCATTGATAAAAAACTACC 0.342 0.50 37 37 MSH3 4437 broad.mit.edu 37 5 79965925 79965926 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr5:79965925_79965926insT uc003kgz.2 + 4 842_843 c.589_590insT c.(589-591)CTTfs p.L197fs NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 197 Interaction with EXO1. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) GGACACAACACTTTTTGATCTC 0.272 0.40 100 68 HAPLN1 1404 broad.mit.edu 37 5 82948434 82948434 + Frame_Shift_Del DEL T - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr5:82948434delT uc003kim.2 - 2 381 c.310delA c.(310-312)ACCfs p.T104fs HAPLN1_uc003kin.2_Frame_Shift_Del_p.T104fs NM_001884 NP_001875 P10915 HPLN1_HUMAN hyaluronan and proteoglycan link protein 1 104 Ig-like V-type. cell adhesion proteinaceous extracellular matrix hyaluronic acid binding p.T104fs*8(2) large_intestine(3)|ovary(1)|skin(1) 5 Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142) OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29) CCTCCATAGGTTTTTTTGTGG 0.443 0.44 154 122 CHD1 1105 broad.mit.edu 37 5 98236919 98236920 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr5:98236919_98236920insT uc003knf.2 - 5 705_706 c.557_558insA c.(556-558)AACfs p.N186fs NM_001270 NP_001261 O14646 CHD1_HUMAN chromodomain helicase DNA binding protein 1 186 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117) COAD - Colon adenocarcinoma(37;0.0717) Epirubicin(DB00445) TTTTGACTTTGTTTTTTGGCTC 0.361 0.51 140 146 APC 324 broad.mit.edu 37 5 112179138 112179140 + In_Frame_Del DEL AAG - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr5:112179138_112179140delAAG uc010jby.2 + 16 8227_8229 c.7847_7849delAAG c.(7846-7851)AAAGAA>AAA p.E2617del APC_uc011cvt.1_In_Frame_Del_p.E2599del|APC_uc003kpz.3_In_Frame_Del_p.E2617del|APC_uc003kpy.3_In_Frame_Del_p.E2617del|APC_uc010jbz.2_In_Frame_Del_p.E2334del|APC_uc010jca.2_In_Frame_Del_p.E1917del NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 2617 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.?(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) AGAAAAATAAAAGAAAATGAATT 0.360 0.46 50 42 HSPA4 3308 broad.mit.edu 37 5 132439602 132439603 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr5:132439602_132439603insA uc003kyj.2 + 18 2484_2485 c.2203_2204insA c.(2203-2205)GAAfs p.E735fs NM_002154 NP_002145 P34932 HSP74_HUMAN heat shock 70kDa protein 4 735 cellular chaperone-mediated protein complex assembly|protein import into mitochondrial outer membrane|response to unfolded protein cytoplasm|nucleus ATP binding lung(1)|breast(1) 2 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GACAAAGGTAGAAAAAAGCACA 0.436 0.45 27 22 CDKL3 51265 broad.mit.edu 37 5 133640173 133640174 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr5:133640173_133640174insA uc003kzf.3 - 11 1662_1663 c.1543_1544insT c.(1543-1545)TCCfs p.S515fs CDKL3_uc011cxm.1_Frame_Shift_Ins_p.S322fs|CDKL3_uc011cxn.1_RNA|CDKL3_uc010jdw.2_Frame_Shift_Ins_p.S122fs|CDKL3_uc011cxo.1_Frame_Shift_Ins_p.S220fs|CDKL3_uc011cxp.1_Frame_Shift_Ins_p.S220fs|CDKL3_uc011cxq.1_Frame_Shift_Ins_p.S322fs NM_001113575 NP_001107047 Q8IVW4 CDKL3_HUMAN cyclin-dependent kinase-like 3 isoform 1 515 cytoplasm ATP binding|cyclin-dependent protein kinase activity breast(1) 1 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GTCAGATCTGGAAAAATTCAGC 0.371 0.43 196 146 ADAMTS2 9509 broad.mit.edu 37 5 178559312 178559313 + Splice_Site INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr5:178559312_178559313insT uc003mjw.2 - 15 2210 c.2210_splice c.e15-1 p.G737_splice NM_014244 NP_055059 O95450 ATS2_HUMAN ADAM metallopeptidase with thrombospondin type 1 collagen catabolic process proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding large_intestine(1)|lung(1)|ovary(1)|pancreas(1) 4 all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326) all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GBM - Glioblastoma multiforme(465;0.0473) TTGATGTAACCTTTTTTTGATG 0.550 0.39 83 53 HNRNPH1 3187 broad.mit.edu 37 5 179044643 179044644 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr5:179044643_179044644insA uc003mkf.3 - 9 1034_1035 c.928_929insT c.(928-930)TCAfs p.S310fs HNRNPH1_uc011dgn.1_Frame_Shift_Ins_p.S40fs|HNRNPH1_uc003mkg.3_Frame_Shift_Ins_p.S218fs|HNRNPH1_uc003mke.3_Frame_Shift_Ins_p.S310fs|HNRNPH1_uc003mkh.3_Frame_Shift_Ins_p.S310fs NM_005520 NP_005511 P31943 HNRH1_HUMAN heterogeneous nuclear ribonucleoprotein H1 310 RRM 3.|2 X 16 AA Gly-rich approximate repeats. regulation of RNA splicing actin cytoskeleton|catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm nucleotide binding|poly(U) RNA binding|protein binding 0 GTTGAGCGGTGAAAAAAACTAC 0.381 0.40 145 97 MSH5 4439 broad.mit.edu 37 6 31710925 31710926 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr6:31710925_31710926insT uc003nwv.1 + 5 472_473 c.393_394insT c.(391-396)ATATTTfs p.I131fs MSH5_uc003nwt.1_Frame_Shift_Ins_p.I131fs|MSH5_uc003nwu.1_Frame_Shift_Ins_p.I131fs|MSH5_uc003nww.1_Frame_Shift_Ins_p.I131fs|MSH5_uc003nwx.1_Frame_Shift_Ins_p.I131fs|MSH5_uc011dof.1_5'Flank NM_172166 NP_751898 O43196 MSH5_HUMAN mutS homolog 5 isoform c 131_132 chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination synaptonemal complex ATP binding|DNA-dependent ATPase activity|mismatched DNA binding ovary(2)|breast(1) 3 CTGAAATCATATTTTTGCCAAG 0.460 0.50 16 16 RUNX2 860 broad.mit.edu 37 6 45514856 45514856 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr6:45514856delG uc011dvx.1 + 9 1590 c.1380delG c.(1378-1380)CCGfs p.P460fs RUNX2_uc011dvy.1_Frame_Shift_Del_p.P438fs|RUNX2_uc003oxt.2_Frame_Shift_Del_p.P446fs NM_001024630 NP_001019801 Q13950 RUNX2_HUMAN runt-related transcription factor 2 isoform a 460 Pro/Ser/Thr-rich.|Interaction with MYST4. negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent nucleus ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity ovary(2)|skin(1) 3 CCATGGTGCCGGGGGGAGACC 0.542 0.38 129 80 DST 667 broad.mit.edu 37 6 56362694 56362695 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr6:56362694_56362695insT uc003pdf.2 - 75 13724_13725 c.13696_13697insA c.(13696-13698)ACAfs p.T4566fs DST_uc003pcz.3_Frame_Shift_Ins_p.T4388fs|DST_uc011dxj.1_Frame_Shift_Ins_p.T4417fs|DST_uc011dxk.1_Frame_Shift_Ins_p.T4428fs|DST_uc003pcy.3_Frame_Shift_Ins_p.T4062fs NM_001144769 NP_001138241 Q03001 DYST_HUMAN dystonin isoform 2 6474 Spectrin 15. cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1) 14 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) CCTTTGTTCTGTTTTTTCCAAA 0.391 0.40 81 54 PHF3 23469 broad.mit.edu 37 6 64408416 64408417 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr6:64408416_64408417insT uc003pep.1 + 7 2929_2930 c.2903_2904insT c.(2902-2904)TCTfs p.S968fs PHF3_uc010kah.1_Frame_Shift_Ins_p.S782fs|PHF3_uc003pen.2_Frame_Shift_Ins_p.S880fs|PHF3_uc011dxs.1_Frame_Shift_Ins_p.S237fs NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 968 TFIIS central. multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) GAGCTTTTCTCTTTTTTTCGGG 0.302 0.39 87 55 AIM1 202 broad.mit.edu 37 6 107009325 107009325 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr6:107009325delG uc003prh.2 + 18 5351 c.4864delG c.(4864-4866)GGGfs p.G1622fs AIM1_uc003pri.2_Frame_Shift_Del_p.G426fs NM_001624 NP_001615 Q9Y4K1 AIM1_HUMAN absent in melanoma 1 1622 Ricin B-type lectin. sugar binding breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1) 9 Breast(9;0.0138)|all_epithelial(6;0.169) all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473) Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305) all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858) GGAGGATGTCGGGGCCGATGA 0.458 0.51 125 130 AKAP12 9590 broad.mit.edu 37 6 151673735 151673735 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr6:151673735delG uc011eep.1 + 4 4449 c.4209delG c.(4207-4209)GAGfs p.E1403fs AKAP12_uc003qoe.2_Frame_Shift_Del_p.E1403fs|AKAP12_uc003qof.2_Frame_Shift_Del_p.E1305fs|AKAP12_uc010kim.2_Intron|AKAP12_uc003qog.2_Frame_Shift_Del_p.E1298fs NM_005100 NP_005091 Q02952 AKA12_HUMAN A kinase (PRKA) anchor protein 12 isoform 1 1403 G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting cell cortex|cytoskeleton|plasma membrane adenylate cyclase binding|protein kinase A binding large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1) 8 Ovarian(120;0.125) BRCA - Breast invasive adenocarcinoma(37;0.175) OV - Ovarian serous cystadenocarcinoma(155;2.98e-11) TAGGTCAAGAGGAGGCAGTAT 0.507 0.42 84 62 PDK4 5166 broad.mit.edu 37 7 95224436 95224437 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr7:95224436_95224437insA uc003uoa.2 - 2 490_491 c.170_171insT c.(169-171)TTGfs p.L57fs PDK4_uc003unz.2_5'Flank NM_002612 NP_002603 Q16654 PDK4_HUMAN pyruvate dehydrogenase kinase 4 precursor 57 glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate mitochondrial matrix ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity 0 all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151) STAD - Stomach adenocarcinoma(171;0.0151) ATTCTTGTCGCAAAAATGCAAA 0.332 0.39 182 116 HIPK2 28996 broad.mit.edu 37 7 139416659 139416659 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr7:139416659delG uc003vvf.3 - 2 349 c.175delC c.(175-177)CTGfs p.L59fs HIPK2_uc003vvd.3_Frame_Shift_Del_p.L59fs NM_022740 NP_073577 Q9H2X6 HIPK2_HUMAN homeodomain interacting protein kinase 2 isoform 59 L -> P (in Ref. 1; AAG41236). apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction centrosome|nuclear membrane|PML body ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding ovary(3)|central_nervous_system(3)|skin(1) 7 Melanoma(164;0.205) GGCTGCGACAGGGGGATGTTC 0.562 0.46 64 55 MLL3 58508 broad.mit.edu 37 7 151874147 151874148 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr7:151874147_151874148insT uc003wla.2 - 38 8609_8610 c.8390_8391insA c.(8389-8391)AAGfs p.K2797fs MLL3_uc003wkz.2_Frame_Shift_Ins_p.K1858fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.K306fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 2797 K -> R (in Ref. 1; AAK00583). intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding p.K2797fs*26(18) large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTTCTTGTTCCTTTTTTTTTGG 0.347 0.31 367 166 WHSC1L1 54904 broad.mit.edu 37 8 38146944 38146945 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr8:38146944_38146945insT uc003xli.2 - 18 3715_3716 c.3197_3198insA c.(3196-3198)AACfs p.N1066fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.N1066fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.N1017fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 1066 Potential. cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) GTTTTCTTGAGTTTTTTTCAAT 0.371 0.53 59 66 PRKDC 5591 broad.mit.edu 37 8 48866909 48866910 + Frame_Shift_Ins INS - TT TT EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr8:48866909_48866910insTT uc003xqi.2 - 5 553_554 c.496_497insAA c.(496-498)ATAfs p.I166fs PRKDC_uc003xqj.2_Frame_Shift_Ins_p.I166fs|PRKDC_uc011ldh.1_Frame_Shift_Ins_p.I166fs NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic 166 cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) TGTATCTGGTATTTTTTTTTTC 0.267 0.35 55 29 ARFGEF1 10565 broad.mit.edu 37 8 68200287 68200288 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr8:68200287_68200288insT uc003xxo.1 - 7 1319_1320 c.929_930insA c.(928-930)AATfs p.N310fs NM_006421 NP_006412 Q9Y6D6 BIG1_HUMAN brefeldin A-inhibited guanine 310 exocytosis|regulation of ARF protein signal transduction cytoplasm ARF guanyl-nucleotide exchange factor activity|myosin binding ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1) 8 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206) ATAACACTTCATTTTTAGATAA 0.297 0.45 110 89 ARFGEF1 10565 broad.mit.edu 37 8 68211527 68211528 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr8:68211527_68211528insT uc003xxo.1 - 4 765_766 c.375_376insA c.(373-378)AAATTAfs p.K125fs NM_006421 NP_006412 Q9Y6D6 BIG1_HUMAN brefeldin A-inhibited guanine 125_126 exocytosis|regulation of ARF protein signal transduction cytoplasm ARF guanyl-nucleotide exchange factor activity|myosin binding ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1) 8 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206) CTATCAATTAATTTTTTGCCTG 0.351 0.39 97 63 WWP1 11059 broad.mit.edu 37 8 87464833 87464834 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr8:87464833_87464834insA uc003ydt.2 + 21 2599_2600 c.2319_2320insA c.(2317-2322)ACCAAAfs p.T773fs NM_007013 NP_008944 Q9H0M0 WWP1_HUMAN WW domain containing E3 ubiquitin protein ligase 773_774 HECT. central nervous system development|entry of virus into host cell|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|signal transduction cytoplasm|nucleus|plasma membrane|ubiquitin ligase complex protein binding|ubiquitin-protein ligase activity lung(1)|liver(1) 2 0.000 0.51 176 184 VPS13B 157680 broad.mit.edu 37 8 100286529 100286529 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr8:100286529delG uc003yiv.2 + 18 2730 c.2619delG c.(2617-2619)ATGfs p.M873fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.M873fs|VPS13B_uc003yiu.1_Frame_Shift_Del_p.M873fs|VPS13B_uc003yix.1_Frame_Shift_Del_p.M344fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 873 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) CTGGGACCATGGGATCAATAA 0.443 0.44 90 71 UBR5 51366 broad.mit.edu 37 8 103338834 103338835 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr8:103338834_103338835insT uc003ykr.1 - 13 1571_1572 c.1538_1539insA c.(1537-1539)AATfs p.N513fs UBR5_uc003yks.1_Frame_Shift_Ins_p.N513fs NM_015902 NP_056986 O95071 UBR5_HUMAN ubiquitin protein ligase E3 component n-recognin 513 cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus nucleus|soluble fraction protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1) 28 all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05) OV - Ovarian serous cystadenocarcinoma(57;0.000442) TAGGCTTTTTATTTTTTGCTCT 0.376 0.40 111 74 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 10 RECQL4 9401 broad.mit.edu 37 8 145741276 145741277 + Splice_Site INS - G G EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr8:145741276_145741277insG uc003zdj.2 - 6 1164 c.1132_splice c.e6-1 p.A378_splice LRRC14_uc003zdk.1_5'Flank|LRRC14_uc003zdl.1_5'Flank NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) CTTCCATGCCTGGGGGGTGCCC 0.589 0.42 34 25 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.39 415 267 TAF1L 138474 broad.mit.edu 37 9 32633583 32633584 + Frame_Shift_Ins INS - TT TT EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr9:32633583_32633584insTT uc003zrg.1 - 1 2084_2085 c.1994_1995insAA c.(1993-1995)AAGfs p.K665fs uc003zrh.1_RNA NM_153809 NP_722516 Q8IZX4 TAF1L_HUMAN TBP-associated factor RNA polymerase 1-like 665 male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent transcription factor TFIID complex DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding p.K665fs*4(2) lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1) 26 LUSC - Lung squamous cell carcinoma(29;0.0181) GBM - Glioblastoma multiforme(74;0.00301) TCATCTTGGCCTTTTTTTTGAT 0.480 0.30 236 102 OMD 4958 broad.mit.edu 37 9 95179799 95179799 + Frame_Shift_Del DEL A - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr9:95179799delA uc004asd.3 - 2 411 c.42delT c.(40-42)TTTfs p.F14fs CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron NM_005014 NP_005005 Q99983 OMD_HUMAN osteomodulin precursor 14 cell adhesion proteinaceous extracellular matrix ovary(2) 2 CTTTGACTCCAAAAAAGAAGA 0.338 0.35 143 77 PTCH1 5727 broad.mit.edu 37 9 98270530 98270530 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr9:98270530delC uc004avk.3 - 1 302 c.114delG c.(112-114)GGGfs p.G38fs PTCH1_uc010mro.2_5'Flank|PTCH1_uc010mrp.2_5'Flank|PTCH1_uc010mrq.2_5'Flank|PTCH1_uc004avl.3_5'Flank|PTCH1_uc010mrr.2_Intron|PTCH1_uc004avm.3_Intron|PTCH1_uc010mrt.1_5'Flank|PTCH1_uc010mru.1_5'Flank|PTCH1_uc004avo.2_Intron|PTCH1_uc010mrv.1_Intron|PTCH1_uc010mrw.1_Intron NM_000264 NP_000255 Q13635 PTC1_HUMAN patched isoform L 38 Cytoplasmic (Potential). embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway integral to plasma membrane hedgehog receptor activity skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1) 379 Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136) 0.000 0.36 417 239 NEK6 10783 broad.mit.edu 37 9 127110067 127110068 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr9:127110067_127110068insC uc004bog.2 + 9 946_947 c.797_798insC c.(796-798)TACfs p.Y266fs NEK6_uc004bof.2_Frame_Shift_Ins_p.Y284fs|NEK6_uc004boh.2_Frame_Shift_Ins_p.Y300fs|NEK6_uc010mwj.2_Frame_Shift_Ins_p.Y219fs|NEK6_uc010mwk.2_Frame_Shift_Ins_p.Y266fs|NEK6_uc004boi.2_Frame_Shift_Ins_p.Y266fs NM_014397 NP_055212 Q9HC98 NEK6_HUMAN NIMA-related kinase 6 isoform 2 266 Protein kinase. apoptosis|cell division|chromosome segregation|mitosis|peptidyl-serine phosphorylation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of mitotic metaphase/anaphase transition cytoplasm|nucleus ATP binding|kinesin binding|magnesium ion binding|protein kinase binding|protein serine/threonine kinase activity|signal transducer activity p.Y259C(1) ovary(2)|kidney(1) 3 CAGTGTGACTACCCCCCACTCC 0.619 0.32 108 50 FNBP1 23048 broad.mit.edu 37 9 132687242 132687243 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr9:132687242_132687243insT uc004byw.1 - 9 1202_1203 c.983_984insA c.(982-984)AATfs p.N328fs FNBP1_uc011mbv.1_Frame_Shift_Ins_p.N328fs|FNBP1_uc011mbw.1_Frame_Shift_Ins_p.N328fs|FNBP1_uc004bza.2_Frame_Shift_Ins_p.N328fs|FNBP1_uc004byz.1_Frame_Shift_Ins_p.N328fs|FNBP1_uc004byx.1_Frame_Shift_Ins_p.N249fs|FNBP1_uc004byy.1_Frame_Shift_Ins_p.N249fs NM_015033 NP_055848 Q96RU3 FNBP1_HUMAN formin binding protein 1 328 Interaction with microtubules (By similarity).|Required for self-association and induction of membrane tubulation. endocytosis cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane identical protein binding|lipid binding 0 Ovarian(14;0.000536) GBM - Glioblastoma multiforme(294;0.0378) TCAGTACCTTATTTTTTTTGAT 0.381 0.46 122 105 NUP214 8021 broad.mit.edu 37 9 134007992 134007993 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr9:134007992_134007993insA uc004cag.2 + 6 784_785 c.673_674insA c.(673-675)GAAfs p.E225fs NUP214_uc004cah.2_Frame_Shift_Ins_p.E225fs|NUP214_uc004caf.1_Frame_Shift_Ins_p.E225fs NM_005085 NP_005076 P35658 NU214_HUMAN nucleoporin 214kDa 225 carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear pore|nucleoplasm protein binding breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1) 16 all_hematologic(7;0.0028) Myeloproliferative disorder(178;0.204) OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256) GACTTTGCAGGAAAAAAAAGTC 0.361 0.33 133 65 TSC1 7248 broad.mit.edu 37 9 135772950 135772951 + Frame_Shift_Ins INS - T T rs118203724 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr9:135772950_135772951insT uc004cca.2 - 21 2906_2907 c.2672_2673insA c.(2671-2673)AACfs p.N891fs TSC1_uc004ccb.3_Frame_Shift_Ins_p.N890fs|TSC1_uc011mcq.1_Frame_Shift_Ins_p.N840fs|TSC1_uc011mcr.1_Intron NM_000368 NP_000359 Q92574 TSC1_HUMAN tuberous sclerosis 1 protein isoform 1 891 Potential. activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus cell cortex|lamellipodium|membrane|TSC1-TSC2 complex chaperone binding|protein N-terminus binding p.?(1) lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1) 14 OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06) CATGGCTTCTGTTTTTTTCTAG 0.381 0.47 130 117 MAMDC4 158056 broad.mit.edu 37 9 139751265 139751266 + Frame_Shift_Ins INS - G G EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr9:139751265_139751266insG uc004cjs.2 + 15 1874_1875 c.1824_1825insG c.(1822-1827)CACACCfs p.H608fs MAMDC4_uc011mej.1_5'UTR NM_206920 NP_996803 Q6UXC1 AEGP_HUMAN apical early endosomal glycoprotein precursor 687_688 MAM 4.|Extracellular (Potential). protein transport integral to membrane p.H608Y(1) breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1) 7 all_cancers(76;0.0763)|all_epithelial(76;0.198) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171) ACCACGACCACACCACAGGCCA 0.639 0.53 7 8 CUBN 8029 broad.mit.edu 37 10 16949568 16949569 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr10:16949568_16949569insA uc001ioo.2 - 49 7695_7696 c.7643_7644insT c.(7642-7644)TTCfs p.F2548fs CUBN_uc009xjq.1_Intron|CUBN_uc009xjr.1_Intron NM_001081 NP_001072 O60494 CUBN_HUMAN cubilin precursor 2548 CUB 18. cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1) 19 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) ATCCATCCGTGAAAAAAATGAC 0.421 0.47 99 89 CACNB2 783 broad.mit.edu 37 10 18828598 18828599 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr10:18828598_18828599insA uc001ipr.2 + 14 1988_1989 c.1928_1929insA c.(1927-1929)TCAfs p.S643fs CACNB2_uc009xjz.1_Frame_Shift_Ins_p.S393fs|CACNB2_uc001ips.2_Frame_Shift_Ins_p.S619fs|CACNB2_uc001ipt.2_Frame_Shift_Ins_p.S605fs|CACNB2_uc001ipu.2_Frame_Shift_Ins_p.S615fs|CACNB2_uc001ipv.2_Frame_Shift_Ins_p.S591fs|CACNB2_uc009xka.1_Frame_Shift_Ins_p.S577fs|CACNB2_uc001ipw.2_Frame_Shift_Ins_p.S550fs|CACNB2_uc001ipx.2_Frame_Shift_Ins_p.S588fs|CACNB2_uc001ipz.2_Frame_Shift_Ins_p.S565fs|CACNB2_uc001ipy.2_Frame_Shift_Ins_p.S589fs|CACNB2_uc010qco.1_Frame_Shift_Ins_p.S557fs|CACNB2_uc001iqa.2_Frame_Shift_Ins_p.S595fs|NSUN6_uc001iqb.2_Intron NM_201596 NP_963890 Q08289 CACB2_HUMAN calcium channel, voltage-dependent, beta 2 643 axon guidance|neuromuscular junction development integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity large_intestine(1)|central_nervous_system(1)|skin(1) 3 Magnesium Sulfate(DB00653)|Verapamil(DB00661) GAAGTGATATCAAAAAAACGGA 0.450 0.45 74 60 MYO3A 53904 broad.mit.edu 37 10 26462759 26462760 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr10:26462759_26462760insA uc001isn.2 + 30 3926_3927 c.3566_3567insA c.(3565-3567)CCAfs p.P1189fs MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron NM_017433 NP_059129 Q8NEV4 MYO3A_HUMAN myosin IIIA 1189 protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception cytoplasm|filamentous actin|filopodium|myosin complex actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 18 TATCAGACTCCAAAAAAAATGA 0.401 0.45 114 93 ERCC6 2074 broad.mit.edu 37 10 50681033 50681033 + Frame_Shift_Del DEL G - - rs2229760 byFrequency;by1000genomes EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr10:50681033delG uc001jhs.3 - 15 2905 c.2751delC c.(2749-2751)GGCfs p.G917fs ERCC6_uc009xod.2_Frame_Shift_Del_p.G77fs|ERCC6_uc010qgr.1_Frame_Shift_Del_p.G287fs|ERCC6_uc001jhr.3_Frame_Shift_Del_p.G285fs NM_000124 NP_000115 Q03468 ERCC6_HUMAN excision repair cross-complementing rodent 917 Helicase C-terminal. base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair nucleolus|soluble fraction|transcription elongation factor complex ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1) 16 CACCTAAGCCGCCCACCCGCG 0.473 0.59 73 105 TET1 80312 broad.mit.edu 37 10 70332161 70332162 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr10:70332161_70332162insA uc001jok.3 + 2 571_572 c.66_67insA c.(64-69)AAGAAAfs p.K22fs NM_030625 NP_085128 Q8NFU7 TET1_HUMAN CXXC finger 6 22_23 DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding ovary(5)|lung(2)|prostate(1)|breast(1) 9 ACAAAAAAAAGAAAAACAGCCA 0.411 0.48 11 10 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.79 5 19 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 312 101 BIRC2 329 broad.mit.edu 37 11 102239231 102239232 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr11:102239231_102239232insA uc001pgy.2 + 6 2717_2718 c.1318_1319insA c.(1318-1320)GAAfs p.E440fs BIRC2_uc010ruq.1_Frame_Shift_Ins_p.E391fs|BIRC2_uc010rur.1_Frame_Shift_Ins_p.E440fs NM_001166 NP_001157 Q13490 BIRC2_HUMAN baculoviral IAP repeat-containing protein 2 440 cell surface receptor linked signaling pathway|cellular component disassembly involved in apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteasomal ubiquitin-dependent protein catabolic process|protein polyubiquitination CD40 receptor complex|cytosol|internal side of plasma membrane protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding ovary(1)|lung(1)|breast(1) 3 all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227) Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093) Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151) BRCA - Breast invasive adenocarcinoma(274;0.0144) TGCTGAAGATGAAAAAAGAGAA 0.386 0.47 117 102 NPAT 4863 broad.mit.edu 37 11 108032273 108032274 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr11:108032273_108032274insT uc001pjz.3 - 17 3641_3642 c.3539_3540insA c.(3538-3540)AATfs p.N1180fs NPAT_uc010rvv.1_Frame_Shift_Ins_p.N236fs NM_002519 NP_002510 Q14207 NPAT_HUMAN nuclear protein, ataxia-telangiectasia locus 1180 positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle Cajal body protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity ovary(2) 2 all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116) AATTTTCTGGATTTTTCTGTCT 0.361 0.41 271 189 MLL 4297 broad.mit.edu 37 11 118307394 118307394 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr11:118307394delC uc001pta.2 + 1 190 c.167delC c.(166-168)TCCfs p.S56fs MLL_uc001ptb.2_Frame_Shift_Del_p.S56fs|uc001psy.2_5'Flank|MLL_uc001psz.1_Frame_Shift_Del_p.S56fs NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 56 Ala/Gly/Ser-rich. apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) 0.000 0.35 418 222 GRAMD1B 57476 broad.mit.edu 37 11 123474220 123474221 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr11:123474220_123474221insC uc001pyx.2 + 8 1037_1038 c.708_709insC c.(706-711)GTGCCCfs p.V236fs GRAMD1B_uc001pyw.2_Frame_Shift_Ins_p.V243fs|GRAMD1B_uc010rzw.1_Frame_Shift_Ins_p.V196fs|GRAMD1B_uc010rzx.1_Frame_Shift_Ins_p.V196fs|GRAMD1B_uc009zbe.1_Frame_Shift_Ins_p.V232fs NM_020716 NP_065767 Q3KR37 GRM1B_HUMAN GRAM domain containing 1B 236_237 integral to membrane ovary(1) 1 Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394) AGGACTACGTGCCCCCTGACGA 0.446 0.45 96 77 KDM5A 5927 broad.mit.edu 37 12 402030 402031 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:402030_402031insT uc001qif.1 - 27 5123_5124 c.4760_4761insA c.(4759-4761)AAGfs p.K1587fs KDM5A_uc001qie.1_Frame_Shift_Ins_p.K1592fs NM_001042603 NP_001036068 P29375 KDM5A_HUMAN retinoblastoma binding protein 2 isoform 1 1587 Lys-rich. chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter cytoplasm|nucleolus DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding skin(2)|ovary(1) 3 TGTCCAGCACCTTTTTCTCTCT 0.465 0.47 96 84 CHD4 1108 broad.mit.edu 37 12 6701671 6701672 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:6701671_6701672insT uc001qpo.2 - 19 2999_3000 c.2835_2836insA c.(2833-2838)AAACTGfs p.K945fs CHD4_uc001qpn.2_Frame_Shift_Ins_p.K938fs|CHD4_uc001qpp.2_Frame_Shift_Ins_p.K942fs NM_001273 NP_001264 Q14839 CHD4_HUMAN chromodomain helicase DNA binding protein 4 945_946 chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent microtubule organizing center|NuRD complex ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding central_nervous_system(2) 2 ATGTCATGCAGTTTTTTTATCT 0.460 0.38 10 6 ITPR2 3709 broad.mit.edu 37 12 26568292 26568292 + Frame_Shift_Del DEL A - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:26568292delA uc001rhg.2 - 51 7667 c.7250delT c.(7249-7251)TTGfs p.L2417fs ITPR2_uc009zjg.1_Frame_Shift_Del_p.L568fs NM_002223 NP_002214 Q14571 ITPR2_HUMAN inositol 1,4,5-triphosphate receptor, type 2 2417 Extracellular (Potential). activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 14 Colorectal(261;0.0847) GTCATCCTTCAAAAAAAGGAA 0.408 0.37 89 53 WNT1 7471 broad.mit.edu 37 12 49375164 49375164 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:49375164delC uc001rsu.2 + 4 1052 c.854delC c.(853-855)TCCfs p.S285fs NM_005430 NP_005421 P04628 WNT1_HUMAN wingless-type MMTV integration site family, 285 brain segmentation|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|central nervous system morphogenesis|cerebellum formation|dermatome development|diencephalon development|embryonic axis specification|forebrain anterior/posterior pattern formation|fourth ventricle development|hemopoietic stem cell proliferation|hepatocyte differentiation|inner ear morphogenesis|mesoderm morphogenesis|midbrain development|midbrain-hindbrain boundary maturation during brain development|negative regulation of cell-cell adhesion|negative regulation of cell-substrate adhesion|negative regulation of DNA damage checkpoint|negative regulation of fat cell differentiation|neuron fate determination|positive regulation of fibroblast proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of lamellipodium assembly|positive regulation of Notch signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to wounding|signal transduction in response to DNA damage|Spemann organizer formation|T cell differentiation in thymus|Wnt receptor signaling pathway, calcium modulating pathway early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix cytokine activity|frizzled-2 binding|transcription regulatory region DNA binding kidney(1) 1 BRCA - Breast invasive adenocarcinoma(357;0.244) 0.000 0.45 790 634 MAP3K12 7786 broad.mit.edu 37 12 53877256 53877256 + Frame_Shift_Del DEL A - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:53877256delA uc001sdm.1 - 11 1489 c.1391delT c.(1390-1392)TTAfs p.L464fs MAP3K12_uc001sdn.1_Frame_Shift_Del_p.L497fs NM_006301 NP_006292 Q12852 M3K12_HUMAN mitogen-activated protein kinase kinase kinase 464 Leucine-zipper 2. histone phosphorylation|JNK cascade|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation cytosol|membrane fraction|plasma membrane ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding lung(2)|ovary(1)|breast(1)|skin(1) 5 CCTCCGCTCTAAAGCTTGCTC 0.572 0.48 89 82 ITGA7 3679 broad.mit.edu 37 12 56091730 56091731 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:56091730_56091731insT uc001shh.2 - 8 1504_1505 c.1284_1285insA c.(1282-1287)AAACCTfs p.K428fs ITGA7_uc001shg.2_Frame_Shift_Ins_p.K424fs|ITGA7_uc010sps.1_Frame_Shift_Ins_p.K331fs|ITGA7_uc009znw.2_5'Flank|ITGA7_uc009znx.2_Frame_Shift_Ins_p.K311fs NM_001144996 NP_001138468 Q13683 ITA7_HUMAN integrin alpha 7 isoform 1 precursor 468_469 Extracellular (Potential). cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development|regulation of cell shape integrin complex receptor activity ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1) 5 ACCTGTGAAGGTTTGGCGACAA 0.594 0.41 63 44 IRAK3 11213 broad.mit.edu 37 12 66605315 66605316 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:66605315_66605316insT uc001sth.2 + 5 628_629 c.526_527insT c.(526-528)ATTfs p.I176fs IRAK3_uc010ssy.1_Frame_Shift_Ins_p.I115fs NM_007199 NP_009130 Q9Y616 IRAK3_HUMAN interleukin-1 receptor-associated kinase 3 176 ATP (By similarity).|Protein kinase. interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|negative regulation of innate immune response|negative regulation of interleukin-12 production|negative regulation of interleukin-6 production|negative regulation of macrophage cytokine production|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein catabolic process|negative regulation of protein complex disassembly|negative regulation of toll-like receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of macrophage tolerance induction|positive regulation of NF-kappaB transcription factor activity|response to exogenous dsRNA|response to lipopolysaccharide|response to peptidoglycan cytoplasm|nucleus ATP binding|magnesium ion binding|protein heterodimerization activity|protein homodimerization activity|protein serine/threonine kinase activity lung(3)|ovary(2)|breast(2)|central_nervous_system(1) 8 GBM - Glioblastoma multiforme(28;0.0203) AGAAGGAGAGATTTTTGAGGTA 0.351 0.47 98 87 LGR5 8549 broad.mit.edu 37 12 71977821 71977822 + Frame_Shift_Ins INS - T T rs138932490 byFrequency EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:71977821_71977822insT uc001swl.2 + 18 2079_2080 c.2031_2032insT c.(2029-2034)CCATTTfs p.P677fs LGR5_uc001swm.2_Frame_Shift_Ins_p.P653fs|LGR5_uc001swn.1_Intron NM_003667 NP_003658 O75473 LGR5_HUMAN leucine-rich repeat-containing G protein-coupled 677_678 Cytoplasmic (Potential). integral to plasma membrane protein-hormone receptor activity lung(4)|skin(3)|ovary(1)|pancreas(1) 9 CGAAAGCTCCATTTTCTAGCCT 0.500 0.46 63 53 NAV3 89795 broad.mit.edu 37 12 78443882 78443883 + Splice_Site INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:78443882_78443883insT uc001syp.2 + 10 2305 c.2132_splice c.e10+1 p.S711_splice NAV3_uc001syo.2_Splice_Site_p.S711_splice|NAV3_uc010sub.1_Splice_Site_p.S211_splice NM_014903 NP_055718 Q8IVL0 NAV3_HUMAN neuron navigator 3 nuclear outer membrane ATP binding|nucleoside-triphosphatase activity large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 17 TAAGCCACAGGTTTTTTTCAAT 0.332 0.31 92 41 SCYL2 55681 broad.mit.edu 37 12 100723039 100723040 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:100723039_100723040insA uc001thn.2 + 13 1753_1754 c.1703_1704insA c.(1702-1704)GGAfs p.G568fs SCYL2_uc001thm.1_Frame_Shift_Ins_p.G568fs NM_017988 NP_060458 Q6P3W7 SCYL2_HUMAN SCY1-like 2 protein 568 endosome to lysosome transport|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of clathrin-mediated endocytosis|positive regulation of receptor internalization clathrin-coated vesicle|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm ATP binding|protein kinase activity|receptor binding lung(3)|ovary(2)|skin(1) 6 CAGCTGGCCGGAAAAGTGTTGC 0.332 0.42 203 149 UBE3B 89910 broad.mit.edu 37 12 109939223 109939223 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:109939223delG uc001top.2 + 13 1769 c.1166delG c.(1165-1167)TGGfs p.W389fs UBE3B_uc001toq.2_Frame_Shift_Del_p.W389fs|UBE3B_uc001too.1_RNA|UBE3B_uc009zvj.1_Frame_Shift_Del_p.W389fs NM_130466 NP_569733 Q7Z3V4 UBE3B_HUMAN ubiquitin protein ligase E3B 389 protein ubiquitination involved in ubiquitin-dependent protein catabolic process intracellular ubiquitin-protein ligase activity ovary(2)|lung(2) 4 CAGTTCTTGTGGGGGGTGCCT 0.552 0.52 122 132 CIT 11113 broad.mit.edu 37 12 120287990 120287991 + Frame_Shift_Ins INS - T T rs142505542 by1000genomes EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:120287990_120287991insT uc001txi.1 - 5 556_557 c.503_504insA c.(502-504)AATfs p.N168fs CIT_uc001txj.1_Frame_Shift_Ins_p.N168fs NM_007174 NP_009105 O14578 CTRO_HUMAN citron 168 Protein kinase. intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) GATAAAGGTGATTTTTGTCCTG 0.431 0.53 116 131 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.32 49 23 EP400 57634 broad.mit.edu 37 12 132547136 132547138 + In_Frame_Del DEL CAA - - rs60608267;rs111782215 byFrequency EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr12:132547136_132547138delCAA uc001ujn.2 + 46 8259_8261 c.8224_8226delCAA c.(8224-8226)CAAdel p.Q2748del EP400_uc001ujl.2_In_Frame_Del_p.Q2747del|EP400_uc001ujm.2_In_Frame_Del_p.Q2667del|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784 Poly-Gln.|Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) gcagcagcagcaacagcagcagc 0.325 0.33 57 28 ZMYM2 7750 broad.mit.edu 37 13 20580534 20580535 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr13:20580534_20580535insA uc001umr.2 + 7 1618_1619 c.1320_1321insA c.(1318-1323)TTTAAAfs p.F440fs ZMYM2_uc001umq.2_Frame_Shift_Ins_p.F353fs|ZMYM2_uc001ums.2_Frame_Shift_Ins_p.F440fs|ZMYM2_uc001umt.2_Frame_Shift_Ins_p.F440fs|ZMYM2_uc010tco.1_Intron NM_003453 NP_003444 Q9UBW7 ZMYM2_HUMAN zinc finger protein 198 440_441 regulation of transcription, DNA-dependent|transcription, DNA-dependent PML body ubiquitin conjugating enzyme binding|zinc ion binding lung(3)|ovary(2)|prostate(1) 6 all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856) AAGTCAGCTTTAAAAATATGAC 0.322 0.34 115 59 BRCA2 675 broad.mit.edu 37 13 32953632 32953633 + Frame_Shift_Ins INS - A A rs80359144 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr13:32953632_32953633insA uc001uub.1 + 22 9160_9161 c.8933_8934insA c.(8932-8934)TCAfs p.S2978fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 2978 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) GTAAGCTATTCAAAAAAAGAAA 0.322 0.33 68 34 BRCA2 675 broad.mit.edu 37 13 32954022 32954023 + Frame_Shift_Ins INS - A A rs67201695 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr13:32954022_32954023insA uc001uub.1 + 23 9316_9317 c.9089_9090insA c.(9088-9090)ACAfs p.T3030fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 3030 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) TTAGCAGCGACAAAAAAAACTC 0.312 0.23 92 28 CSNK1A1L 122011 broad.mit.edu 37 13 37678703 37678704 + Frame_Shift_Ins INS - T T rs56252523 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr13:37678703_37678704insT uc001uwm.1 - 1 1098_1099 c.690_691insA c.(688-693)AAACAAfs p.K230fs NM_145203 NP_660204 Q8N752 KC1AL_HUMAN casein kinase 1, alpha 1-like 230_231 Protein kinase. Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity large_intestine(1) 1 Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109) all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407) TCATATTTTTGTTTTTTTGTCA 0.426 0.67 64 128 ERCC5 2073 broad.mit.edu 37 13 103504577 103504578 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr13:103504577_103504578insT uc001vpw.2 + 2 641_642 c.198_199insT c.(196-201)TTATTTfs p.L66fs ERCC5_uc001vpu.1_Frame_Shift_Ins_p.L520fs|ERCC5_uc010tjb.1_Frame_Shift_Ins_p.L66fs|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_5'UTR NM_000123 NP_000114 P28715 ERCC5_HUMAN XPG-complementing protein 66_67 N-domain. negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection nucleoplasm bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding ovary(4)|lung(1)|central_nervous_system(1)|skin(1) 7 all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211) GCAAACTCTTATTTTTTCGAAT 0.381 0.36 158 87 CCNB1IP1 57820 broad.mit.edu 37 14 20779825 20779826 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr14:20779825_20779826insA uc001vwv.2 - 7 1366_1367 c.717_718insT c.(715-720)TTTGCGfs p.F239fs CCNB1IP1_uc001vww.2_Frame_Shift_Ins_p.F239fs|CCNB1IP1_uc001vwx.2_Frame_Shift_Ins_p.F239fs|CCNB1IP1_uc001vwy.2_Frame_Shift_Ins_p.F239fs|CCNB1IP1_uc001vwz.2_Frame_Shift_Ins_p.F239fs NM_182851 NP_878271 Q9NPC3 CIP1_HUMAN cyclin B1 interacting protein 1 isoform 3 239_240 chromosome|nucleus ligase activity|metal ion binding|protein binding HMGA2/CCNB1IP1(2) soft_tissue(2)|ovary(1) 3 all_cancers(95;0.00092) all_lung(585;0.235) Epithelial(56;8.86e-07)|all cancers(55;4.98e-06) GBM - Glioblastoma multiforme(265;0.0164) GGAGAACCCGCAAAAAATGGTC 0.450 0.45 122 100 CHD8 57680 broad.mit.edu 37 14 21853994 21853995 + In_Frame_Ins INS - TGGTGATGG TGGTGATGG EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr14:21853994_21853995insTGGTGATGG uc001was.1 - 38 6780_6781 c.6686_6687insCCATCACCA c.(6685-6687)CAT>CACCATCACCAT p.2229_2229H>HHHH CHD8_uc001war.1_In_Frame_Ins_p.2125_2125H>HHHH|SUPT16H_uc001wao.2_5'Flank|SUPT16H_uc001wap.2_5'Flank|SUPT16H_uc001waq.1_5'Flank NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 2508 His-rich. ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) TCAAGCCTGGAtggtgatggtg 0.391 0.29 32 13 CHD8 57680 broad.mit.edu 37 14 21884030 21884031 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr14:21884030_21884031insT uc001was.1 - 6 1009_1010 c.915_916insA c.(913-918)AAATATfs p.K305fs CHD8_uc001war.1_Frame_Shift_Ins_p.K201fs NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 584_585 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) TCCTCTGTATATTTTTTTCGCT 0.396 0.42 174 127 Unknown 0 broad.mit.edu 37 14 23574095 23574096 + In_Frame_Ins INS - GCA GCA rs139523267;rs142154188 by1000genomes EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr14:23574095_23574096insGCA uc010aki.1 - 1 82_83 c.34_35insTGC c.(34-36)CCG>CTGCCG p.11_12insL Homo sapiens cDNA clone IMAGE:40134016. GACTAGTGgcggcagcagcagc 0.446 0.36 9 5 AKAP6 9472 broad.mit.edu 37 14 33015028 33015029 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr14:33015028_33015029insA uc001wrq.2 + 4 1339_1340 c.1169_1170insA c.(1168-1170)CCAfs p.P390fs AKAP6_uc010aml.2_Frame_Shift_Ins_p.P387fs NM_004274 NP_004265 Q13023 AKAP6_HUMAN A-kinase anchor protein 6 390 protein targeting calcium channel complex|nuclear membrane|sarcoplasmic reticulum protein kinase A binding|receptor binding breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1) 21 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) GBM - Glioblastoma multiforme(265;0.019) CCTACATTGCCAAAAAGAGGAC 0.416 0.49 155 146 FANCM 57697 broad.mit.edu 37 14 45644555 45644556 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr14:45644555_45644556insA uc001wwd.3 + 14 2697_2698 c.2598_2599insA c.(2596-2601)CTTAAAfs p.L866fs FANCM_uc010anf.2_Frame_Shift_Ins_p.L840fs|FANCM_uc001wwe.3_Frame_Shift_Ins_p.L402fs|FANCM_uc010ang.2_Frame_Shift_Ins_p.L80fs NM_020937 NP_065988 Q8IYD8 FANCM_HUMAN Fanconi anemia, complementation group M 866_867 DNA repair Fanconi anaemia nuclear complex ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding ovary(3)|lung(2)|breast(2) 7 AAGATCAGCTTAAAAAAGAAAA 0.262 0.42 100 71 KTN1 3895 broad.mit.edu 37 14 56096770 56096771 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr14:56096770_56096771insA uc001xcb.2 + 8 1478_1479 c.1176_1177insA c.(1174-1179)AACAAAfs p.N392fs KTN1_uc001xce.2_Frame_Shift_Ins_p.N392fs|KTN1_uc001xcc.2_Frame_Shift_Ins_p.N392fs|KTN1_uc001xcd.2_Frame_Shift_Ins_p.N392fs|KTN1_uc010trb.1_Frame_Shift_Ins_p.N392fs|KTN1_uc001xcf.1_Frame_Shift_Ins_p.N392fs NM_182926 NP_891556 Q86UP2 KTN1_HUMAN kinectin 1 isoform a 392_393 Lumenal (Potential).|Potential. microtubule-based movement endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction breast(3)|ovary(2)|lung(1)|central_nervous_system(1) 7 TATTTCAAAACAAAATACATGT 0.292 0.46 106 92 PRKCH 5583 broad.mit.edu 37 14 61952228 61952229 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr14:61952228_61952229insT uc001xfn.2 + 10 1592_1593 c.1287_1288insT c.(1285-1290)CTGTTTfs p.L429fs PRKCH_uc010tsa.1_Frame_Shift_Ins_p.L268fs|PRKCH_uc010tsb.1_5'UTR NM_006255 NP_006246 P24723 KPCL_HUMAN protein kinase C, eta 429_430 Protein kinase. intracellular signal transduction|platelet activation cytosol|plasma membrane ATP binding|enzyme binding|metal ion binding|protein kinase C activity ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1) 6 OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182) AGGATCGTCTGTTTTTTGTGAT 0.460 0.43 182 135 TRIP11 9321 broad.mit.edu 37 14 92466341 92466342 + Frame_Shift_Ins INS - T T rs146690807 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr14:92466341_92466342insT uc001xzy.2 - 12 5456_5457 c.4668_4669insA c.(4666-4671)AAACAAfs p.K1556fs TRIP11_uc010auf.1_Frame_Shift_Ins_p.K1292fs NM_004239 NP_004230 Q15643 TRIPB_HUMAN thyroid hormone receptor interactor 11 1556_1557 Potential. transcription from RNA polymerase II promoter cytoskeleton|Golgi apparatus|membrane|nucleus protein binding|transcription coactivator activity p.Q1557K(1) ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1) 13 COAD - Colon adenocarcinoma(157;0.223) TTTTCCATTTGTTTTTGTTTCA 0.337 0.52 142 155 DICER1 23405 broad.mit.edu 37 14 95562249 95562250 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr14:95562249_95562250insA uc001ydw.2 - 24 5189_5190 c.5007_5008insT c.(5005-5010)TTTGAAfs p.F1669fs DICER1_uc010avh.1_Frame_Shift_Ins_p.F567fs|DICER1_uc001ydv.2_Frame_Shift_Ins_p.F1659fs|DICER1_uc001ydx.2_Frame_Shift_Ins_p.F1669fs|DICER1_uc001ydy.1_Frame_Shift_Ins_p.F521fs NM_030621 NP_085124 Q9UPY3 DICER_HUMAN dicer1 1669_1670 RNase III 2. negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference cytosol|RNA-induced silencing complex ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity skin(2)|ovary(1)|pancreas(1)|lung(1) 5 all_cancers(154;0.0621)|all_epithelial(191;0.223) Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215) ATTTTCTTTTCAAAATTTTCAA 0.386 0.38 351 216 TTBK2 146057 broad.mit.edu 37 15 43044816 43044817 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr15:43044816_43044817insT uc001zqo.2 - 14 3066_3067 c.2627_2628insA c.(2626-2628)AATfs p.N876fs TTBK2_uc010bcy.2_Frame_Shift_Ins_p.N807fs NM_173500 NP_775771 Q6IQ55 TTBK2_HUMAN tau tubulin kinase 2 876 cell death ATP binding|protein serine/threonine kinase activity p.N876fs*2(1) ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1) 7 all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216) GBM - Glioblastoma multiforme(94;3.23e-07) TAGATATCTTATTTTTTTGCAT 0.406 0.35 213 115 UNC13C 440279 broad.mit.edu 37 15 54825249 54825250 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr15:54825249_54825250insT uc002ack.2 + 24 5681_5682 c.5681_5682insT c.(5680-5682)GATfs p.D1894fs NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 1894 MHD2. exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) TCTCTTATGGATTTTTTGGACA 0.342 0.26 57 20 NEDD4 4734 broad.mit.edu 37 15 56125274 56125275 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr15:56125274_56125275insT uc002adj.2 - 23 4015_4016 c.3715_3716insA c.(3715-3717)AGAfs p.R1239fs NEDD4_uc002adl.2_Frame_Shift_Ins_p.R820fs|NEDD4_uc002adi.2_Frame_Shift_Ins_p.R1167fs|NEDD4_uc010ugj.1_Frame_Shift_Ins_p.R1223fs|NEDD4_uc010bfm.2_Frame_Shift_Ins_p.R1222fs|NEDD4_uc002adk.2_RNA NM_198400 NP_006145 P46934 NEDD4_HUMAN neural precursor cell expressed, developmentally 1239 HECT. development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity skin(2)|ovary(1)|breast(1) 4 all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113) 0.000 0.23 197 59 NEDD4 4734 broad.mit.edu 37 15 56132708 56132709 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr15:56132708_56132709insA uc002adj.2 - 17 3524_3525 c.3224_3225insT c.(3223-3225)TTCfs p.F1075fs NEDD4_uc002adl.2_Frame_Shift_Ins_p.F656fs|NEDD4_uc002adi.2_Frame_Shift_Ins_p.F1003fs|NEDD4_uc010ugj.1_Frame_Shift_Ins_p.F1059fs|NEDD4_uc010bfm.2_Frame_Shift_Ins_p.F1058fs|NEDD4_uc002adk.2_RNA NM_198400 NP_006145 P46934 NEDD4_HUMAN neural precursor cell expressed, developmentally 1075 HECT. development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity skin(2)|ovary(1)|breast(1) 4 all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113) 0.000 0.70 55 126 PSMA4 5685 broad.mit.edu 37 15 78834955 78834956 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr15:78834955_78834956insT uc002bdu.3 + 4 335_336 c.177_178insT c.(175-180)GTCTTTfs p.V59fs PSMA4_uc010blf.2_Frame_Shift_Ins_p.V59fs|PSMA4_uc002bdv.3_Intron|PSMA4_uc002bdw.3_Frame_Shift_Ins_p.V35fs|PSMA4_uc002bdx.3_Intron NM_002789 NP_002780 P25789 PSA4_HUMAN proteasome alpha 4 subunit isoform 1 59_60 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction cytoplasm|nucleus|proteasome core complex, alpha-subunit complex identical protein binding|threonine-type endopeptidase activity 0 TTGATGAAGTCTTTTTTTCTGA 0.347 0.29 149 62 BLM 641 broad.mit.edu 37 15 91304138 91304139 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr15:91304138_91304139insA uc002bpr.2 + 7 1632_1633 c.1535_1536insA c.(1534-1536)GGAfs p.G512fs BLM_uc010uqh.1_Frame_Shift_Ins_p.G512fs|BLM_uc010uqi.1_Frame_Shift_Ins_p.G137fs|BLM_uc010bnx.2_Frame_Shift_Ins_p.G512fs|BLM_uc002bps.1_Frame_Shift_Ins_p.G74fs NM_000057 NP_000048 P54132 BLM_HUMAN Bloom syndrome protein 512 double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray cytoplasm|lateral element|nuclear matrix|nucleolus|PML body ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding ovary(3)|skin(2)|breast(1) 6 Lung NSC(78;0.0875)|all_lung(78;0.109) Lung(145;0.189) CCAAGACTAGGAAAAAAAAATG 0.371 0.52 59 65 IL21R 50615 broad.mit.edu 37 16 27460529 27460530 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr16:27460529_27460530insC uc002doq.1 + 9 1775_1776 c.1542_1543insC c.(1540-1545)GGACCCfs p.G514fs IL21R_uc002dor.1_Frame_Shift_Ins_p.G514fs|IL21R_uc002dos.1_Frame_Shift_Ins_p.G514fs|uc002dot.2_RNA NM_181078 NP_851564 Q9HBE5 IL21R_HUMAN interleukin 21 receptor precursor 514_515 Cytoplasmic (Potential). natural killer cell activation integral to membrane interleukin-21 receptor activity ovary(2)|lung(1)|breast(1) 4 GGGACGAAGGACCCCCCCGGAG 0.639 0.37 38 22 ZNF668 79759 broad.mit.edu 37 16 31073419 31073420 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr16:31073419_31073420insC uc010caf.2 - 3 1186_1187 c.829_830insG c.(829-831)GAGfs p.E277fs ZNF668_uc002eao.2_Frame_Shift_Ins_p.E277fs NM_024706 NP_078982 Q96K58 ZN668_HUMAN zinc finger protein 668 277 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(4) 4 0.000 0.47 590 518 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.12 109 15 CHD9 80205 broad.mit.edu 37 16 53243678 53243679 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr16:53243678_53243679insA uc002ehb.2 + 2 1901_1902 c.1737_1738insA c.(1735-1740)AGCAAAfs p.S579fs CHD9_uc002egy.2_Frame_Shift_Ins_p.S579fs|CHD9_uc002egz.1_Frame_Shift_Ins_p.S579fs|CHD9_uc002eha.1_Frame_Shift_Ins_p.S579fs|CHD9_uc002ehc.2_Frame_Shift_Ins_p.S579fs|CHD9_uc002ehd.2_Frame_Shift_Ins_p.S105fs NM_025134 NP_079410 Q3L8U1 CHD9_HUMAN chromodomain helicase DNA binding protein 9 579_580 Lys-rich. cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleoplasm ATP binding|DNA binding|helicase activity|protein binding lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1) 7 all_cancers(37;0.0212) ACAAAGACAGCAAAAAAACAAA 0.332 0.54 6 7 ADAMTS18 170692 broad.mit.edu 37 16 77356310 77356311 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr16:77356310_77356311insA uc002ffc.3 - 14 2504_2505 c.2085_2086insT c.(2083-2088)TTTGCAfs p.F695fs ADAMTS18_uc010chc.1_Frame_Shift_Ins_p.F283fs|ADAMTS18_uc002ffe.1_Frame_Shift_Ins_p.F391fs NM_199355 NP_955387 Q8TE60 ATS18_HUMAN ADAM metallopeptidase with thrombospondin type 1 695_696 Cys-rich. proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding p.A696fs*18(2) large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1) 18 CCGGACATTGCAAAAAAAAATT 0.406 0.43 155 119 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 24 324 FLCN 201163 broad.mit.edu 37 17 17131218 17131219 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:17131218_17131219insT uc002gra.3 - 4 737_738 c.233_234insA c.(232-234)AAGfs p.K78fs PLD6_uc010cpn.2_Intron|FLCN_uc002grb.3_Frame_Shift_Ins_p.K78fs|FLCN_uc002grc.2_Frame_Shift_Ins_p.K78fs NM_144997 NP_659434 Q8NFG4 FLCN_HUMAN folliculin isoform 1 78 regulation of protein phosphorylation cytoplasm|nucleus|plasma membrane protein binding thyroid(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1) 3 ACATGTCCGACTTTTTGGGCCC 0.614 0.48 66 61 KSR1 8844 broad.mit.edu 37 17 25910015 25910016 + Frame_Shift_Ins INS - CC CC EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:25910015_25910016insCC uc010crg.2 + 5 898_899 c.453_454insCC c.(451-456)ACGCCCfs p.T151fs KSR1_uc002gzj.1_RNA NM_014238 NP_055053 Q8IVT5 KSR1_HUMAN kinase suppressor of ras 286_287 Poly-Pro. Ras protein signal transduction cytoplasm|membrane ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity lung(3)|central_nervous_system(1) 4 Lung NSC(42;0.00836) BRCA - Breast invasive adenocarcinoma(3;0.00122) UCEC - Uterine corpus endometrioid carcinoma (53;0.168) CACCACGGACGCCCCCCCCACC 0.678 0.23 30 9 NOS2 4843 broad.mit.edu 37 17 26091135 26091136 + Frame_Shift_Ins INS - G G EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:26091135_26091136insG uc002gzu.2 - 21 2727_2728 c.2463_2464insC c.(2461-2466)CCCTGCfs p.P821fs NM_000625 NP_000616 P35228 NOS2_HUMAN nitric oxide synthase 2A 821_822 FAD-binding FR-type. arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process cytosol|nucleus arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding skin(2)|ovary(1)|breast(1) 4 Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155) CTGAGTGAGCAGGGGGGCAGCC 0.599 0.33 8 4 TAOK1 57551 broad.mit.edu 37 17 27844497 27844498 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:27844497_27844498insA uc002hdz.1 + 16 1925_1926 c.1731_1732insA c.(1729-1734)CCCAAAfs p.P577fs TAOK1_uc010wbe.1_Intron|TAOK1_uc010wbf.1_Frame_Shift_Ins_p.P577fs NM_020791 NP_065842 Q7L7X3 TAOK1_HUMAN TAO kinase 1 577_578 Potential. mitotic prometaphase cytosol|intracellular membrane-bounded organelle ATP binding|protein serine/threonine kinase activity upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1) 4 Colorectal(6;0.198) AGAGTACCCCCAAAAAAGAAAA 0.307 0.42 33 24 TAOK1 57551 broad.mit.edu 37 17 27869780 27869780 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:27869780delG uc002hdz.1 + 20 2940 c.2746delG c.(2746-2748)GGGfs p.G916fs TAOK1_uc010wbe.1_Frame_Shift_Del_p.G768fs|TAOK1_uc010wbf.1_Frame_Shift_Del_p.G916fs NM_020791 NP_065842 Q7L7X3 TAOK1_HUMAN TAO kinase 1 916 mitotic prometaphase cytosol|intracellular membrane-bounded organelle ATP binding|protein serine/threonine kinase activity upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1) 4 Colorectal(6;0.198) CAACCCTACTGGGGGTCCAGG 0.572 0.45 59 49 NF1 4763 broad.mit.edu 37 17 29560074 29560075 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:29560074_29560075insA uc002hgg.2 + 27 3884_3885 c.3551_3552insA c.(3550-3552)ACAfs p.T1184fs NF1_uc002hgh.2_Frame_Shift_Ins_p.T1184fs|NF1_uc010csn.1_Frame_Shift_Ins_p.T1044fs|NF1_uc002hgi.1_Frame_Shift_Ins_p.T217fs NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 1184 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) GAAGTTCTGACAAAAATCCTTC 0.421 0.40 97 65 CCL18 6362 broad.mit.edu 37 17 34397892 34397892 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:34397892delC uc002hku.2 + 2 213 c.153delC c.(151-153)AGCfs p.S51fs NM_002988 NP_002979 P55774 CCL18_HUMAN small inducible cytokine A18 precursor 51 cell-cell signaling|chemotaxis|immune response|inflammatory response|response to biotic stimulus|signal transduction extracellular space chemokine activity 0 Ovarian(249;0.17) UCEC - Uterine corpus endometrioid carcinoma (308;0.0185) CTGAAACCAGCCCCCAGTGCC 0.552 0.65 7 13 HNF1B 6928 broad.mit.edu 37 17 36091625 36091625 + Frame_Shift_Del DEL G - - rs138986885 byFrequency EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:36091625delG uc002hok.3 - 4 1227 c.1006delC c.(1006-1008)CACfs p.H336fs HNF1B_uc010wdi.1_Frame_Shift_Del_p.H310fs|HNF1B_uc010cve.1_Frame_Shift_Del_p.H144fs NM_000458 NP_000449 P35680 HNF1B_HUMAN hepatocyte nuclear factor 1-beta isoform 1 336 endocrine pancreas development|genitalia development|kidney development|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric nephron tubule development|regulation of pronephros size nucleus DNA binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity ovary(3) 3 Breast(25;0.00765)|Ovarian(249;0.15) STAD - Stomach adenocarcinoma(1;0.0142) GGCTGGTGGTGGGGGGAGCCG 0.607 0.56 7 9 CDK12 51755 broad.mit.edu 37 17 37646831 37646831 + Frame_Shift_Del DEL A - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:37646831delA uc010cvv.2 + 3 2539 c.1953delA c.(1951-1953)TCAfs p.S651fs CDK12_uc010wef.1_Frame_Shift_Del_p.S650fs|CDK12_uc002hrw.3_Frame_Shift_Del_p.S651fs NM_016507 NP_057591 Q9NYV4 CDK12_HUMAN Cdc2-related kinase, arginine/serine-rich 651 mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1) 19 CTCTTCCTTCAAAACCTGTGA 0.403 0.22 50 14 COL1A1 1277 broad.mit.edu 37 17 48266300 48266301 + Frame_Shift_Ins INS - G G rs72653168 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:48266300_48266301insG uc002iqm.2 - 41 3134_3135 c.3008_3009insC c.(3007-3009)CCTfs p.P1003fs NM_000088 NP_000079 P02452 CO1A1_HUMAN alpha 1 type I collagen preproprotein 1003 Triple-helical region. axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception collagen type I|extracellular space|plasma membrane identical protein binding|platelet-derived growth factor binding COL1A1/PDGFB(372) soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1) 382 Collagenase(DB00048)|Palifermin(DB00039) 0.000 0.48 436 401 TRIM37 4591 broad.mit.edu 37 17 57134361 57134362 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:57134361_57134362insT uc002iwy.3 - 13 1517_1518 c.1073_1074insA c.(1072-1074)AATfs p.N358fs TRIM37_uc002iwz.3_Frame_Shift_Ins_p.N358fs|TRIM37_uc002ixa.3_Frame_Shift_Ins_p.N236fs|TRIM37_uc010woc.1_Frame_Shift_Ins_p.N324fs NM_001005207 NP_001005207 O94972 TRI37_HUMAN tripartite motif-containing 37 protein 358 MATH. perinuclear region of cytoplasm|peroxisome ligase activity|protein binding|zinc ion binding lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1) 7 Medulloblastoma(34;0.0922)|all_neural(34;0.101) CTCGAATGATATTTTTTGTAGG 0.342 0.44 89 69 CLTC 1213 broad.mit.edu 37 17 57760011 57760012 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:57760011_57760012insA uc002ixq.1 + 23 4065_4066 c.3622_3623insA c.(3622-3624)GAAfs p.E1208fs CLTC_uc002ixp.2_Frame_Shift_Ins_p.E1208fs|CLTC_uc002ixr.1_Frame_Shift_Ins_p.E1212fs NM_004859 NP_004850 Q00610 CLH1_HUMAN clathrin heavy chain 1 1208 Heavy chain arm.|Proximal segment. axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle protein binding|structural molecule activity CLTC/ALK(44)|CLTC/TFE3(2) haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1) 48 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) TTGTTATGATGAAAAAATGTAT 0.376 0.49 80 77 P4HB 5034 broad.mit.edu 37 17 79803763 79803764 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:79803763_79803764insT uc002kbn.1 - 8 1357_1358 c.1160_1161insA c.(1159-1161)AACfs p.N387fs P4HB_uc002kbl.1_Frame_Shift_Ins_p.N64fs|P4HB_uc002kbm.1_Frame_Shift_Ins_p.N64fs NM_000918 NP_000909 P07237 PDIA1_HUMAN prolyl 4-hydroxylase, beta subunit precursor 387 Thioredoxin 2. cell redox homeostasis|glycerol ether metabolic process|lipid metabolic process|lipoprotein metabolic process|peptidyl-proline hydroxylation to 4-hydroxy-L-proline cell surface|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|extracellular region|melanosome|plasma membrane electron carrier activity|procollagen-proline 4-dioxygenase activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity 0 all_neural(118;0.0878)|Ovarian(332;0.12) BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509) CCACAAAGACGTTTTTTTTCTC 0.559 0.48 81 74 P4HB 5034 broad.mit.edu 37 17 79813123 79813124 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr17:79813123_79813124insA uc002kbn.1 - 4 715_716 c.518_519insT c.(517-519)TTGfs p.L173fs P4HB_uc002kbm.1_5'UTR NM_000918 NP_000909 P07237 PDIA1_HUMAN prolyl 4-hydroxylase, beta subunit precursor 173 cell redox homeostasis|glycerol ether metabolic process|lipid metabolic process|lipoprotein metabolic process|peptidyl-proline hydroxylation to 4-hydroxy-L-proline cell surface|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|extracellular region|melanosome|plasma membrane electron carrier activity|procollagen-proline 4-dioxygenase activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity 0 all_neural(118;0.0878)|Ovarian(332;0.12) BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509) CTGCTGCCTGCAAAAACTGCTT 0.530 0.44 101 79 LAMA1 284217 broad.mit.edu 37 18 7038884 7038885 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr18:7038884_7038885insT uc002knm.2 - 11 1581_1582 c.1487_1488insA c.(1486-1488)AACfs p.N496fs LAMA1_uc010wzj.1_5'UTR NM_005559 NP_005550 P25391 LAMA1_HUMAN laminin, alpha 1 precursor 496 Laminin EGF-like 4. axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development extracellular space|laminin-1 complex|laminin-3 complex extracellular matrix structural constituent|receptor binding ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1) 21 Colorectal(10;0.172) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) AGCCCCGGGGGTTTTTTTCCTT 0.535 0.43 43 33 ROCK1 6093 broad.mit.edu 37 18 18629104 18629105 + Frame_Shift_Ins INS - A A rs35810558 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr18:18629104_18629105insA uc002kte.2 - 4 1303_1304 c.362_363insT c.(361-363)TTCfs p.F121fs NM_005406 NP_005397 Q13464 ROCK1_HUMAN Rho-associated, coiled-coil containing protein 121 Protein kinase. actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction centriole|cytosol|Golgi membrane ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity lung(2)|breast(2)|central_nervous_system(1) 5 Melanoma(1;0.165) TTTCTTCCCAGAAAAAAGCAGA 0.361 0.35 162 89 RBBP8 5932 broad.mit.edu 37 18 20573182 20573182 + Frame_Shift_Del DEL T - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr18:20573182delT uc002ktw.2 + 11 1723 c.1392delT c.(1390-1392)TCTfs p.S464fs RBBP8_uc002kty.2_Frame_Shift_Del_p.S464fs|RBBP8_uc002ktz.2_Frame_Shift_Del_p.S464fs|RBBP8_uc002kua.2_Frame_Shift_Del_p.S464fs|RBBP8_uc002ktx.1_Frame_Shift_Del_p.S464fs NM_002894 NP_002885 Q99708 COM1_HUMAN retinoblastoma binding protein 8 isoform a 464 cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter nucleus damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity ovary(1)|lung(1)|skin(1) 3 all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19) OV - Ovarian serous cystadenocarcinoma(1;0.00196) CCCAAGCTTCTTTTGATAAAG 0.403 0.55 59 72 TCF3 6929 broad.mit.edu 37 19 1620978 1620979 + Frame_Shift_Ins INS - G G EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr19:1620978_1620979insG uc002ltr.2 - 13 1148_1149 c.1081_1082insC c.(1081-1083)CAGfs p.Q361fs TCF3_uc002lto.2_Frame_Shift_Ins_p.Q123fs|TCF3_uc002ltt.3_Frame_Shift_Ins_p.Q361fs|TCF3_uc002ltq.2_Frame_Shift_Ins_p.Q310fs|TCF3_uc002lts.1_Frame_Shift_Ins_p.Q277fs|TCF3_uc010dso.1_5'Flank NM_003200 NP_003191 P15923 TFE2_HUMAN transcription factor 3 isoform E12 361 B cell lineage commitment|B cell lineage commitment|G1 phase of mitotic cell cycle|immunoglobulin V(D)J recombination|muscle cell differentiation|positive regulation of B cell proliferation|positive regulation of cell cycle|positive regulation of muscle cell differentiation|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter cytoplasm|nucleus|protein complex|transcription factor complex bHLH transcription factor binding|DNA binding|E-box binding|identical protein binding|mitogen-activated protein kinase kinase kinase binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|vitamin D response element binding lung(2)|breast(2)|ovary(1)|large_intestine(1)|skin(1) 7 Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.22 499 143 NOTCH3 4854 broad.mit.edu 37 19 15296411 15296412 + Frame_Shift_Ins INS - T T EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr19:15296411_15296412insT uc002nan.2 - 13 2106_2107 c.2030_2031insA c.(2029-2031)AATfs p.N677fs NOTCH3_uc002nao.1_Frame_Shift_Ins_p.N677fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 677 Extracellular (Potential).|EGF-like 17; calcium-binding (Potential). Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.45 626 507 NOTCH3 4854 broad.mit.edu 37 19 15302820 15302821 + Frame_Shift_Ins INS - C C rs61336539 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr19:15302820_15302821insC uc002nan.2 - 4 705_706 c.629_630insG c.(628-630)GGCfs p.G210fs NOTCH3_uc002nao.1_Frame_Shift_Ins_p.G210fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 210 Extracellular (Potential).|EGF-like 5. Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.53 456 516 CPAMD8 27151 broad.mit.edu 37 19 17007429 17007429 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr19:17007429delC uc002nfb.2 - 40 5286 c.5254delG c.(5254-5256)GCGfs p.A1752fs CPAMD8_uc010xpj.1_Intron|CPAMD8_uc002nfd.1_Frame_Shift_Del_p.A217fs NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 1705 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 0.000 0.51 164 174 CRTC1 23373 broad.mit.edu 37 19 18879553 18879554 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr19:18879553_18879554insC uc002nkb.3 + 10 1358_1359 c.1270_1271insC c.(1270-1272)TCCfs p.S424fs CRTC1_uc010ebv.2_Frame_Shift_Ins_p.S440fs|CRTC1_uc010ebw.2_Frame_Shift_Ins_p.S289fs|CRTC1_uc002nkc.3_Intron NM_015321 NP_056136 Q6UUV9 CRTC1_HUMAN mucoepidermoid carcinoma translocated 1 isoform 424 interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus|plasma membrane cAMP response element binding protein binding|protein binding CRTC1/MAML2(516) salivary_gland(474)|lung(35)|thyroid(4)|breast(3)|skin(2)|ovary(1) 519 TCTCCCCCAGTCCCCCCCAGAG 0.649 0.40 6 4 MAP3K10 4294 broad.mit.edu 37 19 40719469 40719469 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr19:40719469delC uc002ona.2 + 9 2171 c.1883delC c.(1882-1884)TCCfs p.S628fs MAP3K10_uc002onb.2_Frame_Shift_Del_p.S17fs NM_002446 NP_002437 Q02779 M3K10_HUMAN mitogen-activated protein kinase kinase kinase 628 activation of JUN kinase activity|induction of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of JNK cascade|protein autophosphorylation|smoothened signaling pathway cytoplasm ATP binding|bHLH transcription factor binding|JUN kinase kinase kinase activity|protein homodimerization activity|transcription corepressor activity ovary(2)|lung(2)|skin(1)|pancreas(1) 6 0.000 0.42 320 231 CYP2B6 1555 broad.mit.edu 37 19 41518327 41518327 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr19:41518327delC uc002opr.1 + 7 1096 c.1089delC c.(1087-1089)CTCfs p.L363fs CYP2A7_uc002opo.2_Intron|CYP2B6_uc010xvu.1_Frame_Shift_Del_p.L163fs NM_000767 NP_000758 P20813 CP2B6_HUMAN cytochrome P450, family 2, subfamily B, 363 cellular ketone metabolic process|exogenous drug catabolic process|steroid metabolic process|xenobiotic metabolic process endoplasmic reticulum membrane|microsome aromatase activity|electron carrier activity|heme binding|oxygen binding ovary(1)|skin(1) 2 LUSC - Lung squamous cell carcinoma(20;0.00322) Bupropion(DB01156)|Butalbital(DB00241)|Carbamazepine(DB00564)|Clopidogrel(DB00758)|Cyclophosphamide(DB00531)|Efavirenz(DB00625)|Ifosfamide(DB01181)|Memantine(DB01043)|Meperidine(DB00454)|Mephenytoin(DB00532)|Methadone(DB00333)|Methylphenobarbital(DB00849)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicotine(DB00184)|Orphenadrine(DB01173)|Phenytoin(DB00252)|Propofol(DB00818)|Ritonavir(DB00503)|Selegiline(DB01037)|Sertraline(DB01104)|Ticlopidine(DB00208)|Troleandomycin(DB01361) CCGACCTTCTCCCCATGGGTG 0.547 0.46 153 129 MARK4 57787 broad.mit.edu 37 19 45805663 45805664 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr19:45805663_45805664insC uc002pbb.1 + 17 1959_1960 c.1954_1955insC c.(1954-1956)GCCfs p.A652fs MARK4_uc002pba.1_Frame_Shift_Ins_p.P678fs Q96L34 MARK4_HUMAN RecName: Full=MAP/microtubule affinity-regulating kinase 4; EC=2.7.11.1; AltName: Full=MAP/microtubule affinity-regulating kinase-like 1; 652 microtubule bundle formation|nervous system development|positive regulation of programmed cell death centrosome|neuron projection ATP binding|gamma-tubulin binding|microtubule binding|protein serine/threonine kinase activity|tau-protein kinase activity|ubiquitin binding central_nervous_system(2)|large_intestine(1) 3 all_neural(266;0.224)|Ovarian(192;0.231) OV - Ovarian serous cystadenocarcinoma(262;0.0102) AACGGAAACCGCCCCCCGGCTG 0.639 0.37 39 23 LMTK3 114783 broad.mit.edu 37 19 49002806 49002807 + Frame_Shift_Ins INS - GG GG EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr19:49002806_49002807insGG uc002pjk.2 - 12 1606_1607 c.1606_1607insCC c.(1606-1608)CACfs p.H536fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.43 407 313 NR1H2 7376 broad.mit.edu 37 19 50880996 50880997 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr19:50880996_50880997insC uc010enw.2 + 4 326_327 c.50_51insC c.(49-51)GGCfs p.G17fs NR1H2_uc002prv.3_RNA|NR1H2_uc002prz.3_Frame_Shift_Ins_p.G17fs|NR1H2_uc002psa.3_Frame_Shift_Ins_p.G17fs NM_007121 NP_009052 P55055 NR1H2_HUMAN nuclear receptor subfamily 1, group H, member 2 17 negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of pinocytosis|negative regulation of transcription, DNA-dependent|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor cytoplasm|nucleoplasm sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding 0 all_neural(266;0.057) OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186) 0.000 0.23 727 219 BRSK1 84446 broad.mit.edu 37 19 55823384 55823385 + Frame_Shift_Ins INS - C C rs17855468 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr19:55823384_55823385insC uc002qkg.2 + 19 2562_2563 c.2285_2286insC c.(2284-2286)GGCfs p.G762fs BRSK1_uc002qkf.2_Frame_Shift_Ins_p.G778fs|BRSK1_uc002qkh.2_Frame_Shift_Ins_p.G457fs NM_032430 NP_115806 Q8TDC3 BRSK1_HUMAN BR serine/threonine kinase 1 762 G -> A (in Ref. 9; AAH16681). establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV cell junction|cytoplasm|nucleus magnesium ion binding|protein serine/threonine kinase activity ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1) 6 Renal(1328;0.245) BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.0474) 0.000 0.33 711 351 ZNF334 55713 broad.mit.edu 37 20 45130774 45130774 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr20:45130774delC uc002xsc.2 - 5 1388 c.1204delG c.(1204-1206)GAAfs p.E402fs ZNF334_uc002xsa.2_Frame_Shift_Del_p.E425fs|ZNF334_uc002xsb.2_Frame_Shift_Del_p.E364fs|ZNF334_uc002xsd.2_Frame_Shift_Del_p.E364fs|ZNF334_uc010ghl.2_Frame_Shift_Del_p.E401fs NM_018102 NP_060572 Q9HCZ1 ZN334_HUMAN zinc finger protein 334 isoform a 402 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1)|pancreas(1) 2 Myeloproliferative disorder(115;0.0122) TAGGGTTTTTCCCCTGTGTGA 0.433 0.54 6 7 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 51 7 COL18A1 80781 broad.mit.edu 37 21 46911182 46911183 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr21:46911182_46911183insC uc011afs.1 + 21 3377_3378 c.3356_3357insC c.(3355-3357)GGCfs p.G1119fs COL18A1_uc002zhg.2_Frame_Shift_Ins_p.G704fs|COL18A1_uc002zhi.2_Frame_Shift_Ins_p.G884fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1119 Triple-helical region 4 (COL4). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 73 479 COL18A1 80781 broad.mit.edu 37 21 46917558 46917559 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr21:46917558_46917559insC uc011afs.1 + 31 3932_3933 c.3911_3912insC c.(3910-3912)GGCfs p.G1304fs COL18A1_uc002zhg.2_Frame_Shift_Ins_p.G889fs|COL18A1_uc002zhi.2_Frame_Shift_Ins_p.G1069fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1304 Triple-helical region 7 (COL7). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.52 361 384 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 59 329 RGL4 266747 broad.mit.edu 37 22 24037167 24037168 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr22:24037167_24037168insA uc002zxn.2 + 6 2217_2218 c.1047_1048insA c.(1045-1050)TGCAAAfs p.C349fs LOC91316_uc002zxh.3_5'Flank|LOC91316_uc002zxi.3_5'Flank|LOC91316_uc002zxk.3_RNA|LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_RNA|LOC91316_uc002zxm.3_RNA|RGL4_uc002zxo.2_Frame_Shift_Ins_p.C349fs|RGL4_uc002zxp.1_Frame_Shift_Ins_p.C213fs|RGL4_uc002zxq.2_Frame_Shift_Ins_p.C213fs NM_153615 NP_705843 Q8IZJ4 RGDSR_HUMAN ral guanine nucleotide dissociation 349_350 Ras-GEF. small GTPase mediated signal transduction cytoplasmic membrane-bounded vesicle guanyl-nucleotide exchange factor activity ovary(1) 1 AAGAACTCTGCAAAAAAGACAC 0.441 0.38 13 8 MYO18B 84700 broad.mit.edu 37 22 26164426 26164427 + Frame_Shift_Ins INS - C C EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr22:26164426_26164427insC uc003abz.1 + 4 793_794 c.543_544insC c.(541-546)TCTCCCfs p.S181fs MYO18B_uc003aca.1_Frame_Shift_Ins_p.S62fs|MYO18B_uc010guy.1_Frame_Shift_Ins_p.S62fs|MYO18B_uc010guz.1_Frame_Shift_Ins_p.S62fs|MYO18B_uc011aka.1_5'UTR|MYO18B_uc011akb.1_5'Flank NM_032608 NP_115997 Q8IUG5 MY18B_HUMAN myosin XVIIIB 181_182 nucleus|sarcomere|unconventional myosin complex actin binding|ATP binding|motor activity ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2) 12 0.000 0.22 858 239 TIMP3 7078 broad.mit.edu 37 22 33245479 33245479 + Frame_Shift_Del DEL G - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr22:33245479delG uc003anb.2 + 2 1348 c.162delG c.(160-162)GAGfs p.E54fs SYN3_uc003amx.2_Intron|SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron NM_000362 NP_000353 P35625 TIMP3_HUMAN tissue inhibitor of metalloproteinase 3 54 NTR. negative regulation of membrane protein ectodomain proteolysis|visual perception metal ion binding|metalloendopeptidase inhibitor activity|protein binding lung(1) 1 0.000 0.39 343 218 SOX10 6663 broad.mit.edu 37 22 38369707 38369708 + Frame_Shift_Ins INS - G G EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr22:38369707_38369708insG uc003aun.1 - 4 1473_1474 c.1195_1196insC c.(1195-1197)CAGfs p.Q399fs POLR2F_uc003aum.2_Intron|SOX10_uc003auo.1_Frame_Shift_Ins_p.Q399fs NM_006941 NP_008872 P56693 SOX10_HUMAN SRY (sex determining region Y)-box 10 399 cytoplasm|nucleus DNA binding|identical protein binding|transcription coactivator activity 0 Melanoma(58;0.045) 0.000 0.34 1059 534 MKL1 57591 broad.mit.edu 37 22 40814900 40814900 + Frame_Shift_Del DEL C - - EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr22:40814900delC uc003ayv.1 - 9 1749 c.1542delG c.(1540-1542)GGGfs p.G514fs MKL1_uc003ayw.1_Frame_Shift_Del_p.G514fs|MKL1_uc010gye.1_Frame_Shift_Del_p.G514fs|MKL1_uc010gyf.1_Frame_Shift_Del_p.G464fs NM_020831 NP_065882 Q969V6 MKL1_HUMAN megakaryoblastic leukemia 1 protein 514 positive regulation of transcription from RNA polymerase II promoter|smooth muscle cell differentiation|transcription, DNA-dependent cytoplasm|nucleus actin monomer binding|leucine zipper domain binding|nucleic acid binding|transcription coactivator activity ovary(2)|lung(1)|breast(1)|central_nervous_system(1) 5 GCTCCGCCCGCCCCCCAGGGC 0.677 0.73 3 8 PPARA 5465 broad.mit.edu 37 22 46631062 46631063 + Frame_Shift_Ins INS - A A EN_ENDOMETRIUM NA EN_ENDOMETRIUM NA g.chr22:46631062_46631063insA uc003bgw.1 + 9 1458_1459 c.1192_1193insA c.(1192-1194)GAAfs p.E398fs PPARA_uc003bgx.1_Frame_Shift_Ins_p.E398fs|PPARA_uc010hab.1_Frame_Shift_Ins_p.E398fs|PPARA_uc003bhb.1_Frame_Shift_Ins_p.E398fs|PPARA_uc010hac.1_Frame_Shift_Ins_p.E195fs NM_005036 NP_005027 Q07869 PPARA_HUMAN peroxisome proliferative activated receptor, 398 Ligand-binding.|Required for heterodimerization with RXRA. fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fatty acid beta-oxidation|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor nucleoplasm drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|ubiquitin conjugating enzyme binding|zinc ion binding ovary(1)|central_nervous_system(1) 2 Ovarian(80;0.00965)|all_neural(38;0.0416) UCEC - Uterine corpus endometrioid carcinoma (28;0.00522) Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641) AGGACACATTGAAAAAATGCAG 0.446 0.43 24 18 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 5 64 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 266 59 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.40 6 4 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 56 70 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.23 36 11 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.23 27 8 HNRNPA2B1 3181 broad.mit.edu 37 7 26236457 26236458 + In_Frame_Ins INS - AAA AAA ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chr7:26236457_26236458insAAA uc003sxr.3 - 5 696_697 c.480_481insTTT c.(478-483)insTTT p.160_161insF HNRNPA2B1_uc003sxs.3_In_Frame_Ins_p.148_149insF NM_031243 NP_112533 P22626 ROA2_HUMAN heterogeneous nuclear ribonucleoprotein A2/B1 160_161 RRM 2. RNA transport catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm nucleotide binding|protein binding|protein binding|RNA binding|single-stranded telomeric DNA binding ovary(1)|central_nervous_system(1)|skin(1) 3 TCATGGTCATCAAAAGTAACAA 0.332 0.35 92 50 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 280 104 HSP90AA1 3320 broad.mit.edu 37 14 102551075 102551077 + In_Frame_Del DEL CTC - - ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chr14:102551075_102551077delCTC uc001yku.3 - 5 1112_1114 c.922_924delGAG c.(922-924)GAGdel p.E308del HSP90AA1_uc001ykv.3_In_Frame_Del_p.E430del|HSP90AA1_uc001ykw.1_In_Frame_Del_p.E129del|HSP90AA1_uc001ykx.1_In_Frame_Del_p.E297del NM_005348 NP_005339 P07900 HS90A_HUMAN heat shock 90kDa protein 1, alpha isoform 2 308 axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction cytosol|melanosome|plasma membrane ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding ovary(2)|central_nervous_system(2)|prostate(1)|lung(1)|breast(1) 7 Rifabutin(DB00615) ATTCTCCGTACTCCTCATTAGTA 0.374 0.43 178 133 NF1 4763 broad.mit.edu 37 17 29557945 29557946 + Splice_Site INS - A A ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chr17:29557945_29557946insA uc002hgg.2 + 24 3530 c.3197_splice c.e24+2 p.R1066_splice NF1_uc002hgh.2_Splice_Site_p.R1066_splice|NF1_uc010csn.1_Splice_Site_p.R926_splice|NF1_uc002hgi.1_Splice_Site_p.R99_splice NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) TCTTACAAGGTAAAAAAAGAAT 0.332 0.35 34 18 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.84 6 31 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.22 64 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 119 340 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ESS1_ENDOMETRIUM NA ESS1_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 68 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 31 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.44 183 146 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 1.00 0 13 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.38 20 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 60 89 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 14 35 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.34 29 15 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.60 4 6 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 2 23 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.21 197 52 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 421 160 PML 5371 broad.mit.edu 37 15 74290458 74290458 + Frame_Shift_Del DEL G - - F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:74290458delG uc002awv.2 + 2 383 c.243delG c.(241-243)CTGfs p.L81fs PML_uc002awm.2_Frame_Shift_Del_p.L81fs|PML_uc002awl.2_Frame_Shift_Del_p.L81fs|PML_uc002awj.1_Frame_Shift_Del_p.L81fs|PML_uc002awk.2_Frame_Shift_Del_p.L81fs|PML_uc002awn.2_Frame_Shift_Del_p.L81fs|PML_uc002awo.2_Frame_Shift_Del_p.L81fs|PML_uc002awp.2_Frame_Shift_Del_p.L81fs|PML_uc002awq.2_Frame_Shift_Del_p.L81fs|PML_uc002awr.2_Frame_Shift_Del_p.L81fs|PML_uc002aws.2_Frame_Shift_Del_p.L81fs|PML_uc002awt.2_Frame_Shift_Del_p.L81fs|PML_uc002awu.2_Frame_Shift_Del_p.L81fs|PML_uc010ule.1_Intron|PML_uc002aww.1_5'UTR NM_033238 NP_150241 P29590 PML_HUMAN promyelocytic leukemia protein isoform 1 81 RING-type. cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding central_nervous_system(2)|kidney(2)|breast(1) 5 CAGGATGCCTGGAGGCGTCGG 0.642 0.56 7 9 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 48 364 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.47 60 53 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 598 2163 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 62 KDM6A 7403 broad.mit.edu 37 X 44732828 44732836 + In_Frame_Del DEL GCCGCCGCT - - FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chrX:44732828_44732836delGCCGCCGCT uc004dge.3 + 1 406_414 c.31_39delGCCGCCGCT c.(31-39)GCCGCCGCTdel p.AAA14del KDM6A_uc010nhk.2_In_Frame_Del_p.AAA14del|KDM6A_uc011mkz.1_In_Frame_Del_p.AAA14del|KDM6A_uc011mla.1_In_Frame_Del_p.AAA14del|KDM6A_uc011mlb.1_In_Frame_Del_p.AAA14del|KDM6A_uc011mlc.1_5'UTR NM_021140 NP_066963 O15550 KDM6A_HUMAN ubiquitously transcribed tetratricopeptide 14_16 Poly-Ala. histone H3-K4 methylation metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen p.0(8)|p.0?(6) kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2) 84 0.000 0.15 76 13 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.58 25 35 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.62 5 8 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.17 33 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.31 22 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 54 55 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.91 5 51 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.18 83 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 215 56 FRS2 10818 broad.mit.edu 37 12 69968154 69968155 + In_Frame_Ins INS - GTGCCC GTGCCC FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chr12:69968154_69968155insGTGCCC uc001suy.2 + 10 1456_1457 c.946_947insGTGCCC c.(946-948)AGT>AGTGCCCGT p.316_317insAR FRS2_uc001suz.2_In_Frame_Ins_p.316_317insAR|FRS2_uc009zrj.2_In_Frame_Ins_p.316_317insAR|FRS2_uc009zrk.2_In_Frame_Ins_p.316_317insAR NM_006654 NP_006645 Q8WU20 FRS2_HUMAN fibroblast growth factor receptor substrate 2 316_317 activation of MAPKK activity|activation of phospholipase C activity|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|transmembrane receptor protein tyrosine phosphatase signaling pathway endomembrane system|endosome|integral to plasma membrane|membrane fraction fibroblast growth factor receptor binding|insulin receptor binding|phosphatase activator activity|transmembrane receptor protein tyrosine kinase adaptor activity prostate(1)|kidney(1) 2 Breast(13;2.15e-06)|Esophageal squamous(21;0.187) Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24) ATCTATCCCTAGTGCCTCAGGG 0.436 0.30 87 38 MAP3K9 4293 broad.mit.edu 37 14 71209189 71209198 + Frame_Shift_Del DEL CCGTTCCAGG - - FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chr14:71209189_71209198delCCGTTCCAGG uc001xmm.2 - 6 1437_1446 c.1437_1446delCCTGGAACGG c.(1435-1446)ATCCTGGAACGGfs p.I479fs MAP3K9_uc010ttk.1_Frame_Shift_Del_p.I216fs|MAP3K9_uc001xmk.2_Frame_Shift_Del_p.I173fs|MAP3K9_uc001xml.2_Frame_Shift_Del_p.I479fs NM_033141 NP_149132 P80192 M3K9_HUMAN mitogen-activated protein kinase kinase kinase 479_482 Leucine-zipper 2. activation of JUN kinase activity|protein autophosphorylation ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity stomach(2)|lung(1)|central_nervous_system(1)|skin(1) 5 all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08) TGTTGAGCTCCCGTTCCAGGATGTCAATCT 0.619 1.00 0 68 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.45 31 25 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 142 410 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 FADU_UPPER_AERODIGESTIVE_TRACT NA FADU_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 3 30 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 FTC133_THYROID NA FTC133_THYROID NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.40 42 28 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 FTC133_THYROID NA FTC133_THYROID NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.05 -1 22 MSH6 2956 broad.mit.edu 37 2 48028257 48028257 + Frame_Shift_Del DEL G - - FTC133_THYROID NA FTC133_THYROID NA g.chr2:48028257delG uc002rwd.3 + 4 3287 c.3135delG c.(3133-3135)AAGfs p.K1045fs MSH6_uc002rwc.2_Frame_Shift_Del_p.K1045fs|MSH6_uc010fbj.2_Frame_Shift_Del_p.K743fs|MSH6_uc010yoi.1_Frame_Shift_Del_p.K915fs|MSH6_uc010yoj.1_Frame_Shift_Del_p.K743fs NM_000179 NP_000170 P52701 MSH6_HUMAN mutS homolog 6 1045 determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes MutSalpha complex ATP binding|DNA-dependent ATPase activity|protein binding large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1) 168 Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) AAAATTACAAGGACTGGCAGT 0.413 0.97 2 59 EPHA6 285220 broad.mit.edu 37 3 96963082 96963082 + Frame_Shift_Del DEL T - - FTC133_THYROID NA FTC133_THYROID NA g.chr3:96963082delT uc010how.1 + 5 1600 c.1557delT c.(1555-1557)AGTfs p.S519fs EPHA6_uc003drp.1_Frame_Shift_Del_p.S519fs NM_001080448 NP_001073917 Q9UF33 EPHA6_HUMAN EPH receptor A6 isoform a 424 Fibronectin type-III 1.|Extracellular (Potential). integral to plasma membrane ATP binding|ephrin receptor activity stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1) 16 CTGAGTTGAGTTTTTCTCCCA 0.403 0.26 52 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 FTC133_THYROID NA FTC133_THYROID NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.34 59 30 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 FTC133_THYROID NA FTC133_THYROID NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 15 29 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 FTC133_THYROID NA FTC133_THYROID NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.79 57 220 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 FTC133_THYROID NA FTC133_THYROID NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.32 15 7 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 FTC133_THYROID NA FTC133_THYROID NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 1 10 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - FTC133_THYROID NA FTC133_THYROID NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 285 33 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 FTC133_THYROID NA FTC133_THYROID NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 103 26 RB1 5925 broad.mit.edu 37 13 48955432 48955437 + In_Frame_Del DEL GATTCT - - FTC133_THYROID NA FTC133_THYROID NA g.chr13:48955432_48955437delGATTCT uc001vcb.2 + 17 1714_1719 c.1548_1553delGATTCT c.(1546-1554)TGGATTCTG>TGG p.IL517del NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 517_518 Domain A.|Pocket; binds T and E1A. androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.?(7) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) CTTTCCCATGGATTCTGAATGTGCTT 0.296 0.93 4 53 CHD8 57680 broad.mit.edu 37 14 21854277 21854278 + Frame_Shift_Del DEL CT - - FTC133_THYROID NA FTC133_THYROID NA g.chr14:21854277_21854278delCT uc001was.1 - 38 6497_6498 c.6403_6404delAG c.(6403-6405)AGCfs p.S2135fs CHD8_uc001war.1_Frame_Shift_Del_p.S2031fs|SUPT16H_uc001wao.2_5'Flank|SUPT16H_uc001wap.2_5'Flank|SUPT16H_uc001waq.1_5'Flank NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 2414 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) CTTCTTGCTGCTCTCTGGTGCA 0.436 0.32 137 64 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C FTC133_THYROID NA FTC133_THYROID NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 6 84 ZNF780B 163131 broad.mit.edu 37 19 40540284 40540286 + In_Frame_Del DEL TGA - - FTC133_THYROID NA FTC133_THYROID NA g.chr19:40540284_40540286delTGA uc002omu.2 - 5 2545_2547 c.2480_2482delTCA c.(2479-2484)ATCAGA>AGA p.I827del ZNF780B_uc002omv.2_In_Frame_Del_p.I679del NM_001005851 NP_001005851 Q9Y6R6 Z780B_HUMAN zinc finger protein 780B 827 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1)|pancreas(1) 2 all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925) ATGAATTTTCTGATGTTCAGTAA 0.365 0.41 16 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 FTC133_THYROID NA FTC133_THYROID NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 55 423 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 FTC133_THYROID NA FTC133_THYROID NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 58 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 FTC238_THYROID NA FTC238_THYROID NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.37 72 43 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 FTC238_THYROID NA FTC238_THYROID NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 60 MSH6 2956 broad.mit.edu 37 2 48028257 48028257 + Frame_Shift_Del DEL G - - FTC238_THYROID NA FTC238_THYROID NA g.chr2:48028257delG uc002rwd.3 + 4 3287 c.3135delG c.(3133-3135)AAGfs p.K1045fs MSH6_uc002rwc.2_Frame_Shift_Del_p.K1045fs|MSH6_uc010fbj.2_Frame_Shift_Del_p.K743fs|MSH6_uc010yoi.1_Frame_Shift_Del_p.K915fs|MSH6_uc010yoj.1_Frame_Shift_Del_p.K743fs NM_000179 NP_000170 P52701 MSH6_HUMAN mutS homolog 6 1045 determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes MutSalpha complex ATP binding|DNA-dependent ATPase activity|protein binding large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1) 168 Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) AAAATTACAAGGACTGGCAGT 0.413 0.99 1 83 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 FTC238_THYROID NA FTC238_THYROID NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 57 65 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 FTC238_THYROID NA FTC238_THYROID NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.27 48 18 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 FTC238_THYROID NA FTC238_THYROID NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.79 57 210 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 FTC238_THYROID NA FTC238_THYROID NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.36 7 4 DGKB 1607 broad.mit.edu 37 7 14378198 14378198 + Frame_Shift_Del DEL T - - FTC238_THYROID NA FTC238_THYROID NA g.chr7:14378198delT uc003ssz.2 - 22 2254 c.2067delA c.(2065-2067)AAAfs p.K689fs DGKB_uc011jxt.1_Frame_Shift_Del_p.K670fs|DGKB_uc003sta.2_Frame_Shift_Del_p.K689fs|DGKB_uc011jxu.1_Frame_Shift_Del_p.K688fs NM_004080 NP_004071 Q9Y6T7 DGKB_HUMAN diacylglycerol kinase, beta isoform 1 689 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation cytoplasm|plasma membrane ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding lung(5)|ovary(4)|breast(2)|skin(1) 12 Phosphatidylserine(DB00144) TGTCAGACCCTTTTTTCTCTA 0.398 0.25 333 113 MLL3 58508 broad.mit.edu 37 7 152012262 152012263 + Frame_Shift_Ins INS - T T rs35319288 FTC238_THYROID NA FTC238_THYROID NA g.chr7:152012262_152012263insT uc003wla.2 - 4 769_770 c.550_551insA c.(550-552)ATGfs p.M184fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 184 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TGAGTTTTGCATTTTCTCATAG 0.356 0.42 316 225 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - FTC238_THYROID NA FTC238_THYROID NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.36 7 4 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 FTC238_THYROID NA FTC238_THYROID NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 2 23 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency FTC238_THYROID NA FTC238_THYROID NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.44 606 477 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - FTC238_THYROID NA FTC238_THYROID NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 504 59 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 FTC238_THYROID NA FTC238_THYROID NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 218 65 CHD8 57680 broad.mit.edu 37 14 21854277 21854278 + Frame_Shift_Del DEL CT - - FTC238_THYROID NA FTC238_THYROID NA g.chr14:21854277_21854278delCT uc001was.1 - 38 6497_6498 c.6403_6404delAG c.(6403-6405)AGCfs p.S2135fs CHD8_uc001war.1_Frame_Shift_Del_p.S2031fs|SUPT16H_uc001wao.2_5'Flank|SUPT16H_uc001wap.2_5'Flank|SUPT16H_uc001waq.1_5'Flank NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 2414 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) CTTCTTGCTGCTCTCTGGTGCA 0.436 0.48 63 58 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C FTC238_THYROID NA FTC238_THYROID NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 20 265 ZNF780B 163131 broad.mit.edu 37 19 40540284 40540286 + In_Frame_Del DEL TGA - - FTC238_THYROID NA FTC238_THYROID NA g.chr19:40540284_40540286delTGA uc002omu.2 - 5 2545_2547 c.2480_2482delTCA c.(2479-2484)ATCAGA>AGA p.I827del ZNF780B_uc002omv.2_In_Frame_Del_p.I679del NM_001005851 NP_001005851 Q9Y6R6 Z780B_HUMAN zinc finger protein 780B 827 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1)|pancreas(1) 2 all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925) ATGAATTTTCTGATGTTCAGTAA 0.365 0.93 1 14 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 FTC238_THYROID NA FTC238_THYROID NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 12 9 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 FTC238_THYROID NA FTC238_THYROID NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 154 594 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 FTC238_THYROID NA FTC238_THYROID NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 78 MAPK8IP2 23542 broad.mit.edu 37 22 51043138 51043146 + In_Frame_Del DEL GAGGACGAA - - FTC238_THYROID NA FTC238_THYROID NA g.chr22:51043138_51043146delGAGGACGAA uc003bmx.2 + 6 1528_1536 c.1411_1419delGAGGACGAA c.(1411-1419)GAGGACGAAdel p.EDE471del MAPK8IP2_uc003bmy.2_In_Frame_Del_p.EDE444del|MAPK8IP2_uc011asc.1_5'Flank NM_012324 NP_036456 Q13387 JIP2_HUMAN mitogen-activated protein kinase 8 interacting 471_473 Asp/Glu-rich (acidic). behavioral fear response|dendrite morphogenesis|MAPKKK cascade|nonassociative learning|positive regulation of anti-apoptosis|regulation of excitatory postsynaptic membrane potential|regulation of JNK cascade|regulation of receptor activity|regulation of synaptic transmission, glutamatergic|signal complex assembly|social behavior cytoplasm|postsynaptic density beta-amyloid binding|kinesin binding|MAP-kinase scaffold activity|protein kinase activator activity|protein kinase binding large_intestine(2)|central_nervous_system(1) 3 all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) OV - Ovarian serous cystadenocarcinoma(4;1.28e-70)|Epithelial(4;3.46e-65)|GBM - Glioblastoma multiforme(4;4.83e-06)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247) 0.000 0.70 3 7 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 FU97_STOMACH NA FU97_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 39 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - FU97_STOMACH NA FU97_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.40 425 278 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes FU97_STOMACH NA FU97_STOMACH NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.36 7 4 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 FU97_STOMACH NA FU97_STOMACH NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.32 13 6 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A FU97_STOMACH NA FU97_STOMACH NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 116 31 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 FU97_STOMACH NA FU97_STOMACH NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.33 14 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 FU97_STOMACH NA FU97_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.42 67 49 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 FU97_STOMACH NA FU97_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.24 48 15 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 FU97_STOMACH NA FU97_STOMACH NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.36 9 5 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 FU97_STOMACH NA FU97_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency FU97_STOMACH NA FU97_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.52 233 248 FADD 8772 broad.mit.edu 37 11 70049816 70049817 + Frame_Shift_Ins INS - G G FU97_STOMACH NA FU97_STOMACH NA g.chr11:70049816_70049817insG uc001opm.2 + 1 548_549 c.251_252insG c.(250-252)GCGfs p.A84fs NM_003824 NP_003815 Q13158 FADD_HUMAN Fas-associated via death domain 84 activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction cytosol death receptor binding|identical protein binding ovary(1)|lung(1)|pancreas(1) 3 Esophageal squamous(2;1.19e-45) LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) 0.000 0.10 698 74 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 FU97_STOMACH NA FU97_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 266 81 CSNK2A2 1459 broad.mit.edu 37 16 58200548 58200560 + Frame_Shift_Del DEL TACAGTTCTTCTG - - FU97_STOMACH NA FU97_STOMACH NA g.chr16:58200548_58200560delTACAGTTCTTCTG uc002enc.2 - 9 897_909 c.755_767delCAGAAGAACTGTA c.(754-768)ACAGAAGAACTGTATfs p.T252fs NM_001896 NP_001887 P19784 CSK22_HUMAN casein kinase 2, alpha prime polypeptide 252_256 Protein kinase. axon guidance|Wnt receptor signaling pathway cytosol|nucleus ATP binding|protein N-terminus binding|protein serine/threonine kinase activity central_nervous_system(1) 1 CAGATACCCATACAGTTCTTCTGTACCCAGAAC 0.465 0.12 239 32 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 FU97_STOMACH NA FU97_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.50 23 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 FU97_STOMACH NA FU97_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 100 364 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 FU97_STOMACH NA FU97_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 56 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 FUOV1_OVARY NA FUOV1_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 3 157 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - FUOV1_OVARY NA FUOV1_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.50 524 517 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 FUOV1_OVARY NA FUOV1_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.41 52 36 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A FUOV1_OVARY NA FUOV1_OVARY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 156 36 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 FUOV1_OVARY NA FUOV1_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.47 21 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 FUOV1_OVARY NA FUOV1_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 135 134 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 FUOV1_OVARY NA FUOV1_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.36 99 56 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 FUOV1_OVARY NA FUOV1_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.25 180 61 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes FUOV1_OVARY NA FUOV1_OVARY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.62 5 8 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 FUOV1_OVARY NA FUOV1_OVARY NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.19 60 14 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes FUOV1_OVARY NA FUOV1_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.83 4 19 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 FUOV1_OVARY NA FUOV1_OVARY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.57 25 33 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 FUOV1_OVARY NA FUOV1_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 3 69 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency FUOV1_OVARY NA FUOV1_OVARY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.10 104 12 NUP98 4928 broad.mit.edu 37 11 3797219 3797222 + Frame_Shift_Del DEL AGAG - - FUOV1_OVARY NA FUOV1_OVARY NA g.chr11:3797219_3797222delAGAG uc001lyh.2 - 5 676_679 c.385_388delCTCT c.(385-390)CTCTTTfs p.L129fs NUP98_uc001lyi.2_Frame_Shift_Del_p.L129fs|NUP98_uc001lyj.1_Frame_Shift_Del_p.L129fs|NUP98_uc001lyk.1_Frame_Shift_Del_p.L129fs|NUP98_uc010qxv.1_Frame_Shift_Del_p.L92fs NM_016320 NP_057404 P52948 NUP98_HUMAN nucleoporin 98kD isoform 1 129_130 Gly/Thr-rich. carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex protein binding|structural constituent of nuclear pore|transporter activity breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1) 12 Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227) BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199) GTGGTTCCAAAGAGTCCTCCACTG 0.387 0.28 237 92 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 FUOV1_OVARY NA FUOV1_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 750 278 ATN1 1822 broad.mit.edu 37 12 7045892 7045903 + In_Frame_Del DEL CAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448 byFrequency;byFrequency;by1000genomes;byFrequency FUOV1_OVARY NA FUOV1_OVARY NA g.chr12:7045892_7045903delCAGCAGCAGCAG uc001qrw.1 + 5 1699_1710 c.1462_1473delCAGCAGCAGCAG c.(1462-1473)CAGCAGCAGCAGdel p.QQQQ496del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQ496del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 496_499 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagc 0.467 0.12 147 21 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency FUOV1_OVARY NA FUOV1_OVARY NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.49 29 28 Unknown 0 broad.mit.edu 37 14 23574096 23574098 + In_Frame_Del DEL GCA - - FUOV1_OVARY NA FUOV1_OVARY NA g.chr14:23574096_23574098delGCA uc010aki.1 - 1 80_82 c.32_34delTGC c.(31-36)CTGCCG>CCG p.L11del Homo sapiens cDNA clone IMAGE:40134016. ACTAGTGgcggcagcagcagcag 0.448 0.33 8 4 PLCG2 5336 broad.mit.edu 37 16 81904462 81904464 + In_Frame_Del DEL AGG - - FUOV1_OVARY NA FUOV1_OVARY NA g.chr16:81904462_81904464delAGG uc002fgt.2 + 7 722_724 c.570_572delAGG c.(568-573)ATAGGA>ATA p.G191del PLCG2_uc010chg.1_In_Frame_Del_p.G191del NM_002661 NP_002652 P16885 PLCG2_HUMAN phospholipase C, gamma 2 191 intracellular signal transduction|phospholipid catabolic process|platelet activation plasma membrane phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity large_intestine(4)|lung(2)|ovary(1)|skin(1) 8 TACAGGAAATAGGAGCACACAAA 0.345 0.37 94 55 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 FUOV1_OVARY NA FUOV1_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 41 244 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 FUOV1_OVARY NA FUOV1_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 11 118 Unknown 0 broad.mit.edu 37 X 80185321 80185321 + Frame_Shift_Del DEL A - - G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chrX:80185321delA uc004eec.1 + 1 394 c.220delA c.(220-222)AAAfs p.K74fs SubName: Full=cDNA FLJ16670 fis, clone THYMU3001133, highly similar to Voltage-dependent anion-selective channel protein 1; SubName: Full=Voltage-dependent anion channel 1, isoform CRA_a; TAACACTGGGAAAAAAAATGC 0.483 0.83 31 149 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.49 18 17 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.54 12 14 HTT 3064 broad.mit.edu 37 4 3076672 3076673 + In_Frame_Ins INS - CCGCCGCCG CCGCCGCCG rs76533208 G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr4:3076672_3076673insCCGCCGCCG uc011bvq.1 + 2 271_272 c.126_127insCCGCCGCCG c.(124-129)insCCGCCGCCG p.51_52insPPP NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 49_50 establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) aacagccgccaccgccgccgcc 0.084 0.40 89 60 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.18 98 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.72 104 265 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 37 63 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 12 ADCK5 203054 broad.mit.edu 37 8 145617362 145617364 + In_Frame_Del DEL GGA - - G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr8:145617362_145617364delGGA uc003zch.2 + 11 1221_1223 c.1167_1169delGGA c.(1165-1170)CTGGAG>CTG p.E391del ADCK5_uc003zcg.2_RNA|ADCK5_uc003zci.2_5'UTR NM_174922 NP_777582 Q3MIX3 ADCK5_HUMAN aarF domain containing kinase 5 391 Protein kinase. integral to membrane protein serine/threonine kinase activity stomach(1) 1 all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;8.96e-41)|Epithelial(56;4.08e-40)|all cancers(56;4.51e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055) ACCAGTTCCTGGAGGAGAAGTGA 0.680 0.33 12 6 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 36 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.52 529 570 MEF2A 4205 broad.mit.edu 37 15 100252710 100252724 + In_Frame_Del DEL CAGCAGCAGCAGCAG - - rs72276751;rs72236998;rs72416294 G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr15:100252710_100252724delCAGCAGCAGCAGCAG uc010urw.1 + 11 1617_1631 c.1258_1272delCAGCAGCAGCAGCAG c.(1258-1272)CAGCAGCAGCAGCAGdel p.QQQQQ425del MEF2A_uc010urv.1_In_Frame_Del_p.QQQQQ355del|MEF2A_uc010bos.2_In_Frame_Del_p.QQQQQ415del|MEF2A_uc002bvf.2_In_Frame_Del_p.QQQQQ417del|MEF2A_uc002bve.2_In_Frame_Del_p.QQQQQ423del|MEF2A_uc002bvg.2_In_Frame_Del_p.QQQQQ415del|MEF2A_uc002bvi.2_In_Frame_Del_p.QQQQQ415del|MEF2A_uc010bot.2_In_Frame_Del_p.QQQQQ347del NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 425_429 Gln/Pro-rich. apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) ATCGGGCTTCcagcagcagcagcagcagcagcagc 0.498 0.47 48 42 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.10 302 34 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 24 120 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 72 300 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 G292CLONEA141B1_BONE NA G292CLONEA141B1_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 100 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 G361_SKIN NA G361_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 11 158 CTNNA2 1496 broad.mit.edu 37 2 79971696 79971708 + Frame_Shift_Del DEL GTGCGCAAACAAG - - G361_SKIN NA G361_SKIN NA g.chr2:79971696_79971708delGTGCGCAAACAAG uc010ysh.1 + 2 291_303 c.286_298delGTGCGCAAACAAG c.(286-300)GTGCGCAAACAAGGTfs p.V96fs CTNNA2_uc010yse.1_Frame_Shift_Del_p.V96fs|CTNNA2_uc010ysf.1_Frame_Shift_Del_p.V96fs|CTNNA2_uc010ysg.1_Frame_Shift_Del_p.V96fs NM_004389 NP_004380 P26232 CTNA2_HUMAN catenin, alpha 2 isoform 1 96_100 axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity actin cytoskeleton|axon|cytosol cadherin binding|structural constituent of cytoskeleton pancreas(4)|lung(3)|breast(1)|skin(1) 9 TGTAGAGGATGTGCGCAAACAAGGTAGGCAGAA 0.413 0.35 333 182 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes G361_SKIN NA G361_SKIN NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.21 26 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 G361_SKIN NA G361_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.32 98 47 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A G361_SKIN NA G361_SKIN NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.13 433 62 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 G361_SKIN NA G361_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 96 69 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 G361_SKIN NA G361_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 313 400 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 G361_SKIN NA G361_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.55 71 86 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 G361_SKIN NA G361_SKIN NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.22 69 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 G361_SKIN NA G361_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 402 190 Unknown 0 broad.mit.edu 37 14 23574096 23574098 + In_Frame_Del DEL GCA - - G361_SKIN NA G361_SKIN NA g.chr14:23574096_23574098delGCA uc010aki.1 - 1 80_82 c.32_34delTGC c.(31-36)CTGCCG>CCG p.L11del Homo sapiens cDNA clone IMAGE:40134016. ACTAGTGgcggcagcagcagcag 0.448 0.18 31 7 CDH3 1001 broad.mit.edu 37 16 68679613 68679614 + Frame_Shift_Ins INS - A A G361_SKIN NA G361_SKIN NA g.chr16:68679613_68679614insA uc002ewf.2 + 2 1252_1253 c.120_121insA c.(118-123)GCGGGAfs p.A40fs CDH3_uc010vli.1_Intron NM_001793 NP_001784 P22223 CADH3_HUMAN cadherin 3, type 1 preproprotein 40_41 adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception integral to membrane calcium ion binding p.?(1) ovary(3)|breast(1)|skin(1) 5 Ovarian(137;0.0564) OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384) 0.000 1.00 0 13 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C G361_SKIN NA G361_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 22 257 STK11 6794 broad.mit.edu 37 19 1221314 1221314 + Frame_Shift_Del DEL C - - rs67873004 G361_SKIN NA G361_SKIN NA g.chr19:1221314delC uc002lrl.1 + 6 1952 c.837delC c.(835-837)GGCfs p.G279fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 279 Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.P281fs*6(2)|p.?(2)|p.Y246fs*3(1)|p.G279F(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) GCGACTGTGGCCCCCCGCTCT 0.607 0.89 15 124 STXBP2 6813 broad.mit.edu 37 19 7707005 7707006 + Splice_Site DEL GT - - G361_SKIN NA G361_SKIN NA g.chr19:7707005_7707006delGT uc002mha.3 + 8 708 c.663_splice c.e8+1 p.E221_splice STXBP2_uc002mhb.3_Splice_Site_p.E218_splice|STXBP2_uc010dvj.2_Splice_Site|STXBP2_uc010xjr.1_Splice_Site_p.E232_splice|STXBP2_uc010dvk.2_Splice_Site_p.E189_splice|STXBP2_uc002mhc.3_Splice_Site|STXBP2_uc002mhe.1_5'Flank NM_006949 NP_008880 Q15833 STXB2_HUMAN syntaxin binding protein 2 isoform a leukocyte mediated cytotoxicity|neutrophil degranulation|protein transport|regulation of mast cell degranulation|vesicle docking involved in exocytosis azurophil granule|cytolytic granule|cytosol|specific granule|tertiary granule syntaxin-3 binding central_nervous_system(1) 1 0.000 1.00 0 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 G361_SKIN NA G361_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.75 87 266 LMTK3 114783 broad.mit.edu 37 19 49001791 49001792 + Frame_Shift_Ins INS - G G G361_SKIN NA G361_SKIN NA g.chr19:49001791_49001792insG uc002pjk.2 - 12 2621_2622 c.2621_2622insC c.(2620-2622)CCGfs p.P874fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) CCCGGGGCCCCGGGAGTGGGAG 0.718 0.11 169 21 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes G361_SKIN NA G361_SKIN NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.47 38 34 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 G361_SKIN NA G361_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 80 384 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 G401_SOFT_TISSUE NA G401_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 21 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 G401_SOFT_TISSUE NA G401_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 59 85 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 G401_SOFT_TISSUE NA G401_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.58 27 38 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 G401_SOFT_TISSUE NA G401_SOFT_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.31 144 65 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 G401_SOFT_TISSUE NA G401_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 231 42 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 G401_SOFT_TISSUE NA G401_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 6 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 G401_SOFT_TISSUE NA G401_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 110 433 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 G401_SOFT_TISSUE NA G401_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 51 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 48 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.25 24 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 117 80 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.48 42 39 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.19 59 14 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.16 49 9 MAML2 84441 broad.mit.edu 37 11 95825203 95825204 + In_Frame_Ins INS - TGC TGC rs149006316 by1000genomes G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr11:95825203_95825204insTGC uc001pfw.1 - 2 3276_3277 c.1991_1992insGCA c.(1990-1992)CAA>CAGCAA p.664_664Q>QQ NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 664 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) aagatggttgttgctgctgctg 0.178 0.26 447 159 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 489 136 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.23 53 16 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.26 23 8 PKN1 5585 broad.mit.edu 37 19 14580627 14580634 + Splice_Site DEL GTGTGTGC - - G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr19:14580627_14580634delGTGTGTGC uc002myp.2 + 17 2384 c.2216_splice c.e17+1 p.R739_splice PKN1_uc002myq.2_Splice_Site_p.R745_splice|PKN1_uc002myr.2_Splice_Site_p.R79_splice NM_002741 NP_002732 Q16512 PKN1_HUMAN protein kinase N1 isoform 2 activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent endosome|nucleus|plasma membrane androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1) 8 TCGTCTACAGGTGTGTGCGTGTGTGCAT 0.596 0.28 265 104 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.36 106 59 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 89 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.94 76 1177 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 G402_SOFT_TISSUE NA G402_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 88 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 55 ARID1A 8289 broad.mit.edu 37 1 27024002 27024002 + Frame_Shift_Del DEL G - - GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:27024002delG uc001bmv.1 + 1 1481 c.1108delG c.(1108-1110)GGGfs p.G370fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.G370fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.G370fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 370 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.Q372fs*19(1)|p.Q372fs*28(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.40 127 85 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 889 185 ABL2 27 broad.mit.edu 37 1 179077737 179077738 + Frame_Shift_Ins INS - G G GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:179077737_179077738insG uc001gmj.3 - 12 2951_2952 c.2664_2665insC c.(2662-2667)CCCAAGfs p.P888fs ABL2_uc010pnf.1_Frame_Shift_Ins_p.P785fs|ABL2_uc010png.1_Frame_Shift_Ins_p.P764fs|ABL2_uc010pnh.1_Frame_Shift_Ins_p.P867fs|ABL2_uc001gmg.3_Frame_Shift_Ins_p.P770fs|ABL2_uc001gmi.3_Frame_Shift_Ins_p.P873fs|ABL2_uc001gmh.3_Frame_Shift_Ins_p.P852fs|ABL2_uc010pne.1_Frame_Shift_Ins_p.P749fs NM_007314 NP_009298 P42684 ABL2_HUMAN arg tyrosine kinase isoform b 888_889 F-actin-binding (By similarity).|Pro-rich. axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction cytoskeleton|cytosol ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(8)|breast(3)|ovary(2)|central_nervous_system(1) 14 Adenosine triphosphate(DB00171)|Dasatinib(DB01254) TCTTTACCCTTGGGGGCAGCTG 0.619 0.10 428 49 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.64 18 32 HTT 3064 broad.mit.edu 37 4 3076603 3076604 + Splice_Site INS - CAG CAG rs10618869 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:3076603_3076604insCAG uc011bvq.1 + 1 196 c.51_splice c.e1+1 p.F17_splice NM_002111 NP_002102 P42858 HD_HUMAN huntingtin establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) TCAAGTCCTTCcagcagcagca 0.342 0.19 104 24 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.22 71 20 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 134 308 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 56 109 ATXN1 6310 broad.mit.edu 37 6 16327915 16327916 + In_Frame_Ins INS - TGC TGC rs11969612 by1000genomes GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:16327915_16327916insTGC uc003nbt.2 - 8 1597_1598 c.626_627insGCA c.(625-627)CAT>CAGCAT p.208_209insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.208_209insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 208_209 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) gctgatgctgatgctgctgctg 0.381 0.19 144 33 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.16 51 10 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.21 250 68 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 11 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 59 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.42 14 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.53 579 649 ATN1 1822 broad.mit.edu 37 12 7045880 7045885 + In_Frame_Del DEL CAGCAA - - GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:7045880_7045885delCAGCAA uc001qrw.1 + 5 1687_1692 c.1450_1455delCAGCAA c.(1450-1455)CAGCAAdel p.QQ500del ATN1_uc001qrx.1_In_Frame_Del_p.QQ500del|ATN1_uc001qry.1_In_Frame_Del_p.QQ485del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 500_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 CCATCACCACcagcaacagcaacagc 0.447 0.36 111 62 MAP2K5 5607 broad.mit.edu 37 15 67885267 67885269 + In_Frame_Del DEL AAA - - GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:67885267_67885269delAAA uc002aqu.2 + 7 1088_1090 c.435_437delAAA c.(433-438)TTAAAG>TTG p.K147del MAP2K5_uc002aqt.1_In_Frame_Del_p.K147del|MAP2K5_uc002aqv.2_In_Frame_Del_p.K147del|MAP2K5_uc002aqw.2_5'UTR|MAP2K5_uc010ujw.1_In_Frame_Del_p.K111del NM_145160 NP_660143 Q13163 MP2K5_HUMAN mitogen-activated protein kinase kinase 5 147 nerve growth factor receptor signaling pathway ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(2) 2 TTTTCAGCTTAAAGAAGTCTTCT 0.325 0.46 68 57 SALL1 6299 broad.mit.edu 37 16 51175655 51175656 + In_Frame_Ins INS - GCT GCT rs113614842 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:51175655_51175656insGCT uc010vgs.1 - 2 508_509 c.477_478insAGC c.(475-480)insAGC p.159_160insS SALL1_uc010vgr.1_In_Frame_Ins_p.62_63insS|SALL1_uc010cbv.2_Intron NM_002968 NP_002959 Q9NSC2 SALL1_HUMAN sal-like 1 isoform a 159_160 Poly-Gly. adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development chromocenter|cytoplasm|heterochromatin|nucleus beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding skin(5)|ovary(3) 8 all_cancers(37;0.0322) COAD - Colon adenocarcinoma(2;0.24) ccgccgccgccgctgctgctgc 0.460 0.48 11 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 57 563 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.13 79 12 VEZF1 7716 broad.mit.edu 37 17 56056604 56056605 + In_Frame_Ins INS - TGCTGC TGCTGC rs138088904;rs61731354 byFrequency GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:56056604_56056605insTGCTGC uc002ivf.1 - 5 1189_1190 c.1046_1047insGCAGCA c.(1045-1047)CAA>CAGCAGCAA p.349_349Q>QQQ VEZF1_uc010dcn.1_In_Frame_Ins_p.199_199Q>QQQ NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 gttgttgttgttgctgctgctg 0.307 0.20 82 20 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.44 120 95 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 302 36 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 136 500 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 6 164 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 GAMG_CENTRAL_NERVOUS_SYSTEM NA GAMG_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 62 PRDM2 7799 broad.mit.edu 37 1 14105104 14105105 + Frame_Shift_Ins INS - A A GAMG_CENTRAL_NERVOUS_SYSTEM NA GAMG_CENTRAL_NERVOUS_SYSTEM NA g.chr1:14105104_14105105insA uc001avi.2 + 8 1670_1671 c.814_815insA c.(814-816)GAGfs p.E272fs PRDM2_uc001avg.2_Intron|PRDM2_uc001avh.2_Frame_Shift_Ins_p.E272fs|PRDM2_uc001avj.2_Intron|PRDM2_uc009vod.1_Intron|PRDM2_uc001avk.2_Frame_Shift_Ins_p.E71fs|PRDM2_uc009voe.2_Intron|PRDM2_uc009vof.2_Intron NM_012231 NP_036363 Q13029 PRDM2_HUMAN retinoblastoma protein-binding zinc finger 272 Asp/Glu-rich (acidic). Golgi apparatus|nucleus DNA binding|histone-lysine N-methyltransferase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1) 1 Ovarian(185;0.249) all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255) GBM - Glioblastoma multiforme(2;0.00182) UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145) 0.000 0.71 5 12 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 GAMG_CENTRAL_NERVOUS_SYSTEM NA GAMG_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.33 10 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 GAMG_CENTRAL_NERVOUS_SYSTEM NA GAMG_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 48 55 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 GAMG_CENTRAL_NERVOUS_SYSTEM NA GAMG_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.57 28 37 DST 667 broad.mit.edu 37 6 56457036 56457037 + Frame_Shift_Ins INS - T T GAMG_CENTRAL_NERVOUS_SYSTEM NA GAMG_CENTRAL_NERVOUS_SYSTEM NA g.chr6:56457036_56457037insT uc003pdf.2 - 43 6517_6518 c.6489_6490insA c.(6487-6492)TTATCTfs p.L2163fs DST_uc003pcz.3_Frame_Shift_Ins_p.L1985fs|DST_uc011dxj.1_Frame_Shift_Ins_p.L2014fs|DST_uc011dxk.1_Frame_Shift_Ins_p.L2025fs|DST_uc003pcy.3_Frame_Shift_Ins_p.L1659fs|DST_uc010kaa.1_RNA NM_001144769 NP_001138241 Q03001 DYST_HUMAN dystonin isoform 2 4071_4072 Spectrin 3. cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1) 14 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) ATAGGTTCAGATAAGTGTTTGC 0.431 0.70 58 136 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - GAMG_CENTRAL_NERVOUS_SYSTEM NA GAMG_CENTRAL_NERVOUS_SYSTEM NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.48 117 109 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - GAMG_CENTRAL_NERVOUS_SYSTEM NA GAMG_CENTRAL_NERVOUS_SYSTEM NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.80 10 39 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 GAMG_CENTRAL_NERVOUS_SYSTEM NA GAMG_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.80 3 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 GAMG_CENTRAL_NERVOUS_SYSTEM NA GAMG_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 237 104 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 GAMG_CENTRAL_NERVOUS_SYSTEM NA GAMG_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.37 92 54 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 GAMG_CENTRAL_NERVOUS_SYSTEM NA GAMG_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 208 457 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 GAMG_CENTRAL_NERVOUS_SYSTEM NA GAMG_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 2 26 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 60 XIAP 331 broad.mit.edu 37 X 123025155 123025157 + In_Frame_Del DEL GAG - - GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chrX:123025155_123025157delGAG uc010nqu.2 + 4 1171_1173 c.1045_1047delGAG c.(1045-1047)GAGdel p.E350del XIAP_uc004etx.2_In_Frame_Del_p.E350del|XIAP_uc010nqv.2_5'UTR NM_001167 NP_001158 P98170 XIAP_HUMAN baculoviral IAP repeat-containing protein 4 350 anti-apoptosis|apoptosis|induction of apoptosis by intracellular signals|response to DNA damage stimulus cytosol caspase inhibitor activity|ligase activity|protein binding|zinc ion binding ovary(1)|lung(1) 2 TCATTCACTTGAGGAGTGTCTGG 0.197 0.92 3 36 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 485 144 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.36 16 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.73 61 163 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.76 24 77 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.50 5 5 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.54 42 50 LATS1 9113 broad.mit.edu 37 6 149983097 149983099 + In_Frame_Del DEL TCC - - GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr6:149983097_149983099delTCC uc003qmu.1 - 8 3707_3709 c.3159_3161delGGA c.(3157-3162)GAGGAA>GAA p.1053_1054EE>E LATS1_uc010kif.1_In_Frame_Del_p.948_949EE>E NM_004690 NP_004681 O95835 LATS1_HUMAN LATS homolog 1 1053_1054 AGC-kinase C-terminal. cell division|cytoplasmic sequestering of protein|G2/M transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|positive regulation of peptidyl-serine phosphorylation|regulation of actin filament polymerization|sister chromatid segregation microtubule organizing center|spindle pole ATP binding|magnesium ion binding|protein kinase binding|protein serine/threonine kinase activity lung(5)|central_nervous_system(1) 6 Ovarian(120;0.0164) OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116) TACATTTTCTTCCTCGTTATCAT 0.355 0.39 193 123 ARID1B 57492 broad.mit.edu 37 6 157099402 157099403 + In_Frame_Ins INS - CAG CAG GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr6:157099402_157099403insCAG uc003qqn.2 + 1 317_318 c.165_166insCAG c.(163-168)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) TAAACCAGTTCcagcagcagca 0.124 0.42 67 48 TMEM229A 730130 broad.mit.edu 37 7 123672456 123672457 + In_Frame_Ins INS - GCT GCT GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr7:123672456_123672457insGCT uc011kob.1 - 1 1067_1068 c.601_602insAGC c.(601-603)CGG>CAGCGG p.200_201insQ uc011koc.1_Intron NM_001136002 NP_001129474 B2RXF0 T229A_HUMAN transmembrane protein 229A 200_201 host cell nucleus|integral to membrane sequence-specific DNA binding transcription factor activity 0 CGCGCCCCTCCgctgctgctgc 0.604 0.38 15 9 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 CSMD3 114788 broad.mit.edu 37 8 113304842 113304842 + Frame_Shift_Del DEL C - - GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr8:113304842delC uc003ynu.2 - 55 8871 c.8712delG c.(8710-8712)GGGfs p.G2904fs CSMD3_uc003yns.2_Frame_Shift_Del_p.G2106fs|CSMD3_uc003ynt.2_Frame_Shift_Del_p.G2864fs|CSMD3_uc011lhx.1_Frame_Shift_Del_p.G2735fs NM_198123 NP_937756 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 isoform 1 2904 Extracellular (Potential).|Sushi 19. integral to membrane|plasma membrane ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1) 63 GCATAAGATACCCAATATTGC 0.438 0.22 401 112 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 53 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.47 9 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.48 349 317 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.43 34 26 POLG 5428 broad.mit.edu 37 15 89876821 89876822 + In_Frame_Ins INS - TGCTGT TGCTGT GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr15:89876821_89876822insTGCTGT uc002bns.3 - 2 446_447 c.164_165insACAGCA c.(163-165)CAG>CAACAGCAG p.55_55Q>QQQ POLG_uc002bnr.3_In_Frame_Ins_p.55_55Q>QQQ NM_002693 NP_002684 P54098 DPOG1_HUMAN DNA-directed DNA polymerase gamma 55 Poly-Gln. Q -> QQ.|Q -> QQQ. base-excision repair, gap-filling|cell death|DNA-dependent DNA replication mitochondrial nucleoid DNA binding|DNA-directed DNA polymerase activity|protease binding ovary(1)|lung(1) 2 Lung NSC(78;0.0472)|all_lung(78;0.089) STAD - Stomach adenocarcinoma(125;0.165) gctgctgaggctgctgttgctg 0.455 0.42 28 20 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.84 22 112 TP53 7157 broad.mit.edu 37 17 7577564 7577565 + In_Frame_Ins INS - TTA TTA GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr17:7577564_7577565insTTA uc002gim.2 - 7 910_911 c.716_717insTAA c.(715-717)AAC>AATAAC p.239_239N>NN TP53_uc002gig.1_In_Frame_Ins_p.239_239N>NN|TP53_uc002gih.2_In_Frame_Ins_p.239_239N>NN|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_In_Frame_Ins_p.107_107N>NN|TP53_uc010cng.1_In_Frame_Ins_p.107_107N>NN|TP53_uc002gii.1_In_Frame_Ins_p.107_107N>NN|TP53_uc010cnh.1_In_Frame_Ins_p.239_239N>NN|TP53_uc010cni.1_In_Frame_Ins_p.239_239N>NN|TP53_uc002gij.2_In_Frame_Ins_p.239_239N>NN|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_In_Frame_Ins_p.146_146N>NN|TP53_uc002gio.2_In_Frame_Ins_p.107_107N>NN NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 239 |Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). N -> Y (in sporadic cancers; somatic mutation).|N -> S (in sporadic cancers; somatic mutation).|N -> K (in sporadic cancers; somatic mutation).|N -> D (in sporadic cancers; somatic mutation).|N -> T (in sporadic cancers; somatic mutation).|N -> H (in a sporadic cancer; somatic mutation).|N -> I (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.N239D(31)|p.N239S(19)|p.N239fs*25(12)|p.0?(7)|p.N239Y(6)|p.N239K(6)|p.N239T(4)|p.N239_C242delNSSC(3)|p.N239_S240insX(2)|p.N239fs*8(2)|p.N239_S240delNS(2)|p.Y236_M243delYMCNSSCM(1)|p.N239fs*1(1)|p.N239_S240insN(1)|p.V225fs*23(1)|p.N239fs*6(1)|p.N239fs*4(1)|p.C238_N239insX(1)|p.C238_M246delCNSSCMGGM(1)|p.M237_N239delMCN(1)|p.N239fs*26(1)|p.C238fs*21(1)|p.N239N(1)|p.H233fs*6(1)|p.S240fs*26(1)|p.N239*(1)|p.H233_C242del10(1)|p.N239_C242>S(1)|p.N239fs*0(1)|p.N239_C242del(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) TGCAGGAACTGTTACACATGTA 0.574 0.85 27 151 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 25 124 CIC 23152 broad.mit.edu 37 19 42795438 42795438 + Frame_Shift_Del DEL C - - GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr19:42795438delC uc002otf.1 + 10 2558 c.2518delC c.(2518-2520)CCTfs p.P840fs NM_015125 NP_055940 Q96RK0 CIC_HUMAN capicua homolog 840 Pro-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1) 11 Prostate(69;0.00682) TCAGGTGGCACCTGCCCCAGC 0.677 0.19 48 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 68 350 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 GB1_CENTRAL_NERVOUS_SYSTEM NA GB1_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 8 145 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 GCIY_STOMACH NA GCIY_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 5 47 XIAP 331 broad.mit.edu 37 X 123025155 123025157 + In_Frame_Del DEL GAG - - GCIY_STOMACH NA GCIY_STOMACH NA g.chrX:123025155_123025157delGAG uc010nqu.2 + 4 1171_1173 c.1045_1047delGAG c.(1045-1047)GAGdel p.E350del XIAP_uc004etx.2_In_Frame_Del_p.E350del|XIAP_uc010nqv.2_5'UTR NM_001167 NP_001158 P98170 XIAP_HUMAN baculoviral IAP repeat-containing protein 4 350 anti-apoptosis|apoptosis|induction of apoptosis by intracellular signals|response to DNA damage stimulus cytosol caspase inhibitor activity|ligase activity|protein binding|zinc ion binding ovary(1)|lung(1) 2 TCATTCACTTGAGGAGTGTCTGG 0.197 0.88 7 53 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 GCIY_STOMACH NA GCIY_STOMACH NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.29 24 10 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A GCIY_STOMACH NA GCIY_STOMACH NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 143 31 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 GCIY_STOMACH NA GCIY_STOMACH NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.41 20 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 GCIY_STOMACH NA GCIY_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.39 88 57 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 GCIY_STOMACH NA GCIY_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.55 18 22 ATXN1 6310 broad.mit.edu 37 6 16327907 16327909 + In_Frame_Del DEL TGA - - rs59310777 by1000genomes GCIY_STOMACH NA GCIY_STOMACH NA g.chr6:16327907_16327909delTGA uc003nbt.2 - 8 1604_1606 c.633_635delTCA c.(631-636)CATCAG>CAG p.H211del ATXN1_uc010jpi.2_In_Frame_Del_p.H211del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 211 Poly-Gln. H -> HQ (in Ref. 1; CAA55793). cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgctgatgctgatgct 0.384 0.50 8 8 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 GCIY_STOMACH NA GCIY_STOMACH NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.32 15 7 PMS2L3 5387 broad.mit.edu 37 7 75140405 75140405 + Frame_Shift_Del DEL C - - GCIY_STOMACH NA GCIY_STOMACH NA g.chr7:75140405delC uc003udp.2 - 7 1051 c.507delG c.(505-507)CGGfs p.R169fs PMS2L3_uc003udn.2_RNA|PMS2L3_uc003udq.2_3'UTR NM_005395 NP_005386 SubName: Full=Postmeiotic segregation increased 2-like 3; SubName: Full=Postmeiotic segregation increased 2-like 3, isoform CRA_b; 0 CCAACCTTCACCGACGCGTGG 0.532 0.65 53 98 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes GCIY_STOMACH NA GCIY_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 1 13 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - GCIY_STOMACH NA GCIY_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.41 13 9 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 GCIY_STOMACH NA GCIY_STOMACH NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.41 52 36 PAPPA 5069 broad.mit.edu 37 9 119158852 119158854 + In_Frame_Del DEL AAG - - GCIY_STOMACH NA GCIY_STOMACH NA g.chr9:119158852_119158854delAAG uc004bjn.2 + 22 5222_5224 c.4841_4843delAAG c.(4840-4845)CAAGAA>CAA p.E1615del PAPPA_uc011lxq.1_In_Frame_Del_p.E990del NM_002581 NP_002572 Q13219 PAPP1_HUMAN pregnancy-associated plasma protein A 1615 cell differentiation|female pregnancy cytoplasm|extracellular region|membrane metalloendopeptidase activity|zinc ion binding ovary(4)|skin(4)|pancreas(1) 9 CCCCAGGCCCAAGAACACAGCCG 0.517 0.95 4 74 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 GCIY_STOMACH NA GCIY_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 233 68 CDH1 999 broad.mit.edu 37 16 68842751 68842752 + Splice_Site DEL TG - - GCIY_STOMACH NA GCIY_STOMACH NA g.chr16:68842751_68842752delTG uc002ewg.1 + 5 811 c.687_splice c.e5+1 p.T229_splice CDH1_uc010vlj.1_Splice_Site|CDH1_uc010cfg.1_Splice_Site_p.T229_splice NM_004360 NP_004351 P12830 CADH1_HUMAN cadherin 1, type 1 preproprotein adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm cell adhesion molecule binding|gamma-catenin binding p.?(5) breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1) 243 all_neural(199;0.0189)|Ovarian(137;0.0563) Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261) CCACATACACTGTAAGTATCTC 0.480 0.92 6 68 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C GCIY_STOMACH NA GCIY_STOMACH NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 17 173 CPAMD8 27151 broad.mit.edu 37 19 17115106 17115108 + In_Frame_Del DEL TTG - - GCIY_STOMACH NA GCIY_STOMACH NA g.chr19:17115106_17115108delTTG uc002nfb.2 - 8 821_823 c.789_791delCAA c.(787-792)AACAAG>AAG p.N263del NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 216 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 TTCAAAAGACTTGTTGTACGCGT 0.335 0.36 86 48 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT GCIY_STOMACH NA GCIY_STOMACH NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.11 1479 189 ZNF568 374900 broad.mit.edu 37 19 37441496 37441496 + Frame_Shift_Del DEL A - - GCIY_STOMACH NA GCIY_STOMACH NA g.chr19:37441496delA uc002ofc.2 + 7 1956 c.1441delA c.(1441-1443)AAAfs p.K481fs ZNF568_uc010efg.2_Intron|ZNF568_uc010xtn.1_Intron|ZNF568_uc002ofd.2_Frame_Shift_Del_p.K405fs|ZNF568_uc010efe.2_Frame_Shift_Del_p.K405fs|ZNF568_uc010eff.1_Intron NM_198539 NP_940941 Q3ZCX4 ZN568_HUMAN zinc finger protein 568 481 C2H2-type 10. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding large_intestine(1)|ovary(1) 2 Esophageal squamous(110;0.183) COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177) TGAATGTGGGAAAGCTTTTAT 0.393 0.56 7 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 GCIY_STOMACH NA GCIY_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.25 118 39 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes GCIY_STOMACH NA GCIY_STOMACH NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.43 8 6 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 GCIY_STOMACH NA GCIY_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 162 675 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 GCIY_STOMACH NA GCIY_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 3 46 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 33 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.42 7 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 44 82 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 25 55 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.82 2 9 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.44 10 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 1 18 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.11 385 48 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 443 201 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.58 5 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 43 546 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 14 56 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 50 261 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 GCT_SOFT_TISSUE NA GCT_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 63 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 69 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 120 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 94 106 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 27 44 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.39 51 32 MAML1 9794 broad.mit.edu 37 5 179193548 179193548 + Frame_Shift_Del DEL G - - rs145980075 byFrequency GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:179193548delG uc003mkm.2 + 2 1800 c.1537delG c.(1537-1539)GGCfs p.G513fs MAML1_uc003mkn.1_Frame_Shift_Del_p.G513fs NM_014757 NP_055572 Q92585 MAML1_HUMAN mastermind-like 1 513 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck peptide antigen binding|protein kinase binding|transcription coactivator activity lung(4)|ovary(2) 6 all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218) all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GCTGGACTACGGCAATACAAA 0.572 0.49 105 100 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.16 250 47 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 237 74 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 31 168 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 6 74 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 2 15 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.27 316 119 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 33 41 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.79 10 38 PIK3R1 5295 broad.mit.edu 37 5 67589596 67589598 + In_Frame_Del DEL CAC - - GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chr5:67589596_67589598delCAC uc003jva.2 + 11 1919_1921 c.1359_1361delCAC c.(1357-1362)AACACT>AAT p.T454del PIK3R1_uc003jvb.2_In_Frame_Del_p.T454del|PIK3R1_uc003jvc.2_In_Frame_Del_p.T154del|PIK3R1_uc003jvd.2_In_Frame_Del_p.T184del|PIK3R1_uc003jve.2_In_Frame_Del_p.T133del|PIK3R1_uc011crb.1_In_Frame_Del_p.T124del NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 454 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.N453_T454insN(2)|p.D434_Q475del(2)|p.T454_Q455>Q(1)|p.?(1)|p.453_454insN(1)|p.T454_D464del(1)|p.Y452_Q455>SGGSRIK(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) 0.000 0.99 4 303 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.62 33 54 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.34 29 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 21 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 221 78 CREBBP 1387 broad.mit.edu 37 16 3781324 3781326 + In_Frame_Del DEL AGG - - GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chr16:3781324_3781326delAGG uc002cvv.2 - 30 5243_5245 c.5039_5041delCCT c.(5038-5043)TCCTTG>TTG p.S1680del CREBBP_uc002cvw.2_In_Frame_Del_p.S1642del NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1680 Interaction with TRERF1. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) GAGCGGCGCAAGGAGGAGAACTC 0.645 0.93 1 13 ZFHX3 463 broad.mit.edu 37 16 72822034 72822039 + In_Frame_Del DEL GCTGCT - - rs149197237 GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chr16:72822034_72822039delGCTGCT uc002fck.2 - 10 10809_10814 c.10136_10141delAGCAGC c.(10135-10143)CAGCAGCGG>CGG p.QQ3379del ZFHX3_uc002fcl.2_In_Frame_Del_p.QQ2465del NM_006885 NP_008816 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 isoform A 3379_3380 Poly-Gln. Missing. muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation transcription factor complex enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding ovary(2)|skin(2) 4 Ovarian(137;0.13) tgtagttgccgctgctgctgctgctg 0.442 0.33 8 4 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 8 32 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 89 298 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 GI1_CENTRAL_NERVOUS_SYSTEM NA GI1_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.85 4 23 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 4 69 KCNN3 3782 broad.mit.edu 37 1 154842200 154842214 + In_Frame_Del DEL GCTGCTGCTGCTGCT - - rs56352724;rs67752396;rs72156187 GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr1:154842200_154842214delGCTGCTGCTGCTGCT uc001ffp.2 - 1 541_555 c.227_241delAGCAGCAGCAGCAGC c.(226-243)CAGCAGCAGCAGCAGCCA>CCA p.QQQQQ76del KCNN3_uc009wox.1_In_Frame_Del_p.QQQQQ76del NM_002249 NP_002240 Q9UGI6 KCNN3_HUMAN small conductance calcium-activated potassium 76_80 Poly-Gln. integral to membrane calmodulin binding lung(1) 1 all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245) BRCA - Breast invasive adenocarcinoma(34;0.00819) GGATGCGGTGgctgctgctgctgctgctgctgctg 0.321 0.17 67 14 PMS1 5378 broad.mit.edu 37 2 190718746 190718747 + Frame_Shift_Del DEL CC - - GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr2:190718746_190718747delCC uc002urh.3 + 8 1433_1434 c.904_905delCC c.(904-906)CCTfs p.P302fs PMS1_uc010zga.1_Frame_Shift_Del_p.P263fs|PMS1_uc010zgb.1_Frame_Shift_Del_p.P241fs|PMS1_uc002urk.3_Frame_Shift_Del_p.P263fs|PMS1_uc002uri.3_Frame_Shift_Del_p.P302fs|PMS1_uc010zgc.1_Frame_Shift_Del_p.P126fs|PMS1_uc010zgd.1_Frame_Shift_Del_p.P126fs|PMS1_uc002urj.2_RNA|PMS1_uc010fry.1_Frame_Shift_Del_p.P263fs|PMS1_uc010frz.2_Intron|PMS1_uc002url.2_Frame_Shift_Del_p.P87fs|PMS1_uc002urm.2_RNA|PMS1_uc002urn.1_5'UTR NM_000534 NP_000525 P54277 PMS1_HUMAN postmeiotic segregation 1 isoform a 302 mismatch repair|reciprocal meiotic recombination MutLalpha complex ATP binding|ATPase activity|mismatched DNA binding ovary(2)|kidney(1)|central_nervous_system(1) 4 OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751) AATCGATGTTCCTACAGCTGAT 0.287 0.24 22 7 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.42 18 13 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.43 17 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 143 121 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.48 34 32 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.35 40 22 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 11 UBR5 51366 broad.mit.edu 37 8 103266628 103266629 + Frame_Shift_Del DEL AA - - GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr8:103266628_103266629delAA uc003ykr.1 - 59 8334_8335 c.8301_8302delTT c.(8299-8304)ACTTGCfs p.T2767fs UBR5_uc003yks.1_Frame_Shift_Del_p.T2766fs|UBR5_uc003ykq.2_Frame_Shift_Del_p.T278fs NM_015902 NP_056986 O95071 UBR5_HUMAN ubiquitin protein ligase E3 component n-recognin 2767_2768 HECT. Glycyl thioester intermediate (By similarity). C->A: Loss of ubiquitin binding. cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus nucleus|soluble fraction protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1) 28 all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05) OV - Ovarian serous cystadenocarcinoma(57;0.000442) CGAGAAATGCAAGTATTTGCAG 0.426 0.21 119 32 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 50 CARS 833 broad.mit.edu 37 11 3038404 3038408 + Frame_Shift_Del DEL CTTTC - - GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr11:3038404_3038408delCTTTC uc001lxh.2 - 15 1670_1674 c.1596_1600delGAAAG c.(1594-1602)CGGAAAGCCfs p.R532fs CARS_uc001lxe.2_Frame_Shift_Del_p.R522fs|CARS_uc001lxf.2_Frame_Shift_Del_p.R615fs|CARS_uc001lxg.2_Frame_Shift_Del_p.R532fs|CARS_uc010qxo.1_Frame_Shift_Del_p.R615fs|CARS_uc010qxp.1_Frame_Shift_Del_p.R545fs NM_001751 NP_001742 P49589 SYCC_HUMAN cysteinyl-tRNA synthetase isoform b 532_534 cysteinyl-tRNA aminoacylation cytoplasm|cytosol ATP binding|cysteine-tRNA ligase activity|metal ion binding|protein homodimerization activity|protein homodimerization activity|tRNA binding|tRNA binding CARS/ALK(5) soft_tissue(5)|ovary(2) 7 all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681) BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218) L-Cysteine(DB00151) TTCCTCACGGCTTTCCGGGCTGCCA 0.576 0.19 43 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 836 169 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.12 72 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 29 329 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 48 131 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 136 760 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 GMS10_CENTRAL_NERVOUS_SYSTEM NA GMS10_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 67 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 42 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.20 342 88 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.33 8 4 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.43 8 6 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.56 14 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 112 153 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 41 74 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.62 64 104 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 16 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 18 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.34 450 230 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 592 219 CBL 867 broad.mit.edu 37 11 119077232 119077233 + In_Frame_Ins INS - CAC CAC GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr11:119077232_119077233insCAC uc001pwe.2 + 1 243_244 c.105_106insCAC c.(103-108)insCAC p.42_43insH NM_005188 NP_005179 P22681 CBL_HUMAN Cas-Br-M (murine) ecotropic retroviral 42_43 epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis cytosol|nucleus calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1) 149 Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784) CCTTCCAGCCGcaccaccacca 0.599 0.50 9 9 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.57 6 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.48 46 43 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.36 70 39 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 39 378 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 68 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 GOS3_CENTRAL_NERVOUS_SYSTEM NA GOS3_CENTRAL_NERVOUS_SYSTEM NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 0.000 0.11 245 29 HUWE1 10075 broad.mit.edu 37 X 53561050 53561050 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chrX:53561050delG uc004dsp.2 - 83 13342 c.12940delC c.(12940-12942)CTCfs p.L4314fs HUWE1_uc004dsn.2_Frame_Shift_Del_p.L3122fs NM_031407 NP_113584 Q7Z6Z7 HUWE1_HUMAN HECT, UBA and WWE domain containing 1 4314 HECT. base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process cytoplasm|nucleus DNA binding|protein binding|ubiquitin-protein ligase activity ovary(8)|large_intestine(4)|breast(4)|kidney(1) 17 0.000 0.44 559 448 ATRX 546 broad.mit.edu 37 X 76939674 76939674 + Frame_Shift_Del DEL T - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chrX:76939674delT uc004ecp.3 - 9 1306 c.1074delA c.(1072-1074)AAAfs p.K358fs ATRX_uc004ecq.3_Frame_Shift_Del_p.K320fs|ATRX_uc004eco.3_Frame_Shift_Del_p.K143fs|ATRX_uc004ecr.2_Frame_Shift_Del_p.K319fs|ATRX_uc010nlx.1_Frame_Shift_Del_p.K358fs|ATRX_uc010nly.1_Frame_Shift_Del_p.K303fs NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 358 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) TCTCAATCAGTTTTTTTGCCT 0.368 0.41 47 33 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 72 F8 2157 broad.mit.edu 37 X 154158195 154158195 + Frame_Shift_Del DEL T - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chrX:154158195delT uc004fmt.2 - 14 4041 c.3870delA c.(3868-3870)AAAfs p.K1290fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1290 B. acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) CTTCCTCCCCTTTTTTTGAGA 0.383 0.46 22 19 TNFRSF4 7293 broad.mit.edu 37 1 1147002 1147002 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr1:1147002delC uc001ade.2 - 7 772 c.767delG c.(766-768)GGAfs p.G256fs TNFRSF4_uc001adf.2_Frame_Shift_Del_p.G286fs NM_003327 NP_003318 P43489 TNR4_HUMAN tumor necrosis factor receptor superfamily, 256 Cytoplasmic (Potential). immune response|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|positive regulation of B cell proliferation|positive regulation of immunoglobulin secretion|T cell proliferation integral to plasma membrane tumor necrosis factor receptor activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199) GAAACTGCCTCCCCCTGGGGA 0.677 0.43 8 6 RPL22 6146 broad.mit.edu 37 1 6257785 6257786 + Frame_Shift_Del DEL TT - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr1:6257785_6257786delTT uc001amd.2 - 2 89_90 c.43_44delAA c.(43-45)AAGfs p.K15fs RPL22_uc001ame.2_Frame_Shift_Del_p.K15fs NM_000983 NP_000974 P35268 RL22_HUMAN ribosomal protein L22 proprotein 15 endocrine pancreas development|translational elongation|translational termination|viral transcription cytosolic large ribosomal subunit heparin binding|RNA binding|structural constituent of ribosome 0 Ovarian(185;0.0634) all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211) Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182) AACTTGCTTCTTTTTTTTGCCC 0.396 0.49 40 38 SPEN 23013 broad.mit.edu 37 1 16258944 16258944 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr1:16258944delA uc001axk.1 + 11 6413 c.6209delA c.(6208-6210)GAAfs p.E2070fs SPEN_uc010obp.1_Frame_Shift_Del_p.E2029fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2070 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) CCGGCCCCTGAAAAAAACTCC 0.478 0.56 32 41 ARID1A 8289 broad.mit.edu 37 1 27097622 27097622 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr1:27097622delA uc001bmv.1 + 12 3584 c.3211delA c.(3211-3213)AAAfs p.K1071fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.K1071fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.K1071fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.K688fs|ARID1A_uc001bmx.1_5'UTR|ARID1A_uc009vsm.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1071 ARID. androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.K1072fs*21(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CAACAAGAACAAAAAATGGCG 0.483 0.43 32 24 HDAC1 3065 broad.mit.edu 37 1 32798326 32798328 + In_Frame_Del DEL AGG - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr1:32798326_32798328delAGG uc001bvb.1 + 13 1460_1462 c.1397_1399delAGG c.(1396-1401)AAGGAG>AAG p.E468del HDAC1_uc010ohf.1_In_Frame_Del_p.E439del|HDAC1_uc001bvc.1_In_Frame_Del_p.E224del NM_004964 NP_004955 Q13547 HDAC1_HUMAN histone deacetylase 1 468 Missing: Strongly decreases deacetylase activity, and disrupts interaction with NuRD and SIN3 complexes. anti-apoptosis|blood coagulation|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|histone H3 deacetylation|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of androgen receptor signaling pathway|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter cytosol|NuRD complex|Sin3 complex activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|identical protein binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|RNA polymerase II transcription corepressor activity|sequence-specific DNA binding transcription factor activity ovary(1)|lung(1)|breast(1) 3 Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113) KIRC - Kidney renal clear cell carcinoma(1967;0.138) Vorinostat(DB02546) GAGAAAACCAAGGAGGAGAAGCC 0.557 0.39 23 15 HIPK1 204851 broad.mit.edu 37 1 114514538 114514538 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr1:114514538delG uc001eem.2 + 15 3267 c.3106delG c.(3106-3108)GGGfs p.G1036fs HIPK1_uc001eel.2_Frame_Shift_Del_p.G1036fs|HIPK1_uc001een.2_Frame_Shift_Del_p.G1036fs|HIPK1_uc001eeo.2_Frame_Shift_Del_p.G662fs|HIPK1_uc001eep.2_Frame_Shift_Del_p.G642fs|HIPK1_uc001eeq.2_Frame_Shift_Del_p.G328fs NM_198268 NP_938009 Q86Z02 HIPK1_HUMAN homeodomain-interacting protein kinase 1 isoform 1036 Interaction with TP53. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus ATP binding|protein binding|protein serine/threonine kinase activity ovary(4) 4 Lung SC(450;0.184) all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05) Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133) AGCTCAACGCGGGGGGACCAG 0.522 0.28 162 63 ITGA10 8515 broad.mit.edu 37 1 145533551 145533551 + Frame_Shift_Del DEL G - - rs142042030 byFrequency GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr1:145533551delG uc001eoa.2 + 12 1510 c.1434delG c.(1432-1434)CAGfs p.Q478fs NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Frame_Shift_Del_p.Q347fs|ITGA10_uc009wiw.2_Frame_Shift_Del_p.Q335fs|ITGA10_uc010oyw.1_Frame_Shift_Del_p.Q423fs NM_003637 NP_003628 O75578 ITA10_HUMAN integrin, alpha 10 precursor 478 FG-GAP 5.|Extracellular (Potential). cell-matrix adhesion|integrin-mediated signaling pathway integrin complex collagen binding|receptor activity lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1) 8 all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786) AGAGCCTCCAGGGGGAGCAGG 0.577 0.40 40 27 SETDB1 9869 broad.mit.edu 37 1 150933382 150933382 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr1:150933382delC uc001evu.2 + 16 3034 c.2844delC c.(2842-2844)CACfs p.H948fs SETDB1_uc001evv.2_Frame_Shift_Del_p.H948fs|SETDB1_uc009wmg.1_Frame_Shift_Del_p.H948fs NM_001145415 NP_001138887 Q15047 SETB1_HUMAN SET domain, bifurcated 1 isoform 1 948 SET. regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|Golgi apparatus|nucleus|plasma membrane DNA binding|histone-lysine N-methyltransferase activity|protein binding|zinc ion binding ovary(2)|upper_aerodigestive_tract(1) 3 all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211) AGGACTCCCACCCCCCAGATC 0.572 0.39 129 84 PCP4L1 654790 broad.mit.edu 37 1 161254153 161254154 + In_Frame_Ins INS - GGA GGA GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr1:161254153_161254154insGGA uc001gad.2 + 3 337_338 c.89_90insGGA c.(88-90)GCG>GCGGAG p.35_36insE NM_001102566 NP_001096036 A6NKN8 PC4L1_HUMAN Purkinje cell protein 4 like 1 35_36 0 all_cancers(52;4.16e-18)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.00376) GTCAAGAAGGCGGAGGAGGAGG 0.485 0.38 46 28 CDK18 5129 broad.mit.edu 37 1 205492639 205492639 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr1:205492639delC uc001hcr.2 + 3 378 c.159delC c.(157-159)GACfs p.D53fs CDK18_uc009xbk.1_RNA|CDK18_uc009xbl.1_RNA|CDK18_uc010pri.1_Frame_Shift_Del_p.P74fs|CDK18_uc001hcp.2_Frame_Shift_Del_p.D53fs|CDK18_uc001hcq.2_Frame_Shift_Del_p.D53fs|CDK18_uc010prj.1_5'UTR|CDK18_uc001hcs.2_5'UTR|CDK18_uc009xbm.1_5'UTR NM_212503 NP_997668 Q07002 CDK18_HUMAN PCTAIRE protein kinase 3 isoform a 51 ATP binding|cyclin-dependent protein kinase activity|protein binding|signal transducer activity stomach(2) 2 TTGGCAGAGACCCCCCGCAGG 0.682 0.32 32 15 CDC42BPA 8476 broad.mit.edu 37 1 227182042 227182042 + Frame_Shift_Del DEL G - - rs67581567 GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr1:227182042delG uc001hqr.2 - 36 6030 c.5087delC c.(5086-5088)CCAfs p.P1696fs CDC42BPA_uc001hqq.2_Frame_Shift_Del_p.P995fs|CDC42BPA_uc001hqs.2_Frame_Shift_Del_p.P1615fs|CDC42BPA_uc009xes.2_Frame_Shift_Del_p.P1668fs|CDC42BPA_uc010pvs.1_Frame_Shift_Del_p.P1676fs|CDC42BPA_uc001hqp.2_Frame_Shift_Del_p.P914fs NM_003607 NP_003598 Q5VT25 MRCKA_HUMAN CDC42-binding protein kinase alpha isoform B 1709 actin cytoskeleton reorganization|intracellular signal transduction cell leading edge|cell-cell junction|cytoplasm ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1) 11 all_cancers(173;0.156)|Prostate(94;0.0792) AGCTGGGCTTGGGGGGCTGCT 0.552 0.41 110 76 OBSCN 84033 broad.mit.edu 37 1 228467648 228467648 + Frame_Shift_Del DEL T - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr1:228467648delT uc009xez.1 + 28 7567 c.7523delT c.(7522-7524)CTGfs p.L2508fs OBSCN_uc001hsn.2_Frame_Shift_Del_p.L2508fs|OBSCN_uc001hsp.1_Frame_Shift_Del_p.L207fs|OBSCN_uc001hsq.1_5'Flank NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 2508 Ig-like 24. apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) GACACGCCCCTGTCTCCCTCT 0.612 0.47 139 125 SOX11 6664 broad.mit.edu 37 2 5833217 5833217 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr2:5833217delA uc002qyj.2 + 1 419 c.364delA c.(364-366)AAAfs p.K122fs NM_003108 NP_003099 P35716 SOX11_HUMAN SRY-box 11 122 cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis cytoplasm|nucleolus enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding central_nervous_system(3) 3 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) OV - Ovarian serous cystadenocarcinoma(76;0.132) 0.000 0.30 613 264 MYCN 4613 broad.mit.edu 37 2 16082314 16082314 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr2:16082314delC uc002rci.2 + 2 428 c.128delC c.(127-129)ACCfs p.T43fs MYCNOS_uc002rch.1_5'Flank|MYCN_uc010yjr.1_Frame_Shift_Del_p.T35fs NM_005378 NP_005369 P04198 MYCN_HUMAN v-myc myelocytomatosis viral related oncogene, 43 regulation of transcription from RNA polymerase II promoter chromatin|nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity central_nervous_system(2)|ovary(1)|lung(1)|skin(1) 5 all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197) GBM - Glioblastoma multiforme(3;0.000332) CCCGACTCGACCCCCCCGGGG 0.657 0.45 6 5 AFF3 3899 broad.mit.edu 37 2 100368715 100368716 + Frame_Shift_Ins INS - T T GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr2:100368715_100368716insT uc002tag.2 - 8 1205_1206 c.969_970insA c.(967-972)AAAGTGfs p.K323fs AFF3_uc002taf.2_Frame_Shift_Ins_p.K348fs|AFF3_uc010fiq.1_Frame_Shift_Ins_p.K323fs|AFF3_uc010yvr.1_Frame_Shift_Ins_p.K477fs|AFF3_uc002tah.1_Frame_Shift_Ins_p.K348fs|AFF3_uc010fir.1_Frame_Shift_Ins_p.K400fs NM_002285 NP_002276 P51826 AFF3_HUMAN AF4/FMR2 family, member 3 isoform 1 323_324 multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1) 6 GTTGGTTCCACTTTGCCAGGTG 0.426 0.56 12 15 TTN 7273 broad.mit.edu 37 2 179642691 179642692 + Frame_Shift_Ins INS - GA GA GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr2:179642691_179642692insGA uc010zfg.1 - 25 4443_4444 c.4219_4220insTC c.(4219-4221)CCAfs p.P1407fs TTN_uc010zfh.1_Frame_Shift_Ins_p.P1361fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.P1361fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.P1361fs|TTN_uc002unb.2_Frame_Shift_Ins_p.P1407fs|uc002unc.1_RNA NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 1407 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CACTGAACGTGGAGAGAGAGAT 0.446 0.34 134 68 ITGAV 3685 broad.mit.edu 37 2 187521085 187521085 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr2:187521085delG uc002upq.2 + 17 1952 c.1676delG c.(1675-1677)AGGfs p.R559fs ITGAV_uc010frs.2_Frame_Shift_Del_p.R523fs|ITGAV_uc010zfv.1_Frame_Shift_Del_p.R513fs NM_002210 NP_002201 P06756 ITAV_HUMAN integrin alpha-V isoform 1 precursor 559 Extracellular (Potential). angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance integrin complex receptor activity|transforming growth factor beta binding ovary(2)|kidney(1)|skin(1) 4 OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189) STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108) ACTATTTCAAGGGGGGGACTG 0.428 0.15 89 16 PMS1 5378 broad.mit.edu 37 2 190682810 190682810 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr2:190682810delA uc002urh.3 + 5 1015 c.486delA c.(484-486)GCAfs p.A162fs PMS1_uc010zga.1_Frame_Shift_Del_p.A162fs|PMS1_uc010zgb.1_Frame_Shift_Del_p.A101fs|PMS1_uc002urk.3_Frame_Shift_Del_p.A162fs|PMS1_uc002uri.3_Frame_Shift_Del_p.A162fs|PMS1_uc010zgc.1_5'UTR|PMS1_uc010zgd.1_5'UTR|PMS1_uc002urj.2_RNA|PMS1_uc010fry.1_Frame_Shift_Del_p.A162fs|PMS1_uc010frz.2_Frame_Shift_Del_p.A162fs|PMS1_uc002url.2_5'UTR NM_000534 NP_000525 P54277 PMS1_HUMAN postmeiotic segregation 1 isoform a 162 mismatch repair|reciprocal meiotic recombination MutLalpha complex ATP binding|ATPase activity|mismatched DNA binding ovary(2)|kidney(1)|central_nervous_system(1) 4 OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751) ACTCAACTGCAAAAAAATGTA 0.328 0.31 11 5 SPEG 10290 broad.mit.edu 37 2 220347881 220347881 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr2:220347881delC uc010fwg.2 + 30 5696 c.5696delC c.(5695-5697)GCCfs p.A1899fs NM_005876 NP_005867 Q15772 SPEG_HUMAN SPEG complex locus 1899 muscle organ development|negative regulation of cell proliferation nucleus ATP binding|protein serine/threonine kinase activity stomach(9)|ovary(4)|central_nervous_system(1) 14 Renal(207;0.0183) Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163) 0.000 0.34 1156 593 HDAC4 9759 broad.mit.edu 37 2 240002823 240002823 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr2:240002823delG uc002vyk.3 - 22 3495 c.2703delC c.(2701-2703)CCCfs p.P901fs HDAC4_uc010fyy.2_Frame_Shift_Del_p.P858fs NM_006037 NP_006028 P56524 HDAC4_HUMAN histone deacetylase 4 901 Histone deacetylase. B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent histone deacetylase complex|transcriptional repressor complex activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding breast(3)|skin(2)|ovary(1) 6 all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159) Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04) CGTCTCCCATGGGGGGGTCCA 0.602 0.39 42 27 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.37 12 7 GATA2 2624 broad.mit.edu 37 3 128204842 128204842 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr3:128204842delC uc003ekm.3 - 4 1034 c.599delG c.(598-600)GGTfs p.G200fs GATA2_uc003ekn.3_Frame_Shift_Del_p.G200fs|GATA2_uc003eko.2_Frame_Shift_Del_p.G200fs NM_001145661 NP_001139133 P23769 GATA2_HUMAN GATA binding protein 2 isoform 1 200 blood coagulation|negative regulation of fat cell differentiation|negative regulation of fat cell proliferation|negative regulation of neural precursor cell proliferation|negative regulation of Notch signaling pathway|phagocytosis|positive regulation of angiogenesis|positive regulation of phagocytosis|positive regulation of transcription from RNA polymerase II promoter nucleoplasm C2H2 zinc finger domain binding|chromatin binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding haematopoietic_and_lymphoid_tissue(13)|lung(1)|skin(1) 15 GBM - Glioblastoma multiforme(114;0.173) GGCTGCACTACCCCCCGCGGA 0.632 0.37 146 87 SCD5 79966 broad.mit.edu 37 4 83719663 83719664 + Frame_Shift_Ins INS - C C GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr4:83719663_83719664insC uc003hna.2 - 1 347_348 c.27_28insG c.(25-30)GGGAAGfs p.G9fs SCD5_uc003hnb.3_Frame_Shift_Ins_p.G9fs|SCD5_uc003hnc.2_Frame_Shift_Ins_p.G9fs NM_001037582 NP_001032671 Q86SK9 SCD5_HUMAN stearoyl-CoA desaturase 5 isoform a 9_10 fatty acid biosynthetic process endoplasmic reticulum membrane|integral to membrane iron ion binding|stearoyl-CoA 9-desaturase activity ovary(1) 1 Colorectal(4;0.0323)|Hepatocellular(203;0.115) AAAGGGATCTTCCCCGCGTCGG 0.752 0.26 88 31 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 115 150 IL6ST 3572 broad.mit.edu 37 5 55272066 55272067 + Frame_Shift_Ins INS - G G GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr5:55272066_55272067insG uc003jqq.2 - 3 295_296 c.40_41insC c.(40-42)ATTfs p.I14fs IL6ST_uc010iwb.2_Frame_Shift_Ins_p.I14fs|IL6ST_uc010iwc.2_Frame_Shift_Ins_p.I14fs|IL6ST_uc010iwd.2_5'UTR|IL6ST_uc011cqk.1_5'UTR|IL6ST_uc003jqr.2_Frame_Shift_Ins_p.I14fs|IL6ST_uc010iwf.1_RNA NM_002184 NP_002175 P40189 IL6RB_HUMAN interleukin 6 signal transducer isoform 1 14 interleukin-6-mediated signaling pathway|leukemia inhibitory factor signaling pathway|negative regulation of interleukin-6-mediated signaling pathway|positive regulation of anti-apoptosis|positive regulation of cardiac muscle hypertrophy|positive regulation of osteoblast differentiation|positive regulation of T cell proliferation|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation vascular endothelial growth factor production ciliary neurotrophic factor receptor complex|extracellular region|extracellular space|interleukin-6 receptor complex|oncostatin-M receptor complex ciliary neurotrophic factor receptor activity|ciliary neurotrophic factor receptor binding|growth factor binding|protein homodimerization activity large_intestine(1)|ovary(1) 2 Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223) GGTGAGGAAAATAAACAAGGCT 0.312 0.52 33 36 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 42 26 APC 324 broad.mit.edu 37 5 112175621 112175624 + Frame_Shift_Del DEL CAAA - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr5:112175621_112175624delCAAA uc010jby.2 + 16 4710_4713 c.4330_4333delCAAA c.(4330-4335)CAAACAfs p.Q1444fs APC_uc011cvt.1_Frame_Shift_Del_p.Q1426fs|APC_uc003kpz.3_Frame_Shift_Del_p.Q1444fs|APC_uc003kpy.3_Frame_Shift_Del_p.Q1444fs|APC_uc010jbz.2_Frame_Shift_Del_p.Q1161fs|APC_uc010jca.2_Frame_Shift_Del_p.Q744fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1444_1445 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.T1445fs*27(4)|p.T1445fs*28(2)|p.Q1444fs*29(1)|p.Q1444*(1)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.P1441fs*28(1)|p.S1436fs*22(1)|p.P1441fs*27(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) ACCACCTCCTCAAACAGCTCAAAC 0.471 0.98 1 44 TNF 7124 broad.mit.edu 37 6 31543582 31543582 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr6:31543582delG uc003nui.2 + 1 233 c.64delG c.(64-66)GGGfs p.G22fs TNF_uc003nuj.2_5'Flank NM_000594 NP_000585 P01375 TNFA_HUMAN tumor necrosis factor alpha 22 Cytoplasmic (Potential). activation of caspase activity|activation of MAPK activity|activation of MAPKKK activity|anti-apoptosis|cellular response to nicotine|chronic inflammatory response to antigenic stimulus|embryonic digestive tract development|induction of apoptosis via death domain receptors|induction of necroptosis by extracellular signals|leukocyte tethering or rolling|necrotic cell death|negative regulation of branching involved in lung morphogenesis|negative regulation of cytokine secretion involved in immune response|negative regulation of fat cell differentiation|negative regulation of interleukin-6 production|negative regulation of lipid catabolic process|negative regulation of lipid storage|negative regulation of viral genome replication|positive regulation of calcidiol 1-monooxygenase activity|positive regulation of chemokine biosynthetic process|positive regulation of chemokine production|positive regulation of cytokine secretion|positive regulation of ERK1 and ERK2 cascade|positive regulation of fever generation|positive regulation of heterotypic cell-cell adhesion|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of membrane protein ectodomain proteolysis|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of NFAT protein import into nucleus|positive regulation of nitric oxide biosynthetic process|positive regulation of osteoclast differentiation|positive regulation of peptidyl-serine phosphorylation|positive regulation of podosome assembly|positive regulation of protein complex disassembly|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D biosynthetic process|protein import into nucleus, translocation|receptor biosynthetic process|regulation of insulin secretion|response to glucocorticoid stimulus|response to salt stress|response to virus|sequestering of triglyceride|transformed cell apoptosis|tumor necrosis factor-mediated signaling pathway external side of plasma membrane|extracellular space|integral to plasma membrane|membrane raft|phagocytic cup|recycling endosome cytokine activity|identical protein binding|protease binding|transcription regulatory region DNA binding|tumor necrosis factor receptor binding ovary(1)|pancreas(1)|skin(1) 3 Ovarian(999;0.00556) Adalimumab(DB00051)|Adenosine(DB00640)|Amrinone(DB01427)|Atorvastatin(DB01076)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Etanercept(DB00005)|Glucosamine(DB01296)|Infliximab(DB00065)|Naltrexone(DB00704)|Pranlukast(DB01411)|Procaterol(DB01366)|Saquinavir(DB01232)|Simvastatin(DB00641)|Thalidomide(DB01041) CAAGAAGACAGGGGGGCCCCA 0.642 0.39 67 43 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.32 25 12 DNAH8 1769 broad.mit.edu 37 6 38816440 38816440 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr6:38816440delA uc003ooe.1 + 35 5011 c.4411delA c.(4411-4413)AAAfs p.K1471fs NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 TGCTCCATTTAAAAAAAATAT 0.343 0.93 4 53 TTBK1 84630 broad.mit.edu 37 6 43251480 43251480 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr6:43251480delC uc003ouq.1 + 14 3281 c.3002delC c.(3001-3003)GCCfs p.A1001fs NM_032538 NP_115927 Q5TCY1 TTBK1_HUMAN tau tubulin kinase 1 1001 cell junction|cytoplasm|nucleus ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1) 9 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399) 0.000 0.46 990 853 DST 667 broad.mit.edu 37 6 56463452 56463452 + Frame_Shift_Del DEL T - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr6:56463452delT uc003pdf.2 - 40 5421 c.5393delA c.(5392-5394)AACfs p.N1798fs DST_uc003pcz.3_Frame_Shift_Del_p.N1620fs|DST_uc011dxj.1_Frame_Shift_Del_p.N1649fs|DST_uc011dxk.1_Frame_Shift_Del_p.N1660fs|DST_uc003pcy.3_Frame_Shift_Del_p.N1294fs|DST_uc010kaa.1_RNA NM_001144769 NP_001138241 Q03001 DYST_HUMAN dystonin isoform 2 3706 cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1) 14 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) GTTCTCTGTGTTTTTCACTAC 0.323 0.48 78 71 ARID1B 57492 broad.mit.edu 37 6 157099402 157099403 + In_Frame_Ins INS - CAG CAG GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr6:157099402_157099403insCAG uc003qqn.2 + 1 317_318 c.165_166insCAG c.(163-168)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) TAAACCAGTTCcagcagcagca 0.124 0.18 92 20 MLLT4 4301 broad.mit.edu 37 6 168323556 168323557 + Frame_Shift_Del DEL CA - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr6:168323556_168323557delCA uc003qwd.2 + 21 3047_3048 c.2905_2906delCA c.(2905-2907)CACfs p.H969fs MLLT4_uc003qwb.1_Frame_Shift_Del_p.H954fs|MLLT4_uc003qwc.1_Frame_Shift_Del_p.H970fs|MLLT4_uc003qwg.1_Frame_Shift_Del_p.H279fs NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 970 adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) GTTAATTCCTCACACACGTTCA 0.386 0.38 72 45 DLL1 28514 broad.mit.edu 37 6 170597414 170597414 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr6:170597414delG uc003qxm.2 - 4 1053 c.583delC c.(583-585)CGGfs p.R195fs DLL1_uc011ehc.1_Frame_Shift_Del_p.R195fs NM_005618 NP_005609 O00548 DLL1_HUMAN delta-like 1 precursor 195 Extracellular (Potential).|DSL. cell communication|cell fate determination|hemopoiesis|Notch receptor processing|Notch signaling pathway|regulation of cell adhesion extracellular region|integral to plasma membrane calcium ion binding|Notch binding lung(4)|ovary(1) 5 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584) GCATCGTCCCGGGGACGGCAG 0.627 0.46 80 68 TRRAP 8295 broad.mit.edu 37 7 98528336 98528336 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr7:98528336delG uc003upp.2 + 25 3683 c.3474delG c.(3472-3474)CTGfs p.L1158fs TRRAP_uc011kis.1_Frame_Shift_Del_p.L1158fs|TRRAP_uc003upr.2_Frame_Shift_Del_p.L850fs NM_003496 NP_003487 Q9Y4A5 TRRAP_HUMAN transformation/transcription domain-associated 1158 histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1) 37 all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274) STAD - Stomach adenocarcinoma(171;0.215) ATGCAAAGCTGGGGGGTGTGG 0.507 0.42 157 112 EPHB6 2051 broad.mit.edu 37 7 142561448 142561448 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr7:142561448delG uc011kst.1 + 6 947 c.160delG c.(160-162)GGGfs p.G54fs EPHB6_uc011ksu.1_Frame_Shift_Del_p.G54fs|EPHB6_uc003wbs.2_Intron|EPHB6_uc003wbt.2_5'UTR|EPHB6_uc003wbu.2_Intron NM_004445 NP_004436 O15197 EPHB6_HUMAN ephrin receptor EphB6 precursor 54 Extracellular (Potential). extracellular region|integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1) 19 Melanoma(164;0.059) 0.000 0.46 295 248 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 14 NOS3 4846 broad.mit.edu 37 7 150698398 150698398 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr7:150698398delG uc003wif.2 + 11 1609 c.1313delG c.(1312-1314)AGGfs p.R438fs NOS3_uc011kuy.1_Frame_Shift_Del_p.R232fs|NOS3_uc011kuz.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kva.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kvb.1_Frame_Shift_Del_p.R438fs NM_000603 NP_000594 P29474 NOS3_HUMAN nitric oxide synthase 3 isoform 1 438 Interaction with NOSIP. anti-apoptosis|arginine catabolic process|blood vessel remodeling|endothelial cell migration|mitochondrion organization|negative regulation of muscle hyperplasia|negative regulation of platelet activation|nitric oxide biosynthetic process|platelet activation|positive regulation of angiogenesis|positive regulation of guanylate cyclase activity|positive regulation of vasodilation|regulation of blood vessel size|regulation of nitric-oxide synthase activity|regulation of systemic arterial blood pressure by endothelin|response to fluid shear stress|response to heat|smooth muscle hyperplasia caveola|cytoskeleton|cytosol|Golgi membrane actin monomer binding|arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding central_nervous_system(5)|large_intestine(2)|skin(1) 8 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) L-Arginine(DB00125)|L-Citrulline(DB00155)|Rosuvastatin(DB01098)|Tetrahydrobiopterin(DB00360) 0.000 0.23 1057 311 PRKDC 5591 broad.mit.edu 37 8 48869768 48869769 + Frame_Shift_Ins INS - T T GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr8:48869768_48869769insT uc003xqi.2 - 3 343_344 c.286_287insA c.(286-288)ATGfs p.M96fs PRKDC_uc003xqj.2_Frame_Shift_Ins_p.M96fs|PRKDC_uc011ldh.1_Frame_Shift_Ins_p.M96fs NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic 96 cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) CTTCTGGCCCATTTTTTCTAAG 0.297 0.52 12 13 VPS13B 157680 broad.mit.edu 37 8 100050671 100050671 + Frame_Shift_Del DEL T - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr8:100050671delT uc003yiv.2 + 3 279 c.168delT c.(166-168)ACTfs p.T56fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.T56fs|VPS13B_uc003yit.2_Frame_Shift_Del_p.T56fs|VPS13B_uc003yiu.1_Frame_Shift_Del_p.T56fs|VPS13B_uc003yis.2_Frame_Shift_Del_p.T56fs|VPS13B_uc011lgy.1_5'UTR NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 56 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TACCATTCACTTTTTTAAGTG 0.254 0.38 42 26 COL14A1 7373 broad.mit.edu 37 8 121215953 121215953 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr8:121215953delA uc003yox.2 + 9 1148 c.883delA c.(883-885)AAAfs p.K295fs COL14A1_uc003yoy.2_5'UTR|COL14A1_uc010mde.1_5'UTR NM_021110 NP_066933 Q05707 COEA1_HUMAN collagen, type XIV, alpha 1 precursor 295 VWFA 1. cell-cell adhesion|collagen fibril organization collagen type XIV|extracellular space collagen binding|extracellular matrix structural constituent|protein binding, bridging ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1) 12 Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503) GTAAGGGGTGAAAAACGCGGA 0.493 0.38 8 5 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 45 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.15 99 17 SMC2 10592 broad.mit.edu 37 9 106878490 106878490 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr9:106878490delA uc004bbv.2 + 14 1969 c.1681delA c.(1681-1683)AAAfs p.K561fs SMC2_uc004bbu.1_Frame_Shift_Del_p.K561fs|SMC2_uc004bbw.2_Frame_Shift_Del_p.K561fs|SMC2_uc011lvl.1_Frame_Shift_Del_p.K561fs|SMC2_uc004bbx.2_Frame_Shift_Del_p.K561fs NM_001042551 NP_001036016 O95347 SMC2_HUMAN structural maintenance of chromosomes 2 561 Flexible hinge. cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism condensin complex|cytoplasm|nuclear chromosome ATP binding|protein heterodimerization activity ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1) 9 GGTTACTGGTAAAAAGCTACT 0.259 0.44 29 23 SPTAN1 6709 broad.mit.edu 37 9 131388219 131388221 + In_Frame_Del DEL AAG - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr9:131388219_131388221delAAG uc004bvl.3 + 47 6339_6341 c.6226_6228delAAG c.(6226-6228)AAGdel p.K2078del SPTAN1_uc004bvm.3_In_Frame_Del_p.K2083del|SPTAN1_uc004bvn.3_In_Frame_Del_p.K2058del|SPTAN1_uc010mye.1_5'Flank|SPTAN1_uc010myf.1_5'Flank NM_003127 NP_003118 Q13813 SPTA2_HUMAN spectrin, alpha, non-erythrocytic 1 2078 Spectrin 21. actin filament capping|axon guidance|cellular component disassembly involved in apoptosis cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton breast(5)|ovary(4)|pancreas(1) 10 AGCCGCCCGCAAGAAGAAGCTTC 0.616 0.32 41 19 TCERG1L 256536 broad.mit.edu 37 10 132915126 132915126 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr10:132915126delG uc001lkp.2 - 9 1417 c.1331delC c.(1330-1332)CCGfs p.P444fs TCERG1L_uc009yax.1_RNA NM_174937 NP_777597 Q5VWI1 TCRGL_HUMAN transcription elongation regulator 1-like 444 large_intestine(2)|ovary(2) 4 all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09) all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276) GAGGATCTGCGGGGGCGGCGT 0.622 0.48 31 29 PIK3C2A 5286 broad.mit.edu 37 11 17112906 17112907 + Frame_Shift_Ins INS - T T GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr11:17112906_17112907insT uc001mmq.3 - 31 4918_4919 c.4852_4853insA c.(4852-4854)ACGfs p.T1618fs PIK3C2A_uc009ygu.1_Frame_Shift_Ins_p.T221fs|PIK3C2A_uc010rcw.1_Frame_Shift_Ins_p.T1238fs|PIK3C2A_uc001mmr.3_Intron NM_002645 NP_002636 O00443 P3C2A_HUMAN phosphoinositide-3-kinase, class 2 alpha 1618 Nuclear localization signal.|C2. cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity lung(4)|central_nervous_system(4)|stomach(1)|ovary(1) 10 Phosphatidylserine(DB00144) CGGATTCCTCGTTTTTCGTGAA 0.287 0.54 39 46 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.91 4 39 RELA 5970 broad.mit.edu 37 11 65421971 65421972 + Frame_Shift_Ins INS - G G GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr11:65421971_65421972insG uc001ofg.2 - 11 1673_1674 c.1533_1534insC c.(1531-1536)CCCGACfs p.P511fs RELA_uc001ofh.2_Frame_Shift_Ins_p.P508fs|RELA_uc010ron.1_Frame_Shift_Ins_p.P522fs|RELA_uc009yqr.2_Frame_Shift_Ins_p.P458fs|RELA_uc001ofe.2_3'UTR|RELA_uc001off.2_Frame_Shift_Ins_p.P408fs NM_021975 NP_068810 Q04206 TF65_HUMAN v-rel reticuloendotheliosis viral oncogene 511_512 anti-apoptosis|cellular defense response|cytokine-mediated signaling pathway|defense response to virus|inflammatory response|innate immune response|interspecies interaction between organisms|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription, DNA-dependent|nerve growth factor receptor signaling pathway|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of inflammatory response|response to interleukin-1|response to UV-B|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|transcription factor complex activating transcription factor binding|chromatin binding|identical protein binding|NF-kappaB binding|phosphate binding|protein kinase binding|protein N-terminus binding|repressing transcription factor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|ubiquitin protein ligase binding lung(3)|ovary(1) 4 GGAGCTGGGTCGGGGGGCCTCT 0.624 0.10 75 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 853 181 LRP6 4040 broad.mit.edu 37 12 12274318 12274318 + Frame_Shift_Del DEL G - - rs145639537 byFrequency GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr12:12274318delG uc001rah.3 - 23 4726 c.4584delC c.(4582-4584)CCCfs p.P1528fs BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Frame_Shift_Del_p.P1483fs NM_002336 NP_002327 O75581 LRP6_HUMAN low density lipoprotein receptor-related protein 1528 PPPSP motif B.|Cytoplasmic (Potential). cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1) 12 Prostate(47;0.0865) AGGGTGTGGTGGGGGGTGCAA 0.468 0.41 224 158 IRAK4 51135 broad.mit.edu 37 12 44162032 44162032 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr12:44162032delA uc001rnu.3 + 3 248 c.118delA c.(118-120)AAAfs p.K40fs IRAK4_uc001rnt.3_Frame_Shift_Del_p.K40fs|IRAK4_uc001rnx.3_5'UTR|IRAK4_uc001rny.3_5'UTR|IRAK4_uc010sky.1_Intron|IRAK4_uc001rnv.3_5'UTR|IRAK4_uc001rnw.3_5'UTR NM_001114182 NP_001107654 Q9NWZ3 IRAK4_HUMAN interleukin-1 receptor-associated kinase 4 40 Death. innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol|endosome membrane|plasma membrane ATP binding|magnesium ion binding|protein serine/threonine kinase activity 0 all_cancers(12;0.00149) Lung NSC(34;0.0804)|all_lung(34;0.181) GBM - Glioblastoma multiforme(48;0.04) TGTAGCTATTAAAAAACCATC 0.328 0.49 36 34 LRP1 4035 broad.mit.edu 37 12 57603940 57603940 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr12:57603940delC uc001snd.2 + 81 13034 c.12568delC c.(12568-12570)CCCfs p.P4190fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 4190 Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CTCTCCAACGCCCCCCCCAGA 0.637 0.38 88 54 GLI1 2735 broad.mit.edu 37 12 57860075 57860076 + Frame_Shift_Del DEL GG - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr12:57860075_57860076delGG uc001snx.2 + 8 893_894 c.815_816delGG c.(814-816)TGGfs p.W272fs GLI1_uc009zpq.2_Frame_Shift_Del_p.W144fs NM_005269 NP_005260 P08151 GLI1_HUMAN GLI family zinc finger 1 isoform 1 272 C2H2-type 2. epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter cytosol|nucleus transcription regulatory region DNA binding|zinc ion binding skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1) 15 GBM - Glioblastoma multiforme(3;3.99e-32) GTGTGCCACTGGGGGGGCTGCT 0.594 0.45 326 271 CYP27B1 1594 broad.mit.edu 37 12 58160654 58160654 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr12:58160654delC uc001spz.1 - 1 323 c.171delG c.(169-171)GGGfs p.G57fs CYP27B1_uc001sqa.1_5'UTR|CYP27B1_uc001sqb.1_5'Flank|CYP27B1_uc001sqc.1_5'Flank NM_000785 NP_000776 O15528 CP27B_HUMAN cytochrome P450, family 27, subfamily B, 57 bone mineralization|calcium ion homeostasis|calcium ion transport|decidualization|G1 to G0 transition|hormone biosynthetic process|negative regulation of calcidiol 1-monooxygenase activity|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of keratinocyte differentiation|positive regulation of vitamin D 24-hydroxylase activity|positive regulation of vitamin D receptor signaling pathway|regulation of bone mineralization|response to estrogen stimulus|response to interferon-gamma|response to lipopolysaccharide|response to tumor necrosis factor|response to vitamin D|vitamin D biosynthetic process|xenobiotic metabolic process mitochondrial outer membrane calcidiol 1-monooxygenase activity|electron carrier activity|heme binding central_nervous_system(3) 3 all_cancers(7;8.09e-80)|Lung NSC(6;2.26e-27)|all_lung(6;1.99e-25)|all_epithelial(6;3.62e-18)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122) GBM - Glioblastoma multiforme(5;1.97e-113)|all cancers(5;1.54e-78)|BRCA - Breast invasive adenocarcinoma(9;0.0294) Calcidiol(DB00146)|Calcitriol(DB00136)|Ergocalciferol(DB00153) GCCTCGACAGCCCCCCCTTGC 0.597 0.39 82 52 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.35 90 48 ZMYM2 7750 broad.mit.edu 37 13 20657094 20657094 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr13:20657094delA uc001umr.2 + 24 4040 c.3742delA c.(3742-3744)AAAfs p.K1248fs ZMYM2_uc001ums.2_Frame_Shift_Del_p.K1248fs|ZMYM2_uc001umt.2_Frame_Shift_Del_p.K1248fs|ZMYM2_uc001umv.2_Frame_Shift_Del_p.K628fs|ZMYM2_uc001umw.2_Frame_Shift_Del_p.K701fs NM_003453 NP_003444 Q9UBW7 ZMYM2_HUMAN zinc finger protein 198 1248 regulation of transcription, DNA-dependent|transcription, DNA-dependent PML body ubiquitin conjugating enzyme binding|zinc ion binding lung(3)|ovary(2)|prostate(1) 6 all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856) TAGGCATTGGAAAAAAAATCC 0.363 0.40 54 36 SACS 26278 broad.mit.edu 37 13 23909222 23909222 + Frame_Shift_Del DEL T - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr13:23909222delT uc001uon.2 - 10 9382 c.8793delA c.(8791-8793)AAAfs p.K2931fs SACS_uc001uoo.2_Frame_Shift_Del_p.K2784fs|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 2931 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) GGAAATACCGTTTTTTTAACT 0.358 0.47 115 102 FLT3 2322 broad.mit.edu 37 13 28578215 28578216 + Frame_Shift_Del DEL GA - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr13:28578215_28578216delGA uc001urw.2 - 24 3037_3038 c.2955_2956delTC c.(2953-2958)TCTCCGfs p.S985fs FLT3_uc010aao.2_RNA|FLT3_uc010tdn.1_Frame_Shift_Del_p.S944fs NM_004119 NP_004110 P36888 FLT3_HUMAN fms-related tyrosine kinase 3 precursor 985_986 Cytoplasmic (Potential). positive regulation of cell proliferation integral to plasma membrane ATP binding|vascular endothelial growth factor receptor activity haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1) 8549 Acute lymphoblastic leukemia(6;0.04) Lung SC(185;0.0156)|Ovarian(182;0.0392) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212) Sorafenib(DB00398)|Sunitinib(DB01268) TGAGCCTGCGGAGAGAGTAGCC 0.460 0.41 73 51 EDNRB 1910 broad.mit.edu 37 13 78475267 78475267 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr13:78475267delA uc001vko.2 - 4 1135 c.877delT c.(877-879)TATfs p.Y293fs EDNRB_uc001vkq.1_Frame_Shift_Del_p.Y293fs|uc001vkn.1_Intron|EDNRB_uc010aez.1_Frame_Shift_Del_p.Y293fs|EDNRB_uc001vkp.1_Frame_Shift_Del_p.Y376fs NM_001122659 NP_001116131 P24530 EDNRB_HUMAN endothelin receptor type B isoform 1 precursor 293 Helical; Name=5; (Potential). activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction integral to plasma membrane endothelin-B receptor activity|peptide hormone binding 0 Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037) GBM - Glioblastoma multiforme(99;0.0933) Bosentan(DB00559) ATTAGTGTATAAAAAAATGCA 0.343 0.43 47 35 NOVA1 4857 broad.mit.edu 37 14 27066542 27066542 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr14:27066542delG uc001wpy.2 - 1 419 c.101delC c.(100-102)CCTfs p.P34fs NOVA1_uc001wpz.2_Frame_Shift_Del_p.P34fs|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_Frame_Shift_Del_p.P34fs NM_002515 NP_002506 P51513 NOVA1_HUMAN neuro-oncological ventral antigen 1 isoform 1 34 Bipartite nuclear localization signal (Potential). locomotory behavior|RNA splicing|synaptic transmission nucleus RNA binding skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1) 5 GBM - Glioblastoma multiforme(265;0.0135) 0.000 0.48 867 810 PRKD1 5587 broad.mit.edu 37 14 30047530 30047531 + Frame_Shift_Ins INS - T T GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr14:30047530_30047531insT uc001wqh.2 - 17 2651_2652 c.2470_2471insA c.(2470-2472)ATGfs p.M824fs NM_002742 NP_002733 Q15139 KPCD1_HUMAN protein kinase D1 824 Protein kinase. cell proliferation|intracellular signal transduction|sphingolipid metabolic process cytosol|integral to plasma membrane ATP binding|metal ion binding|protein binding|protein kinase C activity lung(3)|large_intestine(2)|ovary(2)|skin(1) 8 Hepatocellular(127;0.0604) LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252) GBM - Glioblastoma multiforme(265;0.00888) GCGCTTTCTCATTTTTACTTGC 0.322 0.45 34 28 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.59 23 33 SPRED1 161742 broad.mit.edu 37 15 38616977 38616977 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr15:38616977delA uc001zka.3 + 4 725 c.390delA c.(388-390)TCAfs p.S130fs NM_152594 NP_689807 Q7Z699 SPRE1_HUMAN sprouty-related protein 1 with EVH-1 domain 130 inactivation of MAPK activity|multicellular organismal development caveola|nucleus stem cell factor receptor binding ovary(2)|lung(2)|skin(1) 5 all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091) GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244) 0.000 0.18 142 31 SRP14 6727 broad.mit.edu 37 15 40328597 40328599 + In_Frame_Del DEL TGC - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr15:40328597_40328599delTGC uc001zkq.2 - 5 418_420 c.346_348delGCA c.(346-348)GCAdel p.A116del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgcggcaggtgctgctgctgct 0.227 0.27 74 28 TYRO3 7301 broad.mit.edu 37 15 41861146 41861147 + Frame_Shift_Del DEL GT - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr15:41861146_41861147delGT uc001zof.1 + 9 1402_1403 c.1178_1179delGT c.(1177-1179)CGTfs p.R393fs NM_006293 NP_006284 Q06418 TYRO3_HUMAN TYRO3 protein tyrosine kinase precursor 393 Fibronectin type-III 2.|Extracellular (Potential). integral to plasma membrane ATP binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity ovary(3)|lung(2)|central_nervous_system(1) 6 all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262) OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117) CTGATCGTACGTGTGTGCGTCT 0.594 0.18 411 88 SGK269 79834 broad.mit.edu 37 15 77473301 77473301 + Frame_Shift_Del DEL T - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr15:77473301delT uc002bcm.2 - 3 1276 c.968delA c.(967-969)AATfs p.N323fs SGK269_uc002bcn.2_Frame_Shift_Del_p.N323fs NM_024776 NP_079052 Q9H792 PEAK1_HUMAN NKF3 kinase family member 323 cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading actin cytoskeleton|cytoplasm|focal adhesion ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding 0 STAD - Stomach adenocarcinoma(199;0.124) GACCACAGAATTTTCCTCATA 0.428 0.48 105 96 FURIN 5045 broad.mit.edu 37 15 91422043 91422044 + Frame_Shift_Ins INS - C C GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr15:91422043_91422044insC uc002bpu.1 + 9 1106_1107 c.890_891insC c.(889-891)GGCfs p.G297fs NM_002569 NP_002560 P09958 FURIN_HUMAN furin preproprotein 297 cell proliferation|negative regulation of low-density lipoprotein particle receptor catabolic process|negative regulation of transforming growth factor-beta1 production|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|Notch signaling pathway|peptide biosynthetic process|peptidyl-glutamic acid carboxylation|post-translational protein modification|secretion by cell|signal peptide processing|transforming growth factor beta receptor signaling pathway|viral assembly, maturation, egress, and release cell surface|Golgi lumen|Golgi membrane|integral to membrane|membrane raft|plasma membrane|trans-Golgi network|trans-Golgi network transport vesicle metal ion binding|nerve growth factor binding|peptide binding|protease binding|serine-type endopeptidase activity|serine-type endopeptidase inhibitor activity central_nervous_system(4)|lung(2)|breast(1) 7 Lung NSC(78;0.0771)|all_lung(78;0.137) Lung(145;0.189) GGGAACGGGGGCCGGGAACATG 0.629 0.41 13 9 MYH11 4629 broad.mit.edu 37 16 15857685 15857688 + Frame_Shift_Del DEL TTTC - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr16:15857685_15857688delTTTC uc002ddy.2 - 10 1201_1204 c.1094_1097delGAAA c.(1093-1098)AGAAACfs p.R365fs MYH11_uc002ddv.2_Frame_Shift_Del_p.R372fs|MYH11_uc002ddw.2_Frame_Shift_Del_p.R365fs|MYH11_uc002ddx.2_Frame_Shift_Del_p.R372fs|MYH11_uc010bvg.2_Frame_Shift_Del_p.R197fs|MYH11_uc002dea.1_Frame_Shift_Del_p.R71fs NM_002474 NP_002465 P35749 MYH11_HUMAN smooth muscle myosin heavy chain 11 isoform 365_366 Myosin head-like. axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction cytosol|melanosome|muscle myosin complex|myosin filament actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1) 15 CTGGTCTGTGTTTCTTTCCTTCTT 0.505 0.45 30 25 CDH1 999 broad.mit.edu 37 16 68835781 68835781 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr16:68835781delC uc002ewg.1 + 3 496 c.372delC c.(370-372)CGCfs p.R124fs CDH1_uc010vlj.1_RNA|CDH1_uc010cfg.1_Frame_Shift_Del_p.R124fs NM_004360 NP_004351 P12830 CADH1_HUMAN cadherin 1, type 1 preproprotein 124 adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm cell adhesion molecule binding|gamma-catenin binding p.P126fs*89(1)|p.P127fs*41(1) breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1) 243 all_neural(199;0.0189)|Ovarian(137;0.0563) Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261) ACCACCACCGCCCCCCGCCCC 0.433 0.38 103 63 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 9 86 CBFA2T3 863 broad.mit.edu 37 16 88967930 88967931 + Frame_Shift_Ins INS - G G GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr16:88967930_88967931insG uc002fmm.1 - 2 471_472 c.285_286insC c.(283-288)CCCTCCfs p.P95fs CBFA2T3_uc002fml.1_Frame_Shift_Ins_p.P34fs|CBFA2T3_uc010cif.1_Frame_Shift_Ins_p.P34fs|CBFA2T3_uc002fmn.1_Frame_Shift_Ins_p.P95fs NM_005187 NP_005178 O75081 MTG16_HUMAN myeloid translocation gene on chromosome 16 95_96 Mediates localization to the nucleus (By similarity).|Pro-rich.|Mediates interaction with PDE7A (in isoform 2).|Required for nucleolar targeting (in isoform 1). cell proliferation|granulocyte differentiation Golgi membrane|nucleolus|nucleoplasm protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding large_intestine(3)|ovary(1) 4 BRCA - Breast invasive adenocarcinoma(80;0.0275) 0.000 0.34 846 428 MYH1 4619 broad.mit.edu 37 17 10400618 10400618 + Frame_Shift_Del DEL T - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr17:10400618delT uc002gmo.2 - 32 4611 c.4517delA c.(4516-4518)AATfs p.N1506fs uc002gml.1_Intron NM_005963 NP_005954 P12882 MYH1_HUMAN myosin, heavy chain 1, skeletal muscle, adult 1506 Potential. muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1) 21 CAAATTCTTATTTTCCCGTTT 0.308 0.48 37 34 WNK4 65266 broad.mit.edu 37 17 40939870 40939870 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr17:40939870delG uc002ibj.2 + 8 1837 c.1816delG c.(1816-1818)GGGfs p.G606fs WNK4_uc010wgx.1_Frame_Shift_Del_p.G270fs|WNK4_uc002ibk.1_Frame_Shift_Del_p.G378fs|WNK4_uc010wgy.1_Intron NM_032387 NP_115763 Q96J92 WNK4_HUMAN WNK lysine deficient protein kinase 4 606 intracellular protein kinase cascade tight junction ATP binding|protein serine/threonine kinase activity ovary(3)|skin(3)|stomach(1) 7 Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.0749) TCAGCCCCCTGGGGGGGTGCC 0.637 0.36 100 57 AXIN2 8313 broad.mit.edu 37 17 63532585 63532585 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr17:63532585delC uc002jfi.2 - 8 2283 c.1994delG c.(1993-1995)GGCfs p.G665fs AXIN2_uc002jfh.2_Frame_Shift_Del_p.G600fs NM_004655 NP_004646 Q9Y2T1 AXIN2_HUMAN axin 2 665 cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding central_nervous_system(1)|skin(1) 2 CCCGCTGTTGCCCCCCCACAG 0.657 0.48 31 29 TCF3 6929 broad.mit.edu 37 19 1620992 1620992 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr19:1620992delG uc002ltr.2 - 13 1135 c.1068delC c.(1066-1068)CCCfs p.P356fs TCF3_uc002lto.2_Frame_Shift_Del_p.P118fs|TCF3_uc002ltt.3_Frame_Shift_Del_p.P356fs|TCF3_uc002ltq.2_Frame_Shift_Del_p.P305fs|TCF3_uc002lts.1_Frame_Shift_Del_p.P272fs|TCF3_uc010dso.1_5'Flank NM_003200 NP_003191 P15923 TFE2_HUMAN transcription factor 3 isoform E12 356 B cell lineage commitment|B cell lineage commitment|G1 phase of mitotic cell cycle|immunoglobulin V(D)J recombination|muscle cell differentiation|positive regulation of B cell proliferation|positive regulation of cell cycle|positive regulation of muscle cell differentiation|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter cytoplasm|nucleus|protein complex|transcription factor complex bHLH transcription factor binding|DNA binding|E-box binding|identical protein binding|mitogen-activated protein kinase kinase kinase binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|vitamin D response element binding lung(2)|breast(2)|ovary(1)|large_intestine(1)|skin(1) 7 Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.37 276 164 MAST1 22983 broad.mit.edu 37 19 12984594 12984595 + Frame_Shift_Del DEL CA - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr19:12984594_12984595delCA uc002mvm.2 + 26 3751_3752 c.3623_3624delCA c.(3622-3624)GCAfs p.A1208fs NM_014975 NP_055790 Q9Y2H9 MAST1_HUMAN microtubule associated serine/threonine kinase 1208 cytoskeleton organization|intracellular protein kinase cascade cytoplasm|cytoskeleton|plasma membrane ATP binding|magnesium ion binding|protein serine/threonine kinase activity ovary(3)|lung(2)|large_intestine(1)|skin(1) 7 0.000 0.48 692 637 PRKACA 5566 broad.mit.edu 37 19 14203926 14203926 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr19:14203926delA uc002myc.2 - 10 1254 c.1054delT c.(1054-1056)TAGfs p.*352fs SAMD1_uc010xnl.1_5'Flank|PRKACA_uc002myb.2_Frame_Shift_Del_p.*344fs NM_002730 NP_002721 P17612 KAPCA_HUMAN cAMP-dependent protein kinase catalytic subunit 352 activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|G2/M transition of mitotic cell cycle|gluconeogenesis|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|regulation of insulin secretion|transmembrane transport|triglyceride catabolic process|water transport cAMP-dependent protein kinase complex|centrosome|cytosol|nucleoplasm|plasma membrane ATP binding|cAMP-dependent protein kinase activity|cAMP-dependent protein kinase inhibitor activity|protein kinase binding lung(1) 1 GCATGCCCCTAAAACTCAGAA 0.478 0.39 41 26 PKN1 5585 broad.mit.edu 37 19 14552016 14552016 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr19:14552016delC uc002myp.2 + 2 251 c.83delC c.(82-84)GCCfs p.A28fs PKN1_uc002myq.2_Frame_Shift_Del_p.A34fs NM_002741 NP_002732 Q16512 PKN1_HUMAN protein kinase N1 isoform 2 28 activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent endosome|nucleus|plasma membrane androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1) 8 0.000 0.23 805 242 CRTC1 23373 broad.mit.edu 37 19 18870878 18870879 + Frame_Shift_Ins INS - G G GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr19:18870878_18870879insG uc002nkb.3 + 8 814_815 c.726_727insG c.(724-729)ACAGGGfs p.T242fs CRTC1_uc010ebv.2_Frame_Shift_Ins_p.T258fs|CRTC1_uc010ebw.2_Frame_Shift_Ins_p.T107fs|CRTC1_uc002nkc.3_Frame_Shift_Ins_p.T107fs NM_015321 NP_056136 Q6UUV9 CRTC1_HUMAN mucoepidermoid carcinoma translocated 1 isoform 242_243 Nuclear export signal (By similarity). interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus|plasma membrane cAMP response element binding protein binding|protein binding CRTC1/MAML2(516) salivary_gland(474)|lung(35)|thyroid(4)|breast(3)|skin(2)|ovary(1) 519 CCCACAACACAGGGGGGTCCCT 0.658 0.33 22 11 MAP3K10 4294 broad.mit.edu 37 19 40718995 40718995 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr19:40718995delG uc002ona.2 + 8 2025 c.1737delG c.(1735-1737)CTGfs p.L579fs MAP3K10_uc002onb.2_5'UTR NM_002446 NP_002437 Q02779 M3K10_HUMAN mitogen-activated protein kinase kinase kinase 579 activation of JUN kinase activity|induction of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of JNK cascade|protein autophosphorylation|smoothened signaling pathway cytoplasm ATP binding|bHLH transcription factor binding|JUN kinase kinase kinase activity|protein homodimerization activity|transcription corepressor activity ovary(2)|lung(2)|skin(1)|pancreas(1) 6 0.000 0.46 417 358 CIC 23152 broad.mit.edu 37 19 42794627 42794627 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr19:42794627delC uc002otf.1 + 10 1747 c.1707delC c.(1705-1707)GGCfs p.G569fs NM_015125 NP_055940 Q96RK0 CIC_HUMAN capicua homolog 569 Pro-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1) 11 Prostate(69;0.00682) GCACAGCGGGCCCCCTACGGC 0.677 0.43 40 30 CIC 23152 broad.mit.edu 37 19 42798164 42798164 + Frame_Shift_Del DEL C - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr19:42798164delC uc002otf.1 + 17 4158 c.4118delC c.(4117-4119)TCCfs p.S1373fs NM_015125 NP_055940 Q96RK0 CIC_HUMAN capicua homolog 1373 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1) 11 Prostate(69;0.00682) GTGCTGCCCTCCCCCACCCTG 0.637 0.43 165 123 GLTSCR1 29998 broad.mit.edu 37 19 48176865 48176865 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr19:48176865delG uc002phh.3 + 3 228 c.34delG c.(34-36)GTGfs p.V12fs NM_015711 NP_056526 Q9NZM4 GSCR1_HUMAN glioma tumor suppressor candidate region gene 1 12 protein binding pancreas(3) 3 all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086) all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355) CTTACTAGACGTGATTTGGTG 0.323 0.35 135 74 LMTK3 114783 broad.mit.edu 37 19 49002136 49002136 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr19:49002136delG uc002pjk.2 - 12 2277 c.2277delC c.(2275-2277)CCCfs p.P759fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.42 341 250 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 43 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 115 667 MCM3AP 8888 broad.mit.edu 37 21 47663397 47663397 + Frame_Shift_Del DEL G - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr21:47663397delG uc002zir.1 - 24 5314 c.5278delC c.(5278-5280)CGGfs p.R1760fs MCM3APAS_uc002zim.2_Intron|MCM3APAS_uc002zin.2_Intron|MCM3AP_uc002zio.1_Frame_Shift_Del_p.R255fs|MCM3AP_uc002zip.1_Frame_Shift_Del_p.R501fs|MCM3AP_uc002ziq.1_Frame_Shift_Del_p.R687fs|MCM3APAS_uc002zis.1_Intron NM_003906 NP_003897 O60318 MCM3A_HUMAN minichromosome maintenance complex component 3 1760 DNA replication|protein import into nucleus cytosol|nucleus DNA binding|nucleotide binding large_intestine(2)|lung(1)|ovary(1)|skin(1) 5 Breast(49;0.112) ACAGGAAGCCGGGGGGGCGTC 0.527 0.39 104 66 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 8 104 MED15 51586 broad.mit.edu 37 22 20918897 20918899 + In_Frame_Del DEL GCA - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr22:20918897_20918899delGCA uc002zsp.2 + 6 692_694 c.612_614delGCA c.(610-615)GTGCAG>GTG p.Q209del MED15_uc002zsn.1_In_Frame_Del_p.Q128del|MED15_uc002zso.2_In_Frame_Del_p.Q138del|MED15_uc002zsq.2_In_Frame_Del_p.Q209del|MED15_uc010gso.2_In_Frame_Del_p.Q209del|MED15_uc002zsr.2_In_Frame_Del_p.Q183del|MED15_uc011ahs.1_In_Frame_Del_p.Q183del|MED15_uc011aht.1_In_Frame_Del_p.Q183del|MED15_uc002zss.2_In_Frame_Del_p.Q128del|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 209 Poly-Gln. regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) aagcagtagtgcagcagcagcag 0.123 0.31 59 27 MYO18B 84700 broad.mit.edu 37 22 26164298 26164298 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr22:26164298delA uc003abz.1 + 4 665 c.415delA c.(415-417)AAAfs p.K139fs MYO18B_uc003aca.1_Frame_Shift_Del_p.K20fs|MYO18B_uc010guy.1_Frame_Shift_Del_p.K20fs|MYO18B_uc010guz.1_Frame_Shift_Del_p.K20fs|MYO18B_uc011aka.1_5'UTR|MYO18B_uc011akb.1_5'Flank NM_032608 NP_115997 Q8IUG5 MY18B_HUMAN myosin XVIIIB 139 nucleus|sarcomere|unconventional myosin complex actin binding|ATP binding|motor activity ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2) 12 GACACCAACCAAAAAGACTGT 0.607 0.46 20 17 MYO18B 84700 broad.mit.edu 37 22 26287337 26287337 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr22:26287337delA uc003abz.1 + 27 4751 c.4501delA c.(4501-4503)AAAfs p.K1501fs MYO18B_uc003aca.1_Frame_Shift_Del_p.K1382fs|MYO18B_uc010guy.1_Frame_Shift_Del_p.K1383fs|MYO18B_uc010guz.1_Frame_Shift_Del_p.K1382fs|MYO18B_uc011aka.1_Frame_Shift_Del_p.K655fs|MYO18B_uc011akb.1_Frame_Shift_Del_p.K1014fs NM_032608 NP_115997 Q8IUG5 MY18B_HUMAN myosin XVIIIB 1501 Potential.|Tail. nucleus|sarcomere|unconventional myosin complex actin binding|ATP binding|motor activity ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2) 12 0.000 0.47 1280 1125 PPARA 5465 broad.mit.edu 37 22 46631153 46631153 + Frame_Shift_Del DEL A - - GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr22:46631153delA uc003bgw.1 + 9 1549 c.1283delA c.(1282-1284)CAAfs p.Q428fs PPARA_uc003bgx.1_Frame_Shift_Del_p.Q428fs|PPARA_uc010hab.1_Frame_Shift_Del_p.Q428fs|PPARA_uc003bhb.1_Frame_Shift_Del_p.Q428fs|PPARA_uc010hac.1_Frame_Shift_Del_p.Q225fs NM_005036 NP_005027 Q07869 PPARA_HUMAN peroxisome proliferative activated receptor, 428 Ligand-binding.|Required for heterodimerization with RXRA. fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fatty acid beta-oxidation|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor nucleoplasm drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|ubiquitin conjugating enzyme binding|zinc ion binding ovary(1)|central_nervous_system(1) 2 Ovarian(80;0.00965)|all_neural(38;0.0416) UCEC - Uterine corpus endometrioid carcinoma (28;0.00522) Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641) AAACTTCTTCAAAAAATGGCA 0.532 0.41 53 37 MAPK11 5600 broad.mit.edu 37 22 50704059 50704060 + Frame_Shift_Ins INS - G G GP2D_LARGE_INTESTINE NA GP2D_LARGE_INTESTINE NA g.chr22:50704059_50704060insG uc003bkr.2 - 10 850_851 c.792_793insC c.(790-795)CCCATGfs p.P264fs MAPK11_uc010hax.2_Frame_Shift_Ins_p.P86fs|MAPK11_uc011ars.1_RNA|MAPK11_uc010hay.1_Intron NM_002751 NP_002742 Q15759 MK11_HUMAN mitogen-activated protein kinase 11 264_265 Protein kinase. activation of MAPK activity|innate immune response|mRNA metabolic process|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|MAP kinase activity|protein binding lung(1)|breast(1) 2 all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247) TTCTGGGGCATGGGGGGCAGGG 0.634 0.38 31 19 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 69 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.83 2 10 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 23 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 129 178 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 18 31 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.79 3 11 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 11 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.36 7 4 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 54 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.11 101 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 856 369 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.57 38 50 HERC2 8924 broad.mit.edu 37 15 28501091 28501092 + Frame_Shift_Del DEL AG - - GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:28501091_28501092delAG uc001zbj.2 - 19 2903_2904 c.2797_2798delCT c.(2797-2799)CTTfs p.L933fs HERC2_uc001zbl.1_Frame_Shift_Del_p.L628fs NM_004667 NP_004658 O95714 HERC2_HUMAN hect domain and RLD 2 933 DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process nucleus guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1) 13 all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227) all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199) GCCCACCAGAAGATCAATCATG 0.490 0.11 113 14 SRP14 6727 broad.mit.edu 37 15 40328596 40328597 + In_Frame_Ins INS - TGC TGC GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:40328596_40328597insTGC uc001zkq.2 - 5 420_421 c.348_349insGCA c.(346-351)insGCA p.116_117insA SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116_117 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) gctgcggcaggtgctgctgctg 0.228 0.25 105 35 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.23 40 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 181 432 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 107 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 GSS_STOMACH NA GSS_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.74 8 23 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - GSS_STOMACH NA GSS_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.54 150 176 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes GSS_STOMACH NA GSS_STOMACH NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.33 8 4 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 GSS_STOMACH NA GSS_STOMACH NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.48 17 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 GSS_STOMACH NA GSS_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 57 48 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes GSS_STOMACH NA GSS_STOMACH NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.50 466 458 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes GSS_STOMACH NA GSS_STOMACH NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.33 14 7 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - GSS_STOMACH NA GSS_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.44 15 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 GSS_STOMACH NA GSS_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 GSS_STOMACH NA GSS_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 309 64 BCKDK 10295 broad.mit.edu 37 16 31122472 31122473 + Frame_Shift_Ins INS - G G GSS_STOMACH NA GSS_STOMACH NA g.chr16:31122472_31122473insG uc002eaw.3 + 9 1093_1094 c.777_778insG c.(775-780)GCTGCCfs p.A259fs BCKDK_uc002eav.3_Frame_Shift_Ins_p.A259fs|BCKDK_uc010cah.2_RNA|BCKDK_uc010cai.2_Frame_Shift_Ins_p.A259fs NM_005881 NP_005872 O14874 BCKD_HUMAN branched chain ketoacid dehydrogenase kinase 259_260 Histidine kinase. branched chain family amino acid catabolic process|peptidyl-histidine phosphorylation mitochondrial alpha-ketoglutarate dehydrogenase complex [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity|ATP binding|protein binding|protein serine/threonine kinase activity|two-component sensor activity stomach(1)|breast(1) 2 GCCATGTGGCTGCCCGGTTCCC 0.624 0.18 32 7 KEAP1 9817 broad.mit.edu 37 19 10599943 10599943 + Frame_Shift_Del DEL T - - GSS_STOMACH NA GSS_STOMACH NA g.chr19:10599943delT uc002moq.1 - 5 1789 c.1633delA c.(1633-1635)ACTfs p.T545fs KEAP1_uc002mop.1_Intron|KEAP1_uc002mor.1_Frame_Shift_Del_p.T545fs NM_012289 NP_036421 Q14145 KEAP1_HUMAN kelch-like ECH-associated protein 1 545 Kelch 5. regulation of transcription, DNA-dependent|transcription, DNA-dependent centrosome|midbody|nucleus protein binding lung(12)|breast(3)|ovary(1)|pancreas(1) 17 OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05) 0.000 0.72 140 365 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 GSS_STOMACH NA GSS_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.58 33 45 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 GSS_STOMACH NA GSS_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 85 455 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 GSS_STOMACH NA GSS_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 5 65 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HARA_LUNG NA HARA_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 30 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HARA_LUNG NA HARA_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 72 19 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HARA_LUNG NA HARA_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.50 6 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HARA_LUNG NA HARA_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 67 54 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HARA_LUNG NA HARA_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 15 23 CSMD3 114788 broad.mit.edu 37 8 113697806 113697806 + Frame_Shift_Del DEL G - - HARA_LUNG NA HARA_LUNG NA g.chr8:113697806delG uc003ynu.2 - 15 2470 c.2311delC c.(2311-2313)CAGfs p.Q771fs CSMD3_uc003yns.2_Frame_Shift_Del_p.Q43fs|CSMD3_uc003ynt.2_Frame_Shift_Del_p.Q731fs|CSMD3_uc011lhx.1_Frame_Shift_Del_p.Q667fs NM_198123 NP_937756 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 isoform 1 771 Extracellular (Potential).|CUB 4. integral to membrane|plasma membrane ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1) 63 AAATCAAACTGGGATTCCAGG 0.433 0.33 42 21 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HARA_LUNG NA HARA_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 48 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HARA_LUNG NA HARA_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.58 112 153 GRM5 2915 broad.mit.edu 37 11 88338063 88338063 + Frame_Shift_Del DEL G - - HARA_LUNG NA HARA_LUNG NA g.chr11:88338063delG uc001pcq.2 - 4 1417 c.1217delC c.(1216-1218)TCGfs p.S406fs GRM5_uc009yvm.2_Frame_Shift_Del_p.S406fs NM_001143831 NP_001137303 P41594 GRM5_HUMAN glutamate receptor, metabotropic 5 isoform a 406 Extracellular (Potential). activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission integral to plasma membrane G-protein coupled receptor activity|glutamate receptor activity central_nervous_system(4)|ovary(2)|lung(2)|breast(1) 9 Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834) Acamprosate(DB00659) 0.000 0.97 5 157 CHD9 80205 broad.mit.edu 37 16 53358011 53358011 + Frame_Shift_Del DEL G - - HARA_LUNG NA HARA_LUNG NA g.chr16:53358011delG uc002ehb.2 + 38 8062 c.7898delG c.(7897-7899)CGGfs p.R2633fs CHD9_uc002egy.2_Frame_Shift_Del_p.R2617fs|CHD9_uc002ehc.2_Frame_Shift_Del_p.R2618fs|CHD9_uc002ehf.2_Frame_Shift_Del_p.R1731fs|CHD9_uc010cbw.2_Frame_Shift_Del_p.R699fs NM_025134 NP_079410 Q3L8U1 CHD9_HUMAN chromodomain helicase DNA binding protein 9 2633 cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleoplasm ATP binding|DNA binding|helicase activity|protein binding lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1) 7 all_cancers(37;0.0212) CGGGGGAGACGGCCTAAAAGT 0.483 0.35 180 97 MLKL 197259 broad.mit.edu 37 16 74716579 74716579 + Frame_Shift_Del DEL A - - HARA_LUNG NA HARA_LUNG NA g.chr16:74716579delA uc002fdb.2 - 6 1367 c.926delT c.(925-927)CTAfs p.L309fs MLKL_uc002fdc.2_Intron NM_152649 NP_689862 Q8NB16 MLKL_HUMAN mixed lineage kinase domain-like isoform 1 309 Protein kinase. ATP binding|protein binding|protein kinase activity stomach(2) 2 CCCCAGGACTAGGACCATGCG 0.562 0.33 27 13 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HARA_LUNG NA HARA_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.64 4 7 TP53RK 112858 broad.mit.edu 37 20 45318037 45318038 + Frame_Shift_Ins INS - CT CT HARA_LUNG NA HARA_LUNG NA g.chr20:45318037_45318038insCT uc002xsk.2 - 1 239_240 c.16_17insAG c.(16-18)GCTfs p.A6fs TP53RK_uc002xsj.2_Frame_Shift_Ins_p.A6fs NM_033550 NP_291028 Q96S44 PRPK_HUMAN p53-related protein kinase 6 lipopolysaccharide biosynthetic process membrane|nucleus ATP binding|p53 binding|protein serine/threonine kinase activity|protein tyrosine kinase activity 0 Myeloproliferative disorder(115;0.0122) 0.000 0.48 83 78 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HARA_LUNG NA HARA_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 74 217 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HARA_LUNG NA HARA_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 7 61 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC1143_BREAST NA HCC1143_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 3 136 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A HCC1143_BREAST NA HCC1143_BREAST NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 0.88 2 15 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes HCC1143_BREAST NA HCC1143_BREAST NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.26 40 14 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HCC1143_BREAST NA HCC1143_BREAST NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 214 50 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HCC1143_BREAST NA HCC1143_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.38 16 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC1143_BREAST NA HCC1143_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 64 87 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC1143_BREAST NA HCC1143_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 56 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC1143_BREAST NA HCC1143_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 274 114 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HCC1143_BREAST NA HCC1143_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 81 778 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 HCC1143_BREAST NA HCC1143_BREAST NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.29 17 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC1143_BREAST NA HCC1143_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 48 31 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC1143_BREAST NA HCC1143_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 427 1827 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC1143_BREAST NA HCC1143_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 14 181 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC1171_LUNG NA HCC1171_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 17 ACVR2A 92 broad.mit.edu 37 2 148657368 148657369 + Frame_Shift_Ins INS - T T HCC1171_LUNG NA HCC1171_LUNG NA g.chr2:148657368_148657369insT uc002twg.2 + 5 698_699 c.429_430insT c.(427-432)TCCTTGfs p.S143fs ACVR2A_uc010zbn.1_Frame_Shift_Ins_p.S35fs|ACVR2A_uc002twh.2_Frame_Shift_Ins_p.S143fs NM_001616 NP_001607 P27037 AVR2A_HUMAN activin A receptor, type IIA precursor 143_144 Helical; (Potential). activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1) 13 BRCA - Breast invasive adenocarcinoma(221;0.0969) TGCTCTATTCCTTGGTGCCACT 0.441 0.52 116 127 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC1171_LUNG NA HCC1171_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.22 83 23 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC1171_LUNG NA HCC1171_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 23 55 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HCC1171_LUNG NA HCC1171_LUNG NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.54 6 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HCC1171_LUNG NA HCC1171_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 2 12 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HCC1171_LUNG NA HCC1171_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.70 3 7 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HCC1171_LUNG NA HCC1171_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.48 46 42 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC1171_LUNG NA HCC1171_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 11 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 HCC1171_LUNG NA HCC1171_LUNG NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.79 3 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC1171_LUNG NA HCC1171_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 113 16 LRRK2 120892 broad.mit.edu 37 12 40702457 40702460 + Frame_Shift_Del DEL AAAG - - HCC1171_LUNG NA HCC1171_LUNG NA g.chr12:40702457_40702460delAAAG uc001rmg.3 + 29 4269_4272 c.4148_4151delAAAG c.(4147-4152)AAAAGAfs p.K1383fs LRRK2_uc009zjw.2_Frame_Shift_Del_p.K221fs|LRRK2_uc001rmi.2_Frame_Shift_Del_p.K216fs NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 1383_1384 Roc. activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) ATAAGAGACAAAAGAAAGAGAGAT 0.348 0.14 130 22 BIRC8 112401 broad.mit.edu 37 19 53793279 53793280 + Frame_Shift_Ins INS - T T rs111817867 HCC1171_LUNG NA HCC1171_LUNG NA g.chr19:53793279_53793280insT uc002qbk.2 - 1 1596_1597 c.348_349insA c.(346-351)CAAGAAfs p.Q116fs NM_033341 NP_203127 Q96P09 BIRC8_HUMAN baculoviral IAP repeat-containing 8 116_117 apoptosis zinc ion binding lung(1) 1 GBM - Glioblastoma multiforme(134;0.00304) CGTATAGCTTCTTGTAGCATAG 0.386 0.66 24 46 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC1171_LUNG NA HCC1171_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 149 618 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC1171_LUNG NA HCC1171_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 46 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC1187_BREAST NA HCC1187_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 8 133 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT HCC1187_BREAST NA HCC1187_BREAST NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.64 63 112 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC1187_BREAST NA HCC1187_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 89 99 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC1187_BREAST NA HCC1187_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 3 64 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - HCC1187_BREAST NA HCC1187_BREAST NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 137 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC1187_BREAST NA HCC1187_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 798 248 ATN1 1822 broad.mit.edu 37 12 7045892 7045909 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes HCC1187_BREAST NA HCC1187_BREAST NA g.chr12:7045892_7045909delCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1716 c.1462_1479delCAGCAGCAGCAGCAGCAG c.(1462-1479)CAGCAGCAGCAGCAGCAGdel p.QQQQQQ494del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQ494del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 494_499 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagc 0.472 0.56 11 14 NFKBIA 4792 broad.mit.edu 37 14 35872475 35872476 + Frame_Shift_Ins INS - G G HCC1187_BREAST NA HCC1187_BREAST NA g.chr14:35872475_35872476insG uc001wtf.3 - 3 537_538 c.427_428insC c.(427-429)CGAfs p.R143fs NFKBIA_uc001wte.3_Frame_Shift_Ins_p.R53fs|NFKBIA_uc001wtg.3_Frame_Shift_Ins_p.R143fs|NFKBIA_uc010amo.2_RNA NM_020529 NP_065390 P25963 IKBA_HUMAN nuclear factor of kappa light polypeptide gene 143 ANK 3. anti-apoptosis|apoptosis|cellular response to cold|cytoplasmic sequestering of NF-kappaB|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of DNA binding|negative regulation of lipid storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of NF-kappaB transcription factor activity|nerve growth factor receptor signaling pathway|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|I-kappaB/NF-kappaB complex|nucleus|plasma membrane identical protein binding|NF-kappaB binding|nuclear localization sequence binding|ubiquitin protein ligase binding p.R143fs*11(2) breast(2) 2 Breast(36;0.0484)|Hepatocellular(127;0.158) Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891) GBM - Glioblastoma multiforme(112;0.0222) GGTATTTCCTCGAAAGTCTCGG 0.594 0.94 5 76 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HCC1187_BREAST NA HCC1187_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 9 150 TP53 7157 broad.mit.edu 37 17 7579363 7579365 + In_Frame_Del DEL ACC - - HCC1187_BREAST NA HCC1187_BREAST NA g.chr17:7579363_7579365delACC uc002gim.2 - 4 516_518 c.322_324delGGT c.(322-324)GGTdel p.G108del TP53_uc002gig.1_In_Frame_Del_p.G108del|TP53_uc002gih.2_In_Frame_Del_p.G108del|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_In_Frame_Del_p.G108del|TP53_uc010cni.1_In_Frame_Del_p.G108del|TP53_uc002gij.2_In_Frame_Del_p.G108del|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_In_Frame_Del_p.G69del|TP53_uc010cnk.1_In_Frame_Del_p.G123del NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 108 Interaction with HIPK1 (By similarity).||Interaction with WWOX. G -> D (in a sporadic cancer; somatic mutation).|G -> S (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.G59fs*23(3)|p.G108_F109delGF(2)|p.G108del(2)|p.V73fs*9(1)|p.G108fs*41(1)|p.G105_T125del21(1)|p.?_?ins?(1)|p.G108S(1)|p.Y107fs*44(1)|p.W91fs*13(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.G108D(1)|p.G108G(1)|p.Y107fs*38(1)|p.G108fs*15(1)|p.Y103_L111>L(1)|p.Y103fs*15(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.99 11 814 CPAMD8 27151 broad.mit.edu 37 19 17004032 17004032 + Frame_Shift_Del DEL C - - HCC1187_BREAST NA HCC1187_BREAST NA g.chr19:17004032delC uc002nfb.2 - 42 5718 c.5686delG c.(5686-5688)GTGfs p.V1896fs CPAMD8_uc010xpj.1_3'UTR|CPAMD8_uc002nfd.1_3'UTR NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 1849 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 GCCCCCACCACCCGGCCACTA 0.637 0.26 53 19 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC1187_BREAST NA HCC1187_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.67 26 53 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC1187_BREAST NA HCC1187_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 67 509 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC1187_BREAST NA HCC1187_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 88 MYH9 4627 broad.mit.edu 37 22 36688174 36688176 + In_Frame_Del DEL TGC - - rs116972183 by1000genomes HCC1187_BREAST NA HCC1187_BREAST NA g.chr22:36688174_36688176delTGC uc003apg.2 - 31 4431_4433 c.4200_4202delGCA c.(4198-4203)CGGCAC>CGC p.H1401del NM_002473 NP_002464 P35579 MYH9_HUMAN myosin, heavy polypeptide 9, non-muscle 1401 Potential. actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity p.H1401_E1402>E(1)|p.H1401del(1) breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1) 11 CTTCTCCTCGTGCCGCTGGCTCA 0.621 0.97 7 264 FIGF 2277 broad.mit.edu 37 X 15365473 15365473 + Frame_Shift_Del DEL G - - HCC1359_LUNG NA HCC1359_LUNG NA g.chrX:15365473delG uc004cwt.1 - 6 1260 c.751delC c.(751-753)CATfs p.H251fs NM_004469 NP_004460 O43915 VEGFD_HUMAN vascular endothelial growth factor D 251 4 X 16 AA repeats of C-X(10)-C-X-C- X(1,3)-C. angiogenesis|cell differentiation|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of mast cell chemotaxis|vascular endothelial growth factor receptor signaling pathway extracellular space|membrane|platelet alpha granule lumen chemoattractant activity|growth factor activity|platelet-derived growth factor receptor binding ovary(1)|breast(1)|central_nervous_system(1) 3 Hepatocellular(33;0.183) TCCTGGAGATGAGAGTGGTCT 0.433 0.53 30 34 ITIH5L 347365 broad.mit.edu 37 X 54815005 54815006 + Frame_Shift_Del DEL GC - - HCC1359_LUNG NA HCC1359_LUNG NA g.chrX:54815005_54815006delGC uc004dtj.2 - 5 723_724 c.693_694delGC c.(691-696)TTGCAAfs p.L231fs NM_198510 NP_940912 Q6UXX5 ITH5L_HUMAN inter-alpha (globulin) inhibitor H5-like 231_232 hyaluronan metabolic process extracellular region serine-type endopeptidase inhibitor activity lung(2)|skin(2)|ovary(1)|breast(1) 6 GACTGGTCTTGCAATGTCGGGC 0.579 0.56 114 148 ATRX 546 broad.mit.edu 37 X 76937602 76937603 + Frame_Shift_Ins INS - T T HCC1359_LUNG NA HCC1359_LUNG NA g.chrX:76937602_76937603insT uc004ecp.3 - 9 3377_3378 c.3145_3146insA c.(3145-3147)ATAfs p.I1049fs ATRX_uc004ecq.3_Frame_Shift_Ins_p.I1011fs|ATRX_uc004eco.3_Frame_Shift_Ins_p.I834fs|ATRX_uc004ecr.2_Frame_Shift_Ins_p.I981fs|ATRX_uc010nlx.1_Frame_Shift_Ins_p.I1020fs|ATRX_uc010nly.1_Frame_Shift_Ins_p.I994fs NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 1049 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) TTTATCTCTTATTTTTTTACTT 0.327 0.52 47 51 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC1359_LUNG NA HCC1359_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.43 31 23 COL3A1 1281 broad.mit.edu 37 2 189860905 189860905 + Splice_Site DEL G - - HCC1359_LUNG NA HCC1359_LUNG NA g.chr2:189860905delG uc002uqj.1 + 23 1779 c.1662_splice c.e23+1 p.P554_splice NM_000090 NP_000081 P02461 CO3A1_HUMAN collagen type III alpha 1 preproprotein axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway collagen type III|extracellular space extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding central_nervous_system(7)|ovary(4)|large_intestine(2) 13 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141) Collagenase(DB00048)|Palifermin(DB00039) AGGGCCTCCCGTATGTACATT 0.393 0.52 20 22 CXCR2 3579 broad.mit.edu 37 2 218999867 218999867 + Frame_Shift_Del DEL G - - HCC1359_LUNG NA HCC1359_LUNG NA g.chr2:218999867delG uc002vgz.1 + 4 568 c.343delG c.(343-345)GGCfs p.G115fs CXCR2_uc002vha.1_Frame_Shift_Del_p.G115fs|CXCR2_uc002vhb.1_Frame_Shift_Del_p.G115fs NM_001557 NP_001548 P25025 CXCR2_HUMAN interleukin 8 receptor beta 115 Extracellular (Potential). activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cellular defense response|dendritic cell chemotaxis|inflammatory response|neutrophil activation|neutrophil chemotaxis|positive regulation of cell proliferation cell surface|integral to plasma membrane|mast cell granule interleukin-8 receptor activity lung(1)|breast(1) 2 CTGGATTTTTGGCACATTCCT 0.547 0.11 125 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC1359_LUNG NA HCC1359_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.40 52 34 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC1359_LUNG NA HCC1359_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.80 8 33 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HCC1359_LUNG NA HCC1359_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.22 39 11 TMEM229A 730130 broad.mit.edu 37 7 123672457 123672459 + In_Frame_Del DEL GCT - - HCC1359_LUNG NA HCC1359_LUNG NA g.chr7:123672457_123672459delGCT uc011kob.1 - 1 1065_1067 c.599_601delAGC c.(598-603)CAGCGG>CGG p.Q200del uc011koc.1_Intron NM_001136002 NP_001129474 B2RXF0 T229A_HUMAN transmembrane protein 229A 200 host cell nucleus|integral to membrane sequence-specific DNA binding transcription factor activity 0 GCGCCCCTCCgctgctgctgctg 0.601 0.31 9 4 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HCC1359_LUNG NA HCC1359_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.69 4 9 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HCC1359_LUNG NA HCC1359_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.28 58 23 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC1359_LUNG NA HCC1359_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 3 31 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HCC1359_LUNG NA HCC1359_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.22 29 8 NLRP1 22861 broad.mit.edu 37 17 5418227 5418227 + Frame_Shift_Del DEL G - - HCC1359_LUNG NA HCC1359_LUNG NA g.chr17:5418227delG uc002gci.2 - 17 4824 c.4269delC c.(4267-4269)CCCfs p.P1423fs NLRP1_uc002gcg.1_Intron|NLRP1_uc002gck.2_Frame_Shift_Del_p.P1379fs|NLRP1_uc002gcj.2_Frame_Shift_Del_p.P1393fs|NLRP1_uc002gcl.2_Frame_Shift_Del_p.P1349fs|NLRP1_uc002gch.3_Frame_Shift_Del_p.P1379fs NM_033004 NP_127497 Q9C000 NALP1_HUMAN NLR family, pyrin domain containing 1 isoform 1 1423 CARD. defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide cytoplasm|NALP1 inflammasome complex|nucleus ATP binding|caspase activator activity|enzyme binding|protein domain specific binding lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1) 9 Colorectal(1115;3.48e-05) GCATCTGGCTGGGCCTCGTGT 0.572 0.93 18 235 NF1 4763 broad.mit.edu 37 17 29557382 29557382 + Frame_Shift_Del DEL G - - HCC1359_LUNG NA HCC1359_LUNG NA g.chr17:29557382delG uc002hgg.2 + 23 3428 c.3095delG c.(3094-3096)TGCfs p.C1032fs NF1_uc002hgh.2_Frame_Shift_Del_p.C1032fs|NF1_uc010csn.1_Frame_Shift_Del_p.C892fs|NF1_uc002hgi.1_Frame_Shift_Del_p.C65fs NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 1032 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) CTCTCATTTTGCCAAGAGATG 0.368 1.00 0 19 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC1359_LUNG NA HCC1359_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.41 24 17 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HCC1359_LUNG NA HCC1359_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.20 49 12 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC1359_LUNG NA HCC1359_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.86 6 38 TAF1 6872 broad.mit.edu 37 X 70598132 70598137 + In_Frame_Del DEL AGATAT - - HCC1395_BREAST NA HCC1395_BREAST NA g.chrX:70598132_70598137delAGATAT uc004dzu.3 + 7 1029_1034 c.978_983delAGATAT c.(976-984)GGAGATATA>GGA p.DI327del BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_In_Frame_Del_p.DI348del NM_138923 NP_620278 P21675 TAF1_HUMAN TBP-associated factor 1 isoform 2 327_328 Protein kinase 1. G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction MLL1 complex|transcription factor TFIID complex ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity p.I328_K330>K(3) ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1) 17 Renal(35;0.156) all_lung(315;0.000321) AATCAACTGGAGATATAGATAAAGTG 0.485 0.92 8 96 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC1395_BREAST NA HCC1395_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 65 CDC42BPA 8476 broad.mit.edu 37 1 227279608 227279608 + Frame_Shift_Del DEL C - - HCC1395_BREAST NA HCC1395_BREAST NA g.chr1:227279608delC uc001hqr.2 - 16 3277 c.2334delG c.(2332-2334)AAGfs p.K778fs CDC42BPA_uc001hqq.2_Frame_Shift_Del_p.K42fs|CDC42BPA_uc001hqs.2_Frame_Shift_Del_p.K697fs|CDC42BPA_uc009xes.2_Frame_Shift_Del_p.K778fs|CDC42BPA_uc010pvs.1_Frame_Shift_Del_p.K778fs NM_003607 NP_003598 Q5VT25 MRCKA_HUMAN CDC42-binding protein kinase alpha isoform B 778 Potential. actin cytoskeleton reorganization|intracellular signal transduction cell leading edge|cell-cell junction|cytoplasm ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1) 11 all_cancers(173;0.156)|Prostate(94;0.0792) CACTCGTCAGCTTTTTATTTT 0.318 0.15 63 11 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HCC1395_BREAST NA HCC1395_BREAST NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.50 23 23 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 HCC1395_BREAST NA HCC1395_BREAST NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.42 11 8 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HCC1395_BREAST NA HCC1395_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.18 55 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC1395_BREAST NA HCC1395_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 218 254 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC1395_BREAST NA HCC1395_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 22 39 TRIM36 55521 broad.mit.edu 37 5 114466295 114466301 + Frame_Shift_Del DEL CTAACTG - - HCC1395_BREAST NA HCC1395_BREAST NA g.chr5:114466295_114466301delCTAACTG uc003kqs.2 - 9 2329_2335 c.1820_1826delCAGTTAG c.(1819-1827)GCAGTTAGTfs p.A607fs TRIM36_uc011cwc.1_Frame_Shift_Del_p.A595fs|TRIM36_uc003kqt.2_Frame_Shift_Del_p.A452fs NM_018700 NP_061170 Q9NQ86 TRI36_HUMAN tripartite motif-containing 36 isoform 1 607_609 B30.2/SPRY. acrosomal vesicle|cytoskeleton ligase activity|zinc ion binding p.A607fs*27(2) ovary(4)|lung(2)|breast(2) 8 all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195) OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06) CTACCTTGGACTAACTGCATCCCGGGG 0.391 0.93 5 68 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HCC1395_BREAST NA HCC1395_BREAST NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.64 4 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HCC1395_BREAST NA HCC1395_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 5 47 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HCC1395_BREAST NA HCC1395_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.87 5 33 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HCC1395_BREAST NA HCC1395_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.11 157 19 FADD 8772 broad.mit.edu 37 11 70049816 70049817 + Frame_Shift_Ins INS - G G HCC1395_BREAST NA HCC1395_BREAST NA g.chr11:70049816_70049817insG uc001opm.2 + 1 548_549 c.251_252insG c.(250-252)GCGfs p.A84fs NM_003824 NP_003815 Q13158 FADD_HUMAN Fas-associated via death domain 84 activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction cytosol death receptor binding|identical protein binding ovary(1)|lung(1)|pancreas(1) 3 Esophageal squamous(2;1.19e-45) LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) 0.000 0.10 664 70 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC1395_BREAST NA HCC1395_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 637 226 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HCC1395_BREAST NA HCC1395_BREAST NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.61 36 57 HSP90AB4P 664618 broad.mit.edu 37 15 58983559 58983588 + In_Frame_Del DEL TATATATTACCTCGAAGCCCTTCTTCCACT - - rs7163162 by1000genomes HCC1395_BREAST NA HCC1395_BREAST NA g.chr15:58983559_58983588delTATATATTACCTCGAAGCCCTTCTTCCACT uc002afh.1 - 3 1232_1261 c.1232_1261delAGTGGAAGAAGGGCTTCGAGGTAATATATA c.(1231-1263)GAGTGGAAGAAGGGCTTCGAGGTAATATATATG>GTG p.411_421EWKKGFEVIYM>V ADAM10_uc002afd.1_Intron|ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron|ADAM10_uc002afg.2_Intron NR_002927 RecName: Full=Putative heat shock protein HSP 90-beta 4; 0 GGCTCACTCATATATATTACCTCGAAGCCCTTCTTCCACTCTTGCTCCAC 0.487 0.31 41 18 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 HCC1395_BREAST NA HCC1395_BREAST NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.24 29 9 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC1395_BREAST NA HCC1395_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 50 244 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC1395_BREAST NA HCC1395_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 8 90 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC1419_BREAST NA HCC1419_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.73 3 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC1419_BREAST NA HCC1419_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.72 21 55 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC1419_BREAST NA HCC1419_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.85 2 11 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HCC1419_BREAST NA HCC1419_BREAST NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.41 10 7 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT HCC1419_BREAST NA HCC1419_BREAST NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.16 306 60 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HCC1419_BREAST NA HCC1419_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.52 14 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC1419_BREAST NA HCC1419_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 53 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HCC1419_BREAST NA HCC1419_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.56 173 219 MLLT3 4300 broad.mit.edu 37 9 20414311 20414313 + In_Frame_Del DEL CTG - - HCC1419_BREAST NA HCC1419_BREAST NA g.chr9:20414311_20414313delCTG uc003zoe.2 - 5 790_792 c.531_533delCAG c.(529-534)AGCAGT>AGT p.177_178SS>S MLLT3_uc011lne.1_In_Frame_Del_p.145_146SS>S|MLLT3_uc011lnf.1_In_Frame_Del_p.174_175SS>S|MLLT3_uc003zof.2_5'UTR NM_004529 NP_004520 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia 177_178 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding lung(2)|ovary(1) 3 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) gctgctgctactgctgctgctgc 0.143 0.20 39 10 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HCC1419_BREAST NA HCC1419_BREAST NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.50 7 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC1419_BREAST NA HCC1419_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 72 35 TP53 7157 broad.mit.edu 37 17 7579461 7579467 + Frame_Shift_Del DEL CAGGGGC - - HCC1419_BREAST NA HCC1419_BREAST NA g.chr17:7579461_7579467delCAGGGGC uc002gim.2 - 4 414_420 c.220_226delGCCCCTG c.(220-228)GCCCCTGCAfs p.A74fs TP53_uc002gig.1_Frame_Shift_Del_p.A74fs|TP53_uc002gih.2_Frame_Shift_Del_p.A74fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.A74fs|TP53_uc010cni.1_Frame_Shift_Del_p.A74fs|TP53_uc002gij.2_Frame_Shift_Del_p.A74fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.A35fs|TP53_uc010cnk.1_Frame_Shift_Del_p.A89fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 74_76 Interaction with WWOX.|Interaction with HRMT1L2. A -> T (in a sporadic cancer; somatic mutation).|A -> G (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.A76_S90del15(3)|p.G59fs*23(3)|p.P75R(2)|p.P75fs*48(2)|p.V73fs*9(1)|p.R65fs*38(1)|p.E68fs*76(1)|p.A76fs*47(1)|p.A76fs*73(1)|p.D48fs*55(1)|p.A74V(1)|p.A74fs*49(1)|p.A74A(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.D57_A76del20(1)|p.A74fs*71(1)|p.A74fs*47(1)|p.P75S(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.18 256 57 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC1419_BREAST NA HCC1419_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 150 453 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC1419_BREAST NA HCC1419_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 23 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 HCC1438_LUNG NA HCC1438_LUNG NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.38 13 8 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC1438_LUNG NA HCC1438_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.33 22 11 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HCC1438_LUNG NA HCC1438_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.34 43 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC1438_LUNG NA HCC1438_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 56 39 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC1438_LUNG NA HCC1438_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 26 16 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HCC1438_LUNG NA HCC1438_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.38 55 34 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HCC1438_LUNG NA HCC1438_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.19 77 18 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HCC1438_LUNG NA HCC1438_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.18 68 15 FADD 8772 broad.mit.edu 37 11 70049816 70049817 + Frame_Shift_Ins INS - G G HCC1438_LUNG NA HCC1438_LUNG NA g.chr11:70049816_70049817insG uc001opm.2 + 1 548_549 c.251_252insG c.(250-252)GCGfs p.A84fs NM_003824 NP_003815 Q13158 FADD_HUMAN Fas-associated via death domain 84 activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction cytosol death receptor binding|identical protein binding ovary(1)|lung(1)|pancreas(1) 3 Esophageal squamous(2;1.19e-45) LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) 0.000 0.11 203 26 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HCC1438_LUNG NA HCC1438_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.52 14 15 MTUS2 23281 broad.mit.edu 37 13 29599699 29599699 + Frame_Shift_Del DEL G - - HCC1438_LUNG NA HCC1438_LUNG NA g.chr13:29599699delG uc001usl.3 + 1 952 c.894delG c.(892-894)TTGfs p.L298fs NM_001033602 NP_001028774 Q5JR59 MTUS2_HUMAN hypothetical protein LOC23281 isoform a 288 cytoplasm|microtubule microtubule binding|protein homodimerization activity 0 ATTTGACTTTGGCATCGAAGG 0.512 0.99 1 85 BMP4 652 broad.mit.edu 37 14 54418837 54418838 + Frame_Shift_Ins INS - C C HCC1438_LUNG NA HCC1438_LUNG NA g.chr14:54418837_54418838insC uc001xal.3 - 2 290_291 c.103_104insG c.(103-105)GTCfs p.V35fs BMP4_uc010aoh.2_Frame_Shift_Ins_p.V35fs|BMP4_uc001xao.3_Frame_Shift_Ins_p.V35fs|BMP4_uc001xan.3_Frame_Shift_Ins_p.V35fs NM_130851 NP_570912 P12644 BMP4_HUMAN bone morphogenetic protein 4 preproprotein 35 activation of MAPKK activity|blood vessel endothelial cell proliferation involved in sprouting angiogenesis|BMP signaling pathway involved in heart induction|BMP signaling pathway involved in nephric duct formation|branching involved in ureteric bud morphogenesis|bronchus development|bud dilation involved in lung branching|cardiac septum development|cartilage development|endocardial cushion development|epithelial cell proliferation involved in lung morphogenesis|intermediate mesodermal cell differentiation|lung alveolus development|lymphoid progenitor cell differentiation|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway|negative regulation of branching involved in ureteric bud morphogenesis|negative regulation of cell proliferation involved in heart morphogenesis|negative regulation of glomerular mesangial cell proliferation|negative regulation of glomerulus development|negative regulation of immature T cell proliferation in thymus|negative regulation of MAP kinase activity|negative regulation of metanephric comma-shaped body morphogenesis|negative regulation of metanephric S-shaped body morphogenesis|negative regulation of mitosis|negative regulation of myoblast differentiation|negative regulation of phosphorylation|negative regulation of striated muscle tissue development|negative regulation of thymocyte apoptosis|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of apoptosis|positive regulation of bone mineralization|positive regulation of cardiac muscle fiber development|positive regulation of cartilage development|positive regulation of collagen biosynthetic process|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of kidney development|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|protein localization to nucleus|pulmonary artery endothelial tube morphogenesis|secondary heart field specification|SMAD protein signal transduction|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway|steroid hormone mediated signaling pathway extracellular space|proteinaceous extracellular matrix BMP receptor binding|chemoattractant activity|cytokine activity|growth factor activity 0 AATCTCGGCGACTTTTTTCTTC 0.574 0.37 57 34 TP53 7157 broad.mit.edu 37 17 7577139 7577140 + Frame_Shift_Ins INS - A A rs55832599 HCC1438_LUNG NA HCC1438_LUNG NA g.chr17:7577139_7577140insA uc002gim.2 - 8 992_993 c.798_799insT c.(796-801)GGACGGfs p.G266fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Frame_Shift_Ins_p.G266fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Ins_p.G134fs|TP53_uc010cng.1_Frame_Shift_Ins_p.G134fs|TP53_uc002gii.1_Frame_Shift_Ins_p.G134fs|TP53_uc010cnh.1_Frame_Shift_Ins_p.G266fs|TP53_uc010cni.1_Frame_Shift_Ins_p.G266fs|TP53_uc002gij.2_Frame_Shift_Ins_p.G266fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 266_267 |Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). R -> H (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.G266E(45)|p.G266R(42)|p.G266V(31)|p.R267W(20)|p.G266*(12)|p.0?(7)|p.G266fs*79(5)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.G266A(2)|p.G266G(2)|p.G262_S269delGNLLGRNS(2)|p.G266_E271delGRNSFE(2)|p.G266T(1)|p.G266_N268delGRN(1)|p.E258fs*71(1)|p.G266fs*9(1)|p.G262fs*2(1)|p.R267G(1)|p.R267R(1)|p.L265_K305del41(1)|p.L265_R267delLGR(1)|p.G266fs*4(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.48 13 12 TP53 7157 broad.mit.edu 37 17 7578513 7578513 + Frame_Shift_Del DEL C - - HCC1438_LUNG NA HCC1438_LUNG NA g.chr17:7578513delC uc002gim.2 - 5 611 c.417delG c.(415-417)AAGfs p.K139fs TP53_uc002gig.1_Frame_Shift_Del_p.K139fs|TP53_uc002gih.2_Frame_Shift_Del_p.K139fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.K7fs|TP53_uc010cng.1_Frame_Shift_Del_p.K7fs|TP53_uc002gii.1_Frame_Shift_Del_p.K7fs|TP53_uc010cnh.1_Frame_Shift_Del_p.K139fs|TP53_uc010cni.1_Frame_Shift_Del_p.K139fs|TP53_uc002gij.2_Frame_Shift_Del_p.K139fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.K46fs|TP53_uc002gio.2_Frame_Shift_Del_p.K7fs|TP53_uc010vug.1_Frame_Shift_Del_p.K100fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 139 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). K -> N (in sporadic cancers; somatic mutation).|K -> T (in sporadic cancers; somatic mutation).|K -> Q (in sporadic cancers; somatic mutation).|K -> R (in sporadic cancers; somatic mutation).|K -> E (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.K139N(8)|p.K139K(7)|p.0?(7)|p.K139fs*31(4)|p.K139fs*9(3)|p.K139Q(2)|p.K139R(2)|p.K139E(2)|p.N131fs*27(2)|p.K139*(2)|p.K139T(1)|p.L137_W146del10(1)|p.K139fs*4(1)|p.F134_T140>S(1)|p.A138_V143delAKTCPV(1)|p.K139fs*11(1)|p.K139fs*10(1)|p.A138_P142delAKTCP(1)|p.Q136_K139delQLAK(1)|p.K139_C141>N(1)|p.C135_T140delCQLAKT(1)|p.K139fs*29(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) CAGGGCAGGTCTTGGCCAGTT 0.567 1.00 0 47 SMARCA4 6597 broad.mit.edu 37 19 11098392 11098392 + Frame_Shift_Del DEL C - - HCC1438_LUNG NA HCC1438_LUNG NA g.chr19:11098392delC uc002mqf.3 + 6 1194 c.910delC c.(910-912)CCCfs p.P304fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.P304fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.P304fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.P304fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.P304fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.P304fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.P304fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.P304fs|SMARCA4_uc002mqe.2_Frame_Shift_Del_p.P304fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 304 chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) 0.000 0.28 837 326 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC1438_LUNG NA HCC1438_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.42 44 32 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC1438_LUNG NA HCC1438_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 1 12 DDX17 10521 broad.mit.edu 37 22 38897211 38897211 + Frame_Shift_Del DEL T - - HCC1438_LUNG NA HCC1438_LUNG NA g.chr22:38897211delT uc003avy.3 - 2 465 c.362delA c.(361-363)AAGfs p.K121fs DDX17_uc003avx.3_Frame_Shift_Del_p.K121fs|DDX17_uc011anu.1_Frame_Shift_Del_p.K34fs NM_001098504 NP_001091974 Q92841 DDX17_HUMAN DEAD box polypeptide 17 isoform 3 42 RNA processing nucleus ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity skin(3)|upper_aerodigestive_tract(1) 4 Melanoma(58;0.0286) 0.000 0.10 334 37 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC1500_BREAST NA HCC1500_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.86 4 25 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HCC1500_BREAST NA HCC1500_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 229 74 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC1500_BREAST NA HCC1500_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.67 22 44 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC1500_BREAST NA HCC1500_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 9 17 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HCC1500_BREAST NA HCC1500_BREAST NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.33 10 5 ADAM22 53616 broad.mit.edu 37 7 87800876 87800876 + Frame_Shift_Del DEL G - - HCC1500_BREAST NA HCC1500_BREAST NA g.chr7:87800876delG uc003ujn.2 + 26 2379 c.2300delG c.(2299-2301)AGAfs p.R767fs ADAM22_uc003ujk.1_Frame_Shift_Del_p.R767fs|ADAM22_uc003ujl.1_Frame_Shift_Del_p.R767fs|ADAM22_uc003ujm.2_Frame_Shift_Del_p.R767fs|ADAM22_uc003ujo.2_Frame_Shift_Del_p.R767fs|ADAM22_uc003ujp.1_Frame_Shift_Del_p.R819fs NM_021723 NP_068369 Q9P0K1 ADA22_HUMAN ADAM metallopeptidase domain 22 isoform 1 767 Cytoplasmic (Potential). cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis integral to membrane integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding ovary(4)|skin(2)|lung(1)|kidney(1) 8 Esophageal squamous(14;0.00202) STAD - Stomach adenocarcinoma(171;0.215) CGAGAACAGAGGTATGTAATA 0.328 0.16 76 14 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HCC1500_BREAST NA HCC1500_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.92 1 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC1500_BREAST NA HCC1500_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 31 MYST4 23522 broad.mit.edu 37 10 76788653 76788654 + In_Frame_Ins INS - GAA GAA HCC1500_BREAST NA HCC1500_BREAST NA g.chr10:76788653_76788654insGAA uc001jwn.1 + 18 4564_4565 c.4071_4072insGAA c.(4069-4074)insGAA p.1368_1369insE MYST4_uc001jwo.1_In_Frame_Ins_p.1076_1077insE|MYST4_uc001jwp.1_In_Frame_Ins_p.1185_1186insE NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1368_1369 Poly-Glu. histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) aagaggaggaggaggaggaaga 0.233 0.30 42 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC1500_BREAST NA HCC1500_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 115 58 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes HCC1500_BREAST NA HCC1500_BREAST NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.19 42 10 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HCC1500_BREAST NA HCC1500_BREAST NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.28 34 13 C14orf4 64207 broad.mit.edu 37 14 77493762 77493764 + In_Frame_Del DEL TGC - - HCC1500_BREAST NA HCC1500_BREAST NA g.chr14:77493762_77493764delTGC uc001xsy.2 - 1 1271_1273 c.372_374delGCA c.(370-375)CAGCAA>CAA p.124_125QQ>Q NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 124_125 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) GAgctgttgttgctgctgctgct 0.236 0.43 8 6 RBL2 5934 broad.mit.edu 37 16 53485672 53485672 + Frame_Shift_Del DEL C - - HCC1500_BREAST NA HCC1500_BREAST NA g.chr16:53485672delC uc002ehi.3 + 5 813 c.695delC c.(694-696)GCTfs p.A232fs RBL2_uc010vgv.1_Frame_Shift_Del_p.A158fs|RBL2_uc002ehj.2_5'UTR|RBL2_uc010vgw.1_Frame_Shift_Del_p.A16fs NM_005611 NP_005602 Q08999 RBL2_HUMAN retinoblastoma-like 2 (p130) 232 cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleolus DNA binding|protein binding ovary(2)|lung(2)|upper_aerodigestive_tract(1) 5 CTGCTGTGTGCTTTGGACTTA 0.358 0.52 73 79 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC1500_BREAST NA HCC1500_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.66 25 48 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HCC1500_BREAST NA HCC1500_BREAST NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.25 72 24 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC1500_BREAST NA HCC1500_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 126 401 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC1500_BREAST NA HCC1500_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 4 48 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC1599_BREAST NA HCC1599_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.52 23 25 TOP2B 7155 broad.mit.edu 37 3 25661374 25661380 + Frame_Shift_Del DEL AGTTTGA - - HCC1599_BREAST NA HCC1599_BREAST NA g.chr3:25661374_25661380delAGTTTGA uc011awn.1 - 23 3079_3085 c.3036_3042delTCAAACT c.(3034-3042)CTTCAAACTfs p.L1012fs TOP2B_uc003cdj.2_Frame_Shift_Del_p.L1007fs|TOP2B_uc011awm.1_5'UTR|TOP2B_uc010hff.1_Frame_Shift_Del_p.L49fs NM_001068 NP_001059 Q02880 TOP2B_HUMAN DNA topoisomerase II, beta isozyme 1012_1014 DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|resolution of meiotic recombination intermediates|sister chromatid segregation cytosol|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex|WINAC complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity p.K1006fs*18(1)|p.Q1008fs*16(1) breast(2)|ovary(1)|lung(1)|skin(1) 5 AAGTAAGAGTAGTTTGAAGTTTAAAAA 0.319 0.32 28 13 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HCC1599_BREAST NA HCC1599_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.41 10 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC1599_BREAST NA HCC1599_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 22 51 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC1599_BREAST NA HCC1599_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.80 5 20 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HCC1599_BREAST NA HCC1599_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.80 5 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC1599_BREAST NA HCC1599_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 16 FADD 8772 broad.mit.edu 37 11 70049816 70049817 + Frame_Shift_Ins INS - G G HCC1599_BREAST NA HCC1599_BREAST NA g.chr11:70049816_70049817insG uc001opm.2 + 1 548_549 c.251_252insG c.(250-252)GCGfs p.A84fs NM_003824 NP_003815 Q13158 FADD_HUMAN Fas-associated via death domain 84 activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction cytosol death receptor binding|identical protein binding ovary(1)|lung(1)|pancreas(1) 3 Esophageal squamous(2;1.19e-45) LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) 0.000 0.11 523 64 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC1599_BREAST NA HCC1599_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 154 70 BRCA2 675 broad.mit.edu 37 13 32913042 32913051 + Frame_Shift_Del DEL AAGAACCTAC - - rs80359457;rs80359458;rs80358690 HCC1599_BREAST NA HCC1599_BREAST NA g.chr13:32913042_32913051delAAGAACCTAC uc001uub.1 + 11 4777_4786 c.4550_4559delAAGAACCTAC c.(4549-4560)AAAGAACCTACTfs p.K1517fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 1517_1520 BRCA2 4. cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding p.K1517fs*23(1) ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) GAAAAGATCAAAGAACCTACTCTATTGGGT 0.376 0.91 2 20 CRTC1 23373 broad.mit.edu 37 19 18887992 18887993 + Frame_Shift_Ins INS - C C HCC1599_BREAST NA HCC1599_BREAST NA g.chr19:18887992_18887993insC uc002nkb.3 + 14 1793_1794 c.1705_1706insC c.(1705-1707)TCCfs p.S569fs CRTC1_uc010ebv.2_Frame_Shift_Ins_p.S585fs|CRTC1_uc010ebw.2_Frame_Shift_Ins_p.S405fs|CRTC1_uc002nkc.3_Frame_Shift_Ins_p.S267fs NM_015321 NP_056136 Q6UUV9 CRTC1_HUMAN mucoepidermoid carcinoma translocated 1 isoform 569 interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus|plasma membrane cAMP response element binding protein binding|protein binding CRTC1/MAML2(516) salivary_gland(474)|lung(35)|thyroid(4)|breast(3)|skin(2)|ovary(1) 519 GACAGGAGAGTCCCCCCCCAGC 0.614 0.74 10 28 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC1599_BREAST NA HCC1599_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 85 329 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC1599_BREAST NA HCC1599_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 29 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC15_LUNG NA HCC15_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.48 17 16 BMP2K 55589 broad.mit.edu 37 4 79792082 79792083 + In_Frame_Ins INS - CAG CAG rs5859654;rs35071794 HCC15_LUNG NA HCC15_LUNG NA g.chr4:79792082_79792083insCAG uc003hlk.2 + 11 1543_1544 c.1377_1378insCAG c.(1375-1380)insCAG p.486_487insQ BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Ins_p.486_487insQ|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486_487 Gln/His-rich. nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 GTCATCCTCACcagcagcagca 0.262 0.48 36 33 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC15_LUNG NA HCC15_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.76 44 136 FBN2 2201 broad.mit.edu 37 5 127626457 127626457 + Frame_Shift_Del DEL C - - HCC15_LUNG NA HCC15_LUNG NA g.chr5:127626457delC uc003kuu.2 - 50 6851 c.6412delG c.(6412-6414)GACfs p.D2138fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 2138 TB 8. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) TCACAGGGGTCCCCCCAGCCC 0.458 0.43 158 119 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HCC15_LUNG NA HCC15_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.47 8 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HCC15_LUNG NA HCC15_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 2 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC15_LUNG NA HCC15_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 28 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HCC15_LUNG NA HCC15_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.11 291 37 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC15_LUNG NA HCC15_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 489 129 PDZRN4 29951 broad.mit.edu 37 12 41900264 41900264 + Frame_Shift_Del DEL G - - HCC15_LUNG NA HCC15_LUNG NA g.chr12:41900264delG uc010skn.1 + 4 321 c.253delG c.(253-255)GGGfs p.G85fs PDZRN4_uc001rmq.3_Frame_Shift_Del_p.G26fs|PDZRN4_uc009zjz.2_Frame_Shift_Del_p.G24fs NM_013377 NP_037509 Q6ZMN7 PZRN4_HUMAN PDZ domain containing RING finger 4 isoform 2 284 PDZ 1. ubiquitin-protein ligase activity|zinc ion binding lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1) 11 all_cancers(12;0.000673) Lung NSC(34;0.0205)|all_lung(34;0.0264) GTAGGTCAATGGGAAGGATCT 0.438 0.52 44 48 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HCC15_LUNG NA HCC15_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.58 15 21 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HCC15_LUNG NA HCC15_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.60 4 6 SRP14 6727 broad.mit.edu 37 15 40328597 40328605 + In_Frame_Del DEL TGCTGCTGC - - HCC15_LUNG NA HCC15_LUNG NA g.chr15:40328597_40328605delTGCTGCTGC uc001zkq.2 - 5 412_420 c.340_348delGCAGCAGCA c.(340-348)GCAGCAGCAdel p.AAA114del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 114_116 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgcggcaggtgctgctgctgctgctgct 0.239 0.11 56 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HCC15_LUNG NA HCC15_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 27 387 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 HCC15_LUNG NA HCC15_LUNG NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.33 16 8 SMARCA4 6597 broad.mit.edu 37 19 11097625 11097625 + Frame_Shift_Del DEL C - - HCC15_LUNG NA HCC15_LUNG NA g.chr19:11097625delC uc002mqf.3 + 5 1089 c.805delC c.(805-807)CCCfs p.P269fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.P269fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.P269fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.P269fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.P269fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.P269fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.P269fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.P269fs|SMARCA4_uc002mqe.2_Frame_Shift_Del_p.P269fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 269 Necessary for interaction with SS18L1/CREST (By similarity). chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.P270fs*16(1)|p.M272fs*31(1)|p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) 0.000 0.97 15 460 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC15_LUNG NA HCC15_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.64 39 70 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HCC15_LUNG NA HCC15_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 53 10 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC15_LUNG NA HCC15_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 103 446 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC15_LUNG NA HCC15_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 5 63 EP300 2033 broad.mit.edu 37 22 41566524 41566525 + Frame_Shift_Ins INS - A A HCC15_LUNG NA HCC15_LUNG NA g.chr22:41566524_41566525insA uc003azl.3 + 27 4796_4797 c.4401_4402insA c.(4399-4404)TACAAAfs p.Y1467fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1467_1468 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding p.M1470fs*3(3) haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 AGGAATGGTACAAAAAAATGCT 0.470 0.87 12 83 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HCC1806_BREAST NA HCC1806_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.32 19 9 MYLK 4638 broad.mit.edu 37 3 123419184 123419219 + In_Frame_Del DEL GCAGGCTTGGCGTTGCCCATTGGCTTCAGGGTCTCA - - HCC1806_BREAST NA HCC1806_BREAST NA g.chr3:123419184_123419219delGCAGGCTTGGCGTTGCCCATTGGCTTCAGGGTCTCA uc003ego.2 - 18 3378_3413 c.3096_3131delTGAGACCCTGAAGCCAATGGGCAACGCCAAGCCTGC c.(3094-3132)GCTGAGACCCTGAAGCCAATGGGCAACGCCAAGCCTGCC>GCC p.1032_1044AETLKPMGNAKPA>A MYLK_uc011bjw.1_In_Frame_Del_p.1032_1044AETLKPMGNAKPA>A|MYLK_uc003egp.2_In_Frame_Del_p.963_975AETLKPMGNAKPA>A|MYLK_uc003egq.2_In_Frame_Del_p.1032_1044AETLKPMGNAKPA>A|MYLK_uc003egr.2_In_Frame_Del_p.963_975AETLKPMGNAKPA>A|MYLK_uc003egs.2_In_Frame_Del_p.856_868AETLKPMGNAKPA>A|MYLK_uc003egt.2_In_Frame_Del_p.223_235AETLKPMGNAKPA>A NM_053025 NP_444253 Q15746 MYLK_HUMAN myosin light chain kinase isoform 1 1032_1044 6 X 12 AA approximate tandem repeats.|2-5. aorta smooth muscle tissue morphogenesis|muscle contraction cytosol actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity ovary(6)|skin(2)|stomach(1) 9 Lung NSC(201;0.0496) GBM - Glioblastoma multiforme(114;0.0736) CAGGGTCTCGGCAGGCTTGGCGTTGCCCATTGGCTTCAGGGTCTCAGCAGGCTTGG 0.559 0.28 446 175 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HCC1806_BREAST NA HCC1806_BREAST NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.28 122 48 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC1806_BREAST NA HCC1806_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.40 76 51 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC1806_BREAST NA HCC1806_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 26 61 MAML1 9794 broad.mit.edu 37 5 179160355 179160375 + In_Frame_Del DEL CGGCCCCGGCGCCCGCCGCCC - - rs67713510 HCC1806_BREAST NA HCC1806_BREAST NA g.chr5:179160355_179160375delCGGCCCCGGCGCCCGCCGCCC uc003mkm.2 + 1 505_525 c.242_262delCGGCCCCGGCGCCCGCCGCCC c.(241-264)ACGGCCCCGGCGCCCGCCGCCCCG>ACG p.APAPAAP82del MAML1_uc003mkn.1_In_Frame_Del_p.APAPAAP82del NM_014757 NP_055572 Q92585 MAML1_HUMAN mastermind-like 1 82_88 Required for interaction with NOTCH proteins. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck peptide antigen binding|protein kinase binding|transcription coactivator activity lung(4)|ovary(2) 6 all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218) all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) 0.000 0.60 103 155 EXT1 2131 broad.mit.edu 37 8 119122620 119122644 + Frame_Shift_Del DEL ACTGATGCTGGCTTTGGCCAGCATC - - HCC1806_BREAST NA HCC1806_BREAST NA g.chr8:119122620_119122644delACTGATGCTGGCTTTGGCCAGCATC uc003yok.1 - 1 1415_1439 c.642_666delGATGCTGGCCAAAGCCAGCATCAGT c.(640-666)GCGATGCTGGCCAAAGCCAGCATCAGTfs p.A214fs NM_000127 NP_000118 Q16394 EXT1_HUMAN exostosin 1 214_222 Lumenal (Potential). MLAKASIS -> I (in isolated osteochondroma; somatic mutation). glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development Golgi membrane|integral to endoplasmic reticulum membrane glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity ovary(2)|lung(2) 4 all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173) STAD - Stomach adenocarcinoma(47;0.012) AGTTTTCAGTACTGATGCTGGCTTTGGCCAGCATCGCCTGGCCGA 0.471 0.13 117 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC1806_BREAST NA HCC1806_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 19 SIK2 23235 broad.mit.edu 37 11 111571666 111571667 + Frame_Shift_Ins INS - G G HCC1806_BREAST NA HCC1806_BREAST NA g.chr11:111571666_111571667insG uc001plt.2 + 5 653_654 c.535_536insG c.(535-537)AGCfs p.S179fs NM_015191 NP_056006 Q9H0K1 SIK2_HUMAN SNF1-like kinase 2 179 Protein kinase. intracellular protein kinase cascade|regulation of insulin receptor signaling pathway Golgi apparatus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|skin(1) 3 ATGGTGTGGCAGCCCCCCTTAT 0.431 0.11 272 35 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC1806_BREAST NA HCC1806_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.30 23 10 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC1806_BREAST NA HCC1806_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 123 339 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC1806_BREAST NA HCC1806_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 50 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC1833_LUNG NA HCC1833_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.46 50 43 PBRM1 55193 broad.mit.edu 37 3 52678784 52678787 + Frame_Shift_Del DEL TTTT - - HCC1833_LUNG NA HCC1833_LUNG NA g.chr3:52678784_52678787delTTTT uc003des.2 - 8 844_847 c.832_835delAAAA c.(832-837)AAAATAfs p.K278fs PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.K278fs|PBRM1_uc003der.2_Frame_Shift_Del_p.K278fs|PBRM1_uc003det.2_Frame_Shift_Del_p.K278fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.K278fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.K278fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.K278fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.K278fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.K278fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.K176fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 278_279 chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.50 115 116 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HCC1833_LUNG NA HCC1833_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.48 47 44 HTT 3064 broad.mit.edu 37 4 3076672 3076673 + In_Frame_Ins INS - CCG CCG rs76533208 HCC1833_LUNG NA HCC1833_LUNG NA g.chr4:3076672_3076673insCCG uc011bvq.1 + 2 271_272 c.126_127insCCG c.(124-129)insCCG p.51_52insP NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 49_50 establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) aacagccgccaccgccgccgcc 0.084 0.18 126 28 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HCC1833_LUNG NA HCC1833_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.58 16 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC1833_LUNG NA HCC1833_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.66 74 145 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC1833_LUNG NA HCC1833_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 43 72 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HCC1833_LUNG NA HCC1833_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.40 62 41 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 HCC1833_LUNG NA HCC1833_LUNG NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.20 233 58 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HCC1833_LUNG NA HCC1833_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 3 28 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HCC1833_LUNG NA HCC1833_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.85 5 29 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC1833_LUNG NA HCC1833_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 3 101 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HCC1833_LUNG NA HCC1833_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.50 9 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC1833_LUNG NA HCC1833_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.42 899 648 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HCC1833_LUNG NA HCC1833_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.28 253 99 WBP4 11193 broad.mit.edu 37 13 41650183 41650183 + Frame_Shift_Del DEL C - - HCC1833_LUNG NA HCC1833_LUNG NA g.chr13:41650183delC uc001uxt.2 + 8 679 c.566delC c.(565-567)TCCfs p.S189fs WBP4_uc010tfd.1_Frame_Shift_Del_p.S168fs NM_007187 NP_009118 O75554 WBP4_HUMAN WW domain-containing binding protein 4 189 WW 2. nuclear mRNA cis splicing, via spliceosome nuclear speck|spliceosomal complex nucleic acid binding|proline-rich region binding|zinc ion binding breast(2)|kidney(1) 3 Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114) all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07) TGAGCAGAATCCAGATGGGAG 0.318 0.33 126 63 MEF2A 4205 broad.mit.edu 37 15 100252710 100252712 + In_Frame_Del DEL CAG - - HCC1833_LUNG NA HCC1833_LUNG NA g.chr15:100252710_100252712delCAG uc010urw.1 + 11 1617_1619 c.1258_1260delCAG c.(1258-1260)CAGdel p.Q430del MEF2A_uc010urv.1_In_Frame_Del_p.Q360del|MEF2A_uc010bos.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvf.2_In_Frame_Del_p.Q422del|MEF2A_uc002bve.2_In_Frame_Del_p.Q428del|MEF2A_uc002bvg.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvi.2_In_Frame_Del_p.Q420del|MEF2A_uc010bot.2_In_Frame_Del_p.Q352del NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 430 Gln/Pro-rich. Missing (in Ref. 4; AAB17195/AAB17196). apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) ATCGGGCTTCcagcagcagcagc 0.493 0.22 39 11 TP53 7157 broad.mit.edu 37 17 7577080 7577088 + In_Frame_Del DEL TTCCTCTGT - - rs121912667;rs112431538 HCC1833_LUNG NA HCC1833_LUNG NA g.chr17:7577080_7577088delTTCCTCTGT uc002gim.2 - 8 1044_1052 c.850_858delACAGAGGAA c.(850-858)ACAGAGGAAdel p.TEE284del TP53_uc002gig.1_Intron|TP53_uc002gih.2_In_Frame_Del_p.TEE284del|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_In_Frame_Del_p.TEE152del|TP53_uc010cng.1_In_Frame_Del_p.TEE152del|TP53_uc002gii.1_In_Frame_Del_p.TEE152del|TP53_uc010cnh.1_In_Frame_Del_p.TEE284del|TP53_uc010cni.1_In_Frame_Del_p.TEE284del|TP53_uc002gij.2_In_Frame_Del_p.TEE284del NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 284_286 |Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). E -> V (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> G (in sporadic cancers; somatic mutation).|E -> Q (in sporadic cancers; somatic mutation).|E -> A (in LFS; germline mutation and in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.E285K(95)|p.E286K(52)|p.E285*(16)|p.E286*(14)|p.E286G(14)|p.E285V(13)|p.T284P(7)|p.0?(7)|p.E286V(6)|p.E286Q(5)|p.E285Q(4)|p.T284fs*61(3)|p.E285E(3)|p.E285G(3)|p.T284T(3)|p.T284A(3)|p.T284fs*62(2)|p.E285A(2)|p.T284fs*21(2)|p.?(2)|p.E286D(2)|p.E286E(2)|p.R283fs*16(2)|p.E286fs*59(2)|p.E286fs*17(2)|p.E285_N288delEEEN(1)|p.R282_E287delRRTEEE(1)|p.T284_G293del10(1)|p.G279fs*59(1)|p.S269fs*21(1)|p.E285fs*13(1)|p.T284I(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.R283fs*56(1)|p.R283_T284>T(1)|p.E286A(1)|p.V272_K292del21(1)|p.R283fs*59(1)|p.C275fs*20(1)|p.E285_L289delEEENL(1)|p.E285fs*60(1)|p.E285fs*20(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGAGATTCTCTTCCTCTGTGCGCCGGTCT 0.565 0.77 10 33 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 HCC1833_LUNG NA HCC1833_LUNG NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.15 98 17 ALPK2 115701 broad.mit.edu 37 18 56202710 56202710 + Frame_Shift_Del DEL T - - HCC1833_LUNG NA HCC1833_LUNG NA g.chr18:56202710delT uc002lhj.3 - 5 4923 c.4709delA c.(4708-4710)AATfs p.N1570fs ALPK2_uc002lhk.1_Frame_Shift_Del_p.N901fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 1570 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 AACTATGTCATTTTCAGGGAC 0.468 0.93 87 1094 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC1833_LUNG NA HCC1833_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 42 177 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC1833_LUNG NA HCC1833_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 6 60 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HCC1937_BREAST NA HCC1937_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.71 151 370 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 HCC1937_BREAST NA HCC1937_BREAST NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.60 8 12 BMP2K 55589 broad.mit.edu 37 4 79792119 79792136 + In_Frame_Del DEL CAGCAGCAGCAACAGCAA - - HCC1937_BREAST NA HCC1937_BREAST NA g.chr4:79792119_79792136delCAGCAGCAGCAACAGCAA uc003hlk.2 + 11 1580_1597 c.1414_1431delCAGCAGCAGCAACAGCAA c.(1414-1431)CAGCAGCAGCAACAGCAAdel p.QQQQQQ478del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQQQQ478del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 478_483 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 acagcaacagcagcagcagcaacagcaacagcagcagc 0.206 0.22 132 37 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HCC1937_BREAST NA HCC1937_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.65 15 28 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC1937_BREAST NA HCC1937_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 135 254 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HCC1937_BREAST NA HCC1937_BREAST NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.64 5 9 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HCC1937_BREAST NA HCC1937_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 11 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HCC1937_BREAST NA HCC1937_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.29 27 11 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HCC1937_BREAST NA HCC1937_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.11 104 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC1937_BREAST NA HCC1937_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 2 92 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HCC1937_BREAST NA HCC1937_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.10 89 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC1937_BREAST NA HCC1937_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.49 578 558 NCOR2 9612 broad.mit.edu 37 12 124887058 124887059 + In_Frame_Ins INS - GCTGCT GCTGCT rs35831183;rs67031864 HCC1937_BREAST NA HCC1937_BREAST NA g.chr12:124887058_124887059insGCTGCT uc010tba.1 - 14 1648_1649 c.1531_1532insAGCAGC c.(1531-1533)CCC>CAGCAGCCC p.510_511insQQ NCOR2_uc010tay.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010taz.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbb.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbc.1_In_Frame_Ins_p.509_510insQQ|NCOR2_uc001ugj.1_In_Frame_Ins_p.510_511insQQ NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 510_511 cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) GCGGGGCATGGgctgctgctgc 0.312 0.20 92 23 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HCC1937_BREAST NA HCC1937_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.83 34 171 BRCA1 672 broad.mit.edu 37 17 41209079 41209080 + Frame_Shift_Ins INS - G G HCC1937_BREAST NA HCC1937_BREAST NA g.chr17:41209079_41209080insG uc002icq.2 - 19 5498_5499 c.5266_5267insC c.(5266-5268)CAGfs p.Q1756fs BRCA1_uc010whp.1_Frame_Shift_Ins_p.Q605fs|BRCA1_uc010whl.1_Frame_Shift_Ins_p.Q652fs|BRCA1_uc010whm.1_Frame_Shift_Ins_p.Q66fs|BRCA1_uc002icp.3_Frame_Shift_Ins_p.Q1685fs|BRCA1_uc002icu.2_Frame_Shift_Ins_p.Q652fs|BRCA1_uc010cyx.2_Frame_Shift_Ins_p.Q1709fs|BRCA1_uc002ict.2_Frame_Shift_Ins_p.Q1777fs|BRCA1_uc010whn.1_Frame_Shift_Ins_p.Q247fs|BRCA1_uc010who.1_Intron NM_007294 NP_009225 P38398 BRCA1_HUMAN breast cancer 1, early onset isoform 1 1756 BRCT 2. androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding p.Q1756fs*74(2) ovary(24)|breast(21)|lung(4)|central_nervous_system(1)|endometrium(1)|urinary_tract(1) 52 Breast(137;0.000717) BRCA - Breast invasive adenocarcinoma(366;0.126) CTTTCTGTCCTGGGATTCTCTT 0.460 0.93 13 171 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC1937_BREAST NA HCC1937_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 38 165 NCOA6 23054 broad.mit.edu 37 20 33345720 33345721 + In_Frame_Ins INS - TGC TGC rs141107883 HCC1937_BREAST NA HCC1937_BREAST NA g.chr20:33345720_33345721insTGC uc002xav.2 - 8 3401_3402 c.830_831insGCA c.(829-831)CAA>CAGCAA p.277_277Q>QQ NCOA6_uc002xaw.2_In_Frame_Ins_p.277_277Q>QQ|NCOA6_uc010gew.1_In_Frame_Ins_p.234_234Q>QQ NM_014071 NP_054790 Q14686 NCOA6_HUMAN nuclear receptor coactivator 6 277 TBP/GTF2A-binding region.|NCOA1-binding region.|Gln-rich.|CREBBP-binding region. brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter transcription factor complex chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding ovary(3)|breast(3)|central_nervous_system(1) 7 gttgctgttgttgctgctgctg 0.317 0.20 90 23 LAMA5 3911 broad.mit.edu 37 20 60928210 60928210 + Frame_Shift_Del DEL T - - HCC1937_BREAST NA HCC1937_BREAST NA g.chr20:60928210delT uc002ycq.2 - 3 615 c.548delA c.(547-549)CAGfs p.Q183fs NM_005560 NP_005551 O15230 LAMA5_HUMAN laminin alpha 5 precursor 183 Laminin N-terminal. angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex integrin binding ovary(1)|pancreas(1)|skin(1) 3 Breast(26;1.57e-08) BRCA - Breast invasive adenocarcinoma(19;4.36e-06) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) 0.000 1.00 0 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC1937_BREAST NA HCC1937_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 141 393 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC1937_BREAST NA HCC1937_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 112 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC1954_BREAST NA HCC1954_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 9 127 ACVR2A 92 broad.mit.edu 37 2 148657040 148657041 + Frame_Shift_Ins INS - A A HCC1954_BREAST NA HCC1954_BREAST NA g.chr2:148657040_148657041insA uc002twg.2 + 4 546_547 c.277_278insA c.(277-279)GAAfs p.E93fs ACVR2A_uc010zbn.1_5'UTR|ACVR2A_uc002twh.2_Frame_Shift_Ins_p.E93fs NM_001616 NP_001607 P27037 AVR2A_HUMAN activin A receptor, type IIA precursor 93 Extracellular (Potential). activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1) 13 BRCA - Breast invasive adenocarcinoma(221;0.0969) TGATTGTGTAGAAAAAAAAGAC 0.297 0.15 120 21 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HCC1954_BREAST NA HCC1954_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.53 41 46 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC1954_BREAST NA HCC1954_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.21 210 56 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HCC1954_BREAST NA HCC1954_BREAST NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.69 58 129 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HCC1954_BREAST NA HCC1954_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.40 60 40 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC1954_BREAST NA HCC1954_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 30 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HCC1954_BREAST NA HCC1954_BREAST NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.23 124 38 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC1954_BREAST NA HCC1954_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 124 407 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC1954_BREAST NA HCC1954_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 5 190 BRWD3 254065 broad.mit.edu 37 X 79999648 79999649 + Frame_Shift_Del DEL AT - - HCC202_BREAST NA HCC202_BREAST NA g.chrX:79999648_79999649delAT uc004edt.2 - 8 958_959 c.695_696delAT c.(694-696)TATfs p.Y232fs BRWD3_uc004edo.2_5'UTR|BRWD3_uc004edp.2_Frame_Shift_Del_p.Y61fs|BRWD3_uc004edq.2_5'UTR|BRWD3_uc010nmj.1_5'UTR|BRWD3_uc004edr.2_5'UTR|BRWD3_uc004eds.2_5'UTR|BRWD3_uc004edu.2_5'UTR|BRWD3_uc004edv.2_5'UTR|BRWD3_uc004edw.2_5'UTR|BRWD3_uc004edx.2_5'UTR|BRWD3_uc004edy.2_5'UTR|BRWD3_uc004edz.2_5'UTR|BRWD3_uc004eea.2_5'UTR|BRWD3_uc004eeb.2_Intron NM_153252 NP_694984 Q6RI45 BRWD3_HUMAN bromodomain and WD repeat domain containing 3 232 WD 3. ovary(4) 4 GAGTGTTTTCATAGTTAACAGC 0.446 0.19 39 9 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC202_BREAST NA HCC202_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 4 32 AIFM1 9131 broad.mit.edu 37 X 129267296 129267299 + Frame_Shift_Del DEL TGAC - - HCC202_BREAST NA HCC202_BREAST NA g.chrX:129267296_129267299delTGAC uc004evg.2 - 13 1615_1618 c.1437_1440delGTCA c.(1435-1440)CAGTCAfs p.Q479fs AIFM1_uc011mur.1_Frame_Shift_Del_p.Q127fs|AIFM1_uc011mus.1_3'UTR|AIFM1_uc004evh.2_Frame_Shift_Del_p.Q475fs|AIFM1_uc004evi.2_Frame_Shift_Del_p.Q192fs|AIFM1_uc004evk.2_RNA NM_004208 NP_004199 O95831 AIFM1_HUMAN programmed cell death 8 isoform 1 479_480 FAD-dependent oxidoreductase (By similarity). activation of caspase activity|apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|nucleus|perinuclear region of cytoplasm DNA binding|electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity|protein binding ovary(4)|central_nervous_system(1) 5 ACCAGAACATTGACTGATGCCAGT 0.466 0.52 65 70 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HCC202_BREAST NA HCC202_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.34 291 150 MAP3K2 10746 broad.mit.edu 37 2 128081812 128081813 + Frame_Shift_Del DEL CT - - HCC202_BREAST NA HCC202_BREAST NA g.chr2:128081812_128081813delCT uc002toj.1 - 9 747_748 c.682_683delAG c.(682-684)AGCfs p.S228fs MAP3K2_uc010flz.1_Frame_Shift_Del_p.S228fs NM_006609 NP_006600 Q9Y2U5 M3K2_HUMAN mitogen-activated protein kinase kinase kinase 228 activation of JUN kinase activity|cellular response to mechanical stimulus nucleus ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein kinase binding lung(3)|ovary(2)|large_intestine(1)|central_nervous_system(1) 7 Colorectal(110;0.1) BRCA - Breast invasive adenocarcinoma(221;0.0706) TTTTGGATAGCTCTCTCTATAA 0.317 0.35 24 13 PRKG2 5593 broad.mit.edu 37 4 82064060 82064061 + Frame_Shift_Del DEL AG - - HCC202_BREAST NA HCC202_BREAST NA g.chr4:82064060_82064061delAG uc003hmh.2 - 10 1308_1309 c.1294_1295delCT c.(1294-1296)CTGfs p.L432fs PRKG2_uc011ccf.1_Frame_Shift_Del_p.L12fs|PRKG2_uc011ccg.1_Frame_Shift_Del_p.L12fs|PRKG2_uc011cch.1_Frame_Shift_Del_p.L432fs NM_006259 NP_006250 Q13237 KGP2_HUMAN protein kinase, cGMP-dependent, type II 432 platelet activation|signal transduction cytosol ATP binding|cGMP binding|cGMP-dependent protein kinase activity breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1) 7 AATCATTTCCAGAGAGAGTGCT 0.470 0.21 62 16 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HCC202_BREAST NA HCC202_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.58 8 11 ALPK1 80216 broad.mit.edu 37 4 113352188 113352189 + Frame_Shift_Del DEL AG - - HCC202_BREAST NA HCC202_BREAST NA g.chr4:113352188_113352189delAG uc003iap.3 + 11 1764_1765 c.1485_1486delAG c.(1483-1488)ACAGAAfs p.T495fs ALPK1_uc003ian.3_Frame_Shift_Del_p.T495fs|ALPK1_uc011cfx.1_Frame_Shift_Del_p.T417fs|ALPK1_uc003iao.3_Intron|ALPK1_uc010imo.2_Frame_Shift_Del_p.T323fs NM_025144 NP_079420 Q96QP1 ALPK1_HUMAN alpha-kinase 1 495_496 ATP binding|protein serine/threonine kinase activity ovary(5) 5 Ovarian(17;0.0446)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.00325) CTCTAAAAACAGAAATAAAAAA 0.366 0.33 16 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC202_BREAST NA HCC202_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.48 116 107 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC202_BREAST NA HCC202_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.57 23 30 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC202_BREAST NA HCC202_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 31 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC202_BREAST NA HCC202_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 362 131 PKMYT1 9088 broad.mit.edu 37 16 3024396 3024397 + Frame_Shift_Del DEL AG - - HCC202_BREAST NA HCC202_BREAST NA g.chr16:3024396_3024397delAG uc002csn.2 - 6 1444_1445 c.1001_1002delCT c.(1000-1002)TCTfs p.S334fs PKMYT1_uc010uwn.1_RNA|PKMYT1_uc002csm.2_Frame_Shift_Del_p.S334fs|PKMYT1_uc002cso.2_Frame_Shift_Del_p.S265fs|PKMYT1_uc002csp.2_Frame_Shift_Del_p.S325fs|PKMYT1_uc002csq.2_Frame_Shift_Del_p.S325fs|PKMYT1_uc010bsy.1_Frame_Shift_Del_p.S325fs NM_004203 NP_004194 Q99640 PMYT1_HUMAN protein kinase Myt1 isoform 1 334 Protein kinase. G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis endoplasmic reticulum membrane|Golgi membrane|membrane fraction|nucleoplasm ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity stomach(1) 1 TGACAAGGACAGAACGCAGCTC 0.673 0.40 15 10 TP53 7157 broad.mit.edu 37 17 7577086 7577087 + Frame_Shift_Del DEL TG - - HCC202_BREAST NA HCC202_BREAST NA g.chr17:7577086_7577087delTG uc002gim.2 - 8 1045_1046 c.851_852delCA c.(850-852)ACAfs p.T284fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Frame_Shift_Del_p.T284fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.T152fs|TP53_uc010cng.1_Frame_Shift_Del_p.T152fs|TP53_uc002gii.1_Frame_Shift_Del_p.T152fs|TP53_uc010cnh.1_Frame_Shift_Del_p.T284fs|TP53_uc010cni.1_Frame_Shift_Del_p.T284fs|TP53_uc002gij.2_Frame_Shift_Del_p.T284fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 284 |Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). T -> A (in sporadic cancers; somatic mutation).|T -> K (in sporadic cancers; somatic mutation).|T -> P (in sporadic cancers; somatic mutation).|T -> I (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.T284P(7)|p.0?(7)|p.T284fs*61(3)|p.T284A(3)|p.T284T(3)|p.T284fs*21(2)|p.T284fs*62(2)|p.?(2)|p.R283fs*16(2)|p.R282_E287delRRTEEE(1)|p.T284_G293del10(1)|p.G279fs*59(1)|p.S269fs*21(1)|p.R283fs*59(1)|p.T284I(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.R283fs*56(1)|p.R283_T284>T(1)|p.V272_K292del21(1)|p.C275fs*20(1)|p.E285_L289delEEENL(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) TCTCTTCCTCTGTGCGCCGGTC 0.564 0.90 4 35 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HCC202_BREAST NA HCC202_BREAST NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.19 50 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC202_BREAST NA HCC202_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.54 199 236 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC202_BREAST NA HCC202_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 53 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC2157_BREAST NA HCC2157_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 17 LOC642587 642587 broad.mit.edu 37 1 209605637 209605639 + In_Frame_Del DEL AGC - - rs3842530;rs71830217 HCC2157_BREAST NA HCC2157_BREAST NA g.chr1:209605637_209605639delAGC uc009xcn.2 + 4 635_637 c.252_254delAGC c.(250-255)GTAGCA>GTA p.A97del NM_001104548 NP_001098018 hypothetical protein LOC642587 0 OV - Ovarian serous cystadenocarcinoma(81;0.0422) ccaccaccgTagcagcagcagca 0.271 0.46 7 6 ALS2 57679 broad.mit.edu 37 2 202625982 202625984 + In_Frame_Del DEL TTT - - HCC2157_BREAST NA HCC2157_BREAST NA g.chr2:202625982_202625984delTTT uc002uyo.2 - 4 1089_1091 c.733_735delAAA c.(733-735)AAAdel p.K245del ALS2_uc002uyp.3_In_Frame_Del_p.K245del|ALS2_uc002uyq.2_In_Frame_Del_p.K245del|ALS2_uc002uyr.2_In_Frame_Del_p.K245del NM_020919 NP_065970 Q96Q42 ALS2_HUMAN alsin isoform 1 245 cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity p.K245del(1) skin(5)|lung(1)|breast(1) 7 CATGGTCTTCTTTGTCAGTCATA 0.498 0.99 1 82 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC2157_BREAST NA HCC2157_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.43 55 41 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC2157_BREAST NA HCC2157_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.60 25 37 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HCC2157_BREAST NA HCC2157_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 1 13 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HCC2157_BREAST NA HCC2157_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.10 111 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC2157_BREAST NA HCC2157_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 22 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HCC2157_BREAST NA HCC2157_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.53 803 905 CUBN 8029 broad.mit.edu 37 10 16960687 16960693 + Frame_Shift_Del DEL TAACCTC - - HCC2157_BREAST NA HCC2157_BREAST NA g.chr10:16960687_16960693delTAACCTC uc001ioo.2 - 45 6980_6986 c.6928_6934delGAGGTTA c.(6928-6936)GAGGTTATGfs p.E2310fs NM_001081 NP_001072 O60494 CUBN_HUMAN cubilin precursor 2310_2312 CUB 16. cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1) 19 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) CTCAAATACATAACCTCTCCTGAGGAC 0.391 0.52 80 85 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC2157_BREAST NA HCC2157_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 256 64 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HCC2157_BREAST NA HCC2157_BREAST NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.77 3 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HCC2157_BREAST NA HCC2157_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 36 393 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC2157_BREAST NA HCC2157_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.78 8 28 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HCC2157_BREAST NA HCC2157_BREAST NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 70 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC2157_BREAST NA HCC2157_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 195 442 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC2157_BREAST NA HCC2157_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 53 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 HCC2157_BREAST NA HCC2157_BREAST NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.33 31 15 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC2218_BREAST NA HCC2218_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 78 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HCC2218_BREAST NA HCC2218_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.16 624 120 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HCC2218_BREAST NA HCC2218_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.47 17 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC2218_BREAST NA HCC2218_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 76 107 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC2218_BREAST NA HCC2218_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.26 63 22 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HCC2218_BREAST NA HCC2218_BREAST NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.29 17 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HCC2218_BREAST NA HCC2218_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.85 2 11 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HCC2218_BREAST NA HCC2218_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.62 71 114 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 HCC2218_BREAST NA HCC2218_BREAST NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.37 12 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC2218_BREAST NA HCC2218_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 316 129 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HCC2218_BREAST NA HCC2218_BREAST NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.41 36 25 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HCC2218_BREAST NA HCC2218_BREAST NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.53 14 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HCC2218_BREAST NA HCC2218_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 21 196 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC2218_BREAST NA HCC2218_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 12 59 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC2218_BREAST NA HCC2218_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 98 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC2935_LUNG NA HCC2935_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.58 22 30 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HCC2935_LUNG NA HCC2935_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.44 20 16 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HCC2935_LUNG NA HCC2935_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.12 74 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC2935_LUNG NA HCC2935_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 60 101 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC2935_LUNG NA HCC2935_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.79 33 123 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HCC2935_LUNG NA HCC2935_LUNG NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.73 82 221 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HCC2935_LUNG NA HCC2935_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.27 45 17 TBP 6908 broad.mit.edu 37 6 170871038 170871046 + In_Frame_Del DEL CAACAGCAA - - rs145348820;rs71010672;rs10592950;rs62430309 HCC2935_LUNG NA HCC2935_LUNG NA g.chr6:170871038_170871046delCAACAGCAA uc003qxt.2 + 3 446_454 c.214_222delCAACAGCAA c.(214-222)CAACAGCAAdel p.QQQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_95 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding p.Q72del(1) ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcagcagcagcaacagcaacagcagcagc 0.177 0.40 49 33 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HCC2935_LUNG NA HCC2935_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.82 6 28 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC2935_LUNG NA HCC2935_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 429 150 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes HCC2935_LUNG NA HCC2935_LUNG NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.58 5 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC2935_LUNG NA HCC2935_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.61 67 104 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC2935_LUNG NA HCC2935_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 39 146 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC2935_LUNG NA HCC2935_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 6 78 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC33_LUNG NA HCC33_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 35 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC33_LUNG NA HCC33_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.35 112 60 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC33_LUNG NA HCC33_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.43 40 30 MSH5 4439 broad.mit.edu 37 6 31727933 31727934 + Frame_Shift_Ins INS - G G rs28405564 HCC33_LUNG NA HCC33_LUNG NA g.chr6:31727933_31727934insG uc003nwv.1 + 19 1831_1832 c.1752_1753insG c.(1750-1755)AAAGGGfs p.K584fs MSH5_uc003nwt.1_Frame_Shift_Ins_p.K601fs|MSH5_uc003nwu.1_Frame_Shift_Ins_p.K584fs|MSH5_uc003nww.1_Frame_Shift_Ins_p.K584fs|MSH5_uc003nwx.1_Frame_Shift_Ins_p.K601fs|MSH5_uc011dof.1_Frame_Shift_Ins_p.K283fs|MSH5_uc003nwy.1_Frame_Shift_Ins_p.K258fs|MSH5_uc003nwz.3_RNA|C6orf26_uc003nxa.3_5'Flank NM_172166 NP_751898 O43196 MSH5_HUMAN mutS homolog 5 isoform c 584_585 chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination synaptonemal complex ATP binding|DNA-dependent ATPase activity|mismatched DNA binding ovary(2)|breast(1) 3 GTGGGGACAAAGGGAGGGTCAA 0.574 0.12 108 15 EPHA7 2045 broad.mit.edu 37 6 93965680 93965680 + Frame_Shift_Del DEL C - - HCC33_LUNG NA HCC33_LUNG NA g.chr6:93965680delC uc003poe.2 - 13 2489 c.2248delG c.(2248-2250)GCTfs p.A750fs EPHA7_uc003pof.2_Frame_Shift_Del_p.A745fs|EPHA7_uc011eac.1_Frame_Shift_Del_p.A746fs NM_004440 NP_004431 Q15375 EPHA7_HUMAN ephrin receptor EphA7 precursor 750 Cytoplasmic (Potential).|Protein kinase. integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1) 28 all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142) BRCA - Breast invasive adenocarcinoma(108;0.0847) CCCATATCAGCCAAATATCTC 0.418 0.29 79 33 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HCC33_LUNG NA HCC33_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 1 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HCC33_LUNG NA HCC33_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.28 29 11 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC33_LUNG NA HCC33_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 38 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HCC33_LUNG NA HCC33_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.40 6 4 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC33_LUNG NA HCC33_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 384 91 RB1 5925 broad.mit.edu 37 13 48947615 48947615 + Frame_Shift_Del DEL T - - HCC33_LUNG NA HCC33_LUNG NA g.chr13:48947615delT uc001vcb.2 + 12 1368 c.1202delT c.(1201-1203)ATTfs p.I401fs RB1_uc010act.1_Frame_Shift_Del_p.I102fs NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 401 Domain A.|Pocket; binds T and E1A. androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.?(7) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) GAAAATCTGATTTCCTATTTT 0.274 0.93 3 37 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HCC33_LUNG NA HCC33_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 23 207 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC33_LUNG NA HCC33_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.37 42 25 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC33_LUNG NA HCC33_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 126 493 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC33_LUNG NA HCC33_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 7 82 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC366_LUNG NA HCC366_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 53 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HCC366_LUNG NA HCC366_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.34 254 132 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes HCC366_LUNG NA HCC366_LUNG NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.46 19 16 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HCC366_LUNG NA HCC366_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.12 59 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC366_LUNG NA HCC366_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 84 120 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC366_LUNG NA HCC366_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.58 14 19 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HCC366_LUNG NA HCC366_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.47 27 24 ARID1B 57492 broad.mit.edu 37 6 157099402 157099403 + In_Frame_Ins INS - CAG CAG HCC366_LUNG NA HCC366_LUNG NA g.chr6:157099402_157099403insCAG uc003qqn.2 + 1 317_318 c.165_166insCAG c.(163-168)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) TAAACCAGTTCcagcagcagca 0.124 0.18 80 17 NOTCH1 4851 broad.mit.edu 37 9 139405613 139405626 + Frame_Shift_Del DEL CCGTGGGGCAGACA - - HCC366_LUNG NA HCC366_LUNG NA g.chr9:139405613_139405626delCCGTGGGGCAGACA uc004chz.2 - 16 2565_2578 c.2565_2578delTGTCTGCCCCACGG c.(2563-2580)TGTGTCTGCCCCACGGGCfs p.C855fs NOTCH1_uc004cia.1_Frame_Shift_Del_p.C85fs NM_017617 NP_060087 P46531 NOTC1_HUMAN notch1 preproprotein 855_860 Extracellular (Potential).|EGF-like 22. GWQ -> AGAK (in Ref. 1; AAG33848 and 3; AAA60614). aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1) 856 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06) CCTTGCCAGCCCGTGGGGCAGACACAGGAGAAGC 0.664 0.65 16 30 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HCC366_LUNG NA HCC366_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.72 10 26 CIT 11113 broad.mit.edu 37 12 120241182 120241183 + Frame_Shift_Ins INS - G G HCC366_LUNG NA HCC366_LUNG NA g.chr12:120241182_120241183insG uc001txi.1 - 10 1175_1176 c.1122_1123insC c.(1120-1125)CCCTTCfs p.P374fs CIT_uc001txh.1_5'UTR|CIT_uc001txj.1_Frame_Shift_Ins_p.P374fs NM_007174 NP_009105 O14578 CTRO_HUMAN citron 374_375 AGC-kinase C-terminal. intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) GTGGGAACGAAGGGGGGAGGAG 0.500 0.10 74 8 NCOR2 9612 broad.mit.edu 37 12 124887058 124887059 + In_Frame_Ins INS - GCTGCT GCTGCT rs35831183;rs67031864 HCC366_LUNG NA HCC366_LUNG NA g.chr12:124887058_124887059insGCTGCT uc010tba.1 - 14 1648_1649 c.1531_1532insAGCAGC c.(1531-1533)CCC>CAGCAGCCC p.510_511insQQ NCOR2_uc010tay.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010taz.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbb.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbc.1_In_Frame_Ins_p.509_510insQQ|NCOR2_uc001ugj.1_In_Frame_Ins_p.510_511insQQ NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 510_511 cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) GCGGGGCATGGgctgctgctgc 0.312 0.15 46 8 RPGRIP1 57096 broad.mit.edu 37 14 21780627 21780627 + Frame_Shift_Del DEL A - - HCC366_LUNG NA HCC366_LUNG NA g.chr14:21780627delA uc001wag.2 + 9 1113 c.1113delA c.(1111-1113)CGAfs p.R371fs NM_020366 NP_065099 Q96KN7 RPGR1_HUMAN retinitis pigmentosa GTPase regulator 371 Potential. response to stimulus|visual perception cilium ovary(4)|breast(2)|pancreas(1) 7 all_cancers(95;0.0017) all_cancers(140;0.0973) Epithelial(56;6.24e-07)|all cancers(55;6.56e-06) GBM - Glioblastoma multiforme(265;0.00888) AAAAAGAACGAAAATTGCTGA 0.368 0.36 35 20 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes HCC366_LUNG NA HCC366_LUNG NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.13 59 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC366_LUNG NA HCC366_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.79 44 168 CYP2B7P1 1556 broad.mit.edu 37 19 41430277 41430277 + Frame_Shift_Del DEL C - - HCC366_LUNG NA HCC366_LUNG NA g.chr19:41430277delC uc010ehg.1 + 1 108 c.100delC c.(100-102)CCCfs p.P34fs CYP2A7_uc002opo.2_Intron|CYP2B7P1_uc010ehh.1_Frame_Shift_Del_p.P34fs|CYP2B7P1_uc002opq.2_RNA SubName: Full=Cytochrome P450 2B7 short isoform; SubName: Full=CYP2B protein; ovary(1)|skin(1) 2 CCCACCAGGGCCCCGCCCTCT 0.587 0.92 10 118 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC366_LUNG NA HCC366_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 42 573 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC366_LUNG NA HCC366_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 61 CARD10 29775 broad.mit.edu 37 22 37906357 37906358 + Frame_Shift_Ins INS - G G HCC366_LUNG NA HCC366_LUNG NA g.chr22:37906357_37906358insG uc003asx.1 - 4 773_774 c.770_771insC c.(769-771)CCGfs p.P257fs CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_Frame_Shift_Ins_p.P257fs NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 257 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) CCCCAGGGGGCGGGCCCCTGGC 0.515 0.10 183 21 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC38_BREAST NA HCC38_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 6 71 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC38_BREAST NA HCC38_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 63 78 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC38_BREAST NA HCC38_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 23 41 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HCC38_BREAST NA HCC38_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.40 6 4 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HCC38_BREAST NA HCC38_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.44 47 37 MYO3A 53904 broad.mit.edu 37 10 26241109 26241114 + In_Frame_Del DEL ACTGAG - - HCC38_BREAST NA HCC38_BREAST NA g.chr10:26241109_26241114delACTGAG uc001isn.2 + 3 430_435 c.70_75delACTGAG c.(70-75)ACTGAGdel p.TE24del MYO3A_uc009xko.1_In_Frame_Del_p.TE24del|MYO3A_uc009xkp.1_RNA|MYO3A_uc009xkq.1_In_Frame_Del_p.TE24del|MYO3A_uc001ism.2_In_Frame_Del_p.TE24del NM_017433 NP_059129 Q8NEV4 MYO3A_HUMAN myosin IIIA 24_25 Protein kinase. protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception cytoplasm|filamentous actin|filopodium|myosin complex actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity p.E25_I27>I(1) ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 18 ATGGGAAATCACTGAGACAATTGGCA 0.335 0.90 10 88 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HCC38_BREAST NA HCC38_BREAST NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.68 8 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC38_BREAST NA HCC38_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.11 246 31 CNTN5 53942 broad.mit.edu 37 11 100064391 100064391 + Frame_Shift_Del DEL G - - HCC38_BREAST NA HCC38_BREAST NA g.chr11:100064391delG uc001pga.2 + 15 2219 c.1880delG c.(1879-1881)AGGfs p.R627fs CNTN5_uc009ywv.1_Frame_Shift_Del_p.R627fs|CNTN5_uc001pfz.2_Frame_Shift_Del_p.R627fs|CNTN5_uc001pgb.2_Frame_Shift_Del_p.R553fs|CNTN5_uc010ruk.1_5'UTR NM_014361 NP_055176 O94779 CNTN5_HUMAN contactin 5 isoform long 627 Ig-like C2-type 6. cell adhesion anchored to membrane|plasma membrane protein binding skin(3)|ovary(2)|pancreas(2)|breast(1) 8 all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219) BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196) GAAAGCATCAGGGCCGTAAGT 0.358 0.28 81 31 SORL1 6653 broad.mit.edu 37 11 121460807 121460818 + In_Frame_Del DEL CCACTGCATCCC - - HCC38_BREAST NA HCC38_BREAST NA g.chr11:121460807_121460818delCCACTGCATCCC uc001pxx.2 + 30 4217_4228 c.4137_4148delCCACTGCATCCC c.(4135-4149)GGCCACTGCATCCCC>GGC p.HCIP1380del SORL1_uc010rzp.1_In_Frame_Del_p.HCIP226del|SORL1_uc010rzq.1_5'Flank NM_003105 NP_003096 Q92673 SORL_HUMAN sortilin-related receptor containing LDLR class 1380_1383 Extracellular (Potential).|LDL-receptor class A 8. cholesterol metabolic process|lipid transport|receptor-mediated endocytosis integral to plasma membrane|low-density lipoprotein particle low-density lipoprotein particle binding|transmembrane receptor activity p.H1380_P1383del(1) ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1) 15 Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113) BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108) GTGAGAATGGCCACTGCATCCCCAACAGATGG 0.538 0.97 1 36 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HCC38_BREAST NA HCC38_BREAST NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.53 7 8 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes HCC38_BREAST NA HCC38_BREAST NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.15 62 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC38_BREAST NA HCC38_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 66 314 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC38_BREAST NA HCC38_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 5 70 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC4006_LUNG NA HCC4006_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.38 45 28 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HCC4006_LUNG NA HCC4006_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.43 298 223 ITGAV 3685 broad.mit.edu 37 2 187532485 187532492 + Frame_Shift_Del DEL TGTTCAGC - - HCC4006_LUNG NA HCC4006_LUNG NA g.chr2:187532485_187532492delTGTTCAGC uc002upq.2 + 24 2691_2698 c.2415_2422delTGTTCAGC c.(2413-2424)GTTGTTCAGCACfs p.V805fs ITGAV_uc010frs.2_Frame_Shift_Del_p.V769fs|ITGAV_uc010zfv.1_Frame_Shift_Del_p.V759fs NM_002210 NP_002201 P06756 ITAV_HUMAN integrin alpha-V isoform 1 precursor 805_808 Extracellular (Potential). angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance integrin complex receptor activity|transforming growth factor beta binding ovary(2)|kidney(1)|skin(1) 4 OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189) STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108) TTGGGCCAGTTGTTCAGCACATCTATGA 0.418 0.27 175 64 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HCC4006_LUNG NA HCC4006_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.34 35 18 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HCC4006_LUNG NA HCC4006_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.23 106 31 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HCC4006_LUNG NA HCC4006_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.33 12 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC4006_LUNG NA HCC4006_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 60 53 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC4006_LUNG NA HCC4006_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.85 17 96 POU3F2 5454 broad.mit.edu 37 6 99283172 99283173 + In_Frame_Ins INS - CAG CAG HCC4006_LUNG NA HCC4006_LUNG NA g.chr6:99283172_99283173insCAG uc003ppe.2 + 1 593_594 c.423_424insCAG c.(421-426)insCAG p.149_150insQ NM_005604 NP_005595 P20265 PO3F2_HUMAN POU domain, class 3, transcription factor 2 149_150 positive regulation of cell proliferation identical protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197) BRCA - Breast invasive adenocarcinoma(108;0.0355) aacagcagcaacagcagcagca 0.465 0.13 52 8 EGFR 1956 broad.mit.edu 37 7 55242466 55242474 + In_Frame_Del DEL GAATTAAGA - - rs121913426;rs121913425;rs121913435;rs121913436;rs121913441 HCC4006_LUNG NA HCC4006_LUNG NA g.chr7:55242466_55242474delGAATTAAGA uc003tqk.2 + 19 2482_2490 c.2236_2244delGAATTAAGA c.(2236-2244)GAATTAAGAdel p.ELR746del EGFR_uc010kzg.1_In_Frame_Del_p.ELR701del|EGFR_uc011kco.1_In_Frame_Del_p.ELR693del NM_005228 NP_005219 P00533 EGFR_HUMAN epidermal growth factor receptor isoform a 746_748 Cytoplasmic (Potential).|Protein kinase. R -> P (found in a lung cancer sample).|Missing (found in a lung cancer sample).|Missing (found in a lung cancer sample). activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity p.E746_A750del(1613)|p.L747_P753>S(110)|p.L747_A750>P(74)|p.E746_S752>V(67)|p.L747_T751del(62)|p.E746_T751>A(30)|p.L747_S752del(28)|p.L747_T751>P(20)|p.E746_T751del(18)|p.L747_E749del(18)|p.K745_E749del(14)|p.E746_E749del(12)|p.E746_S752del(10)|p.L747_T751>S(7)|p.L747_P753>Q(7)|p.E746_P753>VS(6)|p.E746_A750>IP(5)|p.L747_T751>Q(5)|p.E746_T751>I(5)|p.E746_T751>V(5)|p.E746_S752>A(5)|p.E746_T751>IP(5)|p.E746_A750>QP(4)|p.E746V(4)|p.E746_S752>D(4)|p.K745_A750del(4)|p.L747S(3)|p.L747_S752>Q(3)|p.E746_T751>VA(3)|p.E746_T751>VP(3)|p.E746_A750>RP(2)|p.E746_A750>S(2)|p.E746_S752>T(2)|p.E746_T751>Q(2)|p.E746_T751>S(2)|p.E746_A750>DP(2)|p.E746_T751>L(2)|p.E746K(2)|p.E746_P753del(2)|p.E746_S752>I(2)|p.K745_E746insVPVAIK(2)|p.E746_A750>AP(2)|p.L747_K754>ST(1)|p.E746_A750>A(1)|p.E746_T751>P(1)|p.E746del(1)|p.L747_S752>QH(1)|p.L747P(1)|p.E746_A750>VP(1)|p.L747_K754>N(1)|p.L747_R748>FP(1)|p.K745_L747del(1)|p.L747_T751>A(1)|p.E746_P753>LS(1)|p.E746_P753>VQ(1)|p.E746_T751>LS(1)|p.E746_R748del(1)|p.I744_A750>VK(1)|p.E746I(1)|p.L747_K754del(1)|p.R748I(1)|p.E746_A750>KP(1)|p.E746_A750>EP(1) lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1) 9571 all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318) GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607) Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072) CGCTATCAAGGAATTAAGAGAAGCAACAT 0.478 0.46 120 103 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HCC4006_LUNG NA HCC4006_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.90 1 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC4006_LUNG NA HCC4006_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 2 21 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - HCC4006_LUNG NA HCC4006_LUNG NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.58 49 68 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 HCC4006_LUNG NA HCC4006_LUNG NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.89 2 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC4006_LUNG NA HCC4006_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 507 93 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HCC4006_LUNG NA HCC4006_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.36 29 16 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC4006_LUNG NA HCC4006_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 47 381 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC4006_LUNG NA HCC4006_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 42 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC44_LUNG NA HCC44_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 10 140 STIL 6491 broad.mit.edu 37 1 47746670 47746671 + Frame_Shift_Ins INS - CT CT HCC44_LUNG NA HCC44_LUNG NA g.chr1:47746670_47746671insCT uc001crc.1 - 12 1614_1615 c.1459_1460insAG c.(1459-1461)GGAfs p.G487fs TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Frame_Shift_Ins_p.G440fs|STIL_uc010omo.1_Frame_Shift_Ins_p.G487fs|STIL_uc001crd.1_Frame_Shift_Ins_p.G487fs|STIL_uc001cre.1_Frame_Shift_Ins_p.G487fs|STIL_uc001crf.1_Frame_Shift_Ins_p.G100fs|STIL_uc001crg.1_Frame_Shift_Ins_p.G440fs NM_003035 NP_003026 Q15468 STIL_HUMAN SCL/TAL1 interrupting locus isoform 2 487 cell proliferation|multicellular organismal development centrosome|cytosol lung(2)|skin(1) 3 Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444) ATTTGGTATTCCTCTCAAGGAA 0.450 0.24 957 302 FMN2 56776 broad.mit.edu 37 1 240371579 240371580 + Frame_Shift_Ins INS - A A HCC44_LUNG NA HCC44_LUNG NA g.chr1:240371579_240371580insA uc010pyd.1 + 5 3692_3693 c.3467_3468insA c.(3466-3468)CCAfs p.P1156fs FMN2_uc010pye.1_Frame_Shift_Ins_p.P1160fs NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 1156 Pro-rich.|FH1. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) 0.000 0.29 172 69 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HCC44_LUNG NA HCC44_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 305 62 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HCC44_LUNG NA HCC44_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.52 47 50 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC44_LUNG NA HCC44_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 146 118 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC44_LUNG NA HCC44_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 42 92 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - G G rs34108497;rs146125714 HCC44_LUNG NA HCC44_LUNG NA g.chr8:62550924_62550925insG uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.22 200 57 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC44_LUNG NA HCC44_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 187 37 RB1 5925 broad.mit.edu 37 13 48878142 48878143 + Frame_Shift_Ins INS - A A HCC44_LUNG NA HCC44_LUNG NA g.chr13:48878142_48878143insA uc001vcb.2 + 1 260_261 c.94_95insA c.(94-96)GACfs p.D32fs RB1_uc010acs.1_RNA|uc001vca.2_5'Flank NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 32 androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.0?(13)|p.?(1) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) 0.000 0.47 301 267 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HCC44_LUNG NA HCC44_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.43 8 6 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HCC44_LUNG NA HCC44_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 74 592 STK11 6794 broad.mit.edu 37 19 1207064 1207065 + Frame_Shift_Ins INS - C C HCC44_LUNG NA HCC44_LUNG NA g.chr19:1207064_1207065insC uc002lrl.1 + 1 1267_1268 c.152_153insC c.(151-153)ATGfs p.M51fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 51 Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.?(3)|p.D53fs*11(1)|p.L50_D53del(1)|p.M51fs*14(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.81 457 1978 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC44_LUNG NA HCC44_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.62 45 73 BCL3 602 broad.mit.edu 37 19 45262726 45262729 + Frame_Shift_Del DEL CCCC - - HCC44_LUNG NA HCC44_LUNG NA g.chr19:45262726_45262729delCCCC uc010xxe.1 + 9 1289_1292 c.1219_1222delCCCC c.(1219-1224)CCCCCCfs p.P407fs NM_005178 NP_005169 P20749 BCL3_HUMAN B-cell CLL/lymphoma 3 407_408 Pro/Ser-rich. DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|I-kappaB kinase/NF-kappaB cascade|maintenance of protein location in nucleus|negative regulation of apoptosis|negative regulation of interleukin-8 biosynthetic process|negative regulation of transcription, DNA-dependent|positive regulation of translation|protein import into nucleus, translocation|regulation of DNA binding|regulation of NF-kappaB import into nucleus|response to UV-C|response to virus Bcl3-Bcl10 complex|Bcl3/NF-kappaB2 complex|nucleus|perinuclear region of cytoplasm protein binding, bridging|transcription factor binding ovary(1)|lung(1) 2 Lung NSC(12;0.000698)|all_lung(12;0.002) Ovarian(192;0.0728) CTCCCAGTCTCCCCCCAGGGACCC 0.505 0.40 448 303 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes HCC44_LUNG NA HCC44_LUNG NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.48 22 20 GRIK1 2897 broad.mit.edu 37 21 30959780 30959780 + Frame_Shift_Del DEL C - - HCC44_LUNG NA HCC44_LUNG NA g.chr21:30959780delC uc002yno.1 - 12 2163 c.1699delG c.(1699-1701)GTTfs p.V567fs GRIK1_uc002ynn.2_Frame_Shift_Del_p.V552fs|GRIK1_uc011acs.1_Frame_Shift_Del_p.V567fs|GRIK1_uc011act.1_Frame_Shift_Del_p.V428fs|GRIK1_uc010glq.1_Frame_Shift_Del_p.V410fs NM_000830 NP_000821 P39086 GRIK1_HUMAN glutamate receptor, ionotropic, kainate 1 567 Extracellular (Potential). central nervous system development|synaptic transmission cell junction|postsynaptic membrane kainate selective glutamate receptor activity large_intestine(1)|ovary(1)|skin(1) 3 L-Glutamic Acid(DB00142)|Topiramate(DB00273) AAGGAGAAAACGCCTGGATTG 0.493 0.60 4 6 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC44_LUNG NA HCC44_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 160 488 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC44_LUNG NA HCC44_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 24 295 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC70_BREAST NA HCC70_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 35 FMN2 56776 broad.mit.edu 37 1 240256066 240256067 + In_Frame_Ins INS - CAG CAG HCC70_BREAST NA HCC70_BREAST NA g.chr1:240256066_240256067insCAG uc010pyd.1 + 1 882_883 c.657_658insCAG c.(655-660)insCAG p.225_226insQ FMN2_uc010pye.1_In_Frame_Ins_p.225_226insQ NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 225_226 Potential.|Gln-rich. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) agctccagcaacagcagcagca 0.465 0.21 41 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC70_BREAST NA HCC70_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.37 49 29 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC70_BREAST NA HCC70_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 14 20 GCNT2 2651 broad.mit.edu 37 6 10529403 10529404 + Frame_Shift_Del DEL AC - - HCC70_BREAST NA HCC70_BREAST NA g.chr6:10529403_10529404delAC uc010joo.2 + 3 810_811 c.259_260delAC c.(259-261)ACAfs p.T87fs GCNT2_uc010jol.2_Intron|GCNT2_uc010jom.2_Intron|GCNT2_uc010jop.2_Intron|GCNT2_uc003mza.2_Intron|GCNT2_uc003mzc.3_Frame_Shift_Del_p.T86fs|GCNT2_uc010jon.2_Frame_Shift_Del_p.T86fs NM_145649 NP_663624 Q8N0V5 GNT2A_HUMAN glucosaminyl (N-acetyl) transferase 2, 87 Lumenal (Potential). Golgi membrane|integral to membrane N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity ovary(2) 2 Ovarian(93;0.107)|Breast(50;0.148) all_hematologic(90;0.107) KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119) TGTAACAGAAACACTCTCTGAA 0.446 0.75 39 115 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HCC70_BREAST NA HCC70_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 16 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC70_BREAST NA HCC70_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 1 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HCC70_BREAST NA HCC70_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.48 756 699 PTEN 5728 broad.mit.edu 37 10 89692783 89692783 + Frame_Shift_Del DEL T - - HCC70_BREAST NA HCC70_BREAST NA g.chr10:89692783delT uc001kfb.2 + 6 1298 c.267delT c.(265-267)CCTfs p.P89fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 89 Phosphatase tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R55fs*1(4)|p.?(2)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.F90fs*9(2)|p.Q87_P96del(1)|p.N82_P95del(1)|p.F56fs*2(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) CACAATATCCTTTTGAAGACC 0.338 0.98 2 115 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HCC70_BREAST NA HCC70_BREAST NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.83 4 20 RB1 5925 broad.mit.edu 37 13 48954315 48954317 + In_Frame_Del DEL ACA - - HCC70_BREAST NA HCC70_BREAST NA g.chr13:48954315_48954317delACA uc001vcb.2 + 16 1602_1604 c.1436_1438delACA c.(1435-1440)GACAAC>GAC p.N480del NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 480 Domain A.|Pocket; binds T and E1A. Missing (in RB; mild form). androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.?(7)|p.N480fs*13(1) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) CTTCTGAATGACAACATTTTTCA 0.207 0.95 3 53 PRKD1 5587 broad.mit.edu 37 14 30396619 30396626 + Frame_Shift_Del DEL CGGGCCCG - - rs144938427;rs139860047 by1000genomes HCC70_BREAST NA HCC70_BREAST NA g.chr14:30396619_30396626delCGGGCCCG uc001wqh.2 - 1 274_281 c.93_100delCGGGCCCG c.(91-102)TCCGGGCCCGGGfs p.S31fs NM_002742 NP_002733 Q15139 KPCD1_HUMAN protein kinase D1 31_34 cell proliferation|intracellular signal transduction|sphingolipid metabolic process cytosol|integral to plasma membrane ATP binding|metal ion binding|protein binding|protein kinase C activity lung(3)|large_intestine(2)|ovary(2)|skin(1) 8 Hepatocellular(127;0.0604) LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252) GBM - Glioblastoma multiforme(265;0.00888) 0.000 0.76 195 603 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HCC70_BREAST NA HCC70_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 65 559 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC70_BREAST NA HCC70_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.60 19 28 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC70_BREAST NA HCC70_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 154 497 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC70_BREAST NA HCC70_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 77 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 HCC70_BREAST NA HCC70_BREAST NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.37 36 21 KDM6A 7403 broad.mit.edu 37 X 44929200 44929201 + Frame_Shift_Ins INS - T T HCC78_LUNG NA HCC78_LUNG NA g.chrX:44929200_44929201insT uc004dge.3 + 17 2675_2676 c.2300_2301insT c.(2299-2301)TCTfs p.S767fs KDM6A_uc010nhk.2_Frame_Shift_Ins_p.S733fs|KDM6A_uc011mkz.1_Frame_Shift_Ins_p.S819fs|KDM6A_uc011mla.1_Frame_Shift_Ins_p.S722fs|KDM6A_uc011mlb.1_Frame_Shift_Ins_p.S774fs|KDM6A_uc011mlc.1_Frame_Shift_Ins_p.S471fs|KDM6A_uc011mld.1_Frame_Shift_Ins_p.S406fs NM_021140 NP_066963 O15550 KDM6A_HUMAN ubiquitously transcribed tetratricopeptide 767 histone H3-K4 methylation metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2) 84 CATGGAGATTCTAAGTCACCAG 0.475 0.34 86 44 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC78_LUNG NA HCC78_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 4 51 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes HCC78_LUNG NA HCC78_LUNG NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.64 8 14 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HCC78_LUNG NA HCC78_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.25 27 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC78_LUNG NA HCC78_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.49 127 120 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC78_LUNG NA HCC78_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.52 25 27 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HCC78_LUNG NA HCC78_LUNG NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.53 7 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HCC78_LUNG NA HCC78_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 15 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HCC78_LUNG NA HCC78_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.38 16 10 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HCC78_LUNG NA HCC78_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.41 546 382 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 HCC78_LUNG NA HCC78_LUNG NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.51 17 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC78_LUNG NA HCC78_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 1221 213 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes HCC78_LUNG NA HCC78_LUNG NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.30 76 32 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HCC78_LUNG NA HCC78_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.27 88 32 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HCC78_LUNG NA HCC78_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.56 24 30 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HCC78_LUNG NA HCC78_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 9 70 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC78_LUNG NA HCC78_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 42 104 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HCC78_LUNG NA HCC78_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.22 52 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC78_LUNG NA HCC78_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 57 374 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC78_LUNG NA HCC78_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 98 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC827_LUNG NA HCC827_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 31 TNNI3K 51086 broad.mit.edu 37 1 74819791 74819791 + Frame_Shift_Del DEL T - - HCC827_LUNG NA HCC827_LUNG NA g.chr1:74819791delT uc001dgf.1 + 11 1206 c.1155delT c.(1153-1155)TGTfs p.C385fs TNNI3K_uc001dgc.1_Frame_Shift_Del_p.C486fs|TNNI3K_uc001dgd.2_Frame_Shift_Del_p.C486fs|TNNI3K_uc001dge.1_Frame_Shift_Del_p.C486fs NM_015978 NP_057062 Q59H18 TNI3K_HUMAN TNNI3 interacting kinase isoform b 385 ANK 10. cytoplasm|nucleus ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1) 10 AGCAGACATGTTTGATGTGGG 0.383 0.23 89 26 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HCC827_LUNG NA HCC827_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.26 51 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HCC827_LUNG NA HCC827_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.38 13 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC827_LUNG NA HCC827_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 39 32 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC827_LUNG NA HCC827_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 27 13 EGFR 1956 broad.mit.edu 37 7 55242466 55242480 + In_Frame_Del DEL GAATTAAGAGAAGCA - - rs121913426;rs121913425;rs121913435;rs121913436;rs121913441;rs121913229 HCC827_LUNG NA HCC827_LUNG NA g.chr7:55242466_55242480delGAATTAAGAGAAGCA uc003tqk.2 + 19 2482_2496 c.2236_2250delGAATTAAGAGAAGCA c.(2236-2250)GAATTAAGAGAAGCAdel p.ELREA746del EGFR_uc010kzg.1_In_Frame_Del_p.ELREA701del|EGFR_uc011kco.1_In_Frame_Del_p.ELREA693del NM_005228 NP_005219 P00533 EGFR_HUMAN epidermal growth factor receptor isoform a 746_750 Cytoplasmic (Potential).|Protein kinase. Missing (found in a lung cancer sample). activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity p.E746_A750del(1613)|p.L747_P753>S(110)|p.L747_A750>P(74)|p.E746_S752>V(67)|p.L747_T751del(62)|p.E746_T751>A(30)|p.L747_S752del(28)|p.L747_T751>P(20)|p.E746_T751del(18)|p.L747_E749del(18)|p.K745_E749del(14)|p.E746_E749del(12)|p.E746_S752del(10)|p.L747_T751>S(7)|p.L747_P753>Q(7)|p.E746_P753>VS(6)|p.E746_A750>IP(5)|p.L747_T751>Q(5)|p.E746_T751>I(5)|p.E746_T751>V(5)|p.E746_S752>A(5)|p.E746_T751>IP(5)|p.E746_A750>QP(4)|p.E746V(4)|p.E746_S752>D(4)|p.K745_A750del(4)|p.L747S(3)|p.L747_S752>Q(3)|p.A750P(3)|p.E746_T751>VA(3)|p.E746_T751>VP(3)|p.E746_A750>RP(2)|p.E746_A750>S(2)|p.E746_S752>T(2)|p.A750_E758>P(2)|p.E746_T751>Q(2)|p.E746_T751>S(2)|p.E746_A750>DP(2)|p.E746_T751>L(2)|p.E746K(2)|p.E746_P753del(2)|p.E746_S752>I(2)|p.K745_E746insVPVAIK(2)|p.E746_A750>AP(2)|p.L747_K754>ST(1)|p.E746_A750>A(1)|p.E746_T751>P(1)|p.E746del(1)|p.A750_K754del(1)|p.L747_S752>QH(1)|p.L747P(1)|p.E746_A750>VP(1)|p.L747_K754>N(1)|p.L747_R748>FP(1)|p.K745_L747del(1)|p.L747_T751>A(1)|p.E746_P753>LS(1)|p.E746_P753>VQ(1)|p.E746_T751>LS(1)|p.A750_E758del(1)|p.E746_R748del(1)|p.I744_A750>VK(1)|p.E746I(1)|p.L747_K754del(1)|p.R748I(1)|p.E746_A750>KP(1)|p.T751_E758del(1)|p.E746_A750>EP(1) lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1) 9571 all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318) GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607) Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072) CGCTATCAAGGAATTAAGAGAAGCAACATCTCCGA 0.474 0.95 51 966 ELN 2006 broad.mit.edu 37 7 73474237 73474290 + In_Frame_Del DEL TGGCTCCTGGAGTTGGCGTGGCTCCTGGTGTCGGTGTGGCTCCTGGAGTTGGCT - - rs56307747 HCC827_LUNG NA HCC827_LUNG NA g.chr7:73474237_73474290delTGGCTCCTGGAGTTGGCGTGGCTCCTGGTGTCGGTGTGGCTCCTGGAGTTGGCT uc003tzw.2 + 23 1545_1598 c.1454_1507delTGGCTCCTGGAGTTGGCGTGGCTCCTGGTGTCGGTGTGGCTCCTGGAGTTGGCT c.(1453-1509)GTGGCTCCTGGAGTTGGCGTGGCTCCTGGTGTCGGTGTGGCTCCTGGAGTTGGCTTG>GTG p.APGVGVAPGVGVAPGVGL486del RFC2_uc011kfa.1_Intron|ELN_uc003tzn.2_In_Frame_Del_p.APGVGVAPGVGVAPGVGL480del|ELN_uc003tzz.2_In_Frame_Del_p.APGVGVAPGVGVAPGVGL399del|ELN_uc003tzo.2_In_Frame_Del_p.APGVGVAPGVGVAPGVGL447del|ELN_uc003tzp.2_In_Frame_Del_p.APGVGVAPGVGVAPGVGL391del|ELN_uc003tzq.2_In_Frame_Del_p.APGVGVAPGVGVAPGVGL344del|ELN_uc003tzr.2_Intron|ELN_uc003tzs.2_In_Frame_Del_p.APGVGVAPGVGVAPGVGL461del|ELN_uc003tzt.2_In_Frame_Del_p.APGVGVAPGVGVAPGVGL485del|ELN_uc003tzu.2_In_Frame_Del_p.APGVGVAPGVGVAPGVGL466del|ELN_uc003tzv.2_In_Frame_Del_p.APGVGVAPGVGVAPGVGL451del|ELN_uc003tzx.2_In_Frame_Del_p.APGVGVAPGVGVAPGVGL470del|ELN_uc011kff.1_In_Frame_Del_p.APGVGVAPGVGVAPGVGL480del|ELN_uc003tzy.2_In_Frame_Del_p.APGVGVAPGVGVAPGVGL456del NM_000501 NP_001075224 P15502 ELN_HUMAN elastin isoform a precursor 509_526 Ala-rich. blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange proteinaceous extracellular matrix extracellular matrix constituent conferring elasticity|protein binding ovary(3)|pancreas(2) 5 Lung NSC(55;0.159) Rofecoxib(DB00533) GGTGTCGGCGTGGCTCCTGGAGTTGGCGTGGCTCCTGGTGTCGGTGTGGCTCCTGGAGTTGGCTTGGCTCCTGG 0.496 0.26 145 51 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HCC827_LUNG NA HCC827_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 743 83 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HCC827_LUNG NA HCC827_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.88 2 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC827_LUNG NA HCC827_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 179 63 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HCC827_LUNG NA HCC827_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.50 14 14 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HCC827_LUNG NA HCC827_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.85 35 197 TP53 7157 broad.mit.edu 37 17 7578195 7578197 + In_Frame_Del DEL CAC - - HCC827_LUNG NA HCC827_LUNG NA g.chr17:7578195_7578197delCAC uc002gim.2 - 6 846_848 c.652_654delGTG c.(652-654)GTGdel p.V218del TP53_uc002gig.1_In_Frame_Del_p.V218del|TP53_uc002gih.2_In_Frame_Del_p.V218del|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_In_Frame_Del_p.V86del|TP53_uc010cng.1_In_Frame_Del_p.V86del|TP53_uc002gii.1_In_Frame_Del_p.V86del|TP53_uc010cnh.1_In_Frame_Del_p.V218del|TP53_uc010cni.1_In_Frame_Del_p.V218del|TP53_uc002gij.2_In_Frame_Del_p.V218del|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_In_Frame_Del_p.V125del|TP53_uc002gio.2_In_Frame_Del_p.V86del|TP53_uc010vug.1_In_Frame_Del_p.V179del NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 218 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). V -> A (in sporadic cancers; somatic mutation).|V -> M (in sporadic cancers; somatic mutation).|V -> G (in sporadic cancers; somatic mutation).|V -> L (in sporadic cancers; somatic mutation).|V -> E (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.V218E(8)|p.V218M(7)|p.0?(7)|p.V218G(5)|p.V218del(5)|p.V218A(3)|p.K164_P219del(1)|p.S215fs*27(1)|p.S215fs*29(1)|p.V218_P219insX(1)|p.V218_Y220delVPY(1)|p.V216_Y220delVVVPY(1)|p.D208fs*1(1)|p.V216fs*28(1)|p.?(1)|p.V218L(1)|p.V218_E221delVPYE(1)|p.V218V(1)|p.V218fs*26(1)|p.S215_V218>R(1)|p.T211fs*28(1)|p.V218_E224delVPYEPPE(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GCTCATAGGGCACCACCACACTA 0.552 0.91 8 83 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HCC827_LUNG NA HCC827_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.55 23 28 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC827_LUNG NA HCC827_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 56 335 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC827_LUNG NA HCC827_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 2 39 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HCC95_LUNG NA HCC95_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 25 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HCC95_LUNG NA HCC95_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.33 55 27 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCC95_LUNG NA HCC95_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.44 32 25 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HCC95_LUNG NA HCC95_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HCC95_LUNG NA HCC95_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 10 PAMR1 25891 broad.mit.edu 37 11 35453797 35453797 + Splice_Site DEL C - - rs11344760 HCC95_LUNG NA HCC95_LUNG NA g.chr11:35453797delC uc001mwg.2 - 11 2312 c.2269_splice c.e11+1 PAMR1_uc001mwf.2_Splice_Site|PAMR1_uc010rew.1_3'UTR|PAMR1_uc010rex.1_3'UTR NM_001001991 NP_001001991 Q6UXH9 PAMR1_HUMAN regeneration associated muscle protease isoform proteolysis extracellular region serine-type endopeptidase activity ovary(2) 2 CCTGGCACAGCCCAAGTTCAC 0.522 0.91 2 20 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HCC95_LUNG NA HCC95_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.50 5 5 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HCC95_LUNG NA HCC95_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 120 23 TSC2 7249 broad.mit.edu 37 16 2138578 2138580 + In_Frame_Del DEL CTC - - HCC95_LUNG NA HCC95_LUNG NA g.chr16:2138578_2138580delCTC uc002con.2 + 42 5497_5499 c.5391_5393delCTC c.(5389-5394)ATCTCC>ATC p.S1799del TSC2_uc010bsd.2_In_Frame_Del_p.S1776del|TSC2_uc002coo.2_In_Frame_Del_p.S1732del|TSC2_uc010uvv.1_In_Frame_Del_p.S1696del|TSC2_uc010uvw.1_In_Frame_Del_p.S1684del|TSC2_uc002cop.2_In_Frame_Del_p.S1555del|TSC2_uc002coq.2_In_Frame_Del_p.S574del|TSC2_uc002cor.2_In_Frame_Del_p.S500del NM_000548 NP_000539 P49815 TSC2_HUMAN tuberous sclerosis 2 isoform 1 1799 cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex GTPase activator activity|protein homodimerization activity central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1) 10 Hepatocellular(780;0.0202) AGCGCCTCATCTCCTCGGTGGAG 0.606 0.60 4 6 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HCC95_LUNG NA HCC95_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.83 8 38 TP53 7157 broad.mit.edu 37 17 7574025 7574025 + Frame_Shift_Del DEL C - - HCC95_LUNG NA HCC95_LUNG NA g.chr17:7574025delC uc002gim.2 - 10 1196 c.1002delG c.(1000-1002)GGGfs p.G334fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Intron|TP53_uc010cne.1_Intron|TP53_uc010cnf.1_3'UTR|TP53_uc010cng.1_3'UTR|TP53_uc002gii.1_Frame_Shift_Del_p.G202fs|TP53_uc010cnh.1_3'UTR|TP53_uc010cni.1_3'UTR|TP53_uc002gij.2_Frame_Shift_Del_p.G334fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 334 Oligomerization.|Interaction with HIPK1 (By similarity).|Interaction with CARM1.|Interaction with HIPK2. G -> W (in a sporadic cancer; somatic mutation).|G -> V (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.G334V(3)|p.I332fs*5(1)|p.G334W(1)|p.?(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.98 8 454 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCC95_LUNG NA HCC95_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 36 247 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HCC95_LUNG NA HCC95_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 66 ATRX 546 broad.mit.edu 37 X 76891517 76891519 + In_Frame_Del DEL TGG - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chrX:76891517_76891519delTGG uc004ecp.3 - 16 4818_4820 c.4586_4588delCCA c.(4585-4590)ACCAAG>AAG p.T1529del ATRX_uc004ecq.3_In_Frame_Del_p.T1491del|ATRX_uc004eco.3_In_Frame_Del_p.T1314del NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 1529 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) ATTGGACACTTGGTGGGTGAAGC 0.369 0.88 34 253 DVL1 1855 broad.mit.edu 37 1 1271642 1271642 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr1:1271642delC uc001aer.3 - 15 1940 c.1893delG c.(1891-1893)GGGfs p.G631fs DVL1_uc002quu.2_Frame_Shift_Del_p.G373fs|DVL1_uc009vka.2_Frame_Shift_Del_p.G314fs|DVL1_uc001aeu.1_3'UTR NM_004421 NP_004412 O14640 DVL1_HUMAN dishevelled 1 656 canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome frizzled binding|identical protein binding|protein kinase binding|signal transducer activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145) 0.000 0.32 523 246 PIK3CD 5293 broad.mit.edu 37 1 9782032 9782032 + Splice_Site DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr1:9782032delG uc001aqb.3 + 17 2264 c.2056_splice c.e17-1 p.G686_splice PIK3CD_uc010oaf.1_Splice_Site_p.G685_splice|PIK3CD_uc001aqe.3_Splice_Site_p.G710_splice NM_005026 NP_005017 O00329 PK3CD_HUMAN catalytic phosphatidylinositol 3-kinase delta phosphatidylinositol-mediated signaling|protein phosphorylation phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding lung(4)|skin(2)|central_nervous_system(1) 7 all_lung(157;0.222) all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419) CTGCCCACCAGGGGGAAGCAC 0.667 0.32 13 6 TAL1 6886 broad.mit.edu 37 1 47691376 47691376 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr1:47691376delC uc001cqx.2 - 2 762 c.185delG c.(184-186)GGCfs p.G62fs TAL1_uc009vyq.2_5'Flank|TAL1_uc001cqy.2_Frame_Shift_Del_p.G62fs|TAL1_uc001cra.1_Intron|TAL1_uc001cqz.1_Intron NM_003189 NP_003180 P17542 TAL1_HUMAN T-cell acute lymphocytic leukemia 1 62 basophil differentiation|cell fate commitment|cell proliferation|embryonic hemopoiesis|erythrocyte differentiation|megakaryocyte differentiation|positive regulation of cell division|positive regulation of chromatin assembly or disassembly|positive regulation of erythrocyte differentiation|positive regulation of mitotic cell cycle|positive regulation of protein complex assembly|positive regulation of transcription from RNA polymerase II promoter nuclear chromatin E-box binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity lung(1) 1 0.000 0.10 316 35 STIL 6491 broad.mit.edu 37 1 47717309 47717309 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr1:47717309delT uc001crc.1 - 17 3518 c.3363delA c.(3361-3363)AAAfs p.K1121fs TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Frame_Shift_Del_p.K1075fs|STIL_uc010omo.1_Frame_Shift_Del_p.K1104fs|STIL_uc001crd.1_Frame_Shift_Del_p.K1122fs|STIL_uc001cre.1_Frame_Shift_Del_p.K1121fs NM_003035 NP_003026 Q15468 STIL_HUMAN SCL/TAL1 interrupting locus isoform 2 1121 cell proliferation|multicellular organismal development centrosome|cytosol lung(2)|skin(1) 3 Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444) TCTTCATATATTTTTTGGTTG 0.373 0.43 616 474 LRRC7 57554 broad.mit.edu 37 1 70451966 70451966 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr1:70451966delA uc001dep.2 + 8 744 c.714delA c.(712-714)TCAfs p.S238fs LRRC7_uc009wbg.2_5'UTR NM_020794 NP_065845 Q96NW7 LRRC7_HUMAN leucine rich repeat containing 7 238 LRR 10. centrosome|focal adhesion|nucleolus protein binding ovary(9)|breast(2)|central_nervous_system(2)|liver(1) 14 TGGATATGTCAAAAAACAGAA 0.368 0.43 433 326 HSP90B3P 343477 broad.mit.edu 37 1 92108448 92108448 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr1:92108448delA uc010osx.1 + 3 475 c.475delA c.(475-477)AAAfs p.K159fs NR_003130 SubName: Full=cDNA FLJ58812, highly similar to Endoplasmin (Heat shock protein 90kDa beta member 1); 0 ATATGGATCTAAAAAGAGTGA 0.363 0.44 419 329 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 815 222 MDM4 4194 broad.mit.edu 37 1 204515939 204515939 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr1:204515939delA uc001hba.2 + 10 999 c.837delA c.(835-837)GGAfs p.G279fs MDM4_uc001hbd.1_RNA|MDM4_uc010pqw.1_RNA|MDM4_uc010pqx.1_Frame_Shift_Del_p.G152fs|MDM4_uc001hay.1_Frame_Shift_Del_p.G229fs|MDM4_uc001hbb.2_Frame_Shift_Del_p.G152fs|MDM4_uc010pqy.1_Intron|MDM4_uc001hbc.2_RNA|MDM4_uc009xbe.1_RNA NM_002393 NP_002384 O15151 MDM4_HUMAN mouse double minute 4 homolog 279 Region II.|Asp/Glu-rich (acidic). apoptosis|cell proliferation|cellular response to hypoxia|G0 to G1 transition|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of protein catabolic process|negative regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization nucleus enzyme binding|zinc ion binding upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1) 3 all_cancers(21;0.00146)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.112)|all_epithelial(62;0.118)|Prostate(682;0.227) GBM - Glioblastoma multiforme(2;3.15e-47)|all cancers(3;3.56e-32)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|Epithelial(59;0.143)|BRCA - Breast invasive adenocarcinoma(75;0.143) TTGAAGTGGGAAAAAATGATG 0.373 0.43 451 346 DSTYK 25778 broad.mit.edu 37 1 205129365 205129365 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr1:205129365delC uc001hbw.2 - 8 2046 c.1982delG c.(1981-1983)GGCfs p.G661fs DSTYK_uc001hbx.2_Frame_Shift_Del_p.G661fs|DSTYK_uc001hby.1_Frame_Shift_Del_p.G122fs NM_015375 NP_056190 Q6XUX3 DUSTY_HUMAN receptor interacting protein kinase 5 isoform 1 661 Protein kinase.|ATP (By similarity). cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(1) 1 ACCATACTGGCCCCGGCCCAG 0.507 0.32 269 126 PXDN 7837 broad.mit.edu 37 2 1638058 1638058 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr2:1638058delG uc002qxa.2 - 23 4422 c.4358delC c.(4357-4359)CCTfs p.P1453fs NM_012293 NP_036425 Q92626 PXDN_HUMAN peroxidasin precursor 1453 VWFC. extracellular matrix organization|hydrogen peroxide catabolic process|immune response endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity pancreas(6)|ovary(2) 8 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716) all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228) 0.000 0.39 552 356 BCL11A 53335 broad.mit.edu 37 2 60687759 60687760 + Frame_Shift_Ins INS - T T HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr2:60687759_60687760insT uc002sae.1 - 4 2515_2516 c.2287_2288insA c.(2287-2289)AGCfs p.S763fs BCL11A_uc002sab.2_Intron|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Frame_Shift_Ins_p.S729fs|BCL11A_uc002sad.1_Frame_Shift_Ins_p.S611fs|BCL11A_uc002saf.1_Frame_Shift_Ins_p.S729fs NM_022893 NP_075044 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A isoform 1 763 C2H2-type 4. negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|cytoplasm|nucleus|nucleus nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding central_nervous_system(6)|breast(3)|ovary(2)|skin(2) 13 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) GCCCGTGTGGCTTCTCCTGTGG 0.559 0.45 288 235 RIF1 55183 broad.mit.edu 37 2 152320349 152320350 + Frame_Shift_Ins INS - A A HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr2:152320349_152320350insA uc002txm.2 + 30 4445_4446 c.4315_4316insA c.(4315-4317)CAAfs p.Q1439fs RIF1_uc002txl.2_Frame_Shift_Ins_p.Q1439fs|RIF1_uc002txn.2_Frame_Shift_Ins_p.Q1439fs|RIF1_uc002txo.2_Frame_Shift_Ins_p.Q1439fs|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1439 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) AAATAGTCATCAAAAAAAGGAA 0.376 0.30 200 85 ZAK 51776 broad.mit.edu 37 2 174131371 174131371 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr2:174131371delG uc002uhz.2 + 20 2496 c.2296delG c.(2296-2298)GGGfs p.G766fs uc002uib.2_Intron NM_016653 NP_057737 Q9NYL2 MLTK_HUMAN MLK-related kinase isoform 1 766 activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation cytoplasm|nucleus ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding lung(3)|stomach(1)|ovary(1)|skin(1) 6 OV - Ovarian serous cystadenocarcinoma(117;0.176) AGTCAGCGAAGGGGGCTGGAC 0.557 0.44 55 44 TTN 7273 broad.mit.edu 37 2 179410231 179410231 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr2:179410231delT uc010zfg.1 - 293 88126 c.87902delA c.(87901-87903)AAGfs p.K29301fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.K22996fs|TTN_uc010zfi.1_Frame_Shift_Del_p.K22929fs|TTN_uc010zfj.1_Frame_Shift_Del_p.K22804fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 30228 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GCTGGTCACCTTCAGCCTGGT 0.507 0.40 479 321 TTN 7273 broad.mit.edu 37 2 179486701 179486701 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr2:179486701delT uc010zfg.1 - 193 37468 c.37244delA c.(37243-37245)AAGfs p.K12415fs TTN_uc010zfh.1_Frame_Shift_Del_p.K6110fs|TTN_uc010zfi.1_Frame_Shift_Del_p.K6043fs|TTN_uc010zfj.1_Frame_Shift_Del_p.K5918fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 13342 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTTTTTGCCCTTTTTAATTTC 0.348 0.43 457 346 CTNNB1 1499 broad.mit.edu 37 3 41266134 41266136 + In_Frame_Del DEL CTT - - rs121913407 HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr3:41266134_41266136delCTT uc010hia.1 + 4 287_289 c.131_133delCTT c.(130-135)CCTTCT>CCT p.S45del CTNNB1_uc003ckp.2_In_Frame_Del_p.S45del|CTNNB1_uc003ckq.2_In_Frame_Del_p.S45del|CTNNB1_uc003ckr.2_In_Frame_Del_p.S45del|CTNNB1_uc011azf.1_In_Frame_Del_p.S38del|CTNNB1_uc011azg.1_Intron|uc010hib.1_RNA NM_001904 NP_001895 P35222 CTNB1_HUMAN beta-catenin 45 Missing (in colorectal cancer).|S -> P (in hepatocellular carcinoma).|S -> F (in hepatocellular carcinoma). adherens junction assembly|androgen receptor signaling pathway|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell-cell adhesion|cell-matrix adhesion|cellular component disassembly involved in apoptosis|cellular response to growth factor stimulus|cellular response to indole-3-methanol|central nervous system vasculogenesis|cytoskeletal anchoring at plasma membrane|determination of dorsal/ventral asymmetry|dorsal/ventral axis specification|ectoderm development|embryonic axis specification|embryonic foregut morphogenesis|embryonic leg joint morphogenesis|endodermal cell fate commitment|endothelial tube morphogenesis|epithelial to mesenchymal transition|gastrulation with mouth forming second|glial cell fate determination|hair follicle morphogenesis|hair follicle placode formation|hindbrain development|liver development|lung cell differentiation|lung induction|lung-associated mesenchyme development|male genitalia development|mesenchymal cell proliferation involved in lung development|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of osteoclast differentiation|negative regulation of transcription from RNA polymerase II promoter|nephron tubule formation|odontogenesis of dentine-containing tooth|oocyte development|pancreas development|positive regulation of anti-apoptosis|positive regulation of apoptosis|positive regulation of branching involved in lung morphogenesis|positive regulation of epithelial cell proliferation involved in prostate gland development|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of muscle cell differentiation|positive regulation of osteoblast differentiation|positive regulation of transcription from RNA polymerase II promoter|protein localization at cell surface|proximal/distal pattern formation|regulation of angiogenesis|regulation of calcium ion import|regulation of centriole-centriole cohesion|regulation of centromeric sister chromatid cohesion|regulation of fibroblast proliferation|regulation of nephron tubule epithelial cell differentiation|regulation of protein localization at cell surface|regulation of smooth muscle cell proliferation|regulation of T cell proliferation|renal inner medulla development|renal outer medulla development|renal vesicle formation|response to drug|response to estradiol stimulus|Schwann cell proliferation|smooth muscle cell differentiation|synapse organization|synaptic vesicle transport|T cell differentiation in thymus|thymus development|trachea formation APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin-TCF7L2 complex|catenin complex|cell cortex|cell-substrate adherens junction|centrosome|dendritic shaft|desmosome|fascia adherens|internal side of plasma membrane|lamellipodium|lateral plasma membrane|microvillus membrane|perinuclear region of cytoplasm|protein-DNA complex|synapse|transcription factor complex|Z disc|zonula adherens alpha-catenin binding|androgen receptor binding|cadherin binding|estrogen receptor binding|I-SMAD binding|ion channel binding|protein binding|protein C-terminus binding|protein kinase binding|protein phosphatase binding|R-SMAD binding|RPTP-like protein binding|signal transducer activity|specific RNA polymerase II transcription factor activity|structural molecule activity|transcription coactivator activity|transcription regulatory region DNA binding p.S45F(396)|p.S45P(163)|p.S45del(79)|p.A5_A80del(63)|p.S45Y(21)|p.S45C(18)|p.S45A(10)|p.H24_S47del(9)|p.A5_A80>D(7)|p.A5_Q143del(7)|p.Q28_H134del(5)|p.W25_I140del(4)|p.T3_A126del(2)|p.M5_N141>D(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.V22_L139>V(2)|p.A5_Y142>D(2)|p.?(2)|p.L10_N141del(2)|p.P44L(2)|p.E9_S47del(1)|p.Q28_Q61del(1)|p.A20_R151del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.Y30_A97del(1)|p.A20_A80del(1)|p.E15_I140>V(1)|p.D17_P128del(1)|p.H24_M131del(1)|p.L7_I140del(1)|p.G38_S45del(1)|p.K19_Y142>V(1)|p.A20_L148del(1)|p.V22_A80del(1)|p.V22_G80>NNNNN(1)|p.P44del(1)|p.A20_Q143del(1)|p.A43_E53del(1)|p.A13_R151del(1)|p.S23_I140del(1)|p.M1_A87del(1)|p.P44_N51del(1)|p.V22_T102del(1)|p.S45fs*2(1)|p.S45E(1)|p.A21_A80del(1)|p.S45T(1)|p.S45S(1)|p.D6_I140del(1)|p.Q28_I140del(1)|p.E9_A80del(1)|p.I35_K170del(1)|p.S45_S47>C(1)|p.M14_S45del(1)|p.M8_G50del(1)|p.A5_G80>(1)|p.T42_G48del(1)|p.S45_G48del(1)|p.S45_D58del(1)|p.P16_K133del(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.A5_R90del(1)|p.P44_S45>AP(1)|p.M8_A80del(1)|p.P44_S45insGATTTAP(1)|p.E9_I140del(1)|p.S45_E54del(1)|p.A5_Q143>E(1)|p.H36_E53>L(1)|p.A43_E54del(1)|p.A5_Q72del(1)|p.Y30_A80del(1)|p.S45_L46del(1)|p.D6_K133del(1)|p.V22_Y64del(1)|p.A5_D144>D(1)|p.D17_A126del(1)|p.A5_E54del(1)|p.V22_S71>A(1)|p.W25_A80del(1)|p.A20_Q72del(1)|p.A20_S111del(1) CTNNB1/PLAG1(60) liver(806)|soft_tissue(609)|large_intestine(243)|endometrium(222)|kidney(172)|stomach(157)|central_nervous_system(139)|ovary(104)|skin(97)|pancreas(91)|adrenal_gland(85)|pituitary(81)|salivary_gland(62)|haematopoietic_and_lymphoid_tissue(57)|thyroid(55)|biliary_tract(41)|lung(38)|prostate(24)|bone(20)|small_intestine(17)|cervix(9)|parathyroid(9)|urinary_tract(8)|breast(7)|oesophagus(5)|NS(3)|pleura(2)|upper_aerodigestive_tract(2)|eye(1) 3166 KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294) Lithium(DB01356) ACCACAGCTCCTTCTCTGAGTGG 0.502 0.36 150 83 CCR1 1230 broad.mit.edu 37 3 46245605 46245605 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr3:46245605delT uc003cph.1 - 2 271 c.200delA c.(199-201)AACfs p.N67fs CCR3_uc003cpg.1_Intron NM_001295 NP_001286 P32246 CCR1_HUMAN chemokine (C-C motif) receptor 1 67 Helical; Name=2; (Potential). cell adhesion|cell-cell signaling|cytokine-mediated signaling pathway|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cyclic nucleotide second messenger|immune response|inflammatory response integral to plasma membrane C-C chemokine receptor activity skin(2)|pancreas(1) 3 BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203) GCTGGTCATGTTTTTTAGCCT 0.507 0.42 93 67 SEMA3B 7869 broad.mit.edu 37 3 50311902 50311902 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr3:50311902delG uc003cyu.2 + 13 1488 c.1246delG c.(1246-1248)GGGfs p.G416fs SEMA3B_uc003cyt.2_Frame_Shift_Del_p.G415fs|SEMA3B_uc003cyv.2_Frame_Shift_Del_p.G303fs|SEMA3B_uc003cyw.2_Frame_Shift_Del_p.G139fs|SEMA3B_uc010hli.2_Frame_Shift_Del_p.G308fs|SEMA3B_uc003cyx.2_Frame_Shift_Del_p.G302fs|SEMA3B_uc003cyy.2_Frame_Shift_Del_p.G73fs|SEMA3B_uc011bdo.1_Frame_Shift_Del_p.G73fs NM_004636 NP_004627 Q13214 SEM3B_HUMAN semaphorin 3B isoform 1 precursor 416 Sema. axon guidance|cell-cell signaling endoplasmic reticulum|extracellular region|membrane receptor activity lung(2)|central_nervous_system(2)|kidney(1)|skin(1) 6 BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605) CCTGCCCACTGGGGGGCGCCC 0.562 0.44 106 83 MYLK 4638 broad.mit.edu 37 3 123427729 123427730 + Frame_Shift_Ins INS - G G HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr3:123427729_123427730insG uc003ego.2 - 15 2237_2238 c.1955_1956insC c.(1954-1956)CCTfs p.P652fs MYLK_uc011bjw.1_Frame_Shift_Ins_p.P652fs|MYLK_uc003egp.2_Frame_Shift_Ins_p.P583fs|MYLK_uc003egq.2_Frame_Shift_Ins_p.P652fs|MYLK_uc003egr.2_Frame_Shift_Ins_p.P583fs|MYLK_uc003egs.2_Frame_Shift_Ins_p.P476fs NM_053025 NP_444253 Q15746 MYLK_HUMAN myosin light chain kinase isoform 1 652 Ig-like C2-type 5. P -> A. aorta smooth muscle tissue morphogenesis|muscle contraction cytosol actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity ovary(6)|skin(2)|stomach(1) 9 Lung NSC(201;0.0496) GBM - Glioblastoma multiforme(114;0.0736) AGATGACTTCAGGGGGTGGATT 0.515 0.32 149 70 GATA2 2624 broad.mit.edu 37 3 128204842 128204842 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr3:128204842delC uc003ekm.3 - 4 1034 c.599delG c.(598-600)GGTfs p.G200fs GATA2_uc003ekn.3_Frame_Shift_Del_p.G200fs|GATA2_uc003eko.2_Frame_Shift_Del_p.G200fs NM_001145661 NP_001139133 P23769 GATA2_HUMAN GATA binding protein 2 isoform 1 200 blood coagulation|negative regulation of fat cell differentiation|negative regulation of fat cell proliferation|negative regulation of neural precursor cell proliferation|negative regulation of Notch signaling pathway|phagocytosis|positive regulation of angiogenesis|positive regulation of phagocytosis|positive regulation of transcription from RNA polymerase II promoter nucleoplasm C2H2 zinc finger domain binding|chromatin binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding haematopoietic_and_lymphoid_tissue(13)|lung(1)|skin(1) 15 GBM - Glioblastoma multiforme(114;0.173) GGCTGCACTACCCCCCGCGGA 0.632 0.17 53 11 EPHA5 2044 broad.mit.edu 37 4 66230873 66230873 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr4:66230873delT uc003hcy.2 - 12 2291 c.2098delA c.(2098-2100)AGAfs p.R700fs EPHA5_uc003hcx.2_Frame_Shift_Del_p.R632fs|EPHA5_uc003hcz.2_Frame_Shift_Del_p.R678fs|EPHA5_uc011cah.1_Frame_Shift_Del_p.R701fs|EPHA5_uc011cai.1_Frame_Shift_Del_p.R679fs|EPHA5_uc003hda.2_Frame_Shift_Del_p.R701fs NM_004439 NP_004430 P54756 EPHA5_HUMAN ephrin receptor EphA5 isoform a precursor 700 Cytoplasmic (Potential).|Protein kinase. cAMP-mediated signaling|neuron development dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum ATP binding|transmembrane-ephrin receptor activity lung(19)|stomach(2)|ovary(2)|central_nervous_system(1) 24 GGTAATTCTCTTTTTCCTGGT 0.358 0.41 418 296 CDKL2 8999 broad.mit.edu 37 4 76523333 76523333 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr4:76523333delT uc003hiq.2 - 8 1473 c.948delA c.(946-948)AAAfs p.K316fs CDKL2_uc011cbp.1_Frame_Shift_Del_p.K316fs|CDKL2_uc010iix.1_RNA NM_003948 NP_003939 Q92772 CDKL2_HUMAN cyclin-dependent kinase-like 2 316 sex differentiation|signal transduction cytoplasm|nucleus ATP binding|cyclin-dependent protein kinase activity ovary(2)|stomach(2)|breast(2)|skin(1) 7 Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122) TGTTTTGGGATTTTTTAGATA 0.274 0.49 202 196 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.22 68 19 ALPK1 80216 broad.mit.edu 37 4 113353512 113353512 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr4:113353512delT uc003iap.3 + 11 3088 c.2809delT c.(2809-2811)TTTfs p.F937fs ALPK1_uc003ian.3_Frame_Shift_Del_p.F937fs|ALPK1_uc011cfx.1_Frame_Shift_Del_p.F859fs|ALPK1_uc003iao.3_Intron|ALPK1_uc010imo.2_Frame_Shift_Del_p.F765fs NM_025144 NP_079420 Q96QP1 ALPK1_HUMAN alpha-kinase 1 937 Ser-rich. ATP binding|protein serine/threonine kinase activity ovary(5) 5 Ovarian(17;0.0446)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.00325) ATCACCTGCATTTTCCAGTGG 0.507 0.33 36 18 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.27 65 24 AFF4 27125 broad.mit.edu 37 5 132223814 132223814 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr5:132223814delT uc003kyd.2 - 15 3179 c.2771delA c.(2770-2772)AAGfs p.K924fs AFF4_uc011cxk.1_Frame_Shift_Del_p.K602fs NM_014423 NP_055238 Q9UHB7 AFF4_HUMAN ALL1 fused gene from 5q31 924 transcription from RNA polymerase II promoter mitochondrion|nucleolus protein binding|sequence-specific DNA binding transcription factor activity ovary(2)|kidney(2)|skin(1) 5 all_cancers(142;0.145)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GTGCTTTAGCTTTTTTGCTTC 0.274 0.46 403 339 DEK 7913 broad.mit.edu 37 6 18258250 18258250 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr6:18258250delA uc003ncr.1 - 4 484 c.291delT c.(289-291)TTTfs p.F97fs DEK_uc011djf.1_Frame_Shift_Del_p.F63fs|DEK_uc011djg.1_RNA NM_003472 NP_003463 P35659 DEK_HUMAN DEK oncogene isoform 1 97 chromatin modification|regulation of transcription from RNA polymerase II promoter|signal transduction|transcription from RNA polymerase II promoter|viral genome replication nucleus DNA binding|histone binding kidney(1) 1 Ovarian(93;0.00769)|Breast(50;0.0495) all_hematologic(90;0.053) OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332) TCTTACTTAGAAAAAAATGTA 0.328 0.29 25 10 STK38 11329 broad.mit.edu 37 6 36465583 36465583 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr6:36465583delA uc003omg.2 - 11 1734 c.1146delT c.(1144-1146)TTTfs p.F382fs STK38_uc003omh.2_Frame_Shift_Del_p.F382fs|STK38_uc003omi.2_Frame_Shift_Del_p.F382fs NM_007271 NP_009202 Q15208 STK38_HUMAN serine/threonine kinase 38 382 Protein kinase. intracellular protein kinase cascade|negative regulation of MAP kinase activity cytoplasm|MLL5-L complex ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1) 6 CAACGCCTTCAAAAAAAGAGT 0.368 0.12 434 62 GRM1 2911 broad.mit.edu 37 6 146755345 146755346 + Frame_Shift_Ins INS - C C HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr6:146755345_146755346insC uc010khw.1 + 9 3468_3469 c.2998_2999insC c.(2998-3000)ACCfs p.T1000fs GRM1_uc010khv.1_3'UTR|GRM1_uc003qll.2_3'UTR|GRM1_uc011edz.1_3'UTR|GRM1_uc011eea.1_3'UTR NM_000838 NP_000829 Q13255 GRM1_HUMAN glutamate receptor, metabotropic 1 isoform alpha 1000 Cytoplasmic (Potential). synaptic transmission integral to plasma membrane G-protein coupled receptor activity|glutamate receptor activity lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2) 19 Ovarian(120;0.0387) OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762) Acamprosate(DB00659)|L-Glutamic Acid(DB00142) 0.000 0.45 550 446 LATS1 9113 broad.mit.edu 37 6 150004629 150004629 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr6:150004629delA uc003qmu.1 - 4 2144 c.1596delT c.(1594-1596)TTTfs p.F532fs LATS1_uc010kif.1_Frame_Shift_Del_p.F427fs|LATS1_uc003qmv.1_Frame_Shift_Del_p.F532fs|LATS1_uc003qmw.2_Frame_Shift_Del_p.F532fs|LATS1_uc010kig.1_Frame_Shift_Del_p.F427fs NM_004690 NP_004681 O95835 LATS1_HUMAN LATS homolog 1 532 Interaction with YAP1. cell division|cytoplasmic sequestering of protein|G2/M transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|positive regulation of peptidyl-serine phosphorylation|regulation of actin filament polymerization|sister chromatid segregation microtubule organizing center|spindle pole ATP binding|magnesium ion binding|protein kinase binding|protein serine/threonine kinase activity lung(5)|central_nervous_system(1) 6 Ovarian(120;0.0164) OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116) TTCCCTCAGGAAAAGGACTGG 0.478 0.48 228 209 MLLT4 4301 broad.mit.edu 37 6 168325729 168325729 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr6:168325729delA uc003qwd.2 + 22 3175 c.3033delA c.(3031-3033)CTAfs p.L1011fs MLLT4_uc003qwb.1_Frame_Shift_Del_p.L996fs|MLLT4_uc003qwc.1_Frame_Shift_Del_p.L1012fs|MLLT4_uc003qwg.1_Frame_Shift_Del_p.L321fs NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 1012 PDZ. adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) CTGTGACCCTAAAAAAGCAGA 0.423 0.41 353 250 LMTK2 22853 broad.mit.edu 37 7 97766626 97766626 + Splice_Site DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr7:97766626delG uc003upd.1 + 2 397 c.104_splice c.e2-1 p.G35_splice NM_014916 NP_055731 Q8IWU2 LMTK2_HUMAN lemur tyrosine kinase 2 precursor early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1) 16 all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125) TCTCTTTCCAGGGGAGGCGCC 0.348 0.39 163 103 MET 4233 broad.mit.edu 37 7 116339848 116339848 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr7:116339848delT uc003vij.2 + 2 897 c.710delT c.(709-711)GTTfs p.V237fs MET_uc010lkh.2_Frame_Shift_Del_p.V237fs|MET_uc011knc.1_Frame_Shift_Del_p.V237fs|MET_uc011knd.1_Frame_Shift_Del_p.V237fs|MET_uc011kne.1_Frame_Shift_Del_p.V237fs|MET_uc011knf.1_Frame_Shift_Del_p.V237fs|MET_uc011kng.1_Frame_Shift_Del_p.V237fs|MET_uc011knh.1_Frame_Shift_Del_p.V237fs|MET_uc011kni.1_Frame_Shift_Del_p.V237fs|MET_uc003vii.1_Frame_Shift_Del_p.V256fs|MET_uc010lkg.2_Frame_Shift_Del_p.V237fs|MET_uc011kmz.1_Frame_Shift_Del_p.V237fs|MET_uc011kna.1_Frame_Shift_Del_p.V237fs|MET_uc011knb.1_Frame_Shift_Del_p.V237fs NM_000245 NP_000236 P08581 MET_HUMAN met proto-oncogene isoform b precursor 237 Extracellular (Potential).|Sema. axon guidance|cell proliferation basal plasma membrane|integral to plasma membrane ATP binding|hepatocyte growth factor receptor activity|protein binding upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1) 159 all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125) Ovarian(593;0.133) GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512) TACATTGATGTTTTACCTGAG 0.378 0.46 132 114 MLL3 58508 broad.mit.edu 37 7 151900081 151900081 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr7:151900081delT uc003wla.2 - 26 4249 c.4030delA c.(4030-4032)ATAfs p.I1344fs MLL3_uc003wkz.2_Frame_Shift_Del_p.I405fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 1344 Potential. intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) CTCTTCTTTATTTTTTCAGTG 0.313 0.45 224 180 TOX 9760 broad.mit.edu 37 8 59750809 59750809 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr8:59750809delT uc003xtw.1 - 5 976 c.755delA c.(754-756)AAGfs p.K252fs NM_014729 NP_055544 O94900 TOX_HUMAN thymus high mobility group box protein TOX 252 Nuclear localization signal (Potential). nucleus DNA binding kidney(2)|lung(1)|skin(1) 4 all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607) CTTCTTCTTCTTTTTGGGAGT 0.458 0.39 162 103 ARFGEF1 10565 broad.mit.edu 37 8 68140284 68140284 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr8:68140284delT uc003xxo.1 - 25 3895 c.3505delA c.(3505-3507)ATAfs p.I1169fs ARFGEF1_uc003xxl.1_Frame_Shift_Del_p.I623fs|ARFGEF1_uc003xxn.1_Frame_Shift_Del_p.I152fs NM_006421 NP_006412 Q9Y6D6 BIG1_HUMAN brefeldin A-inhibited guanine 1169 exocytosis|regulation of ARF protein signal transduction cytoplasm ARF guanyl-nucleotide exchange factor activity|myosin binding ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1) 8 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206) ATTTCTACTATTTTTTGTAGA 0.328 0.59 386 545 RUNX1T1 862 broad.mit.edu 37 8 93017471 93017472 + Frame_Shift_Ins INS - T T HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr8:93017471_93017472insT uc003yfd.2 - 5 696_697 c.612_613insA c.(610-615)AAACAGfs p.K204fs RUNX1T1_uc003yfc.1_Frame_Shift_Ins_p.K177fs|RUNX1T1_uc003yfe.1_Frame_Shift_Ins_p.K167fs|RUNX1T1_uc010mao.2_Frame_Shift_Ins_p.K177fs|RUNX1T1_uc011lgi.1_Frame_Shift_Ins_p.K215fs|RUNX1T1_uc003yfb.1_Frame_Shift_Ins_p.K167fs|RUNX1T1_uc003yff.1_Frame_Shift_Ins_p.K167fs NM_175634 NP_783552 Q06455 MTG8_HUMAN acute myelogenous leukemia 1 translocation 1 204_205 TAFH. generation of precursor metabolites and energy nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1) 16 BRCA - Breast invasive adenocarcinoma(11;0.0141) GCAGGGTTCTGTTTGGCCAGTC 0.564 0.51 174 181 TRIB1 10221 broad.mit.edu 37 8 126443309 126443309 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr8:126443309delC uc003yrx.2 + 1 747 c.165delC c.(163-165)AGCfs p.S55fs TRIB1_uc011lis.1_5'Flank|TRIB1_uc010mdn.2_5'Flank NM_025195 NP_079471 Q96RU8 TRIB1_HUMAN G-protein-coupled receptor induced protein 55 Protein kinase. JNK cascade|negative regulation of lipopolysaccharide-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|regulation of MAP kinase activity|response to lipopolysaccharide cytoplasm|nucleus ATP binding|mitogen-activated protein kinase kinase binding|protein kinase activity|protein kinase inhibitor activity|transcription factor binding|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity lung(1) 1 all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108) STAD - Stomach adenocarcinoma(47;0.000918) 0.000 0.31 562 250 BAI1 575 broad.mit.edu 37 8 143558835 143558835 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr8:143558835delC uc003ywm.2 + 5 1495 c.1312delC c.(1312-1314)CCCfs p.P438fs NM_001702 NP_001693 O14514 BAI1_HUMAN brain-specific angiogenesis inhibitor 1 438 Extracellular (Potential).|TSP type-1 3. axonogenesis|cell adhesion|negative regulation of angiogenesis|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development cell-cell junction|integral to plasma membrane G-protein coupled receptor activity|protein binding lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|pancreas(1) 8 all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155) CACCTGCAGGCCCCCCCAGTT 0.652 0.41 22 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.32 571 268 CDKN2A 1029 broad.mit.edu 37 9 21974758 21974759 + Frame_Shift_Ins INS - C C HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr9:21974758_21974759insC uc003zpk.2 - 1 280_281 c.68_69insG c.(67-69)GGTfs p.G23fs MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_Frame_Shift_Ins_p.G23fs|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Intron NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 23 ANK 1. G -> D (in a pancreas tumor and a melanoma; loss of CDK4 binding). cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.?(23)|p.G23fs(2)|p.R24fs*20(1)|p.R22fs*14(1)|p.G23fs*3(1)|p.G23D(1)|p.G23G(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) 0.000 0.37 668 393 CDKN2A 1029 broad.mit.edu 37 9 21994234 21994234 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr9:21994234delC uc003zpl.2 - 1 257 c.220delG c.(220-222)GAGfs p.E74fs MTAP_uc003zpi.1_Intron|CDKN2BAS_uc010miw.1_5'Flank|CDKN2BAS_uc010mix.1_5'Flank|CDKN2BAS_uc003zpm.2_5'Flank NM_058195 NP_478102 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 4 Error:Variant_position_missing_in_P42771_after_alignment cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(197)|p.D74Y(5)|p.D74N(2)|p.D74V(2)|p.D74D(2)|p.E61_L94del(1)|p.D74E(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) 0.000 0.38 1010 614 TAF1L 138474 broad.mit.edu 37 9 32633025 32633025 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr9:32633025delT uc003zrg.1 - 1 2643 c.2553delA c.(2551-2553)AAAfs p.K851fs uc003zrh.1_5'Flank NM_153809 NP_722516 Q8IZX4 TAF1L_HUMAN TBP-associated factor RNA polymerase 1-like 851 male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent transcription factor TFIID complex DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1) 26 LUSC - Lung squamous cell carcinoma(29;0.0181) GBM - Glioblastoma multiforme(74;0.00301) AAGGAAAGGCTTTTTTTATAT 0.443 0.45 261 215 WNK2 65268 broad.mit.edu 37 9 96019305 96019305 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr9:96019305delC uc004ati.1 + 10 2266 c.2266delC c.(2266-2268)CCCfs p.P756fs WNK2_uc011lud.1_Frame_Shift_Del_p.P756fs|WNK2_uc004atj.2_Frame_Shift_Del_p.P756fs|WNK2_uc004atk.2_Frame_Shift_Del_p.P393fs|WNK2_uc010mrc.1_Frame_Shift_Del_p.P704fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 756 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 0.000 0.47 747 661 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.18 109 24 SMC2 10592 broad.mit.edu 37 9 106864838 106864838 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr9:106864838delA uc004bbv.2 + 9 1292 c.1004delA c.(1003-1005)GAAfs p.E335fs SMC2_uc004bbu.1_Frame_Shift_Del_p.E335fs|SMC2_uc004bbw.2_Frame_Shift_Del_p.E335fs|SMC2_uc011lvl.1_Frame_Shift_Del_p.E335fs|SMC2_uc010mtg.1_Frame_Shift_Del_p.E190fs|SMC2_uc010mth.1_Frame_Shift_Del_p.E285fs|SMC2_uc004bbx.2_Frame_Shift_Del_p.E335fs NM_001042551 NP_001036016 O95347 SMC2_HUMAN structural maintenance of chromosomes 2 335 Potential. cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism condensin complex|cytoplasm|nuclear chromosome ATP binding|protein heterodimerization activity ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1) 9 AAAGAGCTGGAAAAAAATATG 0.363 0.40 154 102 NOTCH1 4851 broad.mit.edu 37 9 139418228 139418228 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr9:139418228delC uc004chz.2 - 3 344 c.344delG c.(343-345)GGCfs p.G115fs NM_017617 NP_060087 P46531 NOTC1_HUMAN notch1 preproprotein 115 Extracellular (Potential).|EGF-like 3. aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1) 856 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06) 0.000 0.42 880 647 MLLT10 8028 broad.mit.edu 37 10 21823595 21823595 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr10:21823595delG uc001iqs.2 + 2 370 c.22delG c.(22-24)GTGfs p.V8fs MLLT10_uc001iqt.2_Frame_Shift_Del_p.V8fs|MLLT10_uc001iqv.2_RNA|MLLT10_uc001iqy.2_Frame_Shift_Del_p.V8fs|MLLT10_uc001iqr.1_Frame_Shift_Del_p.V8fs|MLLT10_uc001iqq.1_Frame_Shift_Del_p.V8fs|MLLT10_uc001iqu.1_Frame_Shift_Del_p.V8fs|MLLT10_uc009xke.1_RNA|MLLT10_uc001iqw.1_Frame_Shift_Del_p.V8fs|MLLT10_uc001iqx.1_RNA|MLLT10_uc009xkf.1_RNA NM_004641 NP_004632 P55197 AF10_HUMAN myeloid/lymphoid or mixed-lineage leukemia 8 positive regulation of transcription from RNA polymerase II promoter cytoplasm|nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding lung(1)|skin(1) 2 CGACCGGCCCGTGTCACTGGA 0.517 0.25 30 10 MASTL 84930 broad.mit.edu 37 10 27454334 27454334 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr10:27454334delA uc001itm.2 + 6 1316 c.677delA c.(676-678)GAAfs p.E226fs MASTL_uc001itl.2_Frame_Shift_Del_p.E226fs|MASTL_uc009xkw.1_Frame_Shift_Del_p.E226fs|MASTL_uc009xkx.1_RNA NM_032844 NP_116233 Q96GX5 GWL_HUMAN microtubule associated serine/threonine 226 Protein kinase. cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus centrosome|cleavage furrow|nucleus ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity stomach(1)|ovary(1)|lung(1) 3 CCAATTGCAGAAAAAAATCAA 0.388 0.44 193 153 TNKS2 80351 broad.mit.edu 37 10 93601945 93601946 + Frame_Shift_Ins INS - A A HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr10:93601945_93601946insA uc001khp.2 + 16 2153_2154 c.1856_1857insA c.(1855-1857)ACAfs p.T619fs NM_025235 NP_079511 Q9H2K2 TNKS2_HUMAN tankyrase, TRF1-interacting ankyrin-related 619 ANK 12. positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm NAD+ ADP-ribosyltransferase activity|protein binding kidney(3)|skin(3)|ovary(1)|lung(1) 8 Colorectal(252;0.162) GCAGACCCTACAAAAAAAAACA 0.391 0.19 38 9 TNKS2 80351 broad.mit.edu 37 10 93621902 93621904 + In_Frame_Del DEL GAG - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr10:93621902_93621904delGAG uc001khp.2 + 26 3725_3727 c.3428_3430delGAG c.(3427-3432)AGAGGA>AGA p.G1144del NM_025235 NP_079511 Q9H2K2 TNKS2_HUMAN tankyrase, TRF1-interacting ankyrin-related 1144 PARP catalytic. positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm NAD+ ADP-ribosyltransferase activity|protein binding kidney(3)|skin(3)|ovary(1)|lung(1) 8 Colorectal(252;0.162) GTTATTTACAGAGGAGAACAGGT 0.374 0.40 306 202 SLK 9748 broad.mit.edu 37 10 105762529 105762529 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr10:105762529delG uc001kxo.1 + 9 1627 c.1593delG c.(1591-1593)TTGfs p.L531fs SLK_uc001kxp.1_Frame_Shift_Del_p.L531fs NM_014720 NP_055535 Q9H2G2 SLK_HUMAN serine/threonine kinase 2 531 Glu-rich. apoptosis|nucleotide-excision repair cytoplasm|plasma membrane ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity ovary(2)|stomach(2)|skin(2)|lung(1)|kidney(1) 8 Colorectal(252;0.178) Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165) AAGAGAAATTGGGGGAAGACG 0.418 0.56 594 757 NLRP6 171389 broad.mit.edu 37 11 281700 281700 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr11:281700delG uc010qvs.1 + 4 1966 c.1966delG c.(1966-1968)GTGfs p.V656fs NLRP6_uc010qvt.1_Frame_Shift_Del_p.V656fs NM_138329 NP_612202 P59044 NALP6_HUMAN NLR family, pyrin domain containing 6 656 cytoplasm ATP binding upper_aerodigestive_tract(1)|skin(1) 2 all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122) CCGCATGGACGTGGCTGTTCT 0.627 0.47 21 19 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.69 10 22 WNK1 65125 broad.mit.edu 37 12 1017928 1017928 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr12:1017928delC uc001qio.3 + 28 7626 c.7119delC c.(7117-7119)AACfs p.N2373fs WNK1_uc001qip.3_Frame_Shift_Del_p.N2125fs|WNK1_uc001qir.3_Frame_Shift_Del_p.N1546fs NM_018979 NP_061852 Q9H4A3 WNK1_HUMAN WNK lysine deficient protein kinase 1 2373 intracellular protein kinase cascade|ion transport|neuron development cytoplasm ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1) 23 all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632) Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197) CCATCAGCAACCCCCCAGGCT 0.562 0.33 125 62 PLEKHA5 54477 broad.mit.edu 37 12 19410381 19410381 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr12:19410381delA uc001reb.2 + 6 533 c.447delA c.(445-447)TCAfs p.S149fs PLEKHA5_uc010sie.1_Frame_Shift_Del_p.S149fs|PLEKHA5_uc001rea.2_Frame_Shift_Del_p.S149fs|PLEKHA5_uc009zin.2_5'UTR|PLEKHA5_uc010sif.1_Frame_Shift_Del_p.S41fs|PLEKHA5_uc010sig.1_Frame_Shift_Del_p.S41fs|PLEKHA5_uc010sih.1_Frame_Shift_Del_p.S41fs NM_019012 NP_061885 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A 149 1-phosphatidylinositol binding|protein binding ovary(1)|kidney(1)|skin(1) 3 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) CACGAGCTTCAAAAAAAGTTC 0.318 0.41 138 97 LRP1 4035 broad.mit.edu 37 12 57567696 57567697 + Frame_Shift_Ins INS - C C HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr12:57567696_57567697insC uc001snd.2 + 22 3946_3947 c.3480_3481insC c.(3478-3483)CTGCCCfs p.L1160fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 1160_1161 LDL-receptor class A 10.|Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CAGTCTGCCTGCCCCCTGACAA 0.629 0.37 137 82 LRP1 4035 broad.mit.edu 37 12 57606239 57606239 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr12:57606239delG uc001snd.2 + 89 14002 c.13536delG c.(13534-13536)ATGfs p.M4512fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 4512 Cytoplasmic (Potential).|Interaction with MAFB (By similarity). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CACTCTACATGGGGGGCCATG 0.642 0.39 57 36 ZMYM2 7750 broad.mit.edu 37 13 20657094 20657095 + Frame_Shift_Del DEL AA - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr13:20657094_20657095delAA uc001umr.2 + 24 4040_4041 c.3742_3743delAA c.(3742-3744)AAAfs p.K1248fs ZMYM2_uc001ums.2_Frame_Shift_Del_p.K1248fs|ZMYM2_uc001umt.2_Frame_Shift_Del_p.K1248fs|ZMYM2_uc001umv.2_Frame_Shift_Del_p.K628fs|ZMYM2_uc001umw.2_Frame_Shift_Del_p.K701fs NM_003453 NP_003444 Q9UBW7 ZMYM2_HUMAN zinc finger protein 198 1248 regulation of transcription, DNA-dependent|transcription, DNA-dependent PML body ubiquitin conjugating enzyme binding|zinc ion binding lung(3)|ovary(2)|prostate(1) 6 all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856) TAGGCATTGGAAAAAAAATCCT 0.361 0.43 412 308 FLT3 2322 broad.mit.edu 37 13 28578215 28578216 + Frame_Shift_Del DEL GA - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr13:28578215_28578216delGA uc001urw.2 - 24 3037_3038 c.2955_2956delTC c.(2953-2958)TCTCCGfs p.S985fs FLT3_uc010aao.2_RNA|FLT3_uc010tdn.1_Frame_Shift_Del_p.S944fs NM_004119 NP_004110 P36888 FLT3_HUMAN fms-related tyrosine kinase 3 precursor 985_986 Cytoplasmic (Potential). positive regulation of cell proliferation integral to plasma membrane ATP binding|vascular endothelial growth factor receptor activity haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1) 8549 Acute lymphoblastic leukemia(6;0.04) Lung SC(185;0.0156)|Ovarian(182;0.0392) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212) Sorafenib(DB00398)|Sunitinib(DB01268) TGAGCCTGCGGAGAGAGTAGCC 0.460 0.37 235 138 BRCA2 675 broad.mit.edu 37 13 32937354 32937355 + Frame_Shift_Ins INS - A A HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr13:32937354_32937355insA uc001uub.1 + 18 8242_8243 c.8015_8016insA c.(8014-8016)ATAfs p.I2672fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 2672 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) AGATCGGCTATAAAAAAGATAA 0.332 0.35 294 156 DACH1 1602 broad.mit.edu 37 13 72053384 72053385 + Frame_Shift_Ins INS - T T HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr13:72053384_72053385insT uc010thn.1 - 9 2209_2210 c.1786_1787insA c.(1786-1788)ACTfs p.T596fs DACH1_uc010tho.1_Frame_Shift_Ins_p.T448fs|DACH1_uc010thp.1_Frame_Shift_Ins_p.T394fs NM_080759 NP_542937 Q9UI36 DACH1_HUMAN dachshund homolog 1 isoform a 648 DACHbox-C.|Potential.|Interaction with SIN3A (By similarity). multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus DNA binding|nucleotide binding|protein binding breast(1) 1 Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198) GBM - Glioblastoma multiforme(99;0.00032) CTTCAGCTCAGTTTTTTCCAGT 0.376 0.39 321 201 CHD8 57680 broad.mit.edu 37 14 21862241 21862241 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr14:21862241delG uc001was.1 - 32 4970 c.4876delC c.(4876-4878)CTTfs p.L1626fs CHD8_uc001war.1_Frame_Shift_Del_p.L1522fs|SNORD9_uc001wat.1_5'Flank NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 1905 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) TCTTCCAAAAGGGGGTGGCAT 0.537 0.10 277 30 CHD8 57680 broad.mit.edu 37 14 21897287 21897287 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr14:21897287delT uc001was.1 - 3 308 c.214delA c.(214-216)ATCfs p.I72fs CHD8_uc001war.1_5'UTR NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 351 Gln-rich. ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) ACAATCTGGATTTTTTGCTGT 0.572 0.20 87 22 TRIP11 9321 broad.mit.edu 37 14 92472698 92472698 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr14:92472698delT uc001xzy.2 - 11 2410 c.1622delA c.(1621-1623)AAGfs p.K541fs TRIP11_uc010auf.1_Frame_Shift_Del_p.K277fs NM_004239 NP_004230 Q15643 TRIPB_HUMAN thyroid hormone receptor interactor 11 541 Potential. transcription from RNA polymerase II promoter cytoskeleton|Golgi apparatus|membrane|nucleus protein binding|transcription coactivator activity ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1) 13 COAD - Colon adenocarcinoma(157;0.223) ATGAACTCTCTTTTTTTCATC 0.303 0.44 577 460 MKRN3 7681 broad.mit.edu 37 15 23811405 23811405 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr15:23811405delC uc001ywh.3 + 1 952 c.476delC c.(475-477)GCCfs p.A159fs MKRN3_uc001ywi.2_Intron|MKRN3_uc010ayi.1_Frame_Shift_Del_p.A159fs NM_005664 NP_005655 Q13064 MKRN3_HUMAN makorin ring finger protein 3 159 ribonucleoprotein complex ligase activity|nucleic acid binding|zinc ion binding lung(6)|large_intestine(2)|ovary(2) 10 all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14) all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012) 0.000 0.46 461 393 PLCB2 5330 broad.mit.edu 37 15 40583618 40583620 + In_Frame_Del DEL CTC - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr15:40583618_40583620delCTC uc001zld.2 - 26 3017_3019 c.2716_2718delGAG c.(2716-2718)GAGdel p.E906del PLCB2_uc001zlc.2_5'Flank|PLCB2_uc010bbo.2_In_Frame_Del_p.E902del|PLCB2_uc010ucm.1_In_Frame_Del_p.E891del NM_004573 NP_004564 Q00722 PLCB2_HUMAN phospholipase C, beta 2 906 activation of phospholipase C activity|intracellular signal transduction|lipid catabolic process|phospholipid metabolic process|synaptic transmission cytosol calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity ovary(3)|breast(3)|kidney(1)|pancreas(1) 8 all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508) 0.000 0.39 366 230 UNC13C 440279 broad.mit.edu 37 15 54630643 54630644 + Frame_Shift_Ins INS - T T HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr15:54630643_54630644insT uc002ack.2 + 15 4669_4670 c.4669_4670insT c.(4669-4671)ATTfs p.I1557fs UNC13C_uc002acl.2_Frame_Shift_Ins_p.I387fs NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 1557 exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) ATACAAGTATATTTTTGACAAC 0.436 0.36 214 123 CSPG4 1464 broad.mit.edu 37 15 75968542 75968543 + Frame_Shift_Ins INS - C C HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr15:75968542_75968543insC uc002baw.2 - 10 6410_6411 c.6317_6318insG c.(6316-6318)GGCfs p.G2106fs NM_001897 NP_001888 Q6UVK1 CSPG4_HUMAN chondroitin sulfate proteoglycan 4 precursor 2106 Extracellular (Potential).|CSPG 15.|Cysteine-containing.|Neurite growth inhibition (By similarity). angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane protein kinase binding|signal transducer activity ovary(2)|pancreas(1) 3 0.000 0.53 332 374 PRKCB 5579 broad.mit.edu 37 16 24104123 24104123 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr16:24104123delA uc002dmd.2 + 6 738 c.541delA c.(541-543)AAAfs p.K181fs PRKCB_uc002dme.2_Frame_Shift_Del_p.K181fs NM_212535 NP_997700 P05771 KPCB_HUMAN protein kinase C, beta isoform 1 181 C2. apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent cytosol|nucleus|plasma membrane androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1) 9 Vitamin E(DB00163) AAGAGATGCTAAAAACCTTGT 0.418 0.43 191 142 CDH1 999 broad.mit.edu 37 16 68835766 68835766 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr16:68835766delG uc002ewg.1 + 3 481 c.357delG c.(355-357)GTGfs p.V119fs CDH1_uc010vlj.1_RNA|CDH1_uc010cfg.1_Frame_Shift_Del_p.V119fs NM_004360 NP_004351 P12830 CADH1_HUMAN cadherin 1, type 1 preproprotein 119 adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm cell adhesion molecule binding|gamma-catenin binding p.H121fs*94(2) breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1) 243 all_neural(199;0.0189)|Ovarian(137;0.0563) Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261) TGAATACAGTGGGGCACCACC 0.473 0.31 116 52 BCAR1 9564 broad.mit.edu 37 16 75270878 75270879 + Frame_Shift_Ins INS - G G HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr16:75270878_75270879insG uc002fdv.2 - 4 936_937 c.813_814insC c.(811-816)CCCATGfs p.P271fs BCAR1_uc002fdt.2_5'Flank|BCAR1_uc002fdu.2_Frame_Shift_Ins_p.P61fs|BCAR1_uc010cgu.2_Frame_Shift_Ins_p.P242fs|BCAR1_uc010vna.1_Frame_Shift_Ins_p.P269fs|BCAR1_uc010vnb.1_Frame_Shift_Ins_p.P317fs|BCAR1_uc002fdw.2_Frame_Shift_Ins_p.P271fs|BCAR1_uc010vnc.1_Frame_Shift_Ins_p.P123fs|BCAR1_uc010vnd.1_Frame_Shift_Ins_p.P289fs|BCAR1_uc002fdx.2_Frame_Shift_Ins_p.P289fs NM_014567 NP_055382 P56945 BCAR1_HUMAN breast cancer anti-estrogen resistance 1 271_272 Substrate for kinases (By similarity). actin filament organization|B cell receptor signaling pathway|blood coagulation|cell adhesion|cell division|cell migration|cell proliferation|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|integrin-mediated signaling pathway|nerve growth factor receptor signaling pathway|platelet-derived growth factor receptor signaling pathway|positive regulation of cell migration|regulation of apoptosis|regulation of cell growth|T cell receptor signaling pathway cytosol|focal adhesion|membrane fraction|ruffle protein kinase binding|protein phosphatase binding|SH3 domain binding|signal transducer activity central_nervous_system(5)|breast(2)|prostate(1) 8 BRCA - Breast invasive adenocarcinoma(221;0.169) 0.000 0.42 827 590 FANCA 2175 broad.mit.edu 37 16 89842206 89842206 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr16:89842206delG uc002fou.1 - 21 1886 c.1844delC c.(1843-1845)CCAfs p.P615fs FANCA_uc010vpn.1_Frame_Shift_Del_p.P615fs NM_000135 NP_000126 O15360 FANCA_HUMAN Fanconi anemia, complementation group A isoform 615 DNA repair|protein complex assembly cytoplasm|nucleoplasm protein binding ovary(2)|breast(2)|central_nervous_system(1)|skin(1) 6 Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194) BRCA - Breast invasive adenocarcinoma(80;0.028) GTACAGAGATGGGGGGATTTT 0.438 0.28 293 113 NF1 4763 broad.mit.edu 37 17 29553478 29553478 + Frame_Shift_Del DEL C - - rs145092683 HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr17:29553478delC uc002hgg.2 + 18 2360 c.2027delC c.(2026-2028)ACCfs p.T676fs NF1_uc002hgh.2_Frame_Shift_Del_p.T676fs|NF1_uc010csn.1_Frame_Shift_Del_p.T536fs|NF1_uc002hgi.1_5'UTR NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 676 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2)|p.P678fs*10(1) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) TGCAGCGGAACCCCCCCGATT 0.463 0.58 67 92 TOP2A 7153 broad.mit.edu 37 17 38561120 38561121 + Frame_Shift_Ins INS - T T HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr17:38561120_38561121insT uc002huq.2 - 17 2094_2095 c.1968_1969insA c.(1966-1971)AAACAGfs p.K656fs NM_001067 NP_001058 P11388 TOP2A_HUMAN DNA topoisomerase II, alpha isozyme 656_657 apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1) 7 Breast(137;0.00328) STAD - Stomach adenocarcinoma(5;0.00183) Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385) TCATCTATCTGTTTTTTGCTAA 0.342 0.42 329 236 COL1A1 1277 broad.mit.edu 37 17 48266555 48266556 + Frame_Shift_Del DEL CT - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr17:48266555_48266556delCT uc002iqm.2 - 40 3036_3037 c.2910_2911delAG c.(2908-2913)AGAGGCfs p.R970fs NM_000088 NP_000079 P02452 CO1A1_HUMAN alpha 1 type I collagen preproprotein 970_971 Triple-helical region. axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception collagen type I|extracellular space|plasma membrane identical protein binding|platelet-derived growth factor binding COL1A1/PDGFB(372) soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1) 382 Collagenase(DB00048)|Palifermin(DB00039) 0.000 0.28 549 211 RNF43 54894 broad.mit.edu 37 17 56448298 56448298 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr17:56448298delG uc002iwf.2 - 2 2305 c.349delC c.(349-351)CGCfs p.R117fs RNF43_uc010wnv.1_Intron|RNF43_uc002iwh.3_Frame_Shift_Del_p.R117fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.R117fs|RNF43_uc010dcw.2_5'UTR NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 117 Extracellular (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.80 425 1722 PPM1D 8493 broad.mit.edu 37 17 58740439 58740439 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr17:58740439delT uc002iyt.1 + 6 1566 c.1344delT c.(1342-1344)AATfs p.N448fs PPM1D_uc010ddm.1_RNA NM_003620 NP_003611 O15297 PPM1D_HUMAN protein phosphatase 1D 448 negative regulation of cell proliferation|protein dephosphorylation|response to radiation nucleus|protein serine/threonine phosphatase complex metal ion binding|protein binding|protein serine/threonine phosphatase activity upper_aerodigestive_tract(1) 1 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) Epithelial(12;6.75e-12)|all cancers(12;1.96e-10) 0.000 0.33 1201 579 ASPSCR1 79058 broad.mit.edu 37 17 79954508 79954508 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr17:79954508delC uc002kcx.2 + 7 816 c.719delC c.(718-720)GCCfs p.A240fs ASPSCR1_uc002kcw.1_Frame_Shift_Del_p.A240fs|ASPSCR1_uc002kcy.2_Frame_Shift_Del_p.A240fs|ASPSCR1_uc002kcz.2_Intron|ASPSCR1_uc002kda.2_Frame_Shift_Del_p.A163fs|ASPSCR1_uc002kdb.1_Frame_Shift_Del_p.A163fs NM_024083 NP_076988 Q9BZE9 ASPC1_HUMAN alveolar soft part sarcoma chromosome region, 240 protein binding ASPSCR1/TFE3(161) soft_tissue(118)|kidney(43)|breast(1) 162 all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246) BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191) CCCGCAGCTGCCCCCTTTGTT 0.657 0.38 8 5 SMAD7 4092 broad.mit.edu 37 18 46474795 46474795 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr18:46474795delG uc002ldg.2 - 2 913 c.626delC c.(625-627)CCTfs p.P209fs SMAD7_uc010xde.1_5'UTR NM_005904 NP_005895 O15105 SMAD7_HUMAN SMAD family member 7 209 Poly-Pro.|PY-motif.|Important for interaction with SMURF2. Missing: Diminishes interaction with SMURF2. adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding 0 Colorectal(1;0.0518) GGAGTAAGGAGGGGGGGGAGA 0.388 0.33 102 51 SMARCA4 6597 broad.mit.edu 37 19 11096868 11096869 + Frame_Shift_Ins INS - C C HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr19:11096868_11096869insC uc002mqf.3 + 4 643_644 c.359_360insC c.(358-360)TACfs p.Y120fs SMARCA4_uc010dxp.2_Frame_Shift_Ins_p.Y120fs|SMARCA4_uc010dxo.2_Frame_Shift_Ins_p.Y120fs|SMARCA4_uc002mqg.1_Frame_Shift_Ins_p.Y120fs|SMARCA4_uc010dxq.2_Frame_Shift_Ins_p.Y120fs|SMARCA4_uc010dxr.2_Frame_Shift_Ins_p.Y120fs|SMARCA4_uc002mqj.3_Frame_Shift_Ins_p.Y120fs|SMARCA4_uc010dxs.2_Frame_Shift_Ins_p.Y120fs|SMARCA4_uc002mqe.2_Frame_Shift_Ins_p.Y120fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 120 Necessary for interaction with SS18L1/CREST (By similarity). chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) 0.000 0.51 297 311 ZNF573 126231 broad.mit.edu 37 19 38229651 38229651 + Frame_Shift_Del DEL T - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr19:38229651delT uc002ohe.2 - 4 1762 c.1740delA c.(1738-1740)AAAfs p.K580fs ZNF573_uc010efs.2_Frame_Shift_Del_p.K493fs|ZNF573_uc002ohd.2_Frame_Shift_Del_p.K578fs|ZNF573_uc002ohf.2_Frame_Shift_Del_p.K522fs|ZNF573_uc002ohg.2_Frame_Shift_Del_p.K492fs NM_152360 NP_689573 Q86YE8 ZN573_HUMAN zinc finger protein 573 560 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1) 1 UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146) ATTCATAGGGTTTTTTATCAG 0.368 0.32 17 8 AXL 558 broad.mit.edu 37 19 41744385 41744385 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr19:41744385delC uc010ehj.2 + 8 1195 c.1005delC c.(1003-1005)GGCfs p.G335fs CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Frame_Shift_Del_p.G335fs|AXL_uc010ehk.2_Frame_Shift_Del_p.G335fs NM_021913 NP_068713 P30530 UFO_HUMAN AXL receptor tyrosine kinase isoform 1 335 Extracellular (Potential).|Fibronectin type-III 2. integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1) 13 0.000 0.50 372 371 LMTK3 114783 broad.mit.edu 37 19 49000828 49000829 + Frame_Shift_Ins INS - G G HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr19:49000828_49000829insG uc002pjk.2 - 12 3584_3585 c.3584_3585insC c.(3583-3585)CCGfs p.P1195fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.39 530 342 TFPT 29844 broad.mit.edu 37 19 54617959 54617960 + Frame_Shift_Del DEL AC - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr19:54617959_54617960delAC uc010yej.1 - 2 550_551 c.144_145delGT c.(142-147)GTGTCAfs p.V48fs TFPT_uc010erd.2_Frame_Shift_Del_p.V48fs|PRPF31_uc002qdh.2_5'Flank|PRPF31_uc010yek.1_5'Flank NM_013342 NP_037474 P0C1Z6 TFPT_HUMAN TCF3 (E2A) fusion partner 48_49 apoptosis|DNA recombination|DNA repair|induction of apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|Ino80 complex DNA binding|protein binding 0 all_cancers(19;0.004)|all_epithelial(19;0.00195)|all_lung(19;0.0193)|Lung NSC(19;0.0358)|Breast(117;0.137)|Ovarian(34;0.19) AGACCACCTGACACAAACTCCA 0.624 0.44 28 22 BRSK1 84446 broad.mit.edu 37 19 55823335 55823335 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr19:55823335delC uc002qkg.2 + 19 2513 c.2236delC c.(2236-2238)CCCfs p.P746fs BRSK1_uc002qkf.2_Frame_Shift_Del_p.P762fs|BRSK1_uc002qkh.2_Frame_Shift_Del_p.P441fs NM_032430 NP_115806 Q8TDC3 BRSK1_HUMAN BR serine/threonine kinase 1 746 establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV cell junction|cytoplasm|nucleus magnesium ion binding|protein serine/threonine kinase activity ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1) 6 Renal(1328;0.245) BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.0474) 0.000 0.43 500 378 PTPRT 11122 broad.mit.edu 37 20 40739003 40739003 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr20:40739003delG uc002xkg.2 - 23 3408 c.3224delC c.(3223-3225)CCGfs p.P1075fs PTPRT_uc010ggj.2_Frame_Shift_Del_p.P1094fs|PTPRT_uc010ggi.2_Frame_Shift_Del_p.P278fs NM_007050 NP_008981 O14522 PTPRT_HUMAN protein tyrosine phosphatase, receptor type, T 1075 Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential). homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway cell surface|integral to membrane|plasma membrane alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity skin(8)|ovary(7)|lung(5) 20 Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783) 0.000 0.24 407 131 TIAM1 7074 broad.mit.edu 37 21 32525065 32525065 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr21:32525065delA uc002yow.1 - 20 3727 c.3255delT c.(3253-3255)TTTfs p.F1085fs TIAM1_uc011adk.1_Frame_Shift_Del_p.F1085fs|TIAM1_uc011adl.1_Frame_Shift_Del_p.F1025fs NM_003253 NP_003244 Q13009 TIAM1_HUMAN T-cell lymphoma invasion and metastasis 1 1085 DH. apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cell-cell junction|cytosol receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity lung(3)|breast(3)|ovary(2)|large_intestine(2) 10 TTAAATTTCCAAAAAGCACGT 0.338 0.16 117 22 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 36 466 BCR 613 broad.mit.edu 37 22 23523816 23523816 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr22:23523816delG uc002zww.2 + 1 1265 c.669delG c.(667-669)GTGfs p.V223fs BCR_uc002zwx.2_Frame_Shift_Del_p.V223fs NM_004327 NP_004318 P11274 BCR_HUMAN breakpoint cluster region isoform 1 223 Kinase.|Binding to ABL SH2-domain. regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity BCR/JAK2(6) haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1) 12 0.000 0.59 153 224 MYO18B 84700 broad.mit.edu 37 22 26299684 26299684 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr22:26299684delG uc003abz.1 + 31 5284 c.5034delG c.(5032-5034)CTGfs p.L1678fs MYO18B_uc003aca.1_Frame_Shift_Del_p.L1559fs|MYO18B_uc010guy.1_Frame_Shift_Del_p.L1560fs|MYO18B_uc010guz.1_Frame_Shift_Del_p.L1558fs|MYO18B_uc011aka.1_Frame_Shift_Del_p.L832fs|MYO18B_uc011akb.1_Frame_Shift_Del_p.L1191fs NM_032608 NP_115997 Q8IUG5 MY18B_HUMAN myosin XVIIIB 1678 Potential.|Tail.|Gln-rich. nucleus|sarcomere|unconventional myosin complex actin binding|ATP binding|motor activity ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2) 12 0.000 0.51 676 696 ZNRF3 84133 broad.mit.edu 37 22 29446274 29446275 + Frame_Shift_Ins INS - G G HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr22:29446274_29446275insG uc003aeg.2 + 8 1970_1971 c.1805_1806insG c.(1804-1806)AAGfs p.K602fs ZNRF3_uc003aeh.1_Frame_Shift_Ins_p.K602fs NM_032173 NP_115549 Q9ULT6 ZNRF3_HUMAN zinc and ring finger 3 702 Cytoplasmic (Potential). integral to membrane zinc ion binding ovary(1) 1 0.000 0.37 1005 601 DDX17 10521 broad.mit.edu 37 22 38895455 38895455 + Frame_Shift_Del DEL C - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr22:38895455delC uc003avy.3 - 3 591 c.488delG c.(487-489)GGAfs p.G163fs DDX17_uc003avx.3_Frame_Shift_Del_p.G163fs|DDX17_uc011anu.1_Frame_Shift_Del_p.G76fs NM_001098504 NP_001091974 Q92841 DDX17_HUMAN DEAD box polypeptide 17 isoform 3 84 RNA processing nucleus ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity skin(3)|upper_aerodigestive_tract(1) 4 Melanoma(58;0.0286) 0.000 0.45 499 412 EP300 2033 broad.mit.edu 37 22 41566525 41566525 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr22:41566525delA uc003azl.3 + 27 4797 c.4402delA c.(4402-4404)AAAfs p.K1468fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1468 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding p.M1470fs*3(3) haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 GGAATGGTACAAAAAAATGCT 0.473 0.46 360 306 EP300 2033 broad.mit.edu 37 22 41572810 41572810 + Frame_Shift_Del DEL A - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr22:41572810delA uc003azl.3 + 31 5490 c.5095delA c.(5095-5097)AAAfs p.K1699fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1699 Binding region for E1A adenovirus.|ZZ-type. apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding p.N1700fs*9(4) haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 CTATAACACTAAAAACCATGA 0.443 0.23 24 7 MAPK11 5600 broad.mit.edu 37 22 50704060 50704060 + Frame_Shift_Del DEL G - - HCT116_LARGE_INTESTINE NA HCT116_LARGE_INTESTINE NA g.chr22:50704060delG uc003bkr.2 - 10 850 c.792delC c.(790-792)CCCfs p.P264fs MAPK11_uc010hax.2_Frame_Shift_Del_p.P86fs|MAPK11_uc011ars.1_RNA|MAPK11_uc010hay.1_Intron NM_002751 NP_002742 Q15759 MK11_HUMAN mitogen-activated protein kinase 11 264 Protein kinase. activation of MAPK activity|innate immune response|mRNA metabolic process|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|MAP kinase activity|protein binding lung(1)|breast(1) 2 all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247) TCTGGGGCATGGGGGGCAGGG 0.637 0.38 8 5 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 4 47 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 415 130 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 150 35 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.39 20 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 132 92 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 12 25 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.33 38 19 FADD 8772 broad.mit.edu 37 11 70049816 70049817 + Frame_Shift_Ins INS - G G HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:70049816_70049817insG uc001opm.2 + 1 548_549 c.251_252insG c.(250-252)GCGfs p.A84fs NM_003824 NP_003815 Q13158 FADD_HUMAN Fas-associated via death domain 84 activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction cytosol death receptor binding|identical protein binding ovary(1)|lung(1)|pancreas(1) 3 Esophageal squamous(2;1.19e-45) LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) 0.000 0.10 502 57 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 234 38 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.27 24 9 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 48 356 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 9 72 MAPK12 6300 broad.mit.edu 37 22 50699855 50699874 + Frame_Shift_Del DEL CCGGTACACGGCGCGCACCT - - HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:50699855_50699874delCCGGTACACGGCGCGCACCT uc003bkm.1 - 1 216_235 c.65_84delAGGTGCGCGCCGTGTACCGG c.(64-84)GAGGTGCGCGCCGTGTACCGGfs p.E22fs MAPK12_uc003bkn.2_5'Flank|MAPK12_uc003bko.2_5'Flank|MAPK12_uc003bkl.1_Frame_Shift_Del_p.E22fs|MAPK12_uc003bkq.2_5'Flank|MAPK12_uc010haw.2_Frame_Shift_Del_p.E22fs NM_002969 NP_002960 P53778 MK12_HUMAN mitogen-activated protein kinase 12 22_28 Protein kinase. cell cycle arrest|DNA damage induced protein phosphorylation|muscle organ development|myoblast differentiation|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|Ras protein signal transduction mitochondrion|nucleoplasm ATP binding|magnesium ion binding|MAP kinase activity|protein binding 0 all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247) 0.000 0.98 1 44 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HDQP1_BREAST NA HDQP1_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 44 DFFA 1676 broad.mit.edu 37 1 10523635 10523637 + In_Frame_Del DEL GTA - - HDQP1_BREAST NA HDQP1_BREAST NA g.chr1:10523635_10523637delGTA uc001arj.2 - 4 580_582 c.482_484delTAC c.(481-486)CTACGT>CGT p.L161del DFFA_uc001ark.2_In_Frame_Del_p.L161del NM_004401 NP_004392 O00273 DFFA_HUMAN DNA fragmentation factor, 45kDa, alpha 161 DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction|negative regulation of apoptosis cytosol|mitochondrion|nucleoplasm|plasma membrane deoxyribonuclease activity|identical protein binding 0 Ovarian(185;0.203) all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487) CAACTCTGACGTAGTTCCTGAGC 0.498 0.88 3 23 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HDQP1_BREAST NA HDQP1_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.58 13 18 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HDQP1_BREAST NA HDQP1_BREAST NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.13 157 24 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HDQP1_BREAST NA HDQP1_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.56 14 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HDQP1_BREAST NA HDQP1_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.75 63 192 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HDQP1_BREAST NA HDQP1_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 30 90 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 HDQP1_BREAST NA HDQP1_BREAST NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.90 1 9 DNAH8 1769 broad.mit.edu 37 6 38754578 38754579 + Frame_Shift_Ins INS - C C HDQP1_BREAST NA HDQP1_BREAST NA g.chr6:38754578_38754579insC uc003ooe.1 + 16 2382_2383 c.1782_1783insC c.(1780-1785)ACAGGGfs p.T594fs NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 ATCCAGAAACAGGGAAGTTGCT 0.371 0.29 84 35 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 HDQP1_BREAST NA HDQP1_BREAST NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.16 257 48 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HDQP1_BREAST NA HDQP1_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 26 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HDQP1_BREAST NA HDQP1_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 2 95 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HDQP1_BREAST NA HDQP1_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 855 98 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HDQP1_BREAST NA HDQP1_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.50 448 450 CDH3 1001 broad.mit.edu 37 16 68679613 68679614 + Frame_Shift_Ins INS - A A HDQP1_BREAST NA HDQP1_BREAST NA g.chr16:68679613_68679614insA uc002ewf.2 + 2 1252_1253 c.120_121insA c.(118-123)GCGGGAfs p.A40fs CDH3_uc010vli.1_Intron NM_001793 NP_001784 P22223 CADH3_HUMAN cadherin 3, type 1 preproprotein 40_41 adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception integral to membrane calcium ion binding p.?(1) ovary(3)|breast(1)|skin(1) 5 Ovarian(137;0.0564) OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384) 0.000 1.00 0 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HDQP1_BREAST NA HDQP1_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 6 115 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 HDQP1_BREAST NA HDQP1_BREAST NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.35 17 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HDQP1_BREAST NA HDQP1_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.84 25 131 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HDQP1_BREAST NA HDQP1_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 157 1313 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HDQP1_BREAST NA HDQP1_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 8 63 ARAF 369 broad.mit.edu 37 X 47426420 47426421 + Frame_Shift_Del DEL CG - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chrX:47426420_47426421delCG uc011mlq.1 + 9 896_897 c.763_764delCG c.(763-765)CGGfs p.R255fs ARAF_uc011mln.1_RNA|ARAF_uc011mlo.1_Frame_Shift_Del_p.R121fs|ARAF_uc011mlp.1_Frame_Shift_Del_p.R255fs|ARAF_uc004dic.1_Frame_Shift_Del_p.R36fs NM_001654 NP_001645 P10398 ARAF_HUMAN v-raf murine sarcoma 3611 viral oncogene 255 intracellular signal transduction|negative regulation of apoptosis|positive regulation of peptidyl-serine phosphorylation ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity large_intestine(3)|lung(2)|ovary(1)|skin(1) 7 Adenosine triphosphate(DB00171) TGGAACCCCCCGGGGGAGCCCC 0.644 0.51 37 38 ARAF 369 broad.mit.edu 37 X 47426421 47426421 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chrX:47426421delG uc011mlq.1 + 9 897 c.764delG c.(763-765)CGGfs p.R255fs ARAF_uc011mln.1_RNA|ARAF_uc011mlo.1_Frame_Shift_Del_p.R121fs|ARAF_uc011mlp.1_Frame_Shift_Del_p.R255fs|ARAF_uc004dic.1_Frame_Shift_Del_p.R36fs NM_001654 NP_001645 P10398 ARAF_HUMAN v-raf murine sarcoma 3611 viral oncogene 255 intracellular signal transduction|negative regulation of apoptosis|positive regulation of peptidyl-serine phosphorylation ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity large_intestine(3)|lung(2)|ovary(1)|skin(1) 7 Adenosine triphosphate(DB00171) GGAACCCCCCGGGGGAGCCCC 0.642 0.31 50 22 AR 367 broad.mit.edu 37 X 66931427 66931429 + In_Frame_Del DEL ACG - - rs137852599 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chrX:66931427_66931429delACG uc004dwu.1 + 4 3184_3186 c.2069_2071delACG c.(2068-2073)CACGAC>CAC p.D691del AR_uc004dwv.1_In_Frame_Del_p.D159del NM_000044 NP_000035 P10275 ANDR_HUMAN androgen receptor isoform 1 690 Ligand-binding.|Interaction with MYST2. Missing (in PAIS). cell death|cell growth|cell proliferation|cell-cell signaling|negative regulation of apoptosis|negative regulation of integrin biosynthetic process|positive regulation of cell proliferation|positive regulation of integrin biosynthetic process|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|regulation of establishment of protein localization in plasma membrane|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transport cytoplasm|nuclear chromatin|nucleoplasm androgen binding|androgen receptor activity|beta-catenin binding|enzyme binding|ligand-regulated transcription factor activity|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding ovary(3)|lung(2)|breast(2)|central_nervous_system(1) 8 all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102) all_lung(315;1.3e-11) Bicalutamide(DB01128)|Cyproterone(DB04839)|Dromostanolone(DB00858)|Finasteride(DB01216)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Nandrolone(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Testosterone(DB00624) TGTGCTGGACACGACAACAACCA 0.532 0.91 18 184 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.84 7 38 GPR112 139378 broad.mit.edu 37 X 135443714 135443714 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chrX:135443714delA uc004ezu.1 + 12 7536 c.7245delA c.(7243-7245)ATAfs p.I2415fs GPR112_uc010nsb.1_Frame_Shift_Del_p.I2210fs|GPR112_uc010nsc.1_Frame_Shift_Del_p.I2043fs NM_153834 NP_722576 Q8IZF6 GP112_HUMAN G-protein coupled receptor 112 2415 Extracellular (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1) 12 Acute lymphoblastic leukemia(192;0.000127) CCAGATGCATAAAAAATGAGG 0.408 0.64 13 23 MTM1 4534 broad.mit.edu 37 X 149818284 149818284 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chrX:149818284delA uc004fef.3 + 10 1039 c.963delA c.(961-963)TTAfs p.L321fs MTM1_uc011mxx.1_RNA|MTM1_uc011mxy.1_Frame_Shift_Del_p.L284fs|MTM1_uc011mxz.1_Frame_Shift_Del_p.L206fs|MTM1_uc010nte.2_Frame_Shift_Del_p.L189fs NM_000252 NP_000243 Q13496 MTM1_HUMAN myotubularin 321 Myotubularin phosphatase. endosome to lysosome transport|intermediate filament organization|mitochondrion distribution|mitochondrion morphogenesis|phosphatidylinositol dephosphorylation|protein transport|regulation of vacuole organization filopodium|late endosome|plasma membrane|ruffle intermediate filament binding|phosphatidylinositol binding|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity upper_aerodigestive_tract(1)|ovary(1)|kidney(1) 3 Acute lymphoblastic leukemia(192;6.56e-05) 0.000 0.48 153 144 EPHA2 1969 broad.mit.edu 37 1 16474976 16474977 + Frame_Shift_Ins INS - C C HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:16474976_16474977insC uc001aya.1 - 3 856_857 c.719_720insG c.(718-720)GGTfs p.G240fs EPHA2_uc010oca.1_Frame_Shift_Ins_p.G240fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 240 Extracellular (Potential).|Cys-rich. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) GGGGCTCTTCACCCCCCGGTGG 0.668 0.32 25 12 ARID1A 8289 broad.mit.edu 37 1 27097622 27097622 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:27097622delA uc001bmv.1 + 12 3584 c.3211delA c.(3211-3213)AAAfs p.K1071fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.K1071fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.K1071fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.K688fs|ARID1A_uc001bmx.1_5'UTR|ARID1A_uc009vsm.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1071 ARID. androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.K1072fs*21(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CAACAAGAACAAAAAATGGCG 0.483 0.26 66 23 MAP3K6 9064 broad.mit.edu 37 1 27687423 27687423 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:27687423delC uc001bny.1 - 14 2158 c.1909delG c.(1909-1911)GAGfs p.E637fs MAP3K6_uc009vsw.1_Frame_Shift_Del_p.E629fs|MAP3K6_uc001bnz.1_Frame_Shift_Del_p.E160fs NM_004672 NP_004663 O95382 M3K6_HUMAN mitogen-activated protein kinase kinase kinase 637 activation of JUN kinase activity ATP binding|magnesium ion binding|MAP kinase kinase kinase activity breast(4)|lung(3)|ovary(1)|central_nervous_system(1) 9 all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419) TCCAACATCTCCCCCGCGCCC 0.711 0.33 22 11 TNNI3K 51086 broad.mit.edu 37 1 74905181 74905182 + Frame_Shift_Ins INS - T T HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:74905181_74905182insT uc001dgf.1 + 20 1937_1938 c.1886_1887insT c.(1885-1887)CGTfs p.R629fs TNNI3K_uc001dgd.2_Frame_Shift_Ins_p.R730fs|TNNI3K_uc001dge.1_Frame_Shift_Ins_p.R730fs NM_015978 NP_057062 Q59H18 TNI3K_HUMAN TNNI3 interacting kinase isoform b 629 Protein kinase. R -> G (in a colorectal cancer sample; somatic mutation). R -> L (in Ref. 8; AAH32865). cytoplasm|nucleus ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding p.R629G(1) large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1) 10 CAGAACCTCCGTTGGATGGCTC 0.465 0.25 76 25 PRKACB 5567 broad.mit.edu 37 1 84644898 84644898 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:84644898delA uc001djj.2 + 2 349 c.85delA c.(85-87)AAAfs p.K29fs PRKACB_uc001djl.2_Frame_Shift_Del_p.K76fs|PRKACB_uc010ort.1_Frame_Shift_Del_p.K36fs|PRKACB_uc001djn.2_Frame_Shift_Del_p.K33fs|PRKACB_uc010oru.1_Frame_Shift_Del_p.K17fs|PRKACB_uc001djp.2_Frame_Shift_Del_p.K35fs|PRKACB_uc001djq.2_Frame_Shift_Del_p.K32fs|PRKACB_uc010orv.1_5'Flank|PRKACB_uc001dji.2_Frame_Shift_Del_p.K29fs|PRKACB_uc001djk.2_Frame_Shift_Del_p.K76fs|PRKACB_uc001djo.1_RNA|PRKACB_uc009wcf.1_Frame_Shift_Del_p.K35fs NM_002731 NP_002722 P22694 KAPCB_HUMAN cAMP-dependent protein kinase catalytic subunit 29 activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein signaling, coupled to cAMP nucleotide second messenger|gluconeogenesis|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|regulation of insulin secretion|synaptic transmission|transmembrane transport|triglyceride catabolic process|water transport cAMP-dependent protein kinase complex|centrosome|cytosol|nucleoplasm|plasma membrane ATP binding|cAMP-dependent protein kinase activity|magnesium ion binding|protein binding lung(2)|ovary(1) 3 all cancers(265;0.00536)|Epithelial(280;0.0161)|OV - Ovarian serous cystadenocarcinoma(397;0.141) AGACTTTTTGAAAAAATGGGA 0.239 0.38 26 16 CDC7 8317 broad.mit.edu 37 1 91977476 91977476 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:91977476delA uc001doe.2 + 6 733 c.568delA c.(568-570)AAAfs p.K190fs CDC7_uc001dof.2_Frame_Shift_Del_p.K190fs|CDC7_uc010osw.1_Frame_Shift_Del_p.K162fs|CDC7_uc009wdc.2_Frame_Shift_Del_p.K190fs|CDC7_uc009wdd.2_5'Flank NM_003503 NP_003494 O00311 CDC7_HUMAN cell division cycle 7 190 Protein kinase. cell cycle checkpoint|cell division|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|positive regulation of cell proliferation|regulation of S phase cytoplasm|nucleoplasm ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity stomach(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 5 all_lung(203;0.0165)|Lung NSC(277;0.0562) all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124) TAGGCGCCTGAAAAAGTAAGT 0.234 0.31 79 35 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.44 191 153 FMO4 2329 broad.mit.edu 37 1 171289040 171289041 + Frame_Shift_Ins INS - TGGA TGGA HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:171289040_171289041insTGGA uc001gho.2 + 3 293_294 c.76_77insTGGA c.(76-78)CTGfs p.L26fs NM_002022 NP_002013 P31512 FMO4_HUMAN flavin containing monooxygenase 4 26 xenobiotic metabolic process integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding kidney(2)|skin(1) 3 all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181) GGATGAGGACCTGGAGCCCACC 0.480 0.25 113 38 RNASEL 6041 broad.mit.edu 37 1 182554909 182554909 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:182554909delC uc001gpj.1 - 1 1200 c.1033delG c.(1033-1035)GCAfs p.A345fs RNASEL_uc009wxz.1_Frame_Shift_Del_p.A345fs|RNASEL_uc001gpk.2_Frame_Shift_Del_p.A345fs|RNASEL_uc009wya.1_Frame_Shift_Del_p.A345fs NM_021133 NP_066956 Q05823 RN5A_HUMAN ribonuclease L 345 mRNA processing|response to virus|type I interferon-mediated signaling pathway mitochondrion ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding ovary(4)|stomach(1) 5 TTCAGGGCTGCCCCCCAGTGT 0.453 0.65 33 60 NUAK2 81788 broad.mit.edu 37 1 205273223 205273225 + In_Frame_Del DEL CTT - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:205273223_205273225delCTT uc001hce.2 - 7 1367_1369 c.1240_1242delAAG c.(1240-1242)AAGdel p.K414del NM_030952 NP_112214 Q9H093 NUAK2_HUMAN NUAK family, SNF1-like kinase, 2 414 actin cytoskeleton organization|apoptosis|cellular response to glucose starvation|negative regulation of apoptosis ATP binding|magnesium ion binding|protein serine/threonine kinase activity ovary(3)|stomach(1)|breast(1) 5 Breast(84;0.186) BRCA - Breast invasive adenocarcinoma(75;0.117) AGGCTGACACCTTCTTCTTGAGA 0.616 0.31 147 65 CABC1 56997 broad.mit.edu 37 1 227174192 227174192 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:227174192delG uc001hqm.1 + 20 5117 c.1698delG c.(1696-1698)CTGfs p.L566fs CABC1_uc001hqn.1_Frame_Shift_Del_p.L566fs|CABC1_uc009xeq.1_Frame_Shift_Del_p.L514fs|CABC1_uc010pvq.1_Frame_Shift_Del_p.L287fs|CABC1_uc010pvr.1_Frame_Shift_Del_p.L240fs|CABC1_uc001hqo.1_Frame_Shift_Del_p.L287fs|CABC1_uc009xer.1_Frame_Shift_Del_p.L82fs NM_020247 NP_064632 Q8NI60 ADCK3_HUMAN chaperone, ABC1 activity of bc1 complex like 566 cell death mitochondrion ATP binding|protein serine/threonine kinase activity 0 Prostate(94;0.0771) TCCTCATCCTGGGGGAGGCCT 0.587 0.29 175 72 CDC42BPA 8476 broad.mit.edu 37 1 227213757 227213757 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:227213757delT uc001hqr.2 - 30 5367 c.4424delA c.(4423-4425)AAGfs p.K1475fs CDC42BPA_uc001hqq.2_Frame_Shift_Del_p.K774fs|CDC42BPA_uc001hqs.2_Frame_Shift_Del_p.K1394fs|CDC42BPA_uc009xes.2_Frame_Shift_Del_p.K1447fs|CDC42BPA_uc010pvs.1_Frame_Shift_Del_p.K1455fs|CDC42BPA_uc001hqp.2_Frame_Shift_Del_p.K631fs|CDC42BPA_uc001hqt.2_Frame_Shift_Del_p.K353fs|CDC42BPA_uc001hqu.1_Frame_Shift_Del_p.K682fs NM_003607 NP_003598 Q5VT25 MRCKA_HUMAN CDC42-binding protein kinase alpha isoform B 1488 CNH. actin cytoskeleton reorganization|intracellular signal transduction cell leading edge|cell-cell junction|cytoplasm ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1) 11 all_cancers(173;0.156)|Prostate(94;0.0792) TTAAATTACCTTTTTGAGAGG 0.328 0.64 45 81 CDC42BPA 8476 broad.mit.edu 37 1 227288705 227288706 + Frame_Shift_Ins INS - T T HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:227288705_227288706insT uc001hqr.2 - 15 3179_3180 c.2236_2237insA c.(2236-2238)ACCfs p.T746fs CDC42BPA_uc001hqq.2_Frame_Shift_Ins_p.T10fs|CDC42BPA_uc001hqs.2_Frame_Shift_Ins_p.T665fs|CDC42BPA_uc009xes.2_Frame_Shift_Ins_p.T746fs|CDC42BPA_uc010pvs.1_Frame_Shift_Ins_p.T746fs NM_003607 NP_003598 Q5VT25 MRCKA_HUMAN CDC42-binding protein kinase alpha isoform B 746 Potential. actin cytoskeleton reorganization|intracellular signal transduction cell leading edge|cell-cell junction|cytoplasm ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1) 11 all_cancers(173;0.156)|Prostate(94;0.0792) TTCTCTTCTGGTTTTTTCCAAT 0.183 0.33 63 31 OBSCN 84033 broad.mit.edu 37 1 228456350 228456350 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:228456350delA uc009xez.1 + 17 5025 c.4981delA c.(4981-4983)AAGfs p.K1661fs OBSCN_uc001hsn.2_Frame_Shift_Del_p.K1661fs|OBSCN_uc001hso.2_Frame_Shift_Del_p.K107fs NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 1661 Ig-like 17. apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) GACGTGGTACAAGGATGGGAA 0.682 0.32 192 92 URB2 9816 broad.mit.edu 37 1 229772313 229772313 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:229772313delA uc001hts.1 + 4 2089 c.1953delA c.(1951-1953)GTAfs p.V651fs URB2_uc009xfd.1_Frame_Shift_Del_p.V651fs NM_014777 NP_055592 Q14146 URB2_HUMAN URB2 ribosome biogenesis 2 homolog 651 nucleolus central_nervous_system(2)|ovary(1) 3 TCCCAGGTGTAAAAACACAGC 0.443 0.29 299 125 FMN2 56776 broad.mit.edu 37 1 240371047 240371047 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr1:240371047delC uc010pyd.1 + 5 3160 c.2935delC c.(2935-2937)CCCfs p.P979fs FMN2_uc010pye.1_Frame_Shift_Del_p.P983fs NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 979 Pro-rich.|FH1. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) ACCTCCTCCACCCCCTCTACC 0.716 0.50 9 9 TPO 7173 broad.mit.edu 37 2 1507747 1507748 + Frame_Shift_Ins INS - C C HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:1507747_1507748insC uc002qww.2 + 14 2505_2506 c.2414_2415insC c.(2413-2415)CACfs p.H805fs TPO_uc010ewj.2_RNA|TPO_uc002qwu.2_Frame_Shift_Ins_p.H748fs|TPO_uc002qwr.2_Frame_Shift_Ins_p.H805fs|TPO_uc002qwx.2_Frame_Shift_Ins_p.H748fs|TPO_uc010yio.1_Frame_Shift_Ins_p.H632fs|TPO_uc010yip.1_Intron|TPO_uc002qwy.1_Intron|TPO_uc002qwz.2_Intron NM_000547 NP_000538 P07202 PERT_HUMAN thyroid peroxidase isoform a 805 Extracellular (Potential).|EGF-like; calcium-binding (Potential). cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process cell surface|cytoplasm|integral to plasma membrane calcium ion binding|heme binding|iodide peroxidase activity p.H805L(1) ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1) 20 all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627) all_cancers(51;0.0338) all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12) Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550) 0.000 0.16 1028 197 PXDN 7837 broad.mit.edu 37 2 1652651 1652651 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:1652651delG uc002qxa.2 - 17 2965 c.2901delC c.(2899-2901)CCCfs p.P967fs NM_012293 NP_036425 Q92626 PXDN_HUMAN peroxidasin precursor 967 extracellular matrix organization|hydrogen peroxide catabolic process|immune response endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity pancreas(6)|ovary(2) 8 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716) all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228) 0.000 0.18 1247 268 PXDN 7837 broad.mit.edu 37 2 1652983 1652984 + Frame_Shift_Ins INS - G G HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:1652983_1652984insG uc002qxa.2 - 17 2632_2633 c.2568_2569insC c.(2566-2571)CCCTGCfs p.P856fs NM_012293 NP_036425 Q92626 PXDN_HUMAN peroxidasin precursor 856_857 extracellular matrix organization|hydrogen peroxide catabolic process|immune response endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity pancreas(6)|ovary(2) 8 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716) all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228) ACAGAGAAGCAGGGGGGGTCGT 0.663 0.26 28 10 MYCN 4613 broad.mit.edu 37 2 16082314 16082314 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:16082314delC uc002rci.2 + 2 428 c.128delC c.(127-129)ACCfs p.T43fs MYCNOS_uc002rch.1_5'Flank|MYCN_uc010yjr.1_Frame_Shift_Del_p.T35fs NM_005378 NP_005369 P04198 MYCN_HUMAN v-myc myelocytomatosis viral related oncogene, 43 regulation of transcription from RNA polymerase II promoter chromatin|nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity central_nervous_system(2)|ovary(1)|lung(1)|skin(1) 5 all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197) GBM - Glioblastoma multiforme(3;0.000332) 0.000 0.27 236 88 ALK 238 broad.mit.edu 37 2 29462549 29462549 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:29462549delG uc002rmy.2 - 13 3259 c.2352delC c.(2350-2352)CCCfs p.P784fs NM_004304 NP_004295 Q9UM73 ALK_HUMAN anaplastic lymphoma kinase precursor 784 Extracellular (Potential). protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2) haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1) 1218 Acute lymphoblastic leukemia(172;0.155) Adenosine triphosphate(DB00171) CACTTACACTGGGGCAGGCGT 0.602 0.20 74 19 MSH2 4436 broad.mit.edu 37 2 47702370 47702370 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:47702370delT uc002rvy.1 + 12 2034 c.1966delT c.(1966-1968)TACfs p.Y656fs MSH2_uc010yoh.1_Frame_Shift_Del_p.Y590fs|MSH2_uc002rvz.2_Frame_Shift_Del_p.Y656fs|MSH2_uc010fbg.2_Frame_Shift_Del_p.Y466fs|MSH2_uc010fbi.1_RNA NM_000251 NP_000242 P43246 MSH2_HUMAN mutS homolog 2 656 Interaction with EXO1. Y -> H (in HNPCC1; somatic mutation). B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes MutSalpha complex|MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding p.?(2) large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1) 55 all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) TAATGACGTATACTTTGAAAA 0.318 0.54 71 85 BCL11A 53335 broad.mit.edu 37 2 60689197 60689197 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:60689197delC uc002sae.1 - 4 1078 c.850delG c.(850-852)GCGfs p.A284fs BCL11A_uc002sab.2_Frame_Shift_Del_p.A284fs|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Frame_Shift_Del_p.A250fs|BCL11A_uc002sad.1_Frame_Shift_Del_p.A132fs|BCL11A_uc002saf.1_Frame_Shift_Del_p.A250fs NM_022893 NP_075044 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A isoform 1 284 Pro-rich. negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|cytoplasm|nucleus|nucleus nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding central_nervous_system(6)|breast(3)|ovary(2)|skin(2) 13 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) 0.000 0.33 430 216 BCL11A 53335 broad.mit.edu 37 2 60689254 60689254 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:60689254delG uc002sae.1 - 4 1021 c.793delC c.(793-795)CTGfs p.L265fs BCL11A_uc002sab.2_Frame_Shift_Del_p.L265fs|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Frame_Shift_Del_p.L231fs|BCL11A_uc002sad.1_Frame_Shift_Del_p.L113fs|BCL11A_uc002saf.1_Frame_Shift_Del_p.L231fs NM_022893 NP_075044 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A isoform 1 265 Pro-rich. negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|cytoplasm|nucleus|nucleus nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding central_nervous_system(6)|breast(3)|ovary(2)|skin(2) 13 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) GGACTAAACAGGGGGGGAGTG 0.582 0.25 27 9 EHBP1 23301 broad.mit.edu 37 2 63053336 63053336 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:63053336delA uc002sby.2 + 6 909 c.427delA c.(427-429)AAAfs p.K143fs EHBP1_uc010fcp.2_Frame_Shift_Del_p.K143fs|EHBP1_uc010fcq.1_Frame_Shift_Del_p.K143fs|EHBP1_uc002sbx.2_Frame_Shift_Del_p.K143fs|EHBP1_uc002sbz.2_Frame_Shift_Del_p.K143fs|EHBP1_uc002scb.2_Frame_Shift_Del_p.K143fs NM_015252 NP_056067 Q8NDI1 EHBP1_HUMAN EH domain binding protein 1 isoform 1 143 cytoplasm|membrane ovary(1)|breast(1) 2 Lung NSC(7;0.0951)|all_lung(7;0.169) LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189) GCCATTATCTAAAAAAGTTGT 0.378 0.20 168 41 MAP3K2 10746 broad.mit.edu 37 2 128096510 128096511 + Frame_Shift_Ins INS - T T HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:128096510_128096511insT uc002toj.1 - 2 185_186 c.120_121insA c.(118-123)AAACAGfs p.K40fs MAP3K2_uc010flz.1_Frame_Shift_Ins_p.K40fs NM_006609 NP_006600 Q9Y2U5 M3K2_HUMAN mitogen-activated protein kinase kinase kinase 40_41 activation of JUN kinase activity|cellular response to mechanical stimulus nucleus ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein kinase binding lung(3)|ovary(2)|large_intestine(1)|central_nervous_system(1) 7 Colorectal(110;0.1) BRCA - Breast invasive adenocarcinoma(221;0.0706) ATAAATACCTGTTTTTTTGGTG 0.332 0.40 36 24 LRP1B 53353 broad.mit.edu 37 2 141356336 141356336 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:141356336delT uc002tvj.1 - 43 8030 c.7058delA c.(7057-7059)AATfs p.N2353fs NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 2353 Extracellular (Potential).|LDL-receptor class B 25. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) CACTTGAGCATTTTTCCCAGT 0.368 0.22 239 68 LRP1B 53353 broad.mit.edu 37 2 141819647 141819648 + Frame_Shift_Ins INS - T T HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:141819647_141819648insT uc002tvj.1 - 8 2180_2181 c.1208_1209insA c.(1207-1209)AATfs p.N403fs LRP1B_uc010fnl.1_Intron NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 403 Extracellular (Potential).|LDL-receptor class B 4. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) CAGTGTGTCTATTTTTTCCTTG 0.391 0.19 150 35 RIF1 55183 broad.mit.edu 37 2 152320713 152320715 + In_Frame_Del DEL AAG - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:152320713_152320715delAAG uc002txm.2 + 30 4809_4811 c.4679_4681delAAG c.(4678-4683)AAAGAA>AAA p.E1562del RIF1_uc002txl.2_In_Frame_Del_p.E1562del|RIF1_uc002txn.2_In_Frame_Del_p.E1562del|RIF1_uc002txo.2_In_Frame_Del_p.E1562del|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1562 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) TCGGAGGCAAAAGAAGAAGGTTC 0.404 0.36 46 26 CHN1 1123 broad.mit.edu 37 2 175742640 175742640 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:175742640delT uc002uji.2 - 6 1007 c.477delA c.(475-477)AAAfs p.K159fs CHN1_uc010zeq.1_Frame_Shift_Del_p.K159fs|CHN1_uc002ujj.2_Intron NM_001822 NP_001813 P15882 CHIN_HUMAN chimerin (chimaerin) 1 isoform a 159 regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction cytosol GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity ovary(2)|skin(1) 3 OV - Ovarian serous cystadenocarcinoma(117;0.226) CTGGCATATGTTTTTTGTATG 0.423 0.47 320 280 TTN 7273 broad.mit.edu 37 2 179425450 179425451 + Frame_Shift_Del DEL AG - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:179425450_179425451delAG uc010zfg.1 - 275 77928_77929 c.77704_77705delCT c.(77704-77706)CTTfs p.L25902fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.L19597fs|TTN_uc010zfi.1_Frame_Shift_Del_p.L19530fs|TTN_uc010zfj.1_Frame_Shift_Del_p.L19405fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 26829 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCCCCAGGAAAGAGAGCATTTC 0.480 0.24 64 20 TTN 7273 broad.mit.edu 37 2 179439852 179439852 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:179439852delT uc010zfg.1 - 275 63527 c.63303delA c.(63301-63303)AAAfs p.K21101fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.K14796fs|TTN_uc010zfi.1_Frame_Shift_Del_p.K14729fs|TTN_uc010zfj.1_Frame_Shift_Del_p.K14604fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 22028 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTTGGTCTCCTTTTTTCCATG 0.423 0.22 447 125 TTN 7273 broad.mit.edu 37 2 179597269 179597269 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:179597269delG uc010zfg.1 - 53 13011 c.12787delC c.(12787-12789)CTGfs p.L4263fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.L924fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 5190 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TAGAGTTCCAGGGAACTCTCT 0.438 0.23 297 91 CASP8 841 broad.mit.edu 37 2 202149793 202149794 + Frame_Shift_Del DEL AA - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:202149793_202149794delAA uc002uxr.1 + 9 1266_1267 c.1057_1058delAA c.(1057-1059)AAAfs p.K353fs CASP8_uc002uxp.1_Frame_Shift_Del_p.K370fs|CASP8_uc002uxq.1_Frame_Shift_Del_p.K338fs|CASP8_uc002uxt.1_Frame_Shift_Del_p.K412fs|CASP8_uc002uxu.1_RNA|CASP8_uc002uxw.1_Frame_Shift_Del_p.K338fs|CASP8_uc002uxy.1_Intron|CASP8_uc002uxx.1_Intron|CASP8_uc010ftf.2_Frame_Shift_Del_p.K269fs NM_033355 NP_203519 Q14790 CASP8_HUMAN caspase 8 isoform B precursor 353 activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor centrosome|cytosol|mitochondrial outer membrane cysteine-type endopeptidase activity|protein binding|protein binding upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1) 5 TGGAAAACCCAAAGTGTTTTTT 0.455 0.23 275 81 ALS2 57679 broad.mit.edu 37 2 202591522 202591522 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:202591522delG uc002uyo.2 - 18 3403 c.3047delC c.(3046-3048)CCTfs p.P1016fs ALS2_uc002uyp.3_Frame_Shift_Del_p.P1016fs|ALS2_uc010ftl.2_RNA NM_020919 NP_065970 Q96Q42 ALS2_HUMAN alsin isoform 1 1016 cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity skin(5)|lung(1)|breast(1) 7 ACTTCCATAAGGGGGGAGATC 0.463 0.23 342 100 TRPM8 79054 broad.mit.edu 37 2 234879010 234879010 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:234879010delC uc002vvh.2 + 17 2335 c.2295delC c.(2293-2295)CACfs p.H765fs TRPM8_uc010fyj.2_Intron NM_024080 NP_076985 Q7Z2W7 TRPM8_HUMAN transient receptor potential cation channel, 765 Helical; Name=3; (Potential). integral to membrane skin(4) 4 Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224) Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108) Menthol(DB00825) CGGTGCCACACCCCCCCGAGC 0.577 0.58 218 307 HDAC4 9759 broad.mit.edu 37 2 240002823 240002823 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr2:240002823delG uc002vyk.3 - 22 3495 c.2703delC c.(2701-2703)CCCfs p.P901fs HDAC4_uc010fyy.2_Frame_Shift_Del_p.P858fs NM_006037 NP_006028 P56524 HDAC4_HUMAN histone deacetylase 4 901 Histone deacetylase. B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent histone deacetylase complex|transcriptional repressor complex activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding breast(3)|skin(2)|ovary(1) 6 all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159) Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04) CGTCTCCCATGGGGGGGTCCA 0.602 0.51 33 34 OXSR1 9943 broad.mit.edu 37 3 38284237 38284237 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr3:38284237delC uc003chy.2 + 12 1420 c.1078delC c.(1078-1080)CCCfs p.P360fs OXSR1_uc010hhb.2_Frame_Shift_Del_p.P294fs NM_005109 NP_005100 O95747 OXSR1_HUMAN oxidative-stress responsive 1 360 intracellular protein kinase cascade|response to oxidative stress ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity skin(1) 1 KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738) CGTTTAGTCTCCCCGAGTGAA 0.338 0.35 77 41 ULK4 54986 broad.mit.edu 37 3 41860984 41860985 + Frame_Shift_Ins INS - T T HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr3:41860984_41860985insT uc003ckv.3 - 19 1979_1980 c.1778_1779insA c.(1777-1779)AAGfs p.K593fs ULK4_uc003ckw.2_Frame_Shift_Ins_p.K593fs NM_017886 NP_060356 Q96C45 ULK4_HUMAN unc-51-like kinase 4 593 ATP binding|protein serine/threonine kinase activity 0 KIRC - Kidney renal clear cell carcinoma(284;0.214) CTCTAGGGTTCTTTTTTTTTTC 0.450 0.25 93 31 CCR3 1232 broad.mit.edu 37 3 46307343 46307343 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr3:46307343delA uc003cpg.1 + 4 1237 c.694delA c.(694-696)AAAfs p.K232fs CCR3_uc003cpi.1_Frame_Shift_Del_p.K232fs|CCR3_uc003cpj.1_Frame_Shift_Del_p.K232fs|CCR3_uc003cpk.1_Frame_Shift_Del_p.K253fs|CCR3_uc010hjb.1_Frame_Shift_Del_p.K250fs|CCR3_uc003cpl.1_Frame_Shift_Del_p.K265fs NM_178329 NP_847899 P51677 CCR3_HUMAN CC chemokine receptor 3 isoform 1 232 Cytoplasmic (Potential). cell adhesion|cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cAMP nucleotide second messenger|inflammatory response|interspecies interaction between organisms|positive regulation of angiogenesis integral to plasma membrane ovary(3)|lung(3)|breast(1)|kidney(1) 8 BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216) 0.000 0.22 783 224 FLNB 2317 broad.mit.edu 37 3 58094909 58094909 + Frame_Shift_Del DEL G - - rs148679414 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr3:58094909delG uc003djj.2 + 14 2224 c.2059delG c.(2059-2061)GGGfs p.G687fs FLNB_uc010hne.2_Frame_Shift_Del_p.G687fs|FLNB_uc003djk.2_Frame_Shift_Del_p.G687fs|FLNB_uc010hnf.2_Frame_Shift_Del_p.G687fs|FLNB_uc003djl.2_Frame_Shift_Del_p.G518fs|FLNB_uc003djm.2_Frame_Shift_Del_p.G518fs NM_001457 NP_001448 O75369 FLNB_HUMAN filamin B isoform 2 687 Filamin 5. actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction cell cortex|integral to membrane|nucleus|sarcomere actin binding breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1) 19 BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898) TTTGCAGGATGGGGAAGGCCA 0.547 0.18 103 23 ROBO1 6091 broad.mit.edu 37 3 79639036 79639036 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr3:79639036delA uc003dqe.2 - 2 234 c.26delT c.(25-27)TTGfs p.L9fs NM_002941 NP_002932 Q9Y6N7 ROBO1_HUMAN roundabout 1 isoform a 9 activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway cell surface|cytoplasm|integral to plasma membrane axon guidance receptor activity|identical protein binding|LRR domain binding large_intestine(2) 2 Lung SC(41;0.0257)|Lung NSC(201;0.0439) LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274) TATCATGACCAAAAAAGGAAC 0.393 0.28 87 33 MYLK 4638 broad.mit.edu 37 3 123386003 123386003 + Frame_Shift_Del DEL G - - rs147227509 by1000genomes HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr3:123386003delG uc003ego.2 - 21 3966 c.3684delC c.(3682-3684)CCCfs p.P1228fs MYLK_uc010hrr.2_5'Flank|MYLK_uc011bjv.1_Frame_Shift_Del_p.P28fs|MYLK_uc011bjw.1_Frame_Shift_Del_p.P1228fs|MYLK_uc003egp.2_Frame_Shift_Del_p.P1159fs|MYLK_uc003egq.2_Frame_Shift_Del_p.P1228fs|MYLK_uc003egr.2_Frame_Shift_Del_p.P1159fs|MYLK_uc003egs.2_Frame_Shift_Del_p.P1052fs NM_053025 NP_444253 Q15746 MYLK_HUMAN myosin light chain kinase isoform 1 1228 Actin-binding (calcium/calmodulin- insensitive) (By similarity). aorta smooth muscle tissue morphogenesis|muscle contraction cytosol actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity ovary(6)|skin(2)|stomach(1) 9 Lung NSC(201;0.0496) GBM - Glioblastoma multiforme(114;0.0736) GAGGTGTCTTGGGGGCAGGTT 0.463 0.65 82 155 EIF4A2 1974 broad.mit.edu 37 3 186505300 186505302 + In_Frame_Del DEL AGA - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr3:186505300_186505302delAGA uc003fqs.2 + 9 965_967 c.926_928delAGA c.(925-930)CAGAAG>CAG p.K310del EIF4A2_uc003fqt.2_RNA|EIF4A2_uc003fqu.2_In_Frame_Del_p.K311del|EIF4A2_uc003fqv.2_In_Frame_Del_p.K215del|EIF4A2_uc003fqw.2_In_Frame_Del_p.K215del|EIF4A2_uc011bsb.1_In_Frame_Del_p.K183del|SNORA4_uc010hyx.1_5'Flank NM_001967 NP_001958 Q14240 IF4A2_HUMAN eukaryotic translation initiation factor 4A2 310 Helicase C-terminal. interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation cytosol|eukaryotic translation initiation factor 4F complex ATP binding|ATP-dependent helicase activity|protein binding|translation initiation factor activity ovary(2)|breast(2) 4 all_cancers(143;2.68e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;1.07e-20) GBM - Glioblastoma multiforme(93;0.0704) GACATGGACCAGAAGGAGAGAGA 0.394 0.52 16 17 RFC4 5984 broad.mit.edu 37 3 186507937 186507937 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr3:186507937delT uc003fqz.2 - 10 1213 c.990delA c.(988-990)AAAfs p.K330fs RFC4_uc011bsc.1_Frame_Shift_Del_p.K330fs NM_002916 NP_002907 P35249 RFC4_HUMAN replication factor C 4 330 cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|phosphatidylinositol-mediated signaling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair DNA replication factor C complex|nucleoplasm ATP binding|DNA clamp loader activity|protein binding breast(2)|upper_aerodigestive_tract(1)|ovary(1)|large_intestine(1) 5 all_cancers(143;2.92e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;7.41e-21) GBM - Glioblastoma multiforme(93;0.0739) TTACGGCAAGTTTTTCTGTGA 0.368 0.33 75 37 N4BP2 55728 broad.mit.edu 37 4 40123872 40123872 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr4:40123872delC uc003guy.3 + 9 4479 c.4141delC c.(4141-4143)CCCfs p.P1381fs N4BP2_uc010ifq.2_Frame_Shift_Del_p.P1301fs|N4BP2_uc010ifr.2_Frame_Shift_Del_p.P1301fs NM_018177 NP_060647 Q86UW6 N4BP2_HUMAN Nedd4 binding protein 2 1381 cytoplasm ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding lung(3)|breast(2)|kidney(2)|ovary(1) 8 ATTGGCATTACCCCCTGAACT 0.413 0.32 125 59 N4BP2 55728 broad.mit.edu 37 4 40144449 40144449 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr4:40144449delA uc003guy.3 + 15 5280 c.4942delA c.(4942-4944)AAAfs p.K1648fs N4BP2_uc010ifq.2_Frame_Shift_Del_p.K1568fs|N4BP2_uc010ifr.2_Frame_Shift_Del_p.K1551fs NM_018177 NP_060647 Q86UW6 N4BP2_HUMAN Nedd4 binding protein 2 1648 cytoplasm ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding lung(3)|breast(2)|kidney(2)|ovary(1) 8 TCGGATAGGGAAAAAAAATGT 0.398 0.21 134 36 LPHN3 23284 broad.mit.edu 37 4 62453049 62453049 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr4:62453049delG uc010ihh.2 + 2 333 c.160delG c.(160-162)GAAfs p.E54fs LPHN3_uc003hcq.3_Frame_Shift_Del_p.E54fs|LPHN3_uc010ihg.1_Frame_Shift_Del_p.E122fs NM_015236 NP_056051 Q9HAR2 LPHN3_HUMAN latrophilin 3 precursor 54 SUEL-type lectin.|Extracellular (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity|sugar binding lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1) 18 0.000 0.15 947 164 EPHA5 2044 broad.mit.edu 37 4 66286237 66286238 + Frame_Shift_Ins INS - T T HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr4:66286237_66286238insT uc003hcy.2 - 6 1641_1642 c.1448_1449insA c.(1447-1449)AACfs p.N483fs EPHA5_uc003hcx.2_Frame_Shift_Ins_p.N414fs|EPHA5_uc003hcz.2_Frame_Shift_Ins_p.N483fs|EPHA5_uc011cah.1_Frame_Shift_Ins_p.N483fs|EPHA5_uc011cai.1_Frame_Shift_Ins_p.N483fs|EPHA5_uc003hda.2_Frame_Shift_Ins_p.N483fs NM_004439 NP_004430 P54756 EPHA5_HUMAN ephrin receptor EphA5 isoform a precursor 483 Extracellular (Potential).|Fibronectin type-III 2. cAMP-mediated signaling|neuron development dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum ATP binding|transmembrane-ephrin receptor activity lung(19)|stomach(2)|ovary(2)|central_nervous_system(1) 24 AAGAGATGCTGTTTTTTGCAAT 0.347 0.17 40 8 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.51 25 26 BMPR1B 658 broad.mit.edu 37 4 96052545 96052545 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr4:96052545delT uc003htm.3 + 10 1232 c.958delT c.(958-960)TTTfs p.F320fs BMPR1B_uc010ilb.2_Frame_Shift_Del_p.F320fs|BMPR1B_uc003htn.3_Frame_Shift_Del_p.F320fs NM_001203 NP_001194 O00238 BMR1B_HUMAN bone morphogenetic protein receptor, type IB 320 Cytoplasmic (Potential).|Protein kinase. BMP signaling pathway|cartilage condensation|eye development|limb morphogenesis|ovarian cumulus expansion|positive regulation of bone mineralization|positive regulation of osteoblast differentiation receptor complex ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta receptor activity lung(4)|skin(2)|stomach(1)|breast(1) 8 Hepatocellular(203;0.114) OV - Ovarian serous cystadenocarcinoma(123;6.51e-07) CACAGAAATCTTTAGTACTCA 0.413 0.32 163 78 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 81 149 MAML3 55534 broad.mit.edu 37 4 140810957 140810957 + Frame_Shift_Del DEL G - - rs77951606 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr4:140810957delG uc003ihz.1 - 3 2373 c.1621delC c.(1621-1623)CAAfs p.Q541fs MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 541 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) TTAAAGGCTTGGGGGTACATC 0.428 0.28 419 160 FBXW7 55294 broad.mit.edu 37 4 153249361 153249361 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr4:153249361delT uc003ims.2 - 9 1566 c.1417delA c.(1417-1419)AGAfs p.R473fs FBXW7_uc011cii.1_Frame_Shift_Del_p.R473fs|FBXW7_uc003imt.2_Frame_Shift_Del_p.R473fs|FBXW7_uc011cih.1_Frame_Shift_Del_p.R297fs|FBXW7_uc003imq.2_Frame_Shift_Del_p.R393fs|FBXW7_uc003imr.2_Frame_Shift_Del_p.R355fs NM_033632 NP_361014 Q969H0 FBXW7_HUMAN F-box and WD repeat domain containing 7 isoform 473 WD 3. interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex protein binding|protein binding p.R473fs*4(3)|p.R473fs*25(2) haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1) 308 all_hematologic(180;0.093) Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067) TTCCCTTACCTTTTTTCATGA 0.418 0.31 149 66 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.97 24 841 NIPBL 25836 broad.mit.edu 37 5 36995756 36995756 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr5:36995756delC uc003jkl.3 + 11 3653 c.3154delC c.(3154-3156)CCCfs p.P1052fs NIPBL_uc003jkk.3_Frame_Shift_Del_p.P1052fs|NIPBL_uc003jkm.1_Frame_Shift_Del_p.P931fs NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 1052 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) AAAAGAATTACCCCCTGAACT 0.323 0.12 134 19 NIPBL 25836 broad.mit.edu 37 5 37049317 37049317 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr5:37049317delT uc003jkl.3 + 40 7367 c.6868delT c.(6868-6870)TTTfs p.F2290fs NIPBL_uc003jkk.3_Frame_Shift_Del_p.F2290fs|NIPBL_uc003jkn.2_5'Flank NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 2290 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) GCTTGAGGCATTTTTTCACAC 0.403 0.15 289 50 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.21 260 71 FBN2 2201 broad.mit.edu 37 5 127610311 127610311 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr5:127610311delC uc003kuu.2 - 60 8098 c.7659delG c.(7657-7659)GGGfs p.G2553fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 2553 EGF-like 43; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) TACAGGTAAACCCCCCCAGGG 0.423 0.42 164 121 ADAMTS19 171019 broad.mit.edu 37 5 128864325 128864325 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr5:128864325delG uc003kvb.1 + 6 1265 c.1265delG c.(1264-1266)TGGfs p.W422fs ADAMTS19_uc003kvc.1_RNA NM_133638 NP_598377 Q8TE59 ATS19_HUMAN ADAM metallopeptidase with thrombospondin type 1 422 Peptidase M12B. proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding ovary(5)|breast(2)|lung(1)|skin(1) 9 all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) OV - Ovarian serous cystadenocarcinoma(64;0.222) TCAACAAACTGGGGGGAAGAC 0.363 0.18 76 17 RAD50 10111 broad.mit.edu 37 5 131931451 131931452 + Frame_Shift_Ins INS - A A HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr5:131931451_131931452insA uc003kxi.2 + 13 2543_2544 c.2156_2157insA c.(2155-2157)CTAfs p.L719fs RAD50_uc003kxh.2_Frame_Shift_Ins_p.L580fs NM_005732 NP_005723 Q92878 RAD50_HUMAN RAD50 homolog isoform 1 719 Zinc-hook.|Potential. DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding lung(2)|ovary(1)|skin(1) 4 all_cancers(142;0.0368)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GAATCAGAGCTAAAAAAAAAGG 0.416 0.35 83 44 CDC25C 995 broad.mit.edu 37 5 137627690 137627690 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr5:137627690delT uc003lcp.1 - 8 1002 c.731delA c.(730-732)AAGfs p.K244fs CDC25C_uc003lcq.1_Frame_Shift_Del_p.K171fs|CDC25C_uc003lcr.1_Frame_Shift_Del_p.K244fs|CDC25C_uc011cyp.1_Frame_Shift_Del_p.K261fs|CDC25C_uc003lcs.1_Frame_Shift_Del_p.K322fs NM_001790 NP_001781 P30307 MPIP3_HUMAN cell division cycle 25C isoform a 244 cell cycle checkpoint|cell division|cell proliferation|DNA replication|G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis|traversing start control point of mitotic cell cycle cytosol|nucleoplasm protein tyrosine phosphatase activity|WW domain binding lung(3) 3 KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592) AGAAAAATACTTTTTTTTAAC 0.388 0.11 248 32 HMMR 3161 broad.mit.edu 37 5 162917425 162917426 + Frame_Shift_Ins INS - A A HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr5:162917425_162917426insA uc003lzf.2 + 17 2171_2172 c.1989_1990insA c.(1987-1992)GCTAAAfs p.A663fs HMMR_uc003lzh.2_Frame_Shift_Ins_p.A664fs|HMMR_uc003lzg.2_Frame_Shift_Ins_p.A648fs|HMMR_uc011dem.1_Frame_Shift_Ins_p.A577fs|uc003lzi.2_Intron NM_012484 NP_036616 O75330 HMMR_HUMAN hyaluronan-mediated motility receptor isoform b 663_664 Hyaluronic acid-binding (Potential). cell surface|cytoplasm hyaluronic acid binding 0 Renal(175;0.000281) Medulloblastoma(196;0.00853)|all_neural(177;0.0408) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848) GTCAGCTTGCTAAAAAAAAACA 0.307 0.22 47 13 RANBP9 10048 broad.mit.edu 37 6 13632610 13632610 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr6:13632610delT uc003nbb.2 - 12 1998 c.1939delA c.(1939-1941)ATGfs p.M647fs RANBP9_uc003nba.2_Frame_Shift_Del_p.M306fs NM_005493 NP_005484 Q96S59 RANB9_HUMAN RAN binding protein 9 647 Interaction with FMR1. axon guidance|microtubule nucleation|protein complex assembly cytosol|microtubule associated complex|nucleus Ran GTPase binding lung(1)|skin(1) 2 Breast(50;0.00669)|Ovarian(93;0.0634) all_hematologic(90;0.117) Epithelial(50;0.223) ACCTTCAACATTTTTTTGTTT 0.378 0.25 166 56 MAPK14 1432 broad.mit.edu 37 6 36068006 36068006 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr6:36068006delC uc003olp.2 + 9 1205 c.724delC c.(724-726)CCCfs p.P242fs MAPK14_uc003olo.2_Intron|MAPK14_uc003olq.2_Intron|MAPK14_uc003olr.2_Intron|MAPK14_uc011dti.1_Intron NM_001315 NP_001306 Q16539 MK14_HUMAN mitogen-activated protein kinase 14 isoform 1 242 Protein kinase. activation of MAPK activity|cellular component movement|cellular response to ionizing radiation|chemotaxis|innate immune response|mRNA metabolic process|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of muscle cell differentiation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|signal transduction in response to DNA damage|stress-activated MAPK cascade|stress-induced premature senescence|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|MAP kinase activity|MAP kinase kinase activity|protein binding ovary(2)|stomach(1)|lung(1)|central_nervous_system(1)|skin(1) 6 GACAGGAACACCCCCCGCTTA 0.428 0.21 163 43 STK38 11329 broad.mit.edu 37 6 36463593 36463593 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr6:36463593delC uc003omg.2 - 13 1954 c.1366delG c.(1366-1368)GCAfs p.A456fs STK38_uc003omh.2_Frame_Shift_Del_p.A456fs|STK38_uc003omi.2_Frame_Shift_Del_p.A456fs NM_007271 NP_009202 Q15208 STK38_HUMAN serine/threonine kinase 38 456 intracellular protein kinase cascade|negative regulation of MAP kinase activity cytoplasm|MLL5-L complex ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1) 6 GAAGGTATTGCCCCCCTTGCA 0.453 0.23 314 96 RUNX2 860 broad.mit.edu 37 6 45390355 45390355 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr6:45390355delC uc011dvx.1 + 3 294 c.84delC c.(82-84)AGCfs p.S28fs RUNX2_uc011dvy.1_Frame_Shift_Del_p.S28fs|RUNX2_uc003oxt.2_Frame_Shift_Del_p.S14fs NM_001024630 NP_001019801 Q13950 RUNX2_HUMAN runt-related transcription factor 2 isoform a 28 negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent nucleus ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity ovary(2)|skin(1) 3 GGCGCTTCAGCCCCCCCTCCA 0.418 0.18 46 10 PKHD1 5314 broad.mit.edu 37 6 51890014 51890015 + Frame_Shift_Ins INS - A A HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr6:51890014_51890015insA uc003pah.1 - 32 4869_4870 c.4593_4594insT c.(4591-4596)TTTAATfs p.F1531fs PKHD1_uc003pai.2_Frame_Shift_Ins_p.F1531fs NM_138694 NP_619639 P08F94 PKHD1_HUMAN fibrocystin isoform 1 1531_1532 Extracellular (Potential).|IPT/TIG 10. cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body protein binding|receptor activity lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1) 44 Lung NSC(77;0.0605) TGGCTTGCATTAAAAAAAGTTA 0.460 0.19 297 68 AKAP12 9590 broad.mit.edu 37 6 151671833 151671833 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr6:151671833delA uc011eep.1 + 4 2547 c.2307delA c.(2305-2307)AGAfs p.R769fs AKAP12_uc003qoe.2_Frame_Shift_Del_p.R769fs|AKAP12_uc003qof.2_Frame_Shift_Del_p.R671fs|AKAP12_uc010kim.2_Intron|AKAP12_uc003qog.2_Frame_Shift_Del_p.R664fs NM_005100 NP_005091 Q02952 AKA12_HUMAN A kinase (PRKA) anchor protein 12 isoform 1 769 AKAP 2. G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting cell cortex|cytoskeleton|plasma membrane adenylate cyclase binding|protein kinase A binding large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1) 8 Ovarian(120;0.125) BRCA - Breast invasive adenocarcinoma(37;0.175) OV - Ovarian serous cystadenocarcinoma(155;2.98e-11) TCACGCCAAGAAAAAAATCAA 0.507 0.51 20 21 MLLT4 4301 broad.mit.edu 37 6 168272901 168272901 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr6:168272901delA uc003qwd.2 + 4 561 c.419delA c.(418-420)CAAfs p.Q140fs MLLT4_uc003qwb.1_Frame_Shift_Del_p.Q140fs|MLLT4_uc003qwc.1_Frame_Shift_Del_p.Q141fs NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 141 adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) 0.000 0.15 235 42 TBP 6908 broad.mit.edu 37 6 170871004 170871005 + In_Frame_Ins INS - CAA CAA HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr6:170871004_170871005insCAA uc003qxt.2 + 3 412_413 c.180_181insCAA c.(178-183)insCAA p.95_96insQ TBP_uc003qxu.2_In_Frame_Ins_p.95_96insQ|TBP_uc011ehf.1_In_Frame_Ins_p.75_76insQ|TBP_uc011ehg.1_In_Frame_Ins_p.95_96insQ NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 95_96 cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) Ggcagcagcagcaacaacaaca 0.198 0.23 44 13 CLK2P 1197 broad.mit.edu 37 7 23624938 23624938 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr7:23624938delA uc003swk.2 - 1 1209 c.559delT c.(559-561)TACfs p.Y187fs NR_002711 SubName: Full=cDNA FLJ61616, highly similar to Dual specificity protein kinase CLK2 (EC 2.7.12.1); SubName: Full=CDC-like kinase 2, isoform CRA_c; SubName: Full=Putative uncharacterized protein CLK2; 0 CGACCCCGGTAAAAATATTTC 0.512 0.18 177 40 CDK13 8621 broad.mit.edu 37 7 40134547 40134552 + In_Frame_Del DEL GGCAGA - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr7:40134547_40134552delGGCAGA uc003thh.3 + 14 4789_4794 c.4507_4512delGGCAGA c.(4507-4512)GGCAGAdel p.GR1507del CDK13_uc003thi.3_In_Frame_Del_p.GR1447del|CDK13_uc003thj.2_In_Frame_Del_p.GR558del|CDK13_uc003thk.2_In_Frame_Del_p.GR440del NM_003718 NP_003709 Q14004 CDK13_HUMAN cell division cycle 2-like 5 isoform 1 1507_1508 alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity lung(2)|skin(2)|ovary(1) 5 CACATCAACTGGCAGAGGCAGAGGCA 0.485 0.20 149 37 IKZF1 10320 broad.mit.edu 37 7 50467664 50467666 + In_Frame_Del DEL AGA - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr7:50467664_50467666delAGA uc003tow.3 + 9 1067_1069 c.899_901delAGA c.(898-903)GAGAAG>GAG p.K301del IKZF1_uc003tox.3_In_Frame_Del_p.K259del|IKZF1_uc003toy.3_In_Frame_Del_p.K259del|IKZF1_uc011kck.1_In_Frame_Del_p.K214del|IKZF1_uc003toz.3_In_Frame_Del_p.K271del|IKZF1_uc010kyx.2_In_Frame_Del_p.K41del|IKZF1_uc003tpa.3_In_Frame_Del_p.K43del NM_006060 NP_006051 Q13422 IKZF1_HUMAN zinc finger protein, subfamily 1A, 1 (Ikaros) 301 cell cycle|chromatin modification|mesoderm development cytoplasm|nucleus zinc ion binding haematopoietic_and_lymphoid_tissue(147)|lung(1) 148 Glioma(55;0.08)|all_neural(89;0.245) Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07) 0.000 0.45 297 244 DLX6 1750 broad.mit.edu 37 7 96635364 96635369 + In_Frame_Del DEL GCAGCA - - rs34325324 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr7:96635364_96635369delGCAGCA uc003uom.2 + 1 75_80 c.75_80delGCAGCA c.(73-81)GGGCAGCAG>GGG p.QQ30del DLX6AS_uc003uok.2_5'Flank|DLX6AS_uc003uol.2_Intron|DLX6AS_uc010lfo.1_Intron NM_005222 NP_005213 P56179 DLX6_HUMAN distal-less homeobox 6 Error:Variant_position_missing_in_P56179_after_alignment nervous system development|skeletal system development nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity ovary(2) 2 all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858) TGGAGTTCGGgcagcagcagcagcag 0.306 0.44 9 7 SRPK2 6733 broad.mit.edu 37 7 104808539 104808539 + Frame_Shift_Del DEL C - - rs56666353 byFrequency;by1000genomes HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr7:104808539delC uc003vct.2 - 4 496 c.309delG c.(307-309)GGGfs p.G103fs SRPK2_uc003vcu.2_Frame_Shift_Del_p.G103fs|SRPK2_uc003vcv.2_Frame_Shift_Del_p.G114fs|SRPK2_uc003vcw.1_Frame_Shift_Del_p.G103fs NM_182691 NP_872633 P78362 SRPK2_HUMAN serine/arginine-rich protein-specific kinase 2 103 Protein kinase. angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly cytoplasm|nucleolus 14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1) 6 CAAATCTTTTCCCCCTAAAAG 0.259 0.25 50 17 ING3 54556 broad.mit.edu 37 7 120604841 120604841 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr7:120604841delA uc003vjn.2 + 5 447 c.313delA c.(313-315)AAAfs p.K105fs ING3_uc003vjo.2_Intron|ING3_uc003vjp.2_Frame_Shift_Del_p.K105fs|ING3_uc011kns.1_Frame_Shift_Del_p.K90fs NM_019071 NP_061944 Q9NXR8 ING3_HUMAN inhibitor of growth family, member 3 isoform 1 105 histone H2A acetylation|histone H4 acetylation|positive regulation of apoptosis|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent NuA4 histone acetyltransferase complex|Piccolo NuA4 histone acetyltransferase complex zinc ion binding ovary(1) 1 all_neural(327;0.117) 0.000 0.23 229 69 FLNC 2318 broad.mit.edu 37 7 128482323 128482324 + Frame_Shift_Ins INS - A A HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr7:128482323_128482324insA uc003vnz.3 + 14 2369_2370 c.2160_2161insA c.(2158-2163)CCCAACfs p.P720fs FLNC_uc003voa.3_Frame_Shift_Ins_p.P720fs NM_001458 NP_001449 Q14315 FLNC_HUMAN gamma filamin isoform a 720_721 Filamin 5. cell junction assembly cytoskeleton|cytosol|plasma membrane|sarcomere actin binding breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1) 12 AGGTGATCCCCAACGGCGACGG 0.614 0.46 169 142 KIAA1549 57670 broad.mit.edu 37 7 138603524 138603524 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr7:138603524delA uc011kql.1 - 2 897 c.848delT c.(847-849)TTAfs p.L283fs KIAA1549_uc003vuk.3_Frame_Shift_Del_p.L233fs|KIAA1549_uc011kqj.1_Frame_Shift_Del_p.L283fs NM_020910 NP_065961 Q9HCM3 K1549_HUMAN hypothetical protein LOC57670 isoform 1 283 integral to membrane KIAA1549/BRAF(229) central_nervous_system(229)|pancreas(1) 230 CCGGGAGCTTAAAAAAAGGGT 0.517 0.19 142 34 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 2 16 KCNH2 3757 broad.mit.edu 37 7 150644561 150644561 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr7:150644561delC uc003wic.2 - 13 3020 c.3007delG c.(3007-3009)GACfs p.D1003fs KCNH2_uc003wib.2_Frame_Shift_Del_p.D663fs|KCNH2_uc011kux.1_Frame_Shift_Del_p.D907fs NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 1003 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) 0.000 0.18 327 72 KCNH2 3757 broad.mit.edu 37 7 150656679 150656679 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr7:150656679delG uc003wic.2 - 3 466 c.453delC c.(451-453)CCCfs p.P151fs KCNH2_uc011kux.1_Frame_Shift_Del_p.P55fs|KCNH2_uc003wie.2_Frame_Shift_Del_p.P151fs NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 151 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) GCCAGCTGGTGGGGGGGCCCC 0.587 0.16 62 12 MLL3 58508 broad.mit.edu 37 7 152132814 152132815 + Frame_Shift_Ins INS - G G HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr7:152132814_152132815insG uc003wla.2 - 1 276_277 c.57_58insC c.(55-60)CCCGAGfs p.P19fs FABP5L3_uc003wlb.2_5'Flank NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 19_20 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) 0.000 0.26 95 33 TNFRSF10B 8795 broad.mit.edu 37 8 22880255 22880257 + In_Frame_Del DEL TCT - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr8:22880255_22880257delTCT uc003xcu.2 - 9 1543_1545 c.1250_1252delAGA c.(1249-1254)AAGATT>ATT p.K417del TNFRSF10B_uc003xcs.1_In_Frame_Del_p.K182del|TNFRSF10B_uc003xct.2_In_Frame_Del_p.K388del|TNFRSF10B_uc011kzq.1_In_Frame_Del_p.K237del|TNFRSF10B_uc003xcv.2_In_Frame_Del_p.K315del NM_003842 NP_003833 O14763 TR10B_HUMAN tumor necrosis factor receptor superfamily, 417 Death.|Cytoplasmic (Potential). activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cell surface receptor linked signaling pathway|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|positive regulation of I-kappaB kinase/NF-kappaB cascade plasma membrane caspase activator activity|receptor activity|TRAIL binding 0 Prostate(55;0.0421)|Breast(100;0.067) Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703) TGGTCCTCAATCTTCTGCTTGGC 0.498 0.30 421 179 IKBKB 3551 broad.mit.edu 37 8 42129688 42129688 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr8:42129688delG uc003xow.1 + 2 247 c.70delG c.(70-72)GGGfs p.G24fs IKBKB_uc003xov.2_Frame_Shift_Del_p.G24fs|IKBKB_uc010lxh.1_Frame_Shift_Del_p.R13fs|IKBKB_uc011lco.1_RNA|IKBKB_uc010lxj.1_5'UTR|IKBKB_uc003xox.1_5'UTR|IKBKB_uc011lcp.1_RNA|IKBKB_uc011lcq.1_Intron|IKBKB_uc010lxi.1_RNA|IKBKB_uc011lcr.1_5'UTR NM_001556 NP_001547 O14920 IKKB_HUMAN inhibitor of nuclear factor kappa B kinase beta 24 ATP (By similarity).|Protein kinase. anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft ATP binding|identical protein binding|IkappaB kinase activity breast(3)|ovary(2)|lung(1)|skin(1) 7 all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211) all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954) BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264) Arsenic trioxide(DB01169)|Auranofin(DB00995) CCTTGGGACAGGGGGATTTGG 0.562 0.31 11 5 TGS1 96764 broad.mit.edu 37 8 56725621 56725623 + In_Frame_Del DEL AAG - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr8:56725621_56725623delAAG uc003xsj.3 + 12 2770_2772 c.2383_2385delAAG c.(2383-2385)AAGdel p.K796del TGS1_uc010lyh.2_In_Frame_Del_p.R623del NM_024831 NP_079107 Q96RS0 TGS1_HUMAN trimethylguanosine synthase homolog 796 Sufficient for catalytic activity. cellular lipid metabolic process|ncRNA metabolic process|regulation of transcription, DNA-dependent|RNA capping|spliceosomal snRNP assembly|transcription, DNA-dependent Cajal body|cytosol RNA trimethylguanosine synthase activity ovary(1)|lung(1)|breast(1) 3 all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147) Epithelial(17;0.00027)|all cancers(17;0.00251) CAGACTTTCTAAGAAGATCACTA 0.310 0.32 60 28 NBN 4683 broad.mit.edu 37 8 90967512 90967512 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr8:90967512delT uc003yej.1 - 10 1506 c.1396delA c.(1396-1398)AGGfs p.R466fs NBN_uc003yei.1_Frame_Shift_Del_p.R384fs|NBN_uc011lgb.1_Frame_Shift_Del_p.R466fs NM_002485 NP_002476 O60934 NBN_HUMAN nibrin 466 Nuclear localization signal. KR->AA: Blocks the association with KPNA2, and reduces nuclear foci formation in response to ionizing radiation. cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm protein N-terminus binding|transcription factor binding central_nervous_system(3)|kidney(3)|lung(1) 7 BRCA - Breast invasive adenocarcinoma(11;0.0344) AAAACAGACCTTTTTTTGGTA 0.338 0.24 187 59 VPS13B 157680 broad.mit.edu 37 8 100711825 100711825 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr8:100711825delT uc003yiv.2 + 36 6305 c.6194delT c.(6193-6195)CTTfs p.L2065fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.L2040fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 2065 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) CAGATAAACCTTTTTTTAAAG 0.363 0.20 131 33 TRIB1 10221 broad.mit.edu 37 8 126443309 126443309 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr8:126443309delC uc003yrx.2 + 1 747 c.165delC c.(163-165)AGCfs p.S55fs TRIB1_uc011lis.1_5'Flank|TRIB1_uc010mdn.2_5'Flank NM_025195 NP_079471 Q96RU8 TRIB1_HUMAN G-protein-coupled receptor induced protein 55 Protein kinase. JNK cascade|negative regulation of lipopolysaccharide-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|regulation of MAP kinase activity|response to lipopolysaccharide cytoplasm|nucleus ATP binding|mitogen-activated protein kinase kinase binding|protein kinase activity|protein kinase inhibitor activity|transcription factor binding|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity lung(1) 1 all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108) STAD - Stomach adenocarcinoma(47;0.000918) 0.000 0.28 376 143 MAPK15 225689 broad.mit.edu 37 8 144803823 144803823 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr8:144803823delC uc003yzj.2 + 12 1350 c.1309delC c.(1309-1311)CCCfs p.P437fs NM_139021 NP_620590 Q8TD08 MK15_HUMAN mitogen-activated protein kinase 15 437 protein autophosphorylation extracellular region ATP binding|MAP kinase activity|SH3 domain binding lung(2) 2 all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146) 0.000 0.28 1110 426 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.62 350 561 TRPM6 140803 broad.mit.edu 37 9 77354880 77354880 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr9:77354880delA uc004ajl.1 - 34 5484 c.5246delT c.(5245-5247)TTAfs p.L1749fs TRPM6_uc004ajk.1_Frame_Shift_Del_p.L1744fs|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Frame_Shift_Del_p.L700fs|TRPM6_uc010mpd.1_Frame_Shift_Del_p.L582fs|TRPM6_uc010mpe.1_Frame_Shift_Del_p.L296fs|TRPM6_uc004ajj.1_Frame_Shift_Del_p.L705fs NM_017662 NP_060132 Q9BX84 TRPM6_HUMAN transient receptor potential cation channel, 1749 Cytoplasmic (Potential). response to toxin integral to membrane ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1) 8 ATCAAGGTTTAAAGGGGAACT 0.483 0.31 187 83 PTCH1 5727 broad.mit.edu 37 9 98209617 98209617 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr9:98209617delG uc004avk.3 - 23 4109 c.3921delC c.(3919-3921)CCCfs p.P1307fs PTCH1_uc010mrn.2_Frame_Shift_Del_p.P99fs|PTCH1_uc010mro.2_Frame_Shift_Del_p.P1156fs|PTCH1_uc010mrp.2_Frame_Shift_Del_p.P1156fs|PTCH1_uc010mrq.2_Frame_Shift_Del_p.P1156fs|PTCH1_uc004avl.3_Frame_Shift_Del_p.P1156fs|PTCH1_uc010mrr.2_Frame_Shift_Del_p.P1241fs|PTCH1_uc004avm.3_Frame_Shift_Del_p.P1306fs NM_000264 NP_000255 Q13635 PTC1_HUMAN patched isoform L 1307 Cytoplasmic (Potential). embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway integral to plasma membrane hedgehog receptor activity skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1) 379 Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136) 0.000 0.72 169 425 GRIN3A 116443 broad.mit.edu 37 9 104432865 104432865 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr9:104432865delT uc004bbp.1 - 3 2430 c.1829delA c.(1828-1830)AATfs p.N610fs GRIN3A_uc004bbq.1_Frame_Shift_Del_p.N610fs NM_133445 NP_597702 Q8TCU5 NMD3A_HUMAN glutamate receptor, ionotropic, 610 Extracellular (Potential). response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1) 7 Acute lymphoblastic leukemia(62;0.0568) Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740) 0.000 0.20 501 129 ADARB2 105 broad.mit.edu 37 10 1230936 1230936 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr10:1230936delG uc009xhq.2 - 9 2282 c.1908delC c.(1906-1908)CCCfs p.P636fs ADARB2_uc009xhp.2_Frame_Shift_Del_p.P20fs|ADARB2_uc001igl.3_5'UTR|ADARB2_uc001igm.3_Frame_Shift_Del_p.P145fs NM_018702 NP_061172 Q9NS39 RED2_HUMAN adenosine deaminase, RNA-specific, B2 636 A to I editase. mRNA processing mitochondrion|nucleus adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding large_intestine(2)|central_nervous_system(1) 3 all_epithelial(10;0.059)|Colorectal(49;0.0815) all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165) 0.000 0.12 2187 296 CUBN 8029 broad.mit.edu 37 10 17165610 17165610 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr10:17165610delA uc001ioo.2 - 5 518 c.466delT c.(466-468)TGTfs p.C156fs NM_001081 NP_001072 O60494 CUBN_HUMAN cubilin precursor 156 EGF-like 1. cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1) 19 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) GGACAGATACAAAAAAAGGAA 0.438 0.17 96 20 MASTL 84930 broad.mit.edu 37 10 27459056 27459056 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr10:27459056delA uc001itm.2 + 8 1807 c.1168delA c.(1168-1170)AAAfs p.K390fs MASTL_uc001itl.2_Frame_Shift_Del_p.K390fs|MASTL_uc009xkw.1_Frame_Shift_Del_p.K390fs|MASTL_uc009xkx.1_RNA NM_032844 NP_116233 Q96GX5 GWL_HUMAN microtubule associated serine/threonine 390 Protein kinase. cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus centrosome|cleavage furrow|nucleus ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity p.C392fs*17(1) stomach(1)|ovary(1)|lung(1) 3 AAACCTTGCTAAAAAATGCTT 0.418 0.26 90 31 ERCC6 2074 broad.mit.edu 37 10 50732732 50732732 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr10:50732732delA uc001jhs.3 - 5 898 c.744delT c.(742-744)TTTfs p.F248fs PGBD3_uc001jht.2_5'Flank|PGBD3_uc009xoe.2_Frame_Shift_Del_p.F248fs|PGBD3_uc001jhu.2_Frame_Shift_Del_p.F248fs NM_000124 NP_000115 Q03468 ERCC6_HUMAN excision repair cross-complementing rodent 248 base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair nucleolus|soluble fraction|transcription elongation factor complex ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1) 16 TCTGGGTACCAAAAGGTGTCA 0.498 0.23 251 77 CAMK2G 818 broad.mit.edu 37 10 75576686 75576686 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr10:75576686delA uc001jvv.1 - 19 1633 c.1509delT c.(1507-1509)TTTfs p.F503fs CAMK2G_uc001jvm.1_Intron|CAMK2G_uc001jvo.1_Intron|CAMK2G_uc001jvq.1_Intron|CAMK2G_uc001jvr.1_Intron|CAMK2G_uc001jvp.1_Intron|CAMK2G_uc001jvs.1_Intron|CAMK2G_uc001jvt.1_Intron|CAMK2G_uc001jvu.1_Intron|CAMK2G_uc009xrp.1_Intron NM_172171 NP_751911 Q13555 KCC2G_HUMAN calcium/calmodulin-dependent protein kinase II Error:Variant_position_missing_in_Q13555_after_alignment insulin secretion|interferon-gamma-mediated signaling pathway|synaptic transmission calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane ATP binding|calcium-dependent protein serine/threonine phosphatase activity|calmodulin binding|calmodulin-dependent protein kinase activity lung(1)|stomach(1) 2 Prostate(51;0.0112) CAAATAAGGGAAAAGTGGGCA 0.537 0.26 54 19 MYST4 23522 broad.mit.edu 37 10 76744954 76744954 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr10:76744954delA uc001jwn.1 + 12 2983 c.2490delA c.(2488-2490)ACAfs p.T830fs MYST4_uc001jwm.1_Frame_Shift_Del_p.T538fs|MYST4_uc001jwo.1_Frame_Shift_Del_p.T538fs|MYST4_uc001jwp.1_Frame_Shift_Del_p.T647fs NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 830 Catalytic.|Interaction with BRPF1. histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) ATGTCCTTACAAAAAATGATG 0.368 0.27 194 70 PTEN 5728 broad.mit.edu 37 10 89624242 89624243 + Frame_Shift_Del DEL AA - - rs121913290 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr10:89624242_89624243delAA uc001kfb.2 + 2 1047_1048 c.16_17delAA c.(16-18)AAAfs p.K6fs KILLIN_uc009xti.2_5'Flank NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 6 activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.?(13)|p.0?(12)|p.K6fs*4(10)|p.K6I(1)|p.K6N(1)|p.K6R(1)|p.A3fs*14(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) AGCCATCATCAAAGAGATCGTT 0.485 0.49 97 95 PTEN 5728 broad.mit.edu 37 10 89720712 89720712 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr10:89720712delA uc001kfb.2 + 9 1894 c.863delA c.(862-864)GAAfs p.E288fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 288 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.E288fs*3(6)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.E288*(2)|p.G165_*404del(1)|p.S287fs*1(1)|p.G165_K342del(1)|p.E288fs*8(1)|p.S287fs*8(1)|p.W274_F341del(1)|p.E288K(1)|p.E288fs*9(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GAAACCTCAGAAAAAGTAGAA 0.299 0.42 102 74 FAS 355 broad.mit.edu 37 10 90768708 90768708 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr10:90768708delT uc001kfr.2 + 4 743 c.397delT c.(397-399)TTTfs p.F133fs FAS_uc010qna.1_RNA|FAS_uc001kfs.2_Frame_Shift_Del_p.F133fs|FAS_uc001kft.2_Frame_Shift_Del_p.F133fs|FAS_uc010qnb.1_Intron|FAS_uc010qnc.1_Intron|FAS_uc001kfw.2_Intron|FAS_uc010qnd.1_Intron|FAS_uc010qne.1_Intron|FAS_uc009xtp.2_RNA NM_000043 NP_000034 P25445 TNR6_HUMAN tumor necrosis factor receptor superfamily, 133 TNFR-Cys 3.|Extracellular (Potential). activation of caspase activity|activation of pro-apoptotic gene products|anti-apoptosis|cellular response to mechanical stimulus|positive regulation of necrotic cell death cytosol|extracellular region|integral to membrane|soluble fraction identical protein binding|kinase binding upper_aerodigestive_tract(1)|breast(1) 2 Colorectal(252;0.0161) Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193) TAAACCAAACTTTTTTTGTAA 0.368 0.20 194 50 EIF3A 8661 broad.mit.edu 37 10 120797782 120797783 + Frame_Shift_Ins INS - TC TC HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr10:120797782_120797783insTC uc001ldu.2 - 20 3841_3842 c.3695_3696insGA c.(3694-3696)GATfs p.D1232fs EIF3A_uc010qsu.1_Frame_Shift_Ins_p.D1198fs|EIF3A_uc009xzg.1_Frame_Shift_Ins_p.D271fs NM_003750 NP_003741 Q14152 EIF3A_HUMAN eukaryotic translation initiation factor 3, 1232 Asp-rich. formation of translation initiation complex cytosol|eukaryotic translation initiation factor 3 complex protein binding|structural molecule activity|translation initiation factor activity 0 Lung NSC(174;0.094)|all_lung(145;0.123) all cancers(201;0.0236) CTCGATCCACAtctctctctct 0.149 0.20 455 113 CCKBR 887 broad.mit.edu 37 11 6292451 6292451 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr11:6292451delT uc001mcp.2 + 5 1215 c.1022delT c.(1021-1023)CTTfs p.L341fs CCKBR_uc001mcq.2_Frame_Shift_Del_p.L269fs|CCKBR_uc001mcr.2_Frame_Shift_Del_p.L341fs|CCKBR_uc001mcs.2_Frame_Shift_Del_p.L410fs|CCKBR_uc001mct.1_RNA NM_176875 NP_795344 P32239 GASR_HUMAN cholecystokinin B receptor 341 Helical; Name=6; (Potential). activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception 1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding lung(5)|ovary(2)|breast(1) 8 Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029) Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139) Pentagastrin(DB00183) 0.000 0.23 1679 515 PIK3C2A 5286 broad.mit.edu 37 11 17190572 17190573 + Frame_Shift_Ins INS - T T HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr11:17190572_17190573insT uc001mmq.3 - 1 782_783 c.716_717insA c.(715-717)AATfs p.N239fs PIK3C2A_uc009ygu.1_Intron|PIK3C2A_uc010rcw.1_Intron|PIK3C2A_uc001mmr.3_RNA|PIK3C2A_uc010rcx.1_Frame_Shift_Ins_p.N239fs|PIK3C2A_uc009ygv.1_Frame_Shift_Ins_p.N239fs NM_002645 NP_002636 O00443 P3C2A_HUMAN phosphoinositide-3-kinase, class 2 alpha 239 cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity lung(4)|central_nervous_system(4)|stomach(1)|ovary(1) 10 Phosphatidylserine(DB00144) TTGCTTTCCCATTTTTTAAAAA 0.361 0.22 338 98 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.76 5 16 MRE11A 4361 broad.mit.edu 37 11 94189473 94189473 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr11:94189473delT uc001peu.2 - 14 1721 c.1532delA c.(1531-1533)AATfs p.N511fs MRE11A_uc001pev.2_Frame_Shift_Del_p.N511fs|MRE11A_uc009ywj.2_Frame_Shift_Del_p.N514fs NM_005591 NP_005582 P49959 MRE11_HUMAN meiotic recombination 11 homolog A isoform 1 511 DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase Mre11 complex|nucleoplasm 3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity breast(4)|lung(1) 5 Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824) TTCATTAGTATTTTTTTGTCT 0.328 0.37 93 54 MRE11A 4361 broad.mit.edu 37 11 94203691 94203691 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr11:94203691delA uc001peu.2 - 9 1152 c.963delT c.(961-963)TTTfs p.F321fs MRE11A_uc001pev.2_Frame_Shift_Del_p.F321fs|MRE11A_uc009ywj.2_Frame_Shift_Del_p.F324fs NM_005591 NP_005582 P49959 MRE11_HUMAN meiotic recombination 11 homolog A isoform 1 321 DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase Mre11 complex|nucleoplasm 3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity breast(4)|lung(1) 5 Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824) TATCTGGGTTAAAAATGTCTG 0.353 0.22 173 50 MAML2 84441 broad.mit.edu 37 11 95825203 95825204 + In_Frame_Ins INS - TGC TGC rs149006316 by1000genomes HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr11:95825203_95825204insTGC uc001pfw.1 - 2 3276_3277 c.1991_1992insGCA c.(1990-1992)CAA>CAGCAA p.664_664Q>QQ NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 664 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) aagatggttgttgctgctgctg 0.178 0.29 518 208 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 555 245 NPAT 4863 broad.mit.edu 37 11 108056136 108056136 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr11:108056136delA uc001pjz.3 - 9 914 c.812delT c.(811-813)TTAfs p.L271fs NPAT_uc001pka.2_Frame_Shift_Del_p.L66fs NM_002519 NP_002510 Q14207 NPAT_HUMAN nuclear protein, ataxia-telangiectasia locus 271 Mediates transcriptional activation.|Interaction with MIZF. positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle Cajal body protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity ovary(2) 2 all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116) TTACCTAGTTAAAAATTTATT 0.264 0.22 81 23 NCAM1 4684 broad.mit.edu 37 11 113105789 113105790 + Frame_Shift_Ins INS - A A rs141690701 by1000genomes HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr11:113105789_113105790insA uc009yyq.1 + 15 2146_2147 c.1452_1453insA c.(1450-1455)CTGAAGfs p.L484fs NM_001076682 NP_001070150 P13591 NCAM1_HUMAN neural cell adhesion molecule 1 isoform 3 576_577 Extracellular (Potential).|Fibronectin type-III 1. axon guidance|interferon-gamma-mediated signaling pathway anchored to membrane|extracellular region|Golgi membrane|integral to membrane ovary(1) 1 all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207) BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212) TCGTGGGCCTGAAGCCCGAAAC 0.485 0.33 14 7 ATN1 1822 broad.mit.edu 37 12 7045892 7045903 + In_Frame_Del DEL CAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448 byFrequency;byFrequency;by1000genomes;byFrequency HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr12:7045892_7045903delCAGCAGCAGCAG uc001qrw.1 + 5 1699_1710 c.1462_1473delCAGCAGCAGCAG c.(1462-1473)CAGCAGCAGCAGdel p.QQQQ496del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQ496del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 496_499 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagc 0.467 0.25 30 10 ITPR2 3709 broad.mit.edu 37 12 26568291 26568292 + Frame_Shift_Ins INS - A A HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr12:26568291_26568292insA uc001rhg.2 - 51 7667_7668 c.7250_7251insT c.(7249-7251)TTGfs p.L2417fs ITPR2_uc009zjg.1_Frame_Shift_Ins_p.L568fs NM_002223 NP_002214 Q14571 ITPR2_HUMAN inositol 1,4,5-triphosphate receptor, type 2 2417 Extracellular (Potential). activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 14 Colorectal(261;0.0847) AGTCATCCTTCAAAAAAAGGAA 0.411 0.28 135 52 LRRK2 120892 broad.mit.edu 37 12 40671946 40671946 + Frame_Shift_Del DEL A - - rs141585121 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr12:40671946delA uc001rmg.3 + 18 2245 c.2124delA c.(2122-2124)TTAfs p.L708fs LRRK2_uc001rmh.1_Frame_Shift_Del_p.L330fs NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 708 activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) ATGATTACTTAAAAAATGTGA 0.368 0.47 131 118 WNT1 7471 broad.mit.edu 37 12 49374348 49374348 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr12:49374348delG uc001rsu.2 + 3 698 c.500delG c.(499-501)TGGfs p.W167fs NM_005430 NP_005421 P04628 WNT1_HUMAN wingless-type MMTV integration site family, 167 brain segmentation|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|central nervous system morphogenesis|cerebellum formation|dermatome development|diencephalon development|embryonic axis specification|forebrain anterior/posterior pattern formation|fourth ventricle development|hemopoietic stem cell proliferation|hepatocyte differentiation|inner ear morphogenesis|mesoderm morphogenesis|midbrain development|midbrain-hindbrain boundary maturation during brain development|negative regulation of cell-cell adhesion|negative regulation of cell-substrate adhesion|negative regulation of DNA damage checkpoint|negative regulation of fat cell differentiation|neuron fate determination|positive regulation of fibroblast proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of lamellipodium assembly|positive regulation of Notch signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to wounding|signal transduction in response to DNA damage|Spemann organizer formation|T cell differentiation in thymus|Wnt receptor signaling pathway, calcium modulating pathway early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix cytokine activity|frizzled-2 binding|transcription regulatory region DNA binding kidney(1) 1 BRCA - Breast invasive adenocarcinoma(357;0.244) 0.000 0.26 558 198 GLI1 2735 broad.mit.edu 37 12 57864218 57864218 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr12:57864218delC uc001snx.2 + 12 1773 c.1695delC c.(1693-1695)TTCfs p.F565fs GLI1_uc009zpq.2_Frame_Shift_Del_p.F437fs NM_005269 NP_005260 P08151 GLI1_HUMAN GLI family zinc finger 1 isoform 1 565 epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter cytosol|nucleus transcription regulatory region DNA binding|zinc ion binding skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1) 15 GBM - Glioblastoma multiforme(3;3.99e-32) CCTCTCCTTTCCCCCCTGGCT 0.642 0.44 39 31 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.16 62 12 POLE 5426 broad.mit.edu 37 12 133245024 133245024 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr12:133245024delG uc001uks.1 - 19 2135 c.2091delC c.(2089-2091)CCCfs p.P697fs POLE_uc010tbq.1_RNA|POLE_uc009zyu.1_Frame_Shift_Del_p.P670fs NM_006231 NP_006222 Q07864 DPOE1_HUMAN DNA-directed DNA polymerase epsilon 697 base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair nucleoplasm chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding ovary(3)|skin(3)|lung(1)|central_nervous_system(1) 8 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.0416) OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05) 0.000 0.45 653 527 XPO4 64328 broad.mit.edu 37 13 21370942 21370942 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr13:21370942delA uc001unq.3 - 17 2613 c.2577delT c.(2575-2577)TTTfs p.F859fs NM_022459 NP_071904 Q9C0E2 XPO4_HUMAN exportin 4 859 protein transport cytoplasm|nucleus protein binding large_intestine(1)|ovary(1)|kidney(1) 3 all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244) all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548) CAACTTCAACAAAAACTTCTA 0.328 0.22 138 38 IRS2 8660 broad.mit.edu 37 13 110435263 110435263 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr13:110435263delG uc001vqv.2 - 1 3652 c.3138delC c.(3136-3138)CCCfs p.P1046fs NM_003749 NP_003740 Q9Y4H2 IRS2_HUMAN insulin receptor substrate 2 1046 fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus cytosol|plasma membrane insulin receptor binding|signal transducer activity large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|skin(1)|ovary(1)|kidney(1) 8 all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155) Breast(118;0.159) all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147) 0.000 0.11 780 97 TFDP1 7027 broad.mit.edu 37 13 114290382 114290382 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr13:114290382delC uc001vtw.2 + 9 990 c.778delC c.(778-780)CCCfs p.P260fs TFDP1_uc010tkd.1_Frame_Shift_Del_p.P165fs|TFDP1_uc010tke.1_Frame_Shift_Del_p.P165fs|TFDP1_uc001vty.3_Frame_Shift_Del_p.P260fs|TFDP1_uc001vtx.2_Frame_Shift_Del_p.P140fs NM_007111 NP_009042 Q14186 TFDP1_HUMAN transcription factor Dp-1 260 Dimerization (Potential).|Enhances binding of RB protein to E2F.|DCB2. cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|regulation of transcription from RNA polymerase II promoter transcription factor complex DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding lung(4)|ovary(2)|skin(1) 7 Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218) all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153) all cancers(43;0.0576) CATCCACCTGCCCTTCATCAT 0.557 0.21 54 14 NOVA1 4857 broad.mit.edu 37 14 27066542 27066542 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr14:27066542delG uc001wpy.2 - 1 419 c.101delC c.(100-102)CCTfs p.P34fs NOVA1_uc001wpz.2_Frame_Shift_Del_p.P34fs|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_Frame_Shift_Del_p.P34fs NM_002515 NP_002506 P51513 NOVA1_HUMAN neuro-oncological ventral antigen 1 isoform 1 34 Bipartite nuclear localization signal (Potential). locomotory behavior|RNA splicing|synaptic transmission nucleus RNA binding skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1) 5 GBM - Glioblastoma multiforme(265;0.0135) 0.000 0.44 939 723 CDKL1 8814 broad.mit.edu 37 14 50807859 50807860 + Frame_Shift_Ins INS - G G HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr14:50807859_50807860insG uc010anu.1 - 18 2561_2562 c.2561_2562insC c.(2560-2562)CCGfs p.P854fs CDKL1_uc001wxz.2_Frame_Shift_Ins_p.P183fs NM_004196 NP_004187 Q00532 CDKL1_HUMAN cyclin-dependent kinase-like 1 182 Protein kinase. cytoplasm|nucleus ATP binding|cyclin-dependent protein kinase activity ovary(1)|stomach(1) 2 all_epithelial(31;0.000746)|Breast(41;0.0102) AAACATCCACCGGGGGGCCGTA 0.574 0.21 440 117 WDHD1 11169 broad.mit.edu 37 14 55433314 55433315 + Frame_Shift_Ins INS - A A HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr14:55433314_55433315insA uc001xbm.1 - 18 2266_2267 c.2188_2189insT c.(2188-2190)TGGfs p.W730fs WDHD1_uc010aom.1_Frame_Shift_Ins_p.W247fs|WDHD1_uc001xbn.1_Frame_Shift_Ins_p.W607fs NM_007086 NP_009017 O75717 WDHD1_HUMAN WD repeat and HMG-box DNA binding protein 1 730 cytoplasm|nucleoplasm DNA binding skin(1) 1 AACTGAACGCCAAAATTGCTCC 0.312 0.25 97 32 NEK9 91754 broad.mit.edu 37 14 75573355 75573355 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr14:75573355delC uc001xrl.2 - 12 1532 c.1378delG c.(1378-1380)GTGfs p.V460fs NEK9_uc001xrk.2_5'UTR NM_033116 NP_149107 Q8TD19 NEK9_HUMAN NIMA-related kinase 9 460 RCC1 2. cell division|mitosis mitochondrion|nucleus ATP binding|metal ion binding|protein kinase binding|protein serine/threonine kinase activity lung(2)|stomach(2)|ovary(1) 5 BRCA - Breast invasive adenocarcinoma(234;0.00718) ACTTTGTCCACCCCCATGCAG 0.468 0.17 211 44 FBLN5 10516 broad.mit.edu 37 14 92361375 92361376 + Frame_Shift_Ins INS - G G HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr14:92361375_92361376insG uc001xzx.3 - 5 893_894 c.420_421insC c.(418-423)CCCACCfs p.P140fs FBLN5_uc010aud.2_Frame_Shift_Ins_p.P145fs|FBLN5_uc010aue.2_Frame_Shift_Ins_p.P181fs NM_006329 NP_006320 Q9UBX5 FBLN5_HUMAN fibulin 5 precursor 140_141 EGF-like 2; calcium-binding (Potential). cell-matrix adhesion|elastic fiber assembly|protein localization at cell surface|regulation of removal of superoxide radicals extracellular space|proteinaceous extracellular matrix|soluble fraction calcium ion binding|integrin binding|protein C-terminus binding ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1) 6 all_cancers(154;0.0722) CAGATCTGGGTGGGGTTGCACT 0.535 0.49 130 124 JAG2 3714 broad.mit.edu 37 14 105634329 105634329 + Frame_Shift_Del DEL C - - rs149962192 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr14:105634329delC uc001yqg.2 - 2 586 c.182delG c.(181-183)GGCfs p.G61fs JAG2_uc001yqh.2_Frame_Shift_Del_p.G61fs NM_002226 NP_002217 Q9Y219 JAG2_HUMAN jagged 2 isoform a precursor 61 Extracellular (Potential). auditory receptor cell fate commitment|cell communication|cell cycle|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation|spermatogenesis|thymic T cell selection integral to plasma membrane calcium ion binding|growth factor activity|Notch binding lung(3)|breast(2) 5 all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155) OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272) Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208) GTGGCCGCAGCCCCCCGCGCG 0.711 0.20 61 15 MKRN3 7681 broad.mit.edu 37 15 23811405 23811405 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr15:23811405delC uc001ywh.3 + 1 952 c.476delC c.(475-477)GCCfs p.A159fs MKRN3_uc001ywi.2_Intron|MKRN3_uc010ayi.1_Frame_Shift_Del_p.A159fs NM_005664 NP_005655 Q13064 MKRN3_HUMAN makorin ring finger protein 3 159 ribonucleoprotein complex ligase activity|nucleic acid binding|zinc ion binding lung(6)|large_intestine(2)|ovary(2) 10 all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14) all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012) GTGGCGGAAGCCCCCCCGGCT 0.642 0.24 51 16 MGA 23269 broad.mit.edu 37 15 42026746 42026746 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr15:42026746delA uc010ucy.1 + 12 4051 c.3870delA c.(3868-3870)TTAfs p.L1290fs MGA_uc010ucz.1_Frame_Shift_Del_p.L1290fs|MGA_uc010uda.1_5'UTR NM_001164273 NP_001157745 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 1 1290 MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) AGCAGCCCTTAAAACAACTCA 0.343 0.71 47 113 UNC13C 440279 broad.mit.edu 37 15 54306719 54306720 + Frame_Shift_Ins INS - T T HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr15:54306719_54306720insT uc002ack.2 + 1 1619_1620 c.1619_1620insT c.(1618-1620)GATfs p.D540fs NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 540 exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) TCACAGAGTGATTTTTTCACTG 0.366 0.33 158 77 SGK269 79834 broad.mit.edu 37 15 77471654 77471654 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr15:77471654delG uc002bcm.2 - 3 2923 c.2615delC c.(2614-2616)CCGfs p.P872fs SGK269_uc002bcn.2_Frame_Shift_Del_p.P872fs NM_024776 NP_079052 Q9H792 PEAK1_HUMAN NKF3 kinase family member 872 Pro-rich. cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading actin cytoskeleton|cytoplasm|focal adhesion ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding 0 STAD - Stomach adenocarcinoma(199;0.124) AGAGCGTGGCGGGGGAAAGGG 0.532 0.32 38 18 TNFRSF12A 51330 broad.mit.edu 37 16 3071674 3071675 + Frame_Shift_Del DEL GA - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr16:3071674_3071675delGA uc002csv.3 + 3 404_405 c.318_319delGA c.(316-321)AGGAGAfs p.R106fs TNFRSF12A_uc002csw.3_Frame_Shift_Del_p.R71fs|THOC6_uc002ctb.2_5'Flank|THOC6_uc002ctd.2_5'Flank|THOC6_uc002ctc.2_5'Flank|THOC6_uc002cta.2_5'Flank NM_016639 NP_057723 Q9NP84 TNR12_HUMAN tumor necrosis factor receptor superfamily, 106_107 Cytoplasmic (Potential). angiogenesis|apoptosis integral to membrane receptor activity 0 GATGCCGCAGGAGAGAGAAGTT 0.614 0.26 57 20 ERN2 10595 broad.mit.edu 37 16 23718096 23718096 + Frame_Shift_Del DEL G - - rs143761786 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr16:23718096delG uc002dma.3 - 6 779 c.610delC c.(610-612)CGCfs p.R204fs ERN2_uc010bxp.2_Frame_Shift_Del_p.R204fs|ERN2_uc010bxq.1_Frame_Shift_Del_p.R12fs NM_033266 NP_150296 Q76MJ5 ERN2_HUMAN endoplasmic reticulum to nucleus signalling 2 156 Lumenal (Potential). apoptosis|induction of apoptosis|mRNA processing|negative regulation of transcription, DNA-dependent|rRNA catabolic process|transcription, DNA-dependent endoplasmic reticulum membrane|integral to membrane ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein serine/threonine kinase activity large_intestine(2)|lung(2)|ovary(2) 6 GBM - Glioblastoma multiforme(48;0.0156) ATGTAGAGGCGGGGGGTGGAG 0.607 0.17 49 10 FUS 2521 broad.mit.edu 37 16 31202115 31202116 + Frame_Shift_Ins INS - C C HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr16:31202115_31202116insC uc002ebf.2 + 13 1428_1429 c.1345_1346insC c.(1345-1347)GCCfs p.A449fs FUS_uc002ebh.2_Frame_Shift_Ins_p.A448fs|FUS_uc002ebg.2_Frame_Shift_Ins_p.A244fs|FUS_uc002ebi.2_Frame_Shift_Ins_p.A450fs|FUS_uc002ebj.2_Frame_Shift_Ins_p.A245fs NM_004960 NP_004951 P35637 FUS_HUMAN fusion (involved in t(12;16) in malignant 449 RanBP2-type.|Arg/Gly-rich. cell death|nuclear mRNA splicing, via spliceosome nucleoplasm DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding FUS/DDIT3(623)|FUS/ERG(163)|FUS/CREB3L2(158)|FUS/CREB3L1(6)|FUS/ATF1(4)|FUS/FEV(2) soft_tissue(791)|haematopoietic_and_lymphoid_tissue(153)|bone(12)|breast(2) 958 Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121) GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209) CCAGTGTAAGGCCCCTAAACCA 0.505 0.21 210 55 ZFHX3 463 broad.mit.edu 37 16 72821959 72821960 + Frame_Shift_Ins INS - G G HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr16:72821959_72821960insG uc002fck.2 - 10 10888_10889 c.10215_10216insC c.(10213-10218)CCCGGGfs p.P3405fs ZFHX3_uc002fcl.2_Frame_Shift_Ins_p.P2491fs NM_006885 NP_008816 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 isoform A 3405_3406 muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation transcription factor complex enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding ovary(2)|skin(2) 4 Ovarian(137;0.13) GAAGGAGCCCCGGGGGGGACTG 0.416 0.39 28 18 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 13 124 USP6 9098 broad.mit.edu 37 17 5072211 5072211 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr17:5072211delG uc002gau.1 + 35 5608 c.3378delG c.(3376-3378)CAGfs p.Q1126fs USP6_uc002gav.1_Frame_Shift_Del_p.Q1126fs|USP6_uc010ckz.1_Frame_Shift_Del_p.Q809fs NM_004505 NP_004496 P35125 UBP6_HUMAN ubiquitin specific protease 6 1126 protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process lysosome|plasma membrane|recycling endosome calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1) 5 TCACACCCCAGGGGGATGAGC 0.517 0.46 76 66 PER1 5187 broad.mit.edu 37 17 8052019 8052019 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr17:8052019delC uc002gkd.2 - 8 1229 c.991delG c.(991-993)GCCfs p.A331fs PER1_uc010vuq.1_RNA|PER1_uc010vur.1_Frame_Shift_Del_p.A315fs NM_002616 NP_002607 O15534 PER1_HUMAN period 1 331 circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus signal transducer activity lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1) 9 TGTGCAGGGGCCCCATCTGAG 0.637 0.25 96 32 MYH10 4628 broad.mit.edu 37 17 8438774 8438774 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr17:8438774delG uc002gll.2 - 15 1891 c.1795delC c.(1795-1797)CTGfs p.L599fs MYH10_uc002glm.2_Frame_Shift_Del_p.L609fs|MYH10_uc010cnx.2_Frame_Shift_Del_p.L608fs NM_005964 NP_005955 P35580 MYH10_HUMAN myosin, heavy polypeptide 10, non-muscle 599 Myosin head-like. actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape cell cortex|cleavage furrow|midbody|myosin complex|stress fiber actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity ovary(2) 2 TTGTCATTCAGGGGGTCCATA 0.448 0.40 128 84 TOP2A 7153 broad.mit.edu 37 17 38546381 38546381 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr17:38546381delT uc002huq.2 - 34 4429 c.4303delA c.(4303-4305)AGGfs p.R1435fs NM_001067 NP_001058 P11388 TOP2A_HUMAN DNA topoisomerase II, alpha isozyme 1435 apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1) 7 Breast(137;0.00328) STAD - Stomach adenocarcinoma(5;0.00183) Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385) GGGGCAGCCCTTTTTTTGGCA 0.413 0.47 157 141 WNK4 65266 broad.mit.edu 37 17 40948004 40948005 + Frame_Shift_Ins INS - G G HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr17:40948004_40948005insG uc002ibj.2 + 16 3405_3406 c.3384_3385insG c.(3382-3387)AGTGGGfs p.S1128fs WNK4_uc010wgx.1_Frame_Shift_Ins_p.S792fs|CCDC56_uc010wgz.1_Frame_Shift_Ins_p.H85fs|CNTD1_uc002ibm.3_5'Flank|CNTD1_uc010wha.1_5'Flank NM_032387 NP_115763 Q96J92 WNK4_HUMAN WNK lysine deficient protein kinase 4 1128_1129 intracellular protein kinase cascade tight junction ATP binding|protein serine/threonine kinase activity ovary(3)|skin(3)|stomach(1) 7 Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.0749) 0.000 0.22 1084 311 HLF 3131 broad.mit.edu 37 17 53342869 53342869 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr17:53342869delC uc002iug.1 + 1 549 c.24delC c.(22-24)CTCfs p.L8fs HLF_uc010dce.1_5'Flank|HLF_uc002iuh.2_5'Flank|HLF_uc010wni.1_5'Flank NM_002126 NP_002117 Q16534 HLF_HUMAN hepatic leukemia factor 8 multicellular organismal development|rhythmic process|transcription from RNA polymerase II promoter nucleus double-stranded DNA binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity ovary(2) 2 0.000 0.27 128 48 HLF 3131 broad.mit.edu 37 17 53345288 53345288 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr17:53345288delC uc002iug.1 + 2 817 c.292delC c.(292-294)CCCfs p.P98fs HLF_uc010dce.1_Frame_Shift_Del_p.P13fs|HLF_uc002iuh.2_Frame_Shift_Del_p.P13fs|HLF_uc010wni.1_Frame_Shift_Del_p.F46fs NM_002126 NP_002117 Q16534 HLF_HUMAN hepatic leukemia factor 98 multicellular organismal development|rhythmic process|transcription from RNA polymerase II promoter nucleus double-stranded DNA binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity ovary(2) 2 AAATGGCATTCCCCCCAGCCC 0.587 0.40 275 187 RNF43 54894 broad.mit.edu 37 17 56435161 56435161 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr17:56435161delC uc002iwf.2 - 8 3932 c.1976delG c.(1975-1977)GGTfs p.G659fs RNF43_uc010wnv.1_Frame_Shift_Del_p.G618fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.G659fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.G659fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.G532fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 659 Pro-rich.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.29 323 129 PPM1D 8493 broad.mit.edu 37 17 58740727 58740727 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr17:58740727delC uc002iyt.1 + 6 1854 c.1632delC c.(1630-1632)GGCfs p.G544fs PPM1D_uc010ddm.1_RNA NM_003620 NP_003611 O15297 PPM1D_HUMAN protein phosphatase 1D 544 negative regulation of cell proliferation|protein dephosphorylation|response to radiation nucleus|protein serine/threonine phosphatase complex metal ion binding|protein binding|protein serine/threonine phosphatase activity upper_aerodigestive_tract(1) 1 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) Epithelial(12;6.75e-12)|all cancers(12;1.96e-10) 0.000 0.33 1301 652 CDH2 1000 broad.mit.edu 37 18 25589733 25589733 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr18:25589733delC uc002kwg.2 - 5 1109 c.650delG c.(649-651)GGTfs p.G217fs CDH2_uc010xbn.1_Frame_Shift_Del_p.G186fs NM_001792 NP_001783 P19022 CADH2_HUMAN cadherin 2, type 1 preproprotein 217 Cadherin 1.|Extracellular (Potential). adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation catenin complex|integral to membrane alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding ovary(3)|lung(1) 4 CGACAGCTGACCCGAGATGGG 0.478 0.25 49 16 ATP8B1 5205 broad.mit.edu 37 18 55365040 55365040 + Frame_Shift_Del DEL T - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr18:55365040delT uc002lgw.2 - 6 614 c.614delA c.(613-615)AATfs p.N205fs uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 205 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) AACAAAATCATTTTTTTTCAG 0.388 0.27 33 12 CPAMD8 27151 broad.mit.edu 37 19 17081703 17081703 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr19:17081703delG uc002nfb.2 - 18 2384 c.2352delC c.(2350-2352)CCCfs p.P784fs NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 737 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 0.000 0.65 191 357 PAK4 10298 broad.mit.edu 37 19 39664276 39664278 + In_Frame_Del DEL TCC - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr19:39664276_39664278delTCC uc002okj.1 + 6 1185_1187 c.724_726delTCC c.(724-726)TCCdel p.S247del PAK4_uc002okl.1_In_Frame_Del_p.S247del|PAK4_uc002okn.1_In_Frame_Del_p.S247del|PAK4_uc002okm.1_In_Frame_Del_p.S94del|PAK4_uc002oko.1_In_Frame_Del_p.S94del|PAK4_uc002okp.1_In_Frame_Del_p.S157del NM_001014831 NP_001014831 O96013 PAK4_HUMAN p21-activated kinase 4 isoform 1 247 Linker. cellular component movement|signal transduction Golgi apparatus ATP binding|protein binding|protein serine/threonine kinase activity lung(3)|ovary(1) 4 all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454) Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113) 0.000 0.23 1392 410 AXL 558 broad.mit.edu 37 19 41743933 41743933 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr19:41743933delC uc010ehj.2 + 7 1058 c.868delC c.(868-870)CCCfs p.P290fs CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Frame_Shift_Del_p.P290fs|AXL_uc010ehk.2_Frame_Shift_Del_p.P290fs NM_021913 NP_068713 P30530 UFO_HUMAN AXL receptor tyrosine kinase isoform 1 290 Extracellular (Potential).|Fibronectin type-III 1. integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1) 13 AGCATCCGTGCCCCCCCATCA 0.647 0.21 86 23 CIC 23152 broad.mit.edu 37 19 42791339 42791339 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr19:42791339delC uc002otf.1 + 3 439 c.399delC c.(397-399)GGCfs p.G133fs NM_015125 NP_055940 Q96RK0 CIC_HUMAN capicua homolog 133 Pro-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1) 11 Prostate(69;0.00682) AGGCCTCCGGCCCCCCAGGAG 0.662 0.38 16 10 LMTK3 114783 broad.mit.edu 37 19 49000732 49000732 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr19:49000732delG uc002pjk.2 - 12 3681 c.3681delC c.(3679-3681)CCCfs p.P1227fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.17 1036 217 LMTK3 114783 broad.mit.edu 37 19 49002059 49002060 + Frame_Shift_Del DEL GG - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr19:49002059_49002060delGG uc002pjk.2 - 12 2353_2354 c.2353_2354delCC c.(2353-2355)CCGfs p.P785fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.34 566 289 LMTK3 114783 broad.mit.edu 37 19 49002846 49002846 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr19:49002846delC uc002pjk.2 - 12 1567 c.1567delG c.(1567-1569)GCAfs p.A523fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.24 871 274 BRSK1 84446 broad.mit.edu 37 19 55823385 55823385 + Frame_Shift_Del DEL C - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr19:55823385delC uc002qkg.2 + 19 2563 c.2286delC c.(2284-2286)GGCfs p.G762fs BRSK1_uc002qkf.2_Frame_Shift_Del_p.G778fs|BRSK1_uc002qkh.2_Frame_Shift_Del_p.G457fs NM_032430 NP_115806 Q8TDC3 BRSK1_HUMAN BR serine/threonine kinase 1 762 G -> A (in Ref. 9; AAH16681). establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV cell junction|cytoplasm|nucleus magnesium ion binding|protein serine/threonine kinase activity ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1) 6 Renal(1328;0.245) BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.0474) 0.000 0.50 1020 1027 SBK2 646643 broad.mit.edu 37 19 56041329 56041329 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr19:56041329delA uc010ygc.1 - 3 818 c.818delT c.(817-819)TTCfs p.F273fs NM_001101401 NP_001094871 P0C263 SBK2_HUMAN SH3-binding domain kinase family, member 2 273 Protein kinase. ATP binding|protein serine/threonine kinase activity 0 0.000 0.10 1130 127 NCOA6 23054 broad.mit.edu 37 20 33345714 33345715 + In_Frame_Ins INS - TGT TGT HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr20:33345714_33345715insTGT uc002xav.2 - 8 3407_3408 c.836_837insACA c.(835-837)CAG>CAACAG p.279_279Q>QQ NCOA6_uc002xaw.2_In_Frame_Ins_p.279_279Q>QQ|NCOA6_uc010gew.1_In_Frame_Ins_p.236_236Q>QQ NM_014071 NP_054790 Q14686 NCOA6_HUMAN nuclear receptor coactivator 6 279 TBP/GTF2A-binding region.|NCOA1-binding region.|Gln-rich.|CREBBP-binding region. brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter transcription factor complex chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding ovary(3)|breast(3)|central_nervous_system(1) 7 gctgctgttgctgttgttgctg 0.317 0.44 33 26 PTPRT 11122 broad.mit.edu 37 20 40739003 40739003 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr20:40739003delG uc002xkg.2 - 23 3408 c.3224delC c.(3223-3225)CCGfs p.P1075fs PTPRT_uc010ggj.2_Frame_Shift_Del_p.P1094fs|PTPRT_uc010ggi.2_Frame_Shift_Del_p.P278fs NM_007050 NP_008981 O14522 PTPRT_HUMAN protein tyrosine phosphatase, receptor type, T 1075 Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential). homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway cell surface|integral to membrane|plasma membrane alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity skin(8)|ovary(7)|lung(5) 20 Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783) CCCAGCTTCCGGGGGGTTGAG 0.453 0.21 27 7 NCOA3 8202 broad.mit.edu 37 20 46264985 46264985 + Frame_Shift_Del DEL A - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr20:46264985delA uc002xtk.2 + 12 2060 c.1855delA c.(1855-1857)AAAfs p.K619fs NCOA3_uc010ght.1_Frame_Shift_Del_p.K629fs|NCOA3_uc002xtl.2_Frame_Shift_Del_p.K619fs|NCOA3_uc002xtm.2_Frame_Shift_Del_p.K619fs|NCOA3_uc002xtn.2_Frame_Shift_Del_p.K619fs|NCOA3_uc010zyc.1_Frame_Shift_Del_p.K414fs NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 619 Ser-rich. KK->QQ: Abolishes acetylation by CREBBP. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 CAAAGGTCATAAAAAATTACT 0.438 0.41 107 75 TIAM1 7074 broad.mit.edu 37 21 32492713 32492713 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr21:32492713delG uc002yow.1 - 29 5221 c.4749delC c.(4747-4749)CCCfs p.P1583fs TIAM1_uc011adk.1_3'UTR|TIAM1_uc011adl.1_Frame_Shift_Del_p.P1523fs NM_003253 NP_003244 Q13009 TIAM1_HUMAN T-cell lymphoma invasion and metastasis 1 1583 apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cell-cell junction|cytosol receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity lung(3)|breast(3)|ovary(2)|large_intestine(2) 10 GTTTCCTGGAGGGGGCAAAGT 0.562 0.20 209 53 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 77 408 MCM3AP 8888 broad.mit.edu 37 21 47663397 47663397 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr21:47663397delG uc002zir.1 - 24 5314 c.5278delC c.(5278-5280)CGGfs p.R1760fs MCM3APAS_uc002zim.2_Intron|MCM3APAS_uc002zin.2_Intron|MCM3AP_uc002zio.1_Frame_Shift_Del_p.R255fs|MCM3AP_uc002zip.1_Frame_Shift_Del_p.R501fs|MCM3AP_uc002ziq.1_Frame_Shift_Del_p.R687fs|MCM3APAS_uc002zis.1_Intron NM_003906 NP_003897 O60318 MCM3A_HUMAN minichromosome maintenance complex component 3 1760 DNA replication|protein import into nucleus cytosol|nucleus DNA binding|nucleotide binding large_intestine(2)|lung(1)|ovary(1)|skin(1) 5 Breast(49;0.112) ACAGGAAGCCGGGGGGGCGTC 0.527 0.19 131 30 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 9 90 ZNRF3 84133 broad.mit.edu 37 22 29446196 29446196 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr22:29446196delG uc003aeg.2 + 8 1892 c.1727delG c.(1726-1728)AGGfs p.R576fs ZNRF3_uc003aeh.1_Frame_Shift_Del_p.R576fs NM_032173 NP_115549 Q9ULT6 ZNRF3_HUMAN zinc and ring finger 3 676 Cytoplasmic (Potential). integral to membrane zinc ion binding ovary(1) 1 0.000 0.19 2396 573 TIMP3 7078 broad.mit.edu 37 22 33255323 33255324 + Frame_Shift_Ins INS - C C HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr22:33255323_33255324insC uc003anb.2 + 5 1781_1782 c.595_596insC c.(595-597)GCCfs p.A199fs SYN3_uc003amx.2_Intron|SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron NM_000362 NP_000353 P35625 TIMP3_HUMAN tissue inhibitor of metalloproteinase 3 199 negative regulation of membrane protein ectodomain proteolysis|visual perception metal ion binding|metalloendopeptidase inhibitor activity|protein binding lung(1) 1 CCGAGGATGGGCCCCCCCGGAT 0.604 0.18 45 10 CARD10 29775 broad.mit.edu 37 22 37912022 37912024 + In_Frame_Del DEL CTC - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr22:37912022_37912024delCTC uc003asx.1 - 3 658_660 c.655_657delGAG c.(655-657)GAGdel p.E219del CARD10_uc003ast.1_RNA|CARD10_uc003asy.1_In_Frame_Del_p.E219del NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 219 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) CCGAGTTCTTCTCCTCACTGAGC 0.631 0.42 15 11 TNRC6B 23112 broad.mit.edu 37 22 40662617 40662617 + Frame_Shift_Del DEL G - - HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr22:40662617delG uc011aor.1 + 5 2594 c.2383delG c.(2383-2385)GGTfs p.G795fs TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Frame_Shift_Del_p.G795fs|TNRC6B_uc003ayo.2_Frame_Shift_Del_p.G599fs NM_001162501 NP_001155973 Q9UPQ9 TNR6B_HUMAN trinucleotide repeat containing 6B isoform 1 795 gene silencing by RNA|regulation of translation cytoplasmic mRNA processing body nucleotide binding|RNA binding 0 AGCTTCAAAAGGTGGGTGGGA 0.532 0.45 115 93 MKL1 57591 broad.mit.edu 37 22 40816494 40816494 + Frame_Shift_Del DEL G - - rs36003306 HEC108_ENDOMETRIUM NA HEC108_ENDOMETRIUM NA g.chr22:40816494delG uc003ayv.1 - 8 1175 c.968delC c.(967-969)CCTfs p.P323fs MKL1_uc003ayw.1_Frame_Shift_Del_p.P323fs|MKL1_uc010gye.1_Frame_Shift_Del_p.P323fs|MKL1_uc010gyf.1_Frame_Shift_Del_p.P273fs NM_020831 NP_065882 Q969V6 MKL1_HUMAN megakaryoblastic leukemia 1 protein 323 positive regulation of transcription from RNA polymerase II promoter|smooth muscle cell differentiation|transcription, DNA-dependent cytoplasm|nucleus actin monomer binding|leucine zipper domain binding|nucleic acid binding|transcription coactivator activity ovary(2)|lung(1)|breast(1)|central_nervous_system(1) 5 ACAGGGCCCAGGGGCGCCCGA 0.662 0.46 32 27 KDM6A 7403 broad.mit.edu 37 X 44966718 44966718 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chrX:44966718delA uc004dge.3 + 27 4317 c.3942delA c.(3940-3942)GGAfs p.G1314fs KDM6A_uc011mkz.1_Frame_Shift_Del_p.G1366fs|KDM6A_uc011mla.1_Frame_Shift_Del_p.G1269fs|KDM6A_uc011mlb.1_Frame_Shift_Del_p.G1321fs|KDM6A_uc011mlc.1_Frame_Shift_Del_p.G1018fs|KDM6A_uc011mld.1_Frame_Shift_Del_p.G953fs NM_021140 NP_066963 O15550 KDM6A_HUMAN ubiquitously transcribed tetratricopeptide 1314 histone H3-K4 methylation metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2) 84 TTGCTGCAGGAAAAGAGATTA 0.388 0.34 23 12 WAS 7454 broad.mit.edu 37 X 48544133 48544134 + Frame_Shift_Ins INS - G G HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chrX:48544133_48544134insG uc004dkm.3 + 4 428_429 c.371_372insG c.(370-372)GCGfs p.A124fs NM_000377 NP_000368 P42768 WASP_HUMAN Wiskott-Aldrich syndrome protein 124 WH1. blood coagulation|defense response|epidermis development|immune response|T cell receptor signaling pathway actin cytoskeleton|cytosol identical protein binding|small GTPase regulator activity ovary(1) 1 all_lung(315;1.27e-10) GACTGCCAAGCGGGGCTGAACT 0.614 0.49 22 21 CACNA1F 778 broad.mit.edu 37 X 49063086 49063087 + Splice_Site INS - G G HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chrX:49063086_49063087insG uc004dnb.2 - 46 5455 c.5393_splice c.e46-1 p.G1798_splice CACNA1F_uc010nip.2_Splice_Site_p.G1787_splice NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) GCTTCCGACCTGGGGGTGGGTG 0.614 0.53 8 9 FOXO4 4303 broad.mit.edu 37 X 70321277 70321277 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chrX:70321277delG uc004dys.1 + 2 1550 c.1197delG c.(1195-1197)CTGfs p.L399fs FOXO4_uc010nkz.2_Intron|FOXO4_uc004dyt.1_Frame_Shift_Del_p.L344fs NM_005938 NP_005929 P98177 FOXO4_HUMAN forkhead box O4 399 cell cycle arrest|cell differentiation|embryo development|G1 phase of mitotic cell cycle|insulin receptor signaling pathway|mitotic cell cycle G2/M transition DNA damage checkpoint|muscle organ development|negative regulation of angiogenesis|negative regulation of cell proliferation|negative regulation of smooth muscle cell differentiation|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding central_nervous_system(2)|prostate(1) 3 Renal(35;0.156) TTCTGTTGCTGGGGGGGCTTC 0.632 0.36 158 87 MED12 9968 broad.mit.edu 37 X 70360612 70360617 + In_Frame_Del DEL CAGCAA - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chrX:70360612_70360617delCAGCAA uc004dyy.2 + 42 6371_6376 c.6172_6177delCAGCAA c.(6172-6177)CAGCAAdel p.QQ2074del MED12_uc004dyz.2_In_Frame_Del_p.QQ2073del|MED12_uc004dza.2_In_Frame_Del_p.QQ1924del|MED12_uc010nla.2_In_Frame_Del_p.QQ703del NM_005120 NP_005111 Q93074 MED12_HUMAN mediator complex subunit 12 2074_2075 Gln-rich. androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter mediator complex ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding ovary(1)|breast(1)|central_nervous_system(1)|skin(1) 4 Renal(35;0.156) gcagcaacagcagcaacagcaacagc 0.267 0.26 98 35 ATRX 546 broad.mit.edu 37 X 76937602 76937602 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chrX:76937602delA uc004ecp.3 - 9 3378 c.3146delT c.(3145-3147)ATAfs p.I1049fs ATRX_uc004ecq.3_Frame_Shift_Del_p.I1011fs|ATRX_uc004eco.3_Frame_Shift_Del_p.I834fs|ATRX_uc004ecr.2_Frame_Shift_Del_p.I981fs|ATRX_uc010nlx.1_Frame_Shift_Del_p.I1020fs|ATRX_uc010nly.1_Frame_Shift_Del_p.I994fs NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 1049 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) TTTATCTCTTATTTTTTTACT 0.323 0.37 72 43 ATRX 546 broad.mit.edu 37 X 76938089 76938090 + Frame_Shift_Del DEL TC - - rs141180098 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chrX:76938089_76938090delTC uc004ecp.3 - 9 2890_2891 c.2658_2659delGA c.(2656-2661)GAGACTfs p.E886fs ATRX_uc004ecq.3_Frame_Shift_Del_p.E848fs|ATRX_uc004eco.3_Frame_Shift_Del_p.E671fs|ATRX_uc004ecr.2_Frame_Shift_Del_p.E818fs|ATRX_uc010nlx.1_Frame_Shift_Del_p.E857fs|ATRX_uc010nly.1_Frame_Shift_Del_p.E831fs NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 886_887 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) GAAGAGAAAGTCTCTCTCTCTT 0.411 0.41 175 120 ATRX 546 broad.mit.edu 37 X 76939674 76939674 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chrX:76939674delT uc004ecp.3 - 9 1306 c.1074delA c.(1072-1074)AAAfs p.K358fs ATRX_uc004ecq.3_Frame_Shift_Del_p.K320fs|ATRX_uc004eco.3_Frame_Shift_Del_p.K143fs|ATRX_uc004ecr.2_Frame_Shift_Del_p.K319fs|ATRX_uc010nlx.1_Frame_Shift_Del_p.K358fs|ATRX_uc010nly.1_Frame_Shift_Del_p.K303fs NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 358 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) TCTCAATCAGTTTTTTTGCCT 0.368 0.32 76 36 HNRNPH2 3188 broad.mit.edu 37 X 100667776 100667777 + Frame_Shift_Ins INS - T T HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chrX:100667776_100667777insT uc004ehm.2 + 2 970_971 c.800_801insT c.(799-801)TGTfs p.C267fs HNRNPH2_uc004ehn.2_Frame_Shift_Ins_p.C267fs NM_019597 NP_062543 P55795 HNRH2_HUMAN heterogeneous nuclear ribonucleoprotein H2 267 2 X 16 AA Gly-rich approximate repeats. nuclear mRNA splicing, via spliceosome actin cytoskeleton|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm nucleotide binding|protein binding|RNA binding 0 CTCAATTACTGTTTTTCAGGAA 0.475 0.33 79 39 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 66 ODZ1 10178 broad.mit.edu 37 X 123870951 123870951 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chrX:123870951delG uc004euj.2 - 4 696 c.632delC c.(631-633)CCTfs p.P211fs ODZ1_uc011muj.1_Frame_Shift_Del_p.P211fs|ODZ1_uc010nqy.2_Frame_Shift_Del_p.P211fs NM_014253 NP_055068 Q9UKZ4 TEN1_HUMAN odz, odd Oz/ten-m homolog 1 isoform 3 211 Teneurin N-terminal.|Cytoplasmic (Potential). immune response|negative regulation of cell proliferation|nervous system development|signal transduction extracellular region heparin binding ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1) 23 GTCCGCTGCAGGGGGTGGCTT 0.622 0.46 22 19 GPR112 139378 broad.mit.edu 37 X 135488065 135488065 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chrX:135488065delT uc004ezu.1 + 23 9160 c.8869delT c.(8869-8871)TTTfs p.F2957fs GPR112_uc010nsb.1_Frame_Shift_Del_p.F2752fs NM_153834 NP_722576 Q8IZF6 GP112_HUMAN G-protein coupled receptor 112 2957 Helical; Name=6; (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1) 12 Acute lymphoblastic leukemia(192;0.000127) GGGGTTTGCATTTTTTGCTTG 0.453 0.49 154 146 CHD5 26038 broad.mit.edu 37 1 6206784 6206785 + Frame_Shift_Ins INS - CT CT HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:6206784_6206785insCT uc001amb.1 - 10 1630_1631 c.1530_1531insAG c.(1528-1533)GAGTTCfs p.E510fs CHD5_uc001ama.1_5'Flank|CHD5_uc001amc.1_RNA NM_015557 NP_056372 Q8TDI0 CHD5_HUMAN chromodomain helicase DNA binding protein 5 510_511 Chromo 1. chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1) 12 Ovarian(185;0.0634) all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15) Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193) TTGACAAAGAACTCTCTCTCAG 0.663 0.26 56 20 TNFRSF9 3604 broad.mit.edu 37 1 7998254 7998254 + Frame_Shift_Del DEL T - - rs9657965 byFrequency;by1000genomes HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:7998254delT uc001aot.2 - 4 473 c.345delA c.(343-345)AAAfs p.K115fs NM_001561 NP_001552 Q07011 TNR9_HUMAN tumor necrosis factor receptor superfamily, 115 Extracellular (Potential).|TNFR-Cys 3. induction of apoptosis|negative regulation of cell proliferation integral to plasma membrane binding|receptor activity large_intestine(1)|lung(1)|ovary(1)|skin(1) 4 Ovarian(185;0.0634)|all_lung(157;0.151) all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649) CAAACGTACCTTTTTTTGTCA 0.413 0.41 82 56 SPEN 23013 broad.mit.edu 37 1 16259480 16259480 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:16259480delC uc001axk.1 + 11 6949 c.6745delC c.(6745-6747)CCCfs p.P2249fs SPEN_uc010obp.1_Frame_Shift_Del_p.P2208fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2249 RID.|Interaction with MSX2 (By similarity). interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) AGATCTGCAACCCCCCGCAGG 0.557 0.36 141 78 EPHA2 1969 broad.mit.edu 37 1 16461616 16461617 + Frame_Shift_Ins INS - G G HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:16461616_16461617insG uc001aya.1 - 7 1633_1634 c.1496_1497insC c.(1495-1497)CCAfs p.P499fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 499 Extracellular (Potential).|Fibronectin type-III 2. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) AGGTGGTGTCTGGGGCCAGGTC 0.668 0.21 26 7 EPHA2 1969 broad.mit.edu 37 1 16474977 16474977 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:16474977delC uc001aya.1 - 3 856 c.719delG c.(718-720)GGTfs p.G240fs EPHA2_uc010oca.1_Frame_Shift_Del_p.G240fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 240 Extracellular (Potential).|Cys-rich. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) GGGCTCTTCACCCCCCGGTGG 0.667 0.55 30 37 HDAC1 3065 broad.mit.edu 37 1 32798326 32798328 + In_Frame_Del DEL AGG - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:32798326_32798328delAGG uc001bvb.1 + 13 1460_1462 c.1397_1399delAGG c.(1396-1401)AAGGAG>AAG p.E468del HDAC1_uc010ohf.1_In_Frame_Del_p.E439del|HDAC1_uc001bvc.1_In_Frame_Del_p.E224del NM_004964 NP_004955 Q13547 HDAC1_HUMAN histone deacetylase 1 468 Missing: Strongly decreases deacetylase activity, and disrupts interaction with NuRD and SIN3 complexes. anti-apoptosis|blood coagulation|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|histone H3 deacetylation|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of androgen receptor signaling pathway|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter cytosol|NuRD complex|Sin3 complex activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|identical protein binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|RNA polymerase II transcription corepressor activity|sequence-specific DNA binding transcription factor activity ovary(1)|lung(1)|breast(1) 3 Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113) KIRC - Kidney renal clear cell carcinoma(1967;0.138) Vorinostat(DB02546) GAGAAAACCAAGGAGGAGAAGCC 0.557 0.89 4 32 CSF3R 1441 broad.mit.edu 37 1 36935323 36935323 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:36935323delG uc001caw.1 - 11 1582 c.1404delC c.(1402-1404)CCCfs p.P468fs CSF3R_uc001cat.1_Frame_Shift_Del_p.P31fs|CSF3R_uc009vvc.1_Frame_Shift_Del_p.P31fs|CSF3R_uc001cau.1_5'UTR|CSF3R_uc001cav.1_Frame_Shift_Del_p.P468fs|CSF3R_uc001cax.1_Frame_Shift_Del_p.P468fs|CSF3R_uc001cay.1_Frame_Shift_Del_p.P468fs NM_000760 NP_000751 Q99062 CSF3R_HUMAN colony stimulating factor 3 receptor isoform a 468 Extracellular (Potential).|Fibronectin type-III 4. cell adhesion|defense response extracellular region|integral to plasma membrane cytokine receptor activity central_nervous_system(2)|ovary(1) 3 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) Filgrastim(DB00099)|Pegfilgrastim(DB00019) TGCTCGCGCTGGGGGGGCCCA 0.632 0.12 140 19 PLK3 1263 broad.mit.edu 37 1 45268997 45268997 + Frame_Shift_Del DEL C - - rs112574988 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:45268997delC uc001cmn.2 + 8 1106 c.1006delC c.(1006-1008)CCCfs p.P336fs PLK3_uc001cmo.2_RNA NM_004073 NP_004064 Q9H4B4 PLK3_HUMAN polo-like kinase 3 336 membrane ATP binding|protein binding|protein serine/threonine kinase activity 0 Acute lymphoblastic leukemia(166;0.155) AGACCTGACACCCCCCAACCC 0.577 0.44 58 45 PRKAA2 5563 broad.mit.edu 37 1 57157094 57157094 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:57157094delT uc001cyk.3 + 3 335 c.264delT c.(262-264)GATfs p.D88fs NM_006252 NP_006243 P54646 AAPK2_HUMAN AMP-activated protein kinase alpha 2 catalytic 88 Protein kinase. carnitine shuttle|cell cycle arrest|cholesterol biosynthetic process|energy reserve metabolic process|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleoplasm ATP binding|metal ion binding breast(4)|ovary(1)|stomach(1) 6 CTCCAACAGATTTTTTTATGG 0.328 0.37 61 36 JAK1 3716 broad.mit.edu 37 1 65325833 65325833 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:65325833delG uc001dbu.1 - 9 1538 c.1289delC c.(1288-1290)CCGfs p.P430fs JAK1_uc009wam.1_Frame_Shift_Del_p.P418fs NM_002227 NP_002218 P23458 JAK1_HUMAN janus kinase 1 430 interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway cytoskeleton|cytosol|endomembrane system|membrane|nucleus ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity p.P430fs*2(1) haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1) 61 BRCA - Breast invasive adenocarcinoma(111;0.0485) 0.000 0.56 152 192 JAK1 3716 broad.mit.edu 37 1 65339111 65339111 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:65339111delT uc001dbu.1 - 5 674 c.425delA c.(424-426)AAGfs p.K142fs JAK1_uc009wam.1_Frame_Shift_Del_p.K130fs|JAK1_uc001dbv.2_RNA NM_002227 NP_002218 P23458 JAK1_HUMAN janus kinase 1 142 FERM. interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway cytoskeleton|cytosol|endomembrane system|membrane|nucleus ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity p.K142fs*26(3) haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1) 61 BRCA - Breast invasive adenocarcinoma(111;0.0485) ATCTGGAATCTTTTTTTTCTC 0.478 0.38 212 132 ST6GALNAC5 81849 broad.mit.edu 37 1 77334276 77334277 + In_Frame_Ins INS - GCA GCA rs113832855 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:77334276_77334277insGCA uc001dhi.2 + 2 285_286 c.110_111insGCA c.(109-111)CCG>CCGCAG p.49_50insQ ST6GALNAC5_uc010ori.1_In_Frame_Ins_p.49_50insQ|ST6GALNAC5_uc009wbw.2_RNA NM_030965 NP_112227 Q9BVH7 SIA7E_HUMAN sialyltransferase 7E 49_50 Lumenal (Potential). protein glycosylation integral to Golgi membrane sialyltransferase activity pancreas(1)|skin(1) 2 GAGCGGCCCCCgcagcagcagc 0.579 0.41 10 7 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 300 101 ARNT 405 broad.mit.edu 37 1 150789283 150789283 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:150789283delG uc001evr.1 - 18 1926 c.1783delC c.(1783-1785)CGGfs p.R595fs ARNT_uc010pck.1_Frame_Shift_Del_p.R84fs|ARNT_uc001evs.1_Frame_Shift_Del_p.R580fs|ARNT_uc009wmb.1_Frame_Shift_Del_p.R581fs|ARNT_uc009wmc.1_Frame_Shift_Del_p.R595fs|ARNT_uc009wmd.1_Frame_Shift_Del_p.R580fs NM_001668 NP_001659 P27540 ARNT_HUMAN aryl hydrocarbon receptor nuclear translocator 595 positive regulation of hormone biosynthetic process|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|response to hypoxia aryl hydrocarbon receptor binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity skin(4)|lung(3)|central_nervous_system(1)|kidney(1) 9 all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211) TCTGCCGGCCGGGGGGTAGGA 0.527 0.47 110 96 RNASEL 6041 broad.mit.edu 37 1 182554909 182554909 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:182554909delC uc001gpj.1 - 1 1200 c.1033delG c.(1033-1035)GCAfs p.A345fs RNASEL_uc009wxz.1_Frame_Shift_Del_p.A345fs|RNASEL_uc001gpk.2_Frame_Shift_Del_p.A345fs|RNASEL_uc009wya.1_Frame_Shift_Del_p.A345fs NM_021133 NP_066956 Q05823 RN5A_HUMAN ribonuclease L 345 mRNA processing|response to virus|type I interferon-mediated signaling pathway mitochondrion ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding ovary(4)|stomach(1) 5 TTCAGGGCTGCCCCCCAGTGT 0.453 0.30 55 24 FMN2 56776 broad.mit.edu 37 1 240370840 240370840 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr1:240370840delC uc010pyd.1 + 5 2953 c.2728delC c.(2728-2730)CCCfs p.P910fs FMN2_uc010pye.1_Frame_Shift_Del_p.P914fs NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 910 Pro-rich.|FH1. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) AATGCTGCCACCCCCTCCCCC 0.662 0.24 81 25 CAD 790 broad.mit.edu 37 2 27456981 27456982 + Frame_Shift_Ins INS - C C HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr2:27456981_27456982insC uc002rji.2 + 22 3667_3668 c.3505_3506insC c.(3505-3507)ACCfs p.T1169fs CAD_uc010eyw.2_Frame_Shift_Ins_p.T1106fs NM_004341 NP_004332 P27708 PYR1_HUMAN carbamoylphosphate synthetase 2/aspartate 1169 CPSase B.|ATP-grasp 2.|CPSase (Carbamoyl-phosphate synthase). 'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process cytosol|neuronal cell body|nuclear matrix|terminal button aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1) 10 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) L-Aspartic Acid(DB00128)|L-Glutamine(DB00130) GACGCTGGTGACCCCCCCACAA 0.574 0.15 144 26 BCL11A 53335 broad.mit.edu 37 2 60689254 60689254 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr2:60689254delG uc002sae.1 - 4 1021 c.793delC c.(793-795)CTGfs p.L265fs BCL11A_uc002sab.2_Frame_Shift_Del_p.L265fs|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Frame_Shift_Del_p.L231fs|BCL11A_uc002sad.1_Frame_Shift_Del_p.L113fs|BCL11A_uc002saf.1_Frame_Shift_Del_p.L231fs NM_022893 NP_075044 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A isoform 1 265 Pro-rich. negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|cytoplasm|nucleus|nucleus nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding central_nervous_system(6)|breast(3)|ovary(2)|skin(2) 13 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) GGACTAAACAGGGGGGGAGTG 0.582 0.29 22 9 LRP2 4036 broad.mit.edu 37 2 169997025 169997025 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr2:169997025delG uc002ues.2 - 72 13352 c.13139delC c.(13138-13140)CCAfs p.P4380fs NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 4380 EGF-like 17.|Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) 0.000 0.58 90 122 NFE2L2 4780 broad.mit.edu 37 2 178098976 178098979 + Frame_Shift_Del DEL AAGT - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr2:178098976_178098979delAAGT uc002ulh.3 - 2 621_624 c.66_69delACTT c.(64-69)ATACTTfs p.I22fs NFE2L2_uc002ulg.3_Frame_Shift_Del_p.I6fs|NFE2L2_uc010zfa.1_Frame_Shift_Del_p.I6fs|NFE2L2_uc002uli.3_Frame_Shift_Del_p.I6fs|NFE2L2_uc010fra.2_Frame_Shift_Del_p.I6fs|NFE2L2_uc010frb.2_Frame_Shift_Del_p.I6fs NM_006164 NP_006155 Q16236 NF2L2_HUMAN nuclear factor erythroid 2-like 2 isoform 1 22_23 transcription from RNA polymerase II promoter centrosome|cytosol|nucleus|plasma membrane protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity central_nervous_system(1) 1 Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935) 0.000 0.53 92 103 TTN 7273 broad.mit.edu 37 2 179535860 179535860 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr2:179535860delT uc010zfg.1 - 151 31586 c.31362delA c.(31360-31362)AAAfs p.K10454fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.K7115fs|TTN_uc010fre.1_Intron|TTN_uc010zfk.1_5'UTR NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 11381 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TAGTGGGCGGTTTTTTTGGAG 0.368 0.43 83 63 STRADB 55437 broad.mit.edu 37 2 202343320 202343320 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr2:202343320delA uc002uyd.3 + 10 1431 c.1066delA c.(1066-1068)AAAfs p.K356fs NM_018571 NP_061041 Q9C0K7 STRAB_HUMAN STE20-related kinase adaptor beta 356 Protein kinase. activation of protein kinase activity|cell cycle arrest|insulin receptor signaling pathway|protein export from nucleus|regulation of fatty acid oxidation cytosol|nucleus ATP binding|protein binding|protein kinase activity p.K356N(1) skin(2)|stomach(1)|lung(1) 4 AGATCCTGAGAAAAGGTAATA 0.353 0.42 22 16 IRS1 3667 broad.mit.edu 37 2 227660807 227660808 + In_Frame_Ins INS - GCT GCT HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr2:227660807_227660808insGCT uc002voh.3 - 1 2699_2700 c.2647_2648insAGC c.(2647-2649)CCC>CAGCCC p.882_883insQ NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 882_883 fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) GTGCAGCAAGGgctgctgctgc 0.554 0.39 19 12 TRPM8 79054 broad.mit.edu 37 2 234871949 234871949 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr2:234871949delC uc002vvh.2 + 13 1717 c.1677delC c.(1675-1677)CACfs p.H559fs TRPM8_uc010fyj.2_Frame_Shift_Del_p.H247fs NM_024080 NP_076985 Q7Z2W7 TRPM8_HUMAN transient receptor potential cation channel, 559 Cytoplasmic (Potential). integral to membrane skin(4) 4 Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224) Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108) Menthol(DB00825) TTACTCGGCACCCCCTGCAAG 0.512 0.47 72 64 TRPM8 79054 broad.mit.edu 37 2 234879010 234879010 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr2:234879010delC uc002vvh.2 + 17 2335 c.2295delC c.(2293-2295)CACfs p.H765fs TRPM8_uc010fyj.2_Intron NM_024080 NP_076985 Q7Z2W7 TRPM8_HUMAN transient receptor potential cation channel, 765 Helical; Name=3; (Potential). integral to membrane skin(4) 4 Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224) Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108) Menthol(DB00825) CGGTGCCACACCCCCCCGAGC 0.577 0.10 408 46 CNTN6 27255 broad.mit.edu 37 3 1371500 1371501 + Frame_Shift_Ins INS - A A HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr3:1371500_1371501insA uc003boz.2 + 11 1512_1513 c.1245_1246insA c.(1243-1248)GTTAAAfs p.V415fs CNTN6_uc011asj.1_Frame_Shift_Ins_p.V343fs|CNTN6_uc003bpa.2_Frame_Shift_Ins_p.V415fs NM_014461 NP_055276 Q9UQ52 CNTN6_HUMAN contactin 6 precursor 415_416 Ig-like C2-type 5. axon guidance|cell adhesion|central nervous system development|Notch signaling pathway anchored to membrane|plasma membrane skin(3)|lung(2)|breast(2)|pancreas(1) 8 all_cancers(2;0.000164)|all_epithelial(2;0.107) Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139) AAAGTCCAGTTAAAAAAAAGTC 0.391 0.51 38 39 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.32 13 6 DCLK3 85443 broad.mit.edu 37 3 36779823 36779824 + Frame_Shift_Ins INS - G G HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr3:36779823_36779824insG uc003cgi.2 - 2 818_819 c.327_328insC c.(325-330)CCCAGGfs p.P109fs NM_033403 NP_208382 Q9C098 DCLK3_HUMAN doublecortin-like kinase 3 109_110 cytoplasm|nucleus ATP binding|protein serine/threonine kinase activity lung(3)|large_intestine(2)|breast(1)|skin(1)|ovary(1)|kidney(1) 9 GTGGCTTCCCTGGGGGGCTTGC 0.559 0.24 369 116 DOCK3 1795 broad.mit.edu 37 3 51297747 51297747 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr3:51297747delT uc011bds.1 + 23 2368 c.2345delT c.(2344-2346)CTTfs p.L782fs NM_004947 NP_004938 Q8IZD9 DOCK3_HUMAN dedicator of cytokinesis 3 782 cytoplasm GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding 0 BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518) GAAACACTCCTTTTTACTCAG 0.473 0.42 107 78 DOCK3 1795 broad.mit.edu 37 3 51399289 51399290 + Splice_Site INS - C C HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr3:51399289_51399290insC uc011bds.1 + 48 5030 c.5007_splice c.e48-1 p.S1669_splice NM_004947 NP_004938 Q8IZD9 DOCK3_HUMAN dedicator of cytokinesis 3 cytoplasm GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding 0 BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518) CTTGCTCACAGCCCCATGAACT 0.554 0.48 92 86 GRK7 131890 broad.mit.edu 37 3 141497729 141497729 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr3:141497729delT uc011bnd.1 + 1 687 c.603delT c.(601-603)GGTfs p.G201fs NM_139209 NP_631948 Q8WTQ7 GRK7_HUMAN G-protein-coupled receptor kinase 7 precursor 201 ATP (By similarity).|Protein kinase. visual perception membrane ATP binding|G-protein coupled receptor kinase activity|signal transducer activity lung(2)|stomach(1)|ovary(1)|skin(1) 5 GGAAAGGTGGTTTTGGGGAGG 0.468 0.42 141 104 TNK2 10188 broad.mit.edu 37 3 195597005 195597006 + Frame_Shift_Ins INS - G G HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr3:195597005_195597006insG uc003fvu.1 - 11 2065_2066 c.1522_1523insC c.(1522-1524)CAGfs p.Q508fs TNK2_uc003fvq.1_5'Flank|TNK2_uc003fvr.1_Frame_Shift_Ins_p.Q18fs|TNK2_uc003fvs.1_Frame_Shift_Ins_p.Q540fs|TNK2_uc003fvt.1_Frame_Shift_Ins_p.Q571fs|TNK2_uc010hzw.1_RNA|TNK2_uc003fvv.1_Frame_Shift_Ins_p.Q338fs NM_005781 NP_005772 Q07912 ACK1_HUMAN tyrosine kinase, non-receptor, 2 isoform 1 508 Missing (in Ref. 4; AAH08884). positive regulation of peptidyl-tyrosine phosphorylation|protein ubiquitination|small GTPase mediated signal transduction adherens junction|cytoplasmic vesicle membrane|endosome|nucleus ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1) 10 all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206) Lung NSC(153;0.191) Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05) GBM - Glioblastoma multiforme(46;0.000757) Adenosine triphosphate(DB00171) TCCTAGATGCTGGGGGGGCCGG 0.614 0.37 85 49 GRK4 2868 broad.mit.edu 37 4 2986250 2986251 + Frame_Shift_Ins INS - A A rs141511339 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr4:2986250_2986251insA uc003ggn.1 + 2 518_519 c.63_64insA c.(61-66)GGCAAAfs p.G21fs GRK4_uc003ggo.1_Frame_Shift_Ins_p.G21fs|GRK4_uc003ggp.1_Intron|GRK4_uc003ggq.1_Intron NM_182982 NP_892027 P32298 GRK4_HUMAN G protein-coupled receptor kinase 4 isoform 21_22 N-terminal. cell cortex ATP binding|G-protein coupled receptor kinase activity|signal transducer activity lung(1) 1 UCEC - Uterine corpus endometrioid carcinoma (64;0.168) 0.000 0.37 102 59 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 116 163 NIPBL 25836 broad.mit.edu 37 5 37010322 37010322 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr5:37010322delA uc003jkl.3 + 21 5054 c.4555delA c.(4555-4557)AAAfs p.K1519fs NIPBL_uc003jkk.3_Frame_Shift_Del_p.K1519fs NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 1519 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) AGATTCAAATAAAAAAGTAAG 0.299 0.37 29 17 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.37 144 83 FER 2241 broad.mit.edu 37 5 108233470 108233470 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr5:108233470delA uc003kop.1 + 10 1541 c.1157delA c.(1156-1158)CAAfs p.Q386fs FER_uc011cvf.1_Intron|FER_uc011cvg.1_Frame_Shift_Del_p.Q211fs NM_005246 NP_005237 P16591 FER_HUMAN fer (fps/fes related) tyrosine kinase 386 Potential. intracellular signal transduction|peptidyl-tyrosine phosphorylation cytoplasm|nucleus ATP binding|non-membrane spanning protein tyrosine kinase activity lung(2)|stomach(1)|ovary(1)|kidney(1) 5 all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152) OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174) TTACTAGAGCAAAAAGTGCAA 0.403 0.45 33 27 ZNF608 57507 broad.mit.edu 37 5 124079984 124079984 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr5:124079984delC uc003ktq.1 - 1 822 c.699delG c.(697-699)GGGfs p.G233fs ZNF608_uc003ktr.1_RNA|ZNF608_uc003kts.1_Frame_Shift_Del_p.G233fs|ZNF608_uc003ktt.1_Frame_Shift_Del_p.G233fs NM_020747 NP_065798 Q9ULD9 ZN608_HUMAN zinc finger protein 608 233 intracellular zinc ion binding skin(3)|ovary(2)|lung(1) 6 all_cancers(142;0.186)|Prostate(80;0.081) KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221) OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783) CATAGAGGTGCCCCCCGGAAG 0.657 0.39 67 43 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.71 6 15 STK10 6793 broad.mit.edu 37 5 171554400 171554400 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr5:171554400delC uc003mbo.1 - 3 647 c.347delG c.(346-348)GGAfs p.G116fs NM_005990 NP_005981 O94804 STK10_HUMAN serine/threonine kinase 10 116 Protein kinase. ATP binding|protein serine/threonine kinase activity ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1) 8 Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094) Medulloblastoma(196;0.00868)|all_neural(177;0.026) Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516) GTCCACGGCTCCCCCTGGACA 0.567 0.30 52 22 RANBP9 10048 broad.mit.edu 37 6 13632610 13632610 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr6:13632610delT uc003nbb.2 - 12 1998 c.1939delA c.(1939-1941)ATGfs p.M647fs RANBP9_uc003nba.2_Frame_Shift_Del_p.M306fs NM_005493 NP_005484 Q96S59 RANB9_HUMAN RAN binding protein 9 647 Interaction with FMR1. axon guidance|microtubule nucleation|protein complex assembly cytosol|microtubule associated complex|nucleus Ran GTPase binding lung(1)|skin(1) 2 Breast(50;0.00669)|Ovarian(93;0.0634) all_hematologic(90;0.117) Epithelial(50;0.223) ACCTTCAACATTTTTTTGTTT 0.378 0.46 108 91 DNAH8 1769 broad.mit.edu 37 6 38890910 38890910 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr6:38890910delA uc003ooe.1 + 70 10688 c.10088delA c.(10087-10089)GAAfs p.E3363fs uc003oof.1_RNA NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 CTGAGTGGAGAAAAAATCCGG 0.453 0.39 28 18 PTK7 5754 broad.mit.edu 37 6 43097997 43097997 + Frame_Shift_Del DEL C - - rs35848762 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr6:43097997delC uc003oub.1 + 4 698 c.500delC c.(499-501)ACCfs p.T167fs PTK7_uc003ouc.1_Frame_Shift_Del_p.T167fs|PTK7_uc003oud.1_Frame_Shift_Del_p.T167fs|PTK7_uc003oue.1_Frame_Shift_Del_p.T167fs|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_Intron|PTK7_uc011dve.1_Frame_Shift_Del_p.T175fs|PTK7_uc010jyj.1_5'Flank|PTK7_uc003oua.2_Frame_Shift_Del_p.T167fs NM_002821 NP_002812 Q13308 PTK7_HUMAN PTK7 protein tyrosine kinase 7 isoform a 167 Ig-like C2-type 2.|Extracellular (Potential). actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration cell-cell junction|integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ovary(2)|large_intestine(1) 3 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423) CGAGATGGGACCCCCCTTTCT 0.597 0.64 5 9 PKHD1 5314 broad.mit.edu 37 6 51890014 51890015 + Frame_Shift_Ins INS - A A HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr6:51890014_51890015insA uc003pah.1 - 32 4869_4870 c.4593_4594insT c.(4591-4596)TTTAATfs p.F1531fs PKHD1_uc003pai.2_Frame_Shift_Ins_p.F1531fs NM_138694 NP_619639 P08F94 PKHD1_HUMAN fibrocystin isoform 1 1531_1532 Extracellular (Potential).|IPT/TIG 10. cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body protein binding|receptor activity lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1) 44 Lung NSC(77;0.0605) TGGCTTGCATTAAAAAAAGTTA 0.460 0.41 160 110 TTK 7272 broad.mit.edu 37 6 80720539 80720539 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr6:80720539delA uc003pjc.2 + 5 552 c.478delA c.(478-480)AAAfs p.K160fs TTK_uc003pjb.3_Frame_Shift_Del_p.K160fs NM_003318 NP_003309 P33981 TTK_HUMAN TTK protein kinase 160 mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation spindle ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1) 11 all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2) BRCA - Breast invasive adenocarcinoma(397;0.0321) AGGTAATGTCAAAAAAAGTAA 0.383 0.46 7 6 EPHA7 2045 broad.mit.edu 37 6 94068058 94068058 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr6:94068058delA uc003poe.2 - 4 1145 c.904delT c.(904-906)TCTfs p.S302fs EPHA7_uc003pof.2_Frame_Shift_Del_p.S302fs|EPHA7_uc011eac.1_Frame_Shift_Del_p.S302fs NM_004440 NP_004431 Q15375 EPHA7_HUMAN ephrin receptor EphA7 precursor 302 Extracellular (Potential).|Cys-rich. integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1) 28 all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142) BRCA - Breast invasive adenocarcinoma(108;0.0847) TCTTTATCAGAAAAACTGTGA 0.453 0.35 24 13 LIMK1 3984 broad.mit.edu 37 7 73513509 73513509 + Frame_Shift_Del DEL C - - rs150491142 byFrequency HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr7:73513509delC uc003uaa.1 + 5 714 c.549delC c.(547-549)GACfs p.D183fs RFC2_uc011kfa.1_Intron|LIMK1_uc010lbl.1_RNA|LIMK1_uc003uab.2_Frame_Shift_Del_p.D149fs|LIMK1_uc003uac.1_5'UTR NM_002314 NP_002305 P53667 LIMK1_HUMAN LIM domain kinase 1 183 PDZ. actin cytoskeleton organization|axon guidance|negative regulation of ubiquitin-protein ligase activity|positive regulation of actin filament bundle assembly|positive regulation of axon extension|Rho protein signal transduction cytosol|growth cone|nucleus ATP binding|heat shock protein binding|protein serine/threonine kinase activity|zinc ion binding stomach(2)|ovary(1) 3 Lung NSC(55;0.137) TCTCCATTGACCCCCCGCACG 0.677 0.41 83 57 GRM8 2918 broad.mit.edu 37 7 126173278 126173278 + Frame_Shift_Del DEL G - - rs77499554 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr7:126173278delG uc003vlr.2 - 8 2469 c.2158delC c.(2158-2160)CACfs p.H720fs GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Frame_Shift_Del_p.H720fs|GRM8_uc010lkz.1_RNA NM_000845 NP_000836 O00222 GRM8_HUMAN glutamate receptor, metabotropic 8 isoform a 720 Extracellular (Potential). negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception integral to plasma membrane lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1) 23 Prostate(267;0.186) L-Glutamic Acid(DB00142) 0.000 0.88 89 643 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 18 NOS3 4846 broad.mit.edu 37 7 150698398 150698398 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr7:150698398delG uc003wif.2 + 11 1609 c.1313delG c.(1312-1314)AGGfs p.R438fs NOS3_uc011kuy.1_Frame_Shift_Del_p.R232fs|NOS3_uc011kuz.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kva.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kvb.1_Frame_Shift_Del_p.R438fs NM_000603 NP_000594 P29474 NOS3_HUMAN nitric oxide synthase 3 isoform 1 438 Interaction with NOSIP. anti-apoptosis|arginine catabolic process|blood vessel remodeling|endothelial cell migration|mitochondrion organization|negative regulation of muscle hyperplasia|negative regulation of platelet activation|nitric oxide biosynthetic process|platelet activation|positive regulation of angiogenesis|positive regulation of guanylate cyclase activity|positive regulation of vasodilation|regulation of blood vessel size|regulation of nitric-oxide synthase activity|regulation of systemic arterial blood pressure by endothelin|response to fluid shear stress|response to heat|smooth muscle hyperplasia caveola|cytoskeleton|cytosol|Golgi membrane actin monomer binding|arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding central_nervous_system(5)|large_intestine(2)|skin(1) 8 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) L-Arginine(DB00125)|L-Citrulline(DB00155)|Rosuvastatin(DB01098)|Tetrahydrobiopterin(DB00360) CAGAAGGCCAGGGGGGGCTGC 0.617 0.63 10 17 MLL3 58508 broad.mit.edu 37 7 151845523 151845524 + Frame_Shift_Ins INS - A A HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr7:151845523_151845524insA uc003wla.2 - 52 13707_13708 c.13488_13489insT c.(13486-13491)TTTAAGfs p.F4496fs MLL3_uc003wkz.2_Frame_Shift_Ins_p.F3614fs|MLL3_uc003wkx.2_Frame_Shift_Ins_p.F654fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.F2060fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 4496_4497 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) GTTTTGTCCTTAAAAAACATGC 0.431 0.43 219 165 STAR 6770 broad.mit.edu 37 8 38006212 38006212 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr8:38006212delC uc003xkv.1 - 2 389 c.125delG c.(124-126)GGCfs p.G42fs STAR_uc010lwc.1_Intron NM_001007243 NP_001007244 P49675 STAR_HUMAN steroidogenic acute regulatory protein isoform 42 C21-steroid hormone biosynthetic process mitochondrial intermembrane space cholesterol transporter activity ovary(1) 1 Colorectal(12;0.000442) all_lung(54;0.0151)|Lung NSC(58;0.0295) READ - Rectum adenocarcinoma(644;0.188) AGGGGTGGGGCCCCCCAGGGC 0.587 0.43 83 63 BAG4 9530 broad.mit.edu 37 8 38067995 38067995 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr8:38067995delA uc003xky.1 + 5 1640 c.1358delA c.(1357-1359)GAAfs p.E453fs BAG4_uc003xkz.1_Frame_Shift_Del_p.E417fs NM_004874 NP_004865 O95429 BAG4_HUMAN BCL2-associated athanogene 4 453 BAG. anti-apoptosis|apoptosis|protein folding cytoplasm|nucleus receptor signaling protein activity ovary(1) 1 Colorectal(12;0.000442) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121) GAAAAATTAGAAAAAAAAGGA 0.398 0.43 12 9 PLAT 5327 broad.mit.edu 37 8 42038062 42038062 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr8:42038062delC uc003xos.2 - 10 1240 c.1031delG c.(1030-1032)GGCfs p.G344fs PLAT_uc010lxf.1_Frame_Shift_Del_p.G261fs|PLAT_uc010lxg.1_Frame_Shift_Del_p.G169fs|PLAT_uc003xot.2_Frame_Shift_Del_p.G298fs|PLAT_uc011lcm.1_Frame_Shift_Del_p.G255fs|PLAT_uc011lcn.1_Frame_Shift_Del_p.G218fs NM_000930 NP_000921 P00750 TPA_HUMAN plasminogen activator, tissue isoform 1 344 Peptidase S1. blood coagulation|fibrinolysis|negative regulation of proteolysis|protein modification process|proteolysis cell surface|cytoplasm|extracellular space protein binding|serine-type endopeptidase activity breast(1)|skin(1) 2 all_cancers(6;3.84e-26)|all_epithelial(6;9.61e-28)|all_lung(13;7.2e-13)|Lung NSC(13;1.18e-11)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211) all_lung(54;0.000378)|Lung NSC(58;0.00145)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954) BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00135)|Colorectal(10;0.00165)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024) Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Iloprost(DB01088)|Reteplase(DB00015)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013) 0.000 0.14 1581 260 STK3 6788 broad.mit.edu 37 8 99468221 99468221 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr8:99468221delT uc003yip.2 - 11 1466 c.1325delA c.(1324-1326)AATfs p.N442fs STK3_uc003yio.2_Frame_Shift_Del_p.N470fs NM_006281 NP_006272 Q13188 STK3_HUMAN serine/threonine kinase 3 442 SARAH.|Potential. apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis cytoplasm|nucleus ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity lung(3)|ovary(1) 4 Breast(36;2.4e-06) Breast(495;0.106) OV - Ovarian serous cystadenocarcinoma(57;0.0382) KIRC - Kidney renal clear cell carcinoma(542;9.44e-06) TAAACTTAGATTTTTCAACTA 0.348 0.30 109 46 VPS13B 157680 broad.mit.edu 37 8 100654474 100654474 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr8:100654474delA uc003yiv.2 + 34 5842 c.5731delA c.(5731-5733)AAAfs p.K1911fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.K1886fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 1911 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TCCTTCAGGGAAAAAAATAGG 0.458 0.37 63 37 RIMS2 9699 broad.mit.edu 37 8 104927779 104927779 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr8:104927779delA uc003yls.2 + 5 1444 c.1203delA c.(1201-1203)GTAfs p.V401fs RIMS2_uc003ylp.2_Frame_Shift_Del_p.V623fs|RIMS2_uc003ylw.2_Frame_Shift_Del_p.V431fs|RIMS2_uc003ylq.2_Frame_Shift_Del_p.V431fs|RIMS2_uc003ylr.2_Frame_Shift_Del_p.V478fs|RIMS2_uc003ylt.2_Frame_Shift_Del_p.V24fs|RIMS2_uc003ylu.1_Frame_Shift_Del_p.V14fs|RIMS2_uc003ylv.1_Frame_Shift_Del_p.V14fs NM_014677 NP_055492 Q9UQ26 RIMS2_HUMAN regulating synaptic membrane exocytosis 2 701 PDZ. intracellular protein transport cell junction|presynaptic membrane metal ion binding|Rab GTPase binding ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1) 15 OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229) TTACTAAAGTAAAAAAAGGAA 0.323 0.50 67 68 TLE1 7088 broad.mit.edu 37 9 84208104 84208104 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr9:84208104delG uc004aly.2 - 15 1858 c.1417delC c.(1417-1419)CGGfs p.R473fs TLE1_uc004alz.2_Frame_Shift_Del_p.R483fs|TLE1_uc011lsr.1_Frame_Shift_Del_p.R458fs|TLE1_uc004ama.1_Frame_Shift_Del_p.R472fs NM_005077 NP_005068 Q04724 TLE1_HUMAN transducin-like enhancer protein 1 473 WD 1. negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway transcription factor binding ovary(1)|skin(1) 2 CGAGCATGCCGGGGGATTCCG 0.602 0.54 6 7 GRIN3A 116443 broad.mit.edu 37 9 104335503 104335503 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr9:104335503delT uc004bbp.1 - 9 3902 c.3301delA c.(3301-3303)ACGfs p.T1101fs GRIN3A_uc004bbo.1_Frame_Shift_Del_p.T176fs NM_133445 NP_597702 Q8TCU5 NMD3A_HUMAN glutamate receptor, ionotropic, 1101 Cytoplasmic (Potential).|Potential. response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1) 7 Acute lymphoblastic leukemia(62;0.0568) Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740) 0.000 0.29 1202 499 SMC2 10592 broad.mit.edu 37 9 106862450 106862450 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr9:106862450delA uc004bbv.2 + 6 845 c.557delA c.(556-558)GAAfs p.E186fs SMC2_uc004bbu.1_Frame_Shift_Del_p.E186fs|SMC2_uc004bbw.2_Frame_Shift_Del_p.E186fs|SMC2_uc011lvl.1_Frame_Shift_Del_p.E186fs|SMC2_uc010mtg.1_Frame_Shift_Del_p.E41fs|SMC2_uc010mth.1_Frame_Shift_Del_p.E136fs|SMC2_uc004bbx.2_Frame_Shift_Del_p.E186fs NM_001042551 NP_001036016 O95347 SMC2_HUMAN structural maintenance of chromosomes 2 186 Potential. cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism condensin complex|cytoplasm|nuclear chromosome ATP binding|protein heterodimerization activity p.E186K(1) ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1) 9 AAAACTATAGAAAAAAAGGAG 0.299 0.68 6 13 ADARB2 105 broad.mit.edu 37 10 1230936 1230936 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr10:1230936delG uc009xhq.2 - 9 2282 c.1908delC c.(1906-1908)CCCfs p.P636fs ADARB2_uc009xhp.2_Frame_Shift_Del_p.P20fs|ADARB2_uc001igl.3_5'UTR|ADARB2_uc001igm.3_Frame_Shift_Del_p.P145fs NM_018702 NP_061172 Q9NS39 RED2_HUMAN adenosine deaminase, RNA-specific, B2 636 A to I editase. mRNA processing mitochondrion|nucleus adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding large_intestine(2)|central_nervous_system(1) 3 all_epithelial(10;0.059)|Colorectal(49;0.0815) all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165) TCATGCTGAAGGGGGGCGACT 0.677 0.39 33 21 RET 5979 broad.mit.edu 37 10 43609003 43609003 + Splice_Site DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr10:43609003delG uc001jal.2 + 10 1950 c.1760_splice c.e10-1 p.R587_splice RET_uc001jak.1_Splice_Site_p.R587_splice|RET_uc010qez.1_Splice_Site_p.R333_splice NM_020975 NP_066124 P07949 RET_HUMAN ret proto-oncogene isoform a homophilic cell adhesion|positive regulation of metanephric glomerulus development|positive regulation of transcription, DNA-dependent|posterior midgut development integral to membrane ATP binding|calcium ion binding|transmembrane receptor protein tyrosine kinase activity thyroid(404)|adrenal_gland(20)|lung(9)|large_intestine(5)|breast(4)|ovary(4)|central_nervous_system(3)|urinary_tract(1)|NS(1) 451 Ovarian(717;0.0423) Sunitinib(DB01268) 0.000 0.61 181 282 PTEN 5728 broad.mit.edu 37 10 89653796 89653798 + In_Frame_Del DEL ATT - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr10:89653796_89653798delATT uc001kfb.2 + 3 1125_1127 c.94_96delATT c.(94-96)ATTdel p.I33del NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 33 Phosphatase tensin-type. Missing (in CD). activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.?(4)|p.I32del(3)|p.Y27fs*1(2)|p.I33fs*21(2)|p.Y27_N212>Y(2)|p.I32fs*22(2)|p.I33del(1)|p.I33fs*20(1)|p.I33S(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) TTATCCAAACATTATTGCTATGG 0.291 0.42 89 65 PTEN 5728 broad.mit.edu 37 10 89690819 89690820 + Frame_Shift_Del DEL TA - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr10:89690819_89690820delTA uc001kfb.2 + 5 1257_1258 c.226_227delTA c.(226-228)TATfs p.Y76fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 76 Phosphatase tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.Y76fs*1(12)|p.L70fs*7(4)|p.R55fs*1(4)|p.?(2)|p.C71fs*6(2)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.Y76Y(1)|p.Y76*(1)|p.Y76del(1)|p.H75_T78del(1)|p.F56fs*2(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) TGAAAGACATTATGACACCGCC 0.272 0.45 64 53 PDCD11 22984 broad.mit.edu 37 10 105166438 105166441 + Frame_Shift_Del DEL GTCT - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr10:105166438_105166441delGTCT uc001kwy.1 + 7 848_851 c.761_764delGTCT c.(760-765)AGTCTGfs p.S254fs NM_014976 NP_055791 Q14690 RRP5_HUMAN programmed cell death 11 254_255 S1 motif 2. mRNA processing|rRNA processing nucleolus RNA binding|transcription factor binding ovary(2)|breast(2)|skin(2)|central_nervous_system(1) 7 Colorectal(252;0.0747)|Breast(234;0.128) Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208) GGAGTTGTTAGTCTGTCTGTTGGT 0.490 0.38 179 112 PIK3C2A 5286 broad.mit.edu 37 11 17190379 17190379 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr11:17190379delA uc001mmq.3 - 1 976 c.910delT c.(910-912)TGGfs p.W304fs PIK3C2A_uc009ygu.1_Intron|PIK3C2A_uc010rcw.1_Intron|PIK3C2A_uc001mmr.3_RNA|PIK3C2A_uc010rcx.1_Frame_Shift_Del_p.W304fs|PIK3C2A_uc009ygv.1_Frame_Shift_Del_p.W304fs NM_002645 NP_002636 O00443 P3C2A_HUMAN phosphoinositide-3-kinase, class 2 alpha 304 cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity lung(4)|central_nervous_system(4)|stomach(1)|ovary(1) 10 Phosphatidylserine(DB00144) ACAGCATCCCAAGGATCCTTT 0.408 0.47 92 81 DDB2 1643 broad.mit.edu 37 11 47256398 47256401 + Frame_Shift_Del DEL CAAA - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr11:47256398_47256401delCAAA uc001neb.2 + 6 988_991 c.793_796delCAAA c.(793-798)CAAACAfs p.Q265fs DDB2_uc001nec.2_Intron|DDB2_uc009yli.1_Frame_Shift_Del_p.Q201fs|DDB2_uc001ned.2_Intron|DDB2_uc001nee.2_Intron|DDB2_uc001nef.2_Intron|DDB2_uc001neg.2_Frame_Shift_Del_p.Q124fs|DDB2_uc001neh.2_RNA NM_000107 NP_000098 Q92466 DDB2_HUMAN damage-specific DNA binding protein 2 265_266 DWD box.|WD 3. nucleotide-excision repair, DNA damage removal|protein autoubiquitination|protein polyubiquitination|response to UV nucleoplasm|protein complex damaged DNA binding|protein binding kidney(2)|ovary(1) 3 CTCCGTAGATCAAACAGTGAAAAT 0.525 0.46 56 47 SLC3A2 6520 broad.mit.edu 37 11 62623813 62623813 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr11:62623813delG uc001nwd.2 + 1 296 c.72delG c.(70-72)TCGfs p.S24fs SLC3A2_uc001nwb.2_Frame_Shift_Del_p.S24fs|SLC3A2_uc001nwc.2_Frame_Shift_Del_p.S24fs|SLC3A2_uc001nwe.2_Frame_Shift_Del_p.S24fs|SLC3A2_uc001nwf.2_Frame_Shift_Del_p.S24fs|SNHG1_uc001nvp.2_5'Flank|SNHG1_uc001nvo.2_5'Flank|SNHG1_uc001nvq.2_5'Flank|SNHG1_uc001nvs.2_5'Flank|SNHG1_uc001nvr.2_5'Flank|SNHG1_uc001nvt.2_5'Flank|SNHG1_uc001nvu.2_5'Flank|SNORD31_uc009yoj.1_5'Flank|SNORD30_uc001nvw.1_5'Flank|SNORD29_uc001nvx.2_5'Flank|SNORD28_uc001nvy.1_5'Flank|SNORD27_uc001nvz.2_5'Flank|SNORD26_uc009yok.1_5'Flank|SNORD25_uc001nwa.3_5'Flank NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c 24 blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.20 776 189 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.96 1 24 PAK1 5058 broad.mit.edu 37 11 77069989 77069990 + In_Frame_Ins INS - CAT CAT rs149665907 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr11:77069989_77069990insCAT uc001oyh.3 - 6 1083_1084 c.550_551insATG c.(550-552)GCT>GATGCT p.183_184insD PAK1_uc010rso.1_In_Frame_Ins_p.85_86insD|PAK1_uc001oyg.3_In_Frame_Ins_p.183_184insD|PAK1_uc001oyi.1_In_Frame_Ins_p.183_184insD|PAK1_uc010rsn.1_Translation_Start_Site NM_002576 NP_002567 Q13153 PAK1_HUMAN p21-activated kinase 1 isoform 2 183_184 Interaction with CRIPAK. apoptosis|axon guidance|cytoskeleton organization|ER-nucleus signaling pathway|positive regulation of JUN kinase activity|positive regulation of peptidyl-serine phosphorylation|protein autophosphorylation|T cell costimulation|T cell receptor signaling pathway cytosol|focal adhesion|Golgi apparatus ATP binding|collagen binding|protein binding|protein serine/threonine kinase activity skin(2)|stomach(1)|lung(1) 4 all_cancers(14;1.75e-18) TGGTGGGGTAGcatcatcatca 0.426 0.26 199 70 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 650 146 SIK3 23387 broad.mit.edu 37 11 116729328 116729328 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr11:116729328delG uc001ppy.2 - 20 2571 c.2535delC c.(2533-2535)CCCfs p.P845fs SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron|SIK3_uc001ppw.2_Intron|SIK3_uc001ppx.2_Intron|SIK3_uc001pqb.2_Frame_Shift_Del_p.P148fs NM_025164 NP_079440 Q9Y2K2 SIK3_HUMAN serine/threonine-protein kinase QSK 845 Gln-rich. cytoplasm ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1) 12 TGTAGCTGCTGGGGGAACCCC 0.567 0.38 142 87 ADAMTS20 80070 broad.mit.edu 37 12 43896065 43896066 + Frame_Shift_Ins INS - T T rs148832386 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr12:43896065_43896066insT uc010skx.1 - 4 756_757 c.756_757insA c.(754-759)AAACGTfs p.K252fs NM_025003 NP_079279 P59510 ATS20_HUMAN a disintegrin-like and metalloprotease with 252_253 proteinaceous extracellular matrix zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1) 19 all_cancers(12;2.6e-05)|Lung SC(27;0.184) Lung NSC(34;0.0569)|all_lung(34;0.129) GBM - Glioblastoma multiforme(48;0.0473) GATATAAGACGTTTTTTCCTGG 0.327 0.47 93 82 WNT1 7471 broad.mit.edu 37 12 49374348 49374348 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr12:49374348delG uc001rsu.2 + 3 698 c.500delG c.(499-501)TGGfs p.W167fs NM_005430 NP_005421 P04628 WNT1_HUMAN wingless-type MMTV integration site family, 167 brain segmentation|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|central nervous system morphogenesis|cerebellum formation|dermatome development|diencephalon development|embryonic axis specification|forebrain anterior/posterior pattern formation|fourth ventricle development|hemopoietic stem cell proliferation|hepatocyte differentiation|inner ear morphogenesis|mesoderm morphogenesis|midbrain development|midbrain-hindbrain boundary maturation during brain development|negative regulation of cell-cell adhesion|negative regulation of cell-substrate adhesion|negative regulation of DNA damage checkpoint|negative regulation of fat cell differentiation|neuron fate determination|positive regulation of fibroblast proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of lamellipodium assembly|positive regulation of Notch signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to wounding|signal transduction in response to DNA damage|Spemann organizer formation|T cell differentiation in thymus|Wnt receptor signaling pathway, calcium modulating pathway early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix cytokine activity|frizzled-2 binding|transcription regulatory region DNA binding kidney(1) 1 BRCA - Breast invasive adenocarcinoma(357;0.244) gACTGGCACTGGGGGGGCTGC 0.552 0.29 34 14 IKZF4 64375 broad.mit.edu 37 12 56429093 56429093 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr12:56429093delG uc001sjb.1 + 9 1895 c.1736delG c.(1735-1737)CGGfs p.R579fs IKZF4_uc010sqa.1_Frame_Shift_Del_p.R532fs|IKZF4_uc001sjc.1_Frame_Shift_Del_p.R579fs|IKZF4_uc001sjd.1_Frame_Shift_Del_p.R477fs|IKZF4_uc009zoi.1_Frame_Shift_Del_p.R534fs|IKZF4_uc001sje.1_Frame_Shift_Del_p.R538fs NM_022465 NP_071910 Q9H2S9 IKZF4_HUMAN zinc finger protein, subfamily 1A, 4 579 C2H2-type 6. negative regulation of transcription, DNA-dependent nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1) 1 UCEC - Uterine corpus endometrioid carcinoma (6;0.025)|OV - Ovarian serous cystadenocarcinoma(18;0.123) CACATTGTCCGGGGGGAGCAT 0.552 0.54 23 27 STAT6 6778 broad.mit.edu 37 12 57500491 57500491 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr12:57500491delC uc009zpe.2 - 5 714 c.463delG c.(463-465)GCTfs p.A155fs STAT6_uc009zpf.2_Frame_Shift_Del_p.A155fs|STAT6_uc001sna.2_Frame_Shift_Del_p.A155fs|STAT6_uc010srb.1_Frame_Shift_Del_p.A45fs|STAT6_uc010src.1_Frame_Shift_Del_p.A45fs|STAT6_uc010srd.1_Frame_Shift_Del_p.A45fs|STAT6_uc009zpg.2_Frame_Shift_Del_p.A204fs NM_003153 NP_003144 P42226 STAT6_HUMAN signal transducer and activator of transcription 155 regulation of transcription from RNA polymerase II promoter cytosol|nucleus calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity ovary(2)|lung(1)|skin(1) 4 CCAGCCTCAGCCCCCTTCTGC 0.572 0.44 121 97 LRP1 4035 broad.mit.edu 37 12 57556223 57556223 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr12:57556223delC uc001snd.2 + 14 2792 c.2326delC c.(2326-2328)CCCfs p.P776fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 776 Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) AGGAGGCGCACCCCCCACTGT 0.607 0.45 164 134 LRP1 4035 broad.mit.edu 37 12 57560723 57560723 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr12:57560723delC uc001snd.2 + 18 3274 c.2808delC c.(2806-2808)TGCfs p.C936fs LRP1_uc009zph.1_5'Flank|LRP1_uc009zpi.1_5'Flank NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 936 LDL-receptor class A 5.|Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CCCGCACCTGCCCCCCCAACC 0.592 0.52 42 46 PIP4K2C 79837 broad.mit.edu 37 12 57989688 57989688 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr12:57989688delC uc001sou.2 + 4 518 c.387delC c.(385-387)AACfs p.N129fs PIP4K2C_uc001sot.2_Frame_Shift_Del_p.N129fs|PIP4K2C_uc010srs.1_Frame_Shift_Del_p.N111fs|PIP4K2C_uc010srt.1_Intron NM_001146258 NP_001139730 Q8TBX8 PI42C_HUMAN phosphatidylinositol-5-phosphate 4-kinase, type 129 PIPK. cytoplasm|membrane 1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|identical protein binding central_nervous_system(2)|lung(1) 3 Melanoma(17;0.122) TTACCCGAAACCCCCCCAGCG 0.493 0.43 104 78 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.15 91 16 CDX2 1045 broad.mit.edu 37 13 28537278 28537278 + Frame_Shift_Del DEL C - - rs142861632 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr13:28537278delC uc001urv.2 - 3 1090 c.916delG c.(916-918)GTGfs p.V306fs NM_001265 NP_001256 Q99626 CDX2_HUMAN caudal type homeobox 2 306 organ morphogenesis|transcription from RNA polymerase II promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity lung(1) 1 all_cancers(110;0.191)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155) Lung SC(185;0.0156) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199) GGGTTTAGCACCCCCCCAGTT 0.627 0.41 33 23 CSNK1A1L 122011 broad.mit.edu 37 13 37678703 37678704 + Frame_Shift_Ins INS - T T rs56252523 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr13:37678703_37678704insT uc001uwm.1 - 1 1098_1099 c.690_691insA c.(688-693)AAACAAfs p.K230fs NM_145203 NP_660204 Q8N752 KC1AL_HUMAN casein kinase 1, alpha 1-like 230_231 Protein kinase. Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity large_intestine(1) 1 Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109) all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407) TCATATTTTTGTTTTTTTGTCA 0.426 0.39 150 96 CHD8 57680 broad.mit.edu 37 14 21871808 21871808 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr14:21871808delT uc001was.1 - 17 2579 c.2485delA c.(2485-2487)ATCfs p.I829fs CHD8_uc001war.1_Frame_Shift_Del_p.I725fs|CHD8_uc001wav.1_Frame_Shift_Del_p.I271fs NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 1108 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) TCTGTTAGGATTTTTTCTTCA 0.378 0.47 70 63 KIAA1409 57578 broad.mit.edu 37 14 94046589 94046589 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr14:94046589delG uc001ybv.1 + 16 2080 c.1997delG c.(1996-1998)TGGfs p.W666fs KIAA1409_uc001ybs.1_Frame_Shift_Del_p.W666fs NM_020818 NP_065869 Q9P2D8 UNC79_HUMAN hypothetical protein LOC57578 843 integral to membrane p.I654_H670del(1) ovary(10)|skin(4)|large_intestine(3) 17 all_cancers(154;0.0354)|all_epithelial(191;0.216) Epithelial(152;0.188) CAAGCCCCCTGGGGGGGATCC 0.448 0.33 128 62 SRP14 6727 broad.mit.edu 37 15 40328596 40328597 + In_Frame_Ins INS - TGC TGC HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr15:40328596_40328597insTGC uc001zkq.2 - 5 420_421 c.348_349insGCA c.(346-351)insGCA p.116_117insA SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116_117 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) gctgcggcaggtgctgctgctg 0.228 0.29 80 33 BMF 90427 broad.mit.edu 37 15 40396471 40396472 + Frame_Shift_Del DEL GG - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr15:40396471_40396472delGG uc001zkv.2 - 3 448_449 c.362_363delCC c.(361-363)CCCfs p.P121fs BMF_uc001zkt.2_Frame_Shift_Del_p.P121fs|BMF_uc001zku.2_Intron|BMF_uc001zkw.2_Frame_Shift_Del_p.P121fs NM_033503 NP_277038 Q96LC9 BMF_HUMAN Bcl2 modifying factor isoform bmf-1 121 activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria cytosol|mitochondrial outer membrane|myosin complex|plasma membrane protein binding ovary(1) 1 all_cancers(109;4.18e-18)|all_epithelial(112;6.15e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.29e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0516) ACTGCCCTTCGGGGGGCTGCTC 0.564 0.42 190 137 MGA 23269 broad.mit.edu 37 15 42042077 42042077 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr15:42042077delA uc010ucy.1 + 17 6453 c.6272delA c.(6271-6273)GAAfs p.E2091fs MGA_uc010ucz.1_Frame_Shift_Del_p.E1882fs|MGA_uc010uda.1_Frame_Shift_Del_p.E707fs|MGA_uc001zoi.2_Frame_Shift_Del_p.E305fs NM_001164273 NP_001157745 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 1 2052 Basic motif. MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) ACCATTTCTGAAAAAGCCAGT 0.363 0.31 76 34 SGK269 79834 broad.mit.edu 37 15 77474065 77474065 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr15:77474065delT uc002bcm.2 - 3 512 c.204delA c.(202-204)AAAfs p.K68fs SGK269_uc002bcn.2_Frame_Shift_Del_p.K68fs NM_024776 NP_079052 Q9H792 PEAK1_HUMAN NKF3 kinase family member 68 cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading actin cytoskeleton|cytoplasm|focal adhesion ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding 0 STAD - Stomach adenocarcinoma(199;0.124) CTATAGTGGGTTTTTTAGCCA 0.478 0.49 267 254 BLM 641 broad.mit.edu 37 15 91347484 91347484 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr15:91347484delA uc002bpr.2 + 19 3743 c.3646delA c.(3646-3648)AAAfs p.K1216fs BLM_uc010uqh.1_Frame_Shift_Del_p.K1216fs|BLM_uc010uqi.1_Frame_Shift_Del_p.K841fs|BLM_uc010bnx.2_Intron|BLM_uc002bpt.2_Frame_Shift_Del_p.K191fs NM_000057 NP_000048 P54132 BLM_HUMAN Bloom syndrome protein 1216 HRDC. double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray cytoplasm|lateral element|nuclear matrix|nucleolus|PML body ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding ovary(3)|skin(2)|breast(1) 6 Lung NSC(78;0.0875)|all_lung(78;0.109) Lung(145;0.189) AGAGATGGTTAAAAAATGTCT 0.368 0.54 55 65 TSC2 7249 broad.mit.edu 37 16 2121790 2121791 + Frame_Shift_Ins INS - AG AG HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr16:2121790_2121791insAG uc002con.2 + 19 2058_2059 c.1952_1953insAG c.(1951-1953)CCAfs p.P651fs TSC2_uc010bsd.2_Frame_Shift_Ins_p.P651fs|TSC2_uc002coo.2_Frame_Shift_Ins_p.P651fs|TSC2_uc010uvv.1_Frame_Shift_Ins_p.P614fs|TSC2_uc010uvw.1_Frame_Shift_Ins_p.P602fs|TSC2_uc002cop.2_Frame_Shift_Ins_p.P451fs NM_000548 NP_000539 P49815 TSC2_HUMAN tuberous sclerosis 2 isoform 1 651 cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex GTPase activator activity|protein homodimerization activity central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1) 10 Hepatocellular(780;0.0202) TGCAGGGAGCCAGAGAGAGGCT 0.663 0.42 19 14 PALB2 79728 broad.mit.edu 37 16 23632770 23632770 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr16:23632770delG uc002dlx.1 - 10 3226 c.3026delC c.(3025-3027)CCTfs p.P1009fs NM_024675 NP_078951 Q86YC2 PALB2_HUMAN partner and localizer of BRCA2 1009 Interaction with RAD51 and BRCA2.|WD 3. double-strand break repair via homologous recombination nucleoplasm DNA binding|protein binding lung(3)|breast(3)|ovary(2)|skin(1)|kidney(1)|pancreas(1) 11 GBM - Glioblastoma multiforme(48;0.0167) AGTCTCCTCAGGGGGCATCAA 0.368 0.44 84 65 ZNF668 79759 broad.mit.edu 37 16 31072706 31072706 + Frame_Shift_Del DEL G - - rs77284397 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr16:31072706delG uc010caf.2 - 3 1900 c.1543delC c.(1543-1545)CAGfs p.Q515fs ZNF668_uc002eao.2_Frame_Shift_Del_p.Q515fs NM_024706 NP_078982 Q96K58 ZN668_HUMAN zinc finger protein 668 515 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(4) 4 CACACAAACTGGGGGGGCTTC 0.662 0.35 26 14 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.13 112 17 RBL2 5934 broad.mit.edu 37 16 53476704 53476704 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr16:53476704delT uc002ehi.3 + 3 624 c.506delT c.(505-507)ATTfs p.I169fs RBL2_uc010vgv.1_Frame_Shift_Del_p.I95fs NM_005611 NP_005602 Q08999 RBL2_HUMAN retinoblastoma-like 2 (p130) 169 cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleolus DNA binding|protein binding ovary(2)|lung(2)|upper_aerodigestive_tract(1) 5 TATGAACCCATTTTTCAGGAC 0.413 0.52 53 57 THAP11 57215 broad.mit.edu 37 16 67876788 67876796 + In_Frame_Del DEL CAGCAGCAA - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr16:67876788_67876796delCAGCAGCAA uc002euo.2 + 1 576_584 c.331_339delCAGCAGCAA c.(331-339)CAGCAGCAAdel p.QQQ129del CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 129_131 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) acagcagcagcagcagcaacagcagcaac 0.316 0.34 99 51 BCAR1 9564 broad.mit.edu 37 16 75271108 75271108 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr16:75271108delC uc002fdv.2 - 3 891 c.768delG c.(766-768)GGGfs p.G256fs BCAR1_uc002fdt.2_5'Flank|BCAR1_uc002fdu.2_Frame_Shift_Del_p.G46fs|BCAR1_uc010cgu.2_Frame_Shift_Del_p.G227fs|BCAR1_uc010vna.1_Frame_Shift_Del_p.G254fs|BCAR1_uc010vnb.1_Frame_Shift_Del_p.G302fs|BCAR1_uc002fdw.2_Frame_Shift_Del_p.G256fs|BCAR1_uc010vnc.1_Frame_Shift_Del_p.G108fs|BCAR1_uc010vnd.1_Frame_Shift_Del_p.G274fs|BCAR1_uc002fdx.2_Frame_Shift_Del_p.G274fs NM_014567 NP_055382 P56945 BCAR1_HUMAN breast cancer anti-estrogen resistance 1 256 Substrate for kinases (By similarity). actin filament organization|B cell receptor signaling pathway|blood coagulation|cell adhesion|cell division|cell migration|cell proliferation|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|integrin-mediated signaling pathway|nerve growth factor receptor signaling pathway|platelet-derived growth factor receptor signaling pathway|positive regulation of cell migration|regulation of apoptosis|regulation of cell growth|T cell receptor signaling pathway cytosol|focal adhesion|membrane fraction|ruffle protein kinase binding|protein phosphatase binding|SH3 domain binding|signal transducer activity central_nervous_system(5)|breast(2)|prostate(1) 8 BRCA - Breast invasive adenocarcinoma(221;0.169) TGGGAAGCAGCCCCCGAACCG 0.687 0.37 12 7 NLRP1 22861 broad.mit.edu 37 17 5487224 5487226 + In_Frame_Del DEL CTT - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr17:5487224_5487226delCTT uc002gci.2 - 1 607_609 c.52_54delAAG c.(52-54)AAGdel p.K18del NLRP1_uc002gcg.1_In_Frame_Del_p.K18del|NLRP1_uc002gck.2_In_Frame_Del_p.K18del|NLRP1_uc002gcj.2_In_Frame_Del_p.K18del|NLRP1_uc002gcl.2_In_Frame_Del_p.K18del|NLRP1_uc002gch.3_In_Frame_Del_p.K18del|NLRP1_uc010clh.2_In_Frame_Del_p.K18del NM_033004 NP_127497 Q9C000 NALP1_HUMAN NLR family, pyrin domain containing 1 isoform 1 18 DAPIN. defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide cytoplasm|NALP1 inflammasome complex|nucleus ATP binding|caspase activator activity|enzyme binding|protein domain specific binding lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1) 9 Colorectal(1115;3.48e-05) TCAGCTCCTCCTTCTTCAGGAAC 0.601 0.56 8 10 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.33 14 7 CSF3 1440 broad.mit.edu 37 17 38171995 38171995 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr17:38171995delC uc002htp.2 + 2 132 c.92delC c.(91-93)ACCfs p.T31fs CSF3_uc002hto.2_Frame_Shift_Del_p.T31fs|CSF3_uc002htq.2_Frame_Shift_Del_p.T27fs|CSF3_uc010wep.1_Frame_Shift_Del_p.T27fs NM_000759 NP_000750 P09919 CSF3_HUMAN colony stimulating factor 3 isoform a precursor 31 cytokine-mediated signaling pathway|granulocyte differentiation|immune response|positive regulation of cell proliferation extracellular space cytokine activity|enzyme binding|granulocyte colony-stimulating factor receptor binding|growth factor activity ovary(1) 1 Colorectal(19;0.000442) Myeloproliferative disorder(1115;0.0255) Filgrastim(DB00099)|Pegfilgrastim(DB00019) CAGGAAGCCACCCCCCTGGGC 0.642 0.44 35 28 RNF43 54894 broad.mit.edu 37 17 56435161 56435161 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr17:56435161delC uc002iwf.2 - 8 3932 c.1976delG c.(1975-1977)GGTfs p.G659fs RNF43_uc010wnv.1_Frame_Shift_Del_p.G618fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.G659fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.G659fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.G532fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 659 Pro-rich.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.81 57 240 TEX14 56155 broad.mit.edu 37 17 56676292 56676292 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr17:56676292delC uc010dcz.1 - 14 2550 c.2432delG c.(2431-2433)GGTfs p.G811fs TEX14_uc002iwr.1_Frame_Shift_Del_p.G805fs|TEX14_uc002iws.1_Frame_Shift_Del_p.G805fs|TEX14_uc010dda.1_Frame_Shift_Del_p.G585fs NM_198393 NP_938207 Q8IWB6 TEX14_HUMAN testis expressed sequence 14 isoform a 811 cytoplasm ATP binding|protein kinase activity stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1) 17 Medulloblastoma(34;0.127)|all_neural(34;0.237) TGGCTTCTGACCCCCTGAAAG 0.478 0.32 64 30 ERN1 2081 broad.mit.edu 37 17 62142580 62142580 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr17:62142580delC uc002jdz.2 - 9 1023 c.910delG c.(910-912)GTTfs p.V304fs NM_001433 NP_001424 O75460 ERN1_HUMAN endoplasmic reticulum to nucleus signalling 1 304 Lumenal (Potential). activation of signaling protein activity involved in unfolded protein response|apoptosis|cell cycle arrest|induction of apoptosis|mRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent integral to endoplasmic reticulum membrane ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(4)|lung(2)|stomach(1)|ovary(1)|kidney(1) 9 0.000 0.23 544 159 STK11 6794 broad.mit.edu 37 19 1221314 1221314 + Frame_Shift_Del DEL C - - rs67873004 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr19:1221314delC uc002lrl.1 + 6 1952 c.837delC c.(835-837)GGCfs p.G279fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 279 Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.P281fs*6(2)|p.?(2)|p.Y246fs*3(1)|p.G279F(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) GCGACTGTGGCCCCCCGCTCT 0.607 0.80 5 20 NFIX 4784 broad.mit.edu 37 19 13136105 13136105 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr19:13136105delC uc010xmx.1 + 2 375 c.322delC c.(322-324)CCCfs p.P108fs NFIX_uc002mwd.2_Frame_Shift_Del_p.P100fs|NFIX_uc002mwe.2_Frame_Shift_Del_p.P92fs|NFIX_uc002mwf.2_Frame_Shift_Del_p.P103fs|NFIX_uc002mwg.1_Frame_Shift_Del_p.P99fs Q14938 NFIX_HUMAN RecName: Full=Nuclear factor 1; 100 CTF/NF-I. DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter nucleus DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity breast(1)|skin(1) 2 OV - Ovarian serous cystadenocarcinoma(19;8.2e-22) GGGCAAGAAGCCCCCCTGCTG 0.647 0.40 6 4 NOTCH3 4854 broad.mit.edu 37 19 15271908 15271909 + Frame_Shift_Ins INS - G G HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr19:15271908_15271909insG uc002nan.2 - 33 6606_6607 c.6530_6531insC c.(6529-6531)CCAfs p.P2177fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 2177 Cytoplasmic (Potential). Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.47 522 463 NOTCH3 4854 broad.mit.edu 37 19 15289969 15289970 + Frame_Shift_Ins INS - G G HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr19:15289969_15289970insG uc002nan.2 - 22 3660_3661 c.3584_3585insC c.(3583-3585)CCAfs p.P1195fs NOTCH3_uc002nao.1_Frame_Shift_Ins_p.P1143fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 1195 Extracellular (Potential).|EGF-like 30; calcium-binding (Potential). Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) CAGTGTATCCTGGGGGACAGGT 0.668 0.58 5 7 ZNF570 148268 broad.mit.edu 37 19 37975772 37975772 + Frame_Shift_Del DEL T - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr19:37975772delT uc002ogk.1 + 5 1777 c.1248delT c.(1246-1248)TGTfs p.C416fs ZNF570_uc010efl.1_Frame_Shift_Del_p.C472fs|ZNF570_uc010xtr.1_Frame_Shift_Del_p.C213fs NM_144694 NP_653295 Q96NI8 ZN570_HUMAN zinc finger protein 570 416 C2H2-type 8. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1) 1 COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177) CTTATAAGTGTCAGGAATGTA 0.423 0.36 9 5 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.50 71 72 LMTK3 114783 broad.mit.edu 37 19 49001892 49001892 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr19:49001892delC uc002pjk.2 - 12 2521 c.2521delG c.(2521-2523)GCGfs p.A841fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.63 189 324 LMTK3 114783 broad.mit.edu 37 19 49002150 49002151 + Frame_Shift_Ins INS - G G HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr19:49002150_49002151insG uc002pjk.2 - 12 2262_2263 c.2262_2263insC c.(2260-2265)CCCGCCfs p.P754fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.15 304 54 BRSK1 84446 broad.mit.edu 37 19 55816163 55816163 + Frame_Shift_Del DEL C - - rs55892637 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr19:55816163delC uc002qkg.2 + 14 1869 c.1592delC c.(1591-1593)ACCfs p.T531fs BRSK1_uc002qkf.2_Frame_Shift_Del_p.T547fs|BRSK1_uc002qkh.2_Frame_Shift_Del_p.T226fs NM_032430 NP_115806 Q8TDC3 BRSK1_HUMAN BR serine/threonine kinase 1 531 Pro-rich. establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV cell junction|cytoplasm|nucleus magnesium ion binding|protein serine/threonine kinase activity ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1) 6 Renal(1328;0.245) BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.0474) 0.000 0.25 437 145 PLCG1 5335 broad.mit.edu 37 20 39798114 39798114 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr20:39798114delC uc002xjp.1 + 23 2719 c.2598delC c.(2596-2598)AGCfs p.S866fs PLCG1_uc002xjo.1_Frame_Shift_Del_p.S866fs|PLCG1_uc010zwe.1_Frame_Shift_Del_p.S492fs|PLCG1_uc010ggf.2_Frame_Shift_Del_p.S190fs NM_182811 NP_877963 P19174 PLCG1_HUMAN phospholipase C, gamma 1 isoform b 866 activation of phospholipase C activity|axon guidance|blood coagulation|cellular response to epidermal growth factor stimulus|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular signal transduction|leukocyte migration|nerve growth factor receptor signaling pathway|phospholipid catabolic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of epithelial cell migration|T cell receptor signaling pathway cytosol|lamellipodium|plasma membrane|ruffle calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|receptor signaling protein activity lung(3)|breast(3)|skin(2) 8 Myeloproliferative disorder(115;0.00878) ACGAGAACAGCCCCCTAGGGG 0.552 0.47 111 97 TP53RK 112858 broad.mit.edu 37 20 45315634 45315634 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr20:45315634delG uc002xsk.2 - 2 743 c.520delC c.(520-522)CTGfs p.L174fs SLC13A3_uc002xsg.1_5'Flank|SLC13A3_uc010gho.1_5'Flank|TP53RK_uc002xsj.2_3'UTR NM_033550 NP_291028 Q96S44 PRPK_HUMAN p53-related protein kinase 174 Protein kinase. lipopolysaccharide biosynthetic process membrane|nucleus ATP binding|p53 binding|protein serine/threonine kinase activity|protein tyrosine kinase activity 0 Myeloproliferative disorder(115;0.0122) AGCTGTTCCAGGGGGGGTTTC 0.493 0.48 54 49 GNAS 2778 broad.mit.edu 37 20 57428688 57428689 + Frame_Shift_Ins INS - C C HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr20:57428688_57428689insC uc002xzw.2 + 1 653_654 c.368_369insC c.(367-369)TTCfs p.F123fs GNASAS_uc002xzs.1_5'Flank|GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_RNA NM_080425 NP_536350 P63092 GNAS2_HUMAN GNAS complex locus XLas Error:Variant_position_missing_in_P63092_after_alignment activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1) 292 all_lung(29;0.0104) BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109) CAGCCTGGATTCCCCAGTGGGG 0.639 0.44 110 85 COL18A1 80781 broad.mit.edu 37 21 46907379 46907379 + Frame_Shift_Del DEL G - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr21:46907379delG uc011afs.1 + 16 3118 c.3097delG c.(3097-3099)GGGfs p.G1033fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.G618fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.G798fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1033 Nonhelical region 4 (NC4). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.46 159 138 COL18A1 80781 broad.mit.edu 37 21 46917559 46917559 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr21:46917559delC uc011afs.1 + 31 3933 c.3912delC c.(3910-3912)GGCfs p.G1304fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.G889fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.G1069fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1304 Triple-helical region 7 (COL7). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.50 411 409 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.43 286 219 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 108 CLTCL1 8218 broad.mit.edu 37 22 19195739 19195739 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr22:19195739delA uc002zpb.2 - 22 3600 c.3525delT c.(3523-3525)TTTfs p.F1175fs CLTCL1_uc011agv.1_Frame_Shift_Del_p.F1175fs|CLTCL1_uc011agw.1_Frame_Shift_Del_p.F1175fs|CLTCL1_uc011agt.1_5'Flank|CLTCL1_uc011agu.1_5'Flank|CLTCL1_uc010grm.1_Intron|CLTCL1_uc002zpe.2_Frame_Shift_Del_p.F135fs|CLTCL1_uc002zpd.1_Intron NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 1175 Proximal segment.|Heavy chain arm. anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) TAGCCAAGGCAAAAATAAGTT 0.458 0.45 120 100 PHF21B 112885 broad.mit.edu 37 22 45283956 45283956 + Frame_Shift_Del DEL C - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr22:45283956delC uc003bfn.2 - 10 1235 c.1084delG c.(1084-1086)GCCfs p.A362fs PHF21B_uc003bfm.2_Frame_Shift_Del_p.A158fs|PHF21B_uc011aqk.1_Frame_Shift_Del_p.A308fs|PHF21B_uc011aql.1_Frame_Shift_Del_p.A320fs|PHF21B_uc011aqm.1_3'UTR NM_138415 NP_612424 Q96EK2 PF21B_HUMAN PHD finger protein 21B isoform 1 362 PHD-type. zinc ion binding ovary(2)|skin(1) 3 all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731) UCEC - Uterine corpus endometrioid carcinoma (28;0.0203) TGCAGGTTGGCCCCTCGCTTG 0.701 0.64 4 7 FAM118A 55007 broad.mit.edu 37 22 45732267 45732267 + Frame_Shift_Del DEL A - - HEC151_ENDOMETRIUM NA HEC151_ENDOMETRIUM NA g.chr22:45732267delA uc003bfz.3 + 9 1645 c.1029delA c.(1027-1029)TCAfs p.S343fs FAM118A_uc003bga.3_Frame_Shift_Del_p.S343fs|FAM118A_uc011aqr.1_Frame_Shift_Del_p.S161fs NM_001104595 NP_001098065 Q9NWS6 F118A_HUMAN hypothetical protein LOC55007 343 integral to membrane 0 Ovarian(80;0.00965)|all_neural(38;0.0416) UCEC - Uterine corpus endometrioid carcinoma (28;0.0178) TTGAAGTTTCAAAAAAACGCA 0.418 0.43 68 52 TAF1 6872 broad.mit.edu 37 X 70602999 70603000 + Frame_Shift_Ins INS - A A HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chrX:70602999_70603000insA uc004dzu.3 + 12 1980_1981 c.1929_1930insA c.(1927-1932)ATCAAAfs p.I643fs BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Frame_Shift_Ins_p.I664fs NM_138923 NP_620278 P21675 TAF1_HUMAN TBP-associated factor 1 isoform 2 643_644 G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction MLL1 complex|transcription factor TFIID complex ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1) 17 Renal(35;0.156) all_lung(315;0.000321) TAAAGCACATCAAAAAAAAGGC 0.312 0.20 73 18 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 4 66 ODZ1 10178 broad.mit.edu 37 X 123785798 123785799 + Frame_Shift_Ins INS - T T HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chrX:123785798_123785799insT uc004euj.2 - 8 1608_1609 c.1544_1545insA c.(1543-1545)AAGfs p.K515fs ODZ1_uc011muj.1_Frame_Shift_Ins_p.K514fs|ODZ1_uc010nqy.2_Frame_Shift_Ins_p.K515fs NM_014253 NP_055068 Q9UKZ4 TEN1_HUMAN odz, odd Oz/ten-m homolog 1 isoform 3 515 Extracellular (Potential). immune response|negative regulation of cell proliferation|nervous system development|signal transduction extracellular region heparin binding ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1) 23 CTTGCTCCATCTTTTTTCCATC 0.411 0.47 80 72 TNFRSF4 7293 broad.mit.edu 37 1 1147441 1147441 + Frame_Shift_Del DEL G - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr1:1147441delG uc001ade.2 - 5 520 c.515delC c.(514-516)CCAfs p.P172fs TNFRSF4_uc001adf.2_Frame_Shift_Del_p.P176fs NM_003327 NP_003318 P43489 TNR4_HUMAN tumor necrosis factor receptor superfamily, 172 Extracellular (Potential). immune response|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|positive regulation of B cell proliferation|positive regulation of immunoglobulin secretion|T cell proliferation integral to plasma membrane tumor necrosis factor receptor activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199) CTGCGTGGCTGGGGGGTCCCT 0.677 0.53 14 16 PRDM16 63976 broad.mit.edu 37 1 3301765 3301766 + Frame_Shift_Ins INS - G G HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr1:3301765_3301766insG uc001akf.2 + 4 568_569 c.488_489insG c.(487-489)GCGfs p.A163fs PRDM16_uc001akc.2_Frame_Shift_Ins_p.A163fs|PRDM16_uc001akd.2_Frame_Shift_Ins_p.A163fs|PRDM16_uc001ake.2_Frame_Shift_Ins_p.A163fs|PRDM16_uc009vlh.2_5'UTR NM_022114 NP_071397 Q9HAZ2 PRD16_HUMAN PR domain containing 16 isoform 1 163 SET. brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent transcriptional repressor complex protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1) 7 all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111) all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134) Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137) GCAAATCAGGCGGGGGCTGGCA 0.594 0.43 165 123 STIL 6491 broad.mit.edu 37 1 47770571 47770572 + Frame_Shift_Ins INS - GA GA HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr1:47770571_47770572insGA uc001crc.1 - 3 296_297 c.141_142insTC c.(139-144)CTCAGTfs p.L47fs TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Frame_Shift_Ins_p.L47fs|STIL_uc010omo.1_Frame_Shift_Ins_p.L47fs|STIL_uc001crd.1_Frame_Shift_Ins_p.L47fs|STIL_uc001cre.1_Frame_Shift_Ins_p.L47fs|STIL_uc001crg.1_Frame_Shift_Ins_p.L47fs NM_003035 NP_003026 Q15468 STIL_HUMAN SCL/TAL1 interrupting locus isoform 2 47_48 cell proliferation|multicellular organismal development centrosome|cytosol lung(2)|skin(1) 3 Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444) CTGTAGTAACTGAGATGTAAGT 0.361 0.50 50 50 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.44 220 172 INSRR 3645 broad.mit.edu 37 1 156821913 156821914 + Frame_Shift_Ins INS - C C HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr1:156821913_156821914insC uc010pht.1 - 3 961_962 c.707_708insG c.(706-708)GGCfs p.G236fs NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron|INSRR_uc009wsj.1_Frame_Shift_Ins_p.G236fs NM_014215 NP_055030 P14616 INSRR_HUMAN insulin receptor-related receptor precursor 236 protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity lung(11)|ovary(5)|skin(2)|kidney(1)|central_nervous_system(1) 20 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) GCTGGCTGCAGCCCCCCAGGCA 0.658 0.35 88 47 MAP4K3 8491 broad.mit.edu 37 2 39552931 39552932 + Frame_Shift_Del DEL AA - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr2:39552931_39552932delAA uc002rro.2 - 11 837_838 c.746_747delTT c.(745-747)TTTfs p.F249fs MAP4K3_uc002rrp.2_Frame_Shift_Del_p.F249fs|MAP4K3_uc010yns.1_5'UTR NM_003618 NP_003609 Q8IVH8 M4K3_HUMAN mitogen-activated protein kinase kinase kinase 249 Protein kinase. JNK cascade ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity ovary(3)|lung(3)|stomach(1)|pancreas(1) 8 all_hematologic(82;0.211) CCATTTTCACAAAGTGATGAAA 0.252 0.50 17 17 LRP1B 53353 broad.mit.edu 37 2 141081572 141081572 + Frame_Shift_Del DEL T - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr2:141081572delT uc002tvj.1 - 81 13376 c.12404delA c.(12403-12405)AATfs p.N4135fs NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 4135 Extracellular (Potential). protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) AAATACACCATTTTTAGGTCC 0.299 0.27 41 15 TTN 7273 broad.mit.edu 37 2 179411730 179411731 + Frame_Shift_Ins INS - A A HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr2:179411730_179411731insA uc010zfg.1 - 289 87041_87042 c.86817_86818insT c.(86815-86820)GTTGATfs p.V28939fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Ins_p.V22634fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.V22567fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.V22442fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 29866_29867 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TGATACATACCAACTGGATTTT 0.376 0.15 133 24 TRPM8 79054 broad.mit.edu 37 2 234847688 234847688 + Frame_Shift_Del DEL T - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr2:234847688delT uc002vvh.2 + 5 435 c.395delT c.(394-396)CTGfs p.L132fs TRPM8_uc010fyj.2_5'UTR|TRPM8_uc002vvi.3_Frame_Shift_Del_p.L82fs|TRPM8_uc002vvj.3_Frame_Shift_Del_p.L55fs NM_024080 NP_076985 Q7Z2W7 TRPM8_HUMAN transient receptor potential cation channel, 132 Cytoplasmic (Potential). integral to membrane skin(4) 4 Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224) Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108) Menthol(DB00825) CTTTACGAGCTGCTGACCCAG 0.562 0.49 40 39 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.42 32 23 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.46 36 31 MYLK 4638 broad.mit.edu 37 3 123385183 123385184 + Frame_Shift_Ins INS - G G HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr3:123385183_123385184insG uc003ego.2 - 22 3995_3996 c.3713_3714insC c.(3712-3714)CCTfs p.P1238fs MYLK_uc010hrr.2_5'Flank|MYLK_uc011bjv.1_Frame_Shift_Ins_p.P38fs|MYLK_uc011bjw.1_Frame_Shift_Ins_p.P1238fs|MYLK_uc003egp.2_Frame_Shift_Ins_p.P1169fs|MYLK_uc003egq.2_Frame_Shift_Ins_p.P1238fs|MYLK_uc003egr.2_Frame_Shift_Ins_p.P1169fs|MYLK_uc003egs.2_Frame_Shift_Ins_p.P1062fs NM_053025 NP_444253 Q15746 MYLK_HUMAN myosin light chain kinase isoform 1 1238 Actin-binding (calcium/calmodulin- insensitive) (By similarity).|Ig-like C2-type 8. aorta smooth muscle tissue morphogenesis|muscle contraction cytosol actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity ovary(6)|skin(2)|stomach(1) 9 Lung NSC(201;0.0496) GBM - Glioblastoma multiforme(114;0.0736) GGATGATCTGAGGGGGCATTGC 0.564 0.55 111 136 TOPBP1 11073 broad.mit.edu 37 3 133335730 133335731 + Frame_Shift_Ins INS - T T HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr3:133335730_133335731insT uc003eps.2 - 23 3930_3931 c.3798_3799insA c.(3796-3801)AAACAGfs p.K1266fs NM_007027 NP_008958 Q92547 TOPB1_HUMAN topoisomerase (DNA) II binding protein 1 1266_1267 BRCT 7. DNA repair|response to ionizing radiation microtubule organizing center|PML body|spindle pole DNA binding|protein C-terminus binding ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1) 7 AATATGTACTGTTTTTTTAATT 0.282 0.53 35 39 EPHA5 2044 broad.mit.edu 37 4 66189850 66189851 + Frame_Shift_Ins INS - T T HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr4:66189850_66189851insT uc003hcy.2 - 18 3288_3289 c.3095_3096insA c.(3094-3096)AACfs p.N1032fs EPHA5_uc003hcx.2_Frame_Shift_Ins_p.N964fs|EPHA5_uc003hcz.2_Frame_Shift_Ins_p.N1010fs|EPHA5_uc011cah.1_Frame_Shift_Ins_p.N1033fs|EPHA5_uc011cai.1_Frame_Shift_Ins_p.N1011fs NM_004439 NP_004430 P54756 EPHA5_HUMAN ephrin receptor EphA5 isoform a precursor 1032 Cytoplasmic (Potential). N -> S (in a lung large cell carcinoma sample; somatic mutation). cAMP-mediated signaling|neuron development dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum ATP binding|transmembrane-ephrin receptor activity p.N1032S(1) lung(19)|stomach(2)|ovary(2)|central_nervous_system(1) 24 GCACCATTCCGTTTACCAGCTG 0.416 0.27 48 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 90 157 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 27 47 MAP3K1 4214 broad.mit.edu 37 5 56178258 56178258 + Frame_Shift_Del DEL A - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr5:56178258delA uc003jqw.3 + 14 3732 c.3231delA c.(3229-3231)TCAfs p.S1077fs NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 1077 cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) GAGATCCCTCAAAAAATAGCA 0.443 0.47 89 79 AFF4 27125 broad.mit.edu 37 5 132232626 132232627 + Frame_Shift_Ins INS - T T HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr5:132232626_132232627insT uc003kyd.2 - 11 2103_2104 c.1695_1696insA c.(1693-1698)AAACAAfs p.K565fs AFF4_uc011cxk.1_Frame_Shift_Ins_p.K243fs|AFF4_uc003kye.1_Frame_Shift_Ins_p.K565fs NM_014423 NP_055238 Q9UHB7 AFF4_HUMAN ALL1 fused gene from 5q31 565_566 transcription from RNA polymerase II promoter mitochondrion|nucleolus protein binding|sequence-specific DNA binding transcription factor activity ovary(2)|kidney(2)|skin(1) 5 all_cancers(142;0.145)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) TTTTTGGGTTGTTTTTTGCCTA 0.510 0.29 814 326 CDKL3 51265 broad.mit.edu 37 5 133634349 133634349 + Frame_Shift_Del DEL A - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr5:133634349delA uc003kzf.3 - 13 1891 c.1772delT c.(1771-1773)TTCfs p.F591fs CDKL3_uc011cxm.1_Intron|CDKL3_uc011cxn.1_Intron|CDKL3_uc010jdw.2_Intron|CDKL3_uc011cxo.1_Intron|CDKL3_uc011cxp.1_Intron|CDKL3_uc011cxq.1_3'UTR NM_001113575 NP_001107047 Q8IVW4 CDKL3_HUMAN cyclin-dependent kinase-like 3 isoform 1 591 cytoplasm ATP binding|cyclin-dependent protein kinase activity breast(1) 1 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) ACACTACCAGAAAAAAAACCT 0.353 0.72 15 38 NPM1 4869 broad.mit.edu 37 5 170832382 170832383 + Frame_Shift_Ins INS - A A HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr5:170832382_170832383insA uc011dex.1 + 10 881_882 c.746_747insA c.(745-747)GCAfs p.A249fs NPM1_uc003mbh.2_Frame_Shift_Ins_p.A249fs|NPM1_uc003mbi.2_Frame_Shift_Ins_p.A249fs|NPM1_uc003mbj.2_Frame_Shift_Ins_p.A220fs NM_002520 NP_002511 P06748 NPM_HUMAN nucleophosmin 1 isoform 1 249 Required for nucleolar localization. anti-apoptosis|cell aging|CenH3-containing nucleosome assembly at centromere|centrosome cycle|DNA repair|interspecies interaction between organisms|intracellular protein transport|negative regulation of cell proliferation|negative regulation of centrosome duplication|nucleocytoplasmic transport|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|regulation of endodeoxyribonuclease activity|regulation of endoribonuclease activity|ribosome assembly|signal transduction nucleolus|nucleoplasm|ribonucleoprotein complex|spindle pole centrosome histone binding|NF-kappaB binding|protein binding|protein heterodimerization activity|protein homodimerization activity|ribosomal large subunit binding|ribosomal small subunit binding|RNA binding|Tat protein binding|transcription coactivator activity|unfolded protein binding NPM1/ALK(632) haematopoietic_and_lymphoid_tissue(3109)|skin(1) 3110 Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963) Medulloblastoma(196;0.0208)|all_neural(177;0.0416) Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516) GACATTAAAGCAAAAATGCAAG 0.347 0.32 13 6 POU5F1 5460 broad.mit.edu 37 6 31138326 31138326 + Frame_Shift_Del DEL C - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr6:31138326delC uc003nsv.2 - 1 126 c.72delG c.(70-72)GGGfs p.G24fs NM_002701 NP_002692 Q01860 PO5F1_HUMAN POU domain, class 5, transcription factor 1 24 anatomical structure morphogenesis|blastocyst development|BMP signaling pathway involved in heart induction|cardiac cell fate determination|cell fate commitment involved in formation of primary germ layers|mRNA transcription from RNA polymerase II promoter|negative regulation of gene silencing by miRNA|positive regulation of catenin import into nucleus|positive regulation of SMAD protein import into nucleus|positive regulation of transcription from RNA polymerase II promoter|regulation of asymmetric cell division|regulation of heart induction by regulation of canonical Wnt receptor signaling pathway|regulation of methylation-dependent chromatin silencing|response to wounding|somatic stem cell maintenance|somatic stem cell maintenance cytosol|nucleoplasm|transcription factor complex miRNA binding|sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|ubiquitin protein ligase binding EWSR1/POU5F1(10) skin(7)|salivary_gland(2)|bone(2)|lung(1)|ovary(1) 13 CCGGCTCCGGCCCCCCTGGCC 0.701 0.56 15 19 WEE2 494551 broad.mit.edu 37 7 141408736 141408737 + Frame_Shift_Ins INS - T T HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr7:141408736_141408737insT uc003vwn.2 + 1 584_585 c.178_179insT c.(178-180)CTTfs p.L60fs FLJ40852_uc011krh.1_Intron|FLJ40852_uc010lnm.2_Intron|FLJ40852_uc010lnn.2_Intron|FLJ40852_uc003vwm.3_Intron|FLJ40852_uc010lno.2_Intron NM_001105558 NP_001099028 P0C1S8 WEE2_HUMAN WEE1 homolog 2 60 egg activation|female meiosis|female pronucleus assembly|meiotic metaphase II|meiotic prophase I|mitosis|negative regulation of oocyte development|regulation of meiosis I centrosome|nucleus ATP binding|magnesium ion binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Melanoma(164;0.0171) TTGGACTCCCCTTAGCAACGTG 0.500 0.45 59 48 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 2 17 NOS3 4846 broad.mit.edu 37 7 150698398 150698398 + Frame_Shift_Del DEL G - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr7:150698398delG uc003wif.2 + 11 1609 c.1313delG c.(1312-1314)AGGfs p.R438fs NOS3_uc011kuy.1_Frame_Shift_Del_p.R232fs|NOS3_uc011kuz.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kva.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kvb.1_Frame_Shift_Del_p.R438fs NM_000603 NP_000594 P29474 NOS3_HUMAN nitric oxide synthase 3 isoform 1 438 Interaction with NOSIP. anti-apoptosis|arginine catabolic process|blood vessel remodeling|endothelial cell migration|mitochondrion organization|negative regulation of muscle hyperplasia|negative regulation of platelet activation|nitric oxide biosynthetic process|platelet activation|positive regulation of angiogenesis|positive regulation of guanylate cyclase activity|positive regulation of vasodilation|regulation of blood vessel size|regulation of nitric-oxide synthase activity|regulation of systemic arterial blood pressure by endothelin|response to fluid shear stress|response to heat|smooth muscle hyperplasia caveola|cytoskeleton|cytosol|Golgi membrane actin monomer binding|arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding central_nervous_system(5)|large_intestine(2)|skin(1) 8 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) L-Arginine(DB00125)|L-Citrulline(DB00155)|Rosuvastatin(DB01098)|Tetrahydrobiopterin(DB00360) 0.000 0.42 628 463 MLL3 58508 broad.mit.edu 37 7 151874147 151874148 + Frame_Shift_Ins INS - T T HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr7:151874147_151874148insT uc003wla.2 - 38 8609_8610 c.8390_8391insA c.(8389-8391)AAGfs p.K2797fs MLL3_uc003wkz.2_Frame_Shift_Ins_p.K1858fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.K306fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 2797 K -> R (in Ref. 1; AAK00583). intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding p.K2797fs*26(18) large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTTCTTGTTCCTTTTTTTTTGG 0.347 0.60 87 129 VPS13B 157680 broad.mit.edu 37 8 100847792 100847793 + Frame_Shift_Ins INS - A A HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr8:100847792_100847793insA uc003yiv.2 + 54 9954_9955 c.9843_9844insA c.(9841-9846)TGCAAAfs p.C3281fs VPS13B_uc003yiw.2_Frame_Shift_Ins_p.C3256fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 3281_3282 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) AGGTTTATTGCAAAAAAATTCC 0.386 0.17 39 8 TRPS1 7227 broad.mit.edu 37 8 116631783 116631784 + Frame_Shift_Del DEL TG - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr8:116631783_116631784delTG uc003ynz.2 - 2 961_962 c.502_503delCA c.(502-504)CAGfs p.Q168fs TRPS1_uc011lhy.1_Frame_Shift_Del_p.Q172fs|TRPS1_uc003yny.2_Frame_Shift_Del_p.Q181fs|TRPS1_uc010mcy.2_Frame_Shift_Del_p.Q168fs NM_014112 NP_054831 Q9UHF7 TRPS1_HUMAN zinc finger transcription factor TRPS1 168 negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) TTGACCACTCTGTGCTTGCCCT 0.495 0.42 86 63 BAI1 575 broad.mit.edu 37 8 143618407 143618408 + Frame_Shift_Ins INS - G G HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr8:143618407_143618408insG uc003ywm.2 + 25 3813_3814 c.3630_3631insG c.(3628-3633)TCAGGGfs p.S1210fs NM_001702 NP_001693 O14514 BAI1_HUMAN brain-specific angiogenesis inhibitor 1 1210_1211 Cytoplasmic (Potential). axonogenesis|cell adhesion|negative regulation of angiogenesis|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development cell-cell junction|integral to plasma membrane G-protein coupled receptor activity|protein binding lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|pancreas(1) 8 all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155) ACGGGGACTCAGGGGGCTCCTT 0.683 0.44 40 31 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 2 40 TAF1L 138474 broad.mit.edu 37 9 32635092 32635093 + Frame_Shift_Ins INS - G G rs146968712 HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr9:32635092_32635093insG uc003zrg.1 - 1 575_576 c.485_486insC c.(484-486)CCGfs p.P162fs uc003zrh.1_Intron NM_153809 NP_722516 Q8IZX4 TAF1L_HUMAN TBP-associated factor RNA polymerase 1-like 162 Pro-rich. male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent transcription factor TFIID complex DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1) 26 LUSC - Lung squamous cell carcinoma(29;0.0181) GBM - Glioblastoma multiforme(74;0.00301) TCATTGGTCCCGGGGGTGGAGG 0.475 0.38 257 155 CEP110 11064 broad.mit.edu 37 9 123924525 123924525 + Frame_Shift_Del DEL A - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr9:123924525delA uc004bkx.1 + 32 5430 c.5399delA c.(5398-5400)GAAfs p.E1800fs CEP110_uc004blb.1_Frame_Shift_Del_p.E469fs|CEP110_uc010mvp.1_Intron NM_007018 NP_008949 Q7Z7A1 CNTRL_HUMAN centrosomal protein 110kDa 1800 Potential. cell division|G2/M transition of mitotic cell cycle centrosome|cytosol protein binding 0 0.000 0.50 388 390 PIPSL 266971 broad.mit.edu 37 10 95720426 95720426 + Frame_Shift_Del DEL A - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr10:95720426delA uc009xuj.2 - 1 1247 c.728delT c.(727-729)TTGfs p.L243fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTCAGCATCCAAAAAAAGACC 0.483 0.51 62 64 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.67 9 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 804 364 NPAT 4863 broad.mit.edu 37 11 108040772 108040773 + Splice_Site INS - A A rs35747263 HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr11:108040772_108040773insA uc001pjz.3 - 14 2888 c.2786_splice c.e14-1 p.G929_splice NPAT_uc010rvv.1_5'UTR NM_002519 NP_002510 Q14207 NPAT_HUMAN nuclear protein, ataxia-telangiectasia locus positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle Cajal body protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity ovary(2) 2 all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116) TGGCAGATCCTAAAAAAACAAT 0.342 0.25 44 15 MLL 4297 broad.mit.edu 37 11 118307394 118307394 + Frame_Shift_Del DEL C - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr11:118307394delC uc001pta.2 + 1 190 c.167delC c.(166-168)TCCfs p.S56fs MLL_uc001ptb.2_Frame_Shift_Del_p.S56fs|uc001psy.2_5'Flank|MLL_uc001psz.1_Frame_Shift_Del_p.S56fs NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 56 Ala/Gly/Ser-rich. apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) 0.000 0.32 303 143 MAP3K12 7786 broad.mit.edu 37 12 53876614 53876615 + Frame_Shift_Ins INS - C C HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr12:53876614_53876615insC uc001sdm.1 - 12 1971_1972 c.1873_1874insG c.(1873-1875)GCCfs p.A625fs MAP3K12_uc001sdn.1_Frame_Shift_Ins_p.A658fs NM_006301 NP_006292 Q12852 M3K12_HUMAN mitogen-activated protein kinase kinase kinase 625 histone phosphorylation|JNK cascade|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation cytosol|membrane fraction|plasma membrane ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding lung(2)|ovary(1)|breast(1)|skin(1) 5 TCCGCCTGTGGCCCCCCGGCCC 0.673 0.70 3 7 EDNRB 1910 broad.mit.edu 37 13 78475267 78475267 + Frame_Shift_Del DEL A - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr13:78475267delA uc001vko.2 - 4 1135 c.877delT c.(877-879)TATfs p.Y293fs EDNRB_uc001vkq.1_Frame_Shift_Del_p.Y293fs|uc001vkn.1_Intron|EDNRB_uc010aez.1_Frame_Shift_Del_p.Y293fs|EDNRB_uc001vkp.1_Frame_Shift_Del_p.Y376fs NM_001122659 NP_001116131 P24530 EDNRB_HUMAN endothelin receptor type B isoform 1 precursor 293 Helical; Name=5; (Potential). activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction integral to plasma membrane endothelin-B receptor activity|peptide hormone binding 0 Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037) GBM - Glioblastoma multiforme(99;0.0933) Bosentan(DB00559) ATTAGTGTATAAAAAAATGCA 0.343 0.91 7 73 ABCC4 10257 broad.mit.edu 37 13 95696015 95696016 + Frame_Shift_Ins INS - T T HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr13:95696015_95696016insT uc001vmd.3 - 29 3774_3775 c.3655_3656insA c.(3655-3657)ATCfs p.I1219fs ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_Frame_Shift_Ins_p.I1172fs NM_005845 NP_005836 O15439 MRP4_HUMAN ATP-binding cassette, sub-family C, member 4 1219 ABC transporter 2. platelet activation|platelet degranulation integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane 15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity central_nervous_system(3)|skin(1) 4 all_neural(89;0.0878)|Medulloblastoma(90;0.163) Cefazolin(DB01327) TTTCTCCCGGATTTTTTTTTGT 0.376 0.29 59 24 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.57 30 40 SPRED1 161742 broad.mit.edu 37 15 38614463 38614463 + Frame_Shift_Del DEL A - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr15:38614463delA uc001zka.3 + 3 564 c.229delA c.(229-231)AAAfs p.K77fs NM_152594 NP_689807 Q7Z699 SPRE1_HUMAN sprouty-related protein 1 with EVH-1 domain 77 WH1. inactivation of MAPK activity|multicellular organismal development caveola|nucleus stem cell factor receptor binding ovary(2)|lung(2)|skin(1) 5 all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091) GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244) 0.000 0.59 77 112 NEDD4 4734 broad.mit.edu 37 15 56208424 56208425 + Frame_Shift_Ins INS - A A HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr15:56208424_56208425insA uc002adj.2 - 1 905_906 c.605_606insT c.(604-606)TTGfs p.L202fs NEDD4_uc002adl.2_Intron|NEDD4_uc002adi.2_Frame_Shift_Ins_p.L202fs|NEDD4_uc010ugj.1_Frame_Shift_Ins_p.L202fs|NEDD4_uc010bfm.2_Frame_Shift_Ins_p.L202fs|NEDD4_uc002adk.2_RNA NM_198400 NP_006145 P46934 NEDD4_HUMAN neural precursor cell expressed, developmentally 202 Ser-rich. development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity skin(2)|ovary(1)|breast(1) 4 all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113) 0.000 0.44 263 206 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.14 74 12 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.82 13 61 STAT5A 6776 broad.mit.edu 37 17 40453398 40453399 + Frame_Shift_Ins INS - C C rs146398782 HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr17:40453398_40453399insC uc002hzj.1 + 10 1737_1738 c.1095_1096insC c.(1093-1098)AATCCCfs p.N365fs STAT5A_uc010cya.1_Frame_Shift_Ins_p.N365fs|STAT5A_uc010cyb.1_Frame_Shift_Ins_p.N365fs|STAT5A_uc010cyc.1_Frame_Shift_Ins_p.N335fs NM_003152 NP_003143 P42229 STA5A_HUMAN signal transducer and activator of transcription 365_366 2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|oxaloacetate metabolic process|succinate metabolic process|taurine metabolic process|valine metabolic process cytosol|nucleoplasm calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity lung(1) 1 all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.128) TGCACATGAATCCCCCCCAGGT 0.564 0.29 309 124 ATP8B1 5205 broad.mit.edu 37 18 55365039 55365040 + Frame_Shift_Ins INS - T T HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr18:55365039_55365040insT uc002lgw.2 - 6 614_615 c.614_615insA c.(613-615)AATfs p.N205fs uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 205 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) GAACAAAATCATTTTTTTTCAG 0.386 0.49 18 17 SMARCA4 6597 broad.mit.edu 37 19 11097624 11097625 + Frame_Shift_Ins INS - C C HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr19:11097624_11097625insC uc002mqf.3 + 5 1088_1089 c.804_805insC c.(802-807)GTGCCCfs p.V268fs SMARCA4_uc010dxp.2_Frame_Shift_Ins_p.V268fs|SMARCA4_uc010dxo.2_Frame_Shift_Ins_p.V268fs|SMARCA4_uc002mqg.1_Frame_Shift_Ins_p.V268fs|SMARCA4_uc010dxq.2_Frame_Shift_Ins_p.V268fs|SMARCA4_uc010dxr.2_Frame_Shift_Ins_p.V268fs|SMARCA4_uc002mqj.3_Frame_Shift_Ins_p.V268fs|SMARCA4_uc010dxs.2_Frame_Shift_Ins_p.V268fs|SMARCA4_uc002mqe.2_Frame_Shift_Ins_p.V268fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 268_269 Necessary for interaction with SS18L1/CREST (By similarity). chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.P270fs*16(1)|p.M272fs*31(1)|p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) CCTCGGGCGTGCCCCCCGGGAT 0.634 0.36 7 4 PKN1 5585 broad.mit.edu 37 19 14562741 14562741 + Frame_Shift_Del DEL C - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr19:14562741delC uc002myp.2 + 7 1239 c.1071delC c.(1069-1071)CGCfs p.R357fs PKN1_uc002myq.2_Frame_Shift_Del_p.R363fs NM_002741 NP_002732 Q16512 PKN1_HUMAN protein kinase N1 isoform 2 357 C2. activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent endosome|nucleus|plasma membrane androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1) 8 0.000 0.52 814 893 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 104 655 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 108 DDX17 10521 broad.mit.edu 37 22 38897211 38897211 + Frame_Shift_Del DEL T - - HEC1A_ENDOMETRIUM NA HEC1A_ENDOMETRIUM NA g.chr22:38897211delT uc003avy.3 - 2 465 c.362delA c.(361-363)AAGfs p.K121fs DDX17_uc003avx.3_Frame_Shift_Del_p.K121fs|DDX17_uc011anu.1_Frame_Shift_Del_p.K34fs NM_001098504 NP_001091974 Q92841 DDX17_HUMAN DEAD box polypeptide 17 isoform 3 42 RNA processing nucleus ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity skin(3)|upper_aerodigestive_tract(1) 4 Melanoma(58;0.0286) 0.000 0.39 439 277 ATRX 546 broad.mit.edu 37 X 76952093 76952094 + Frame_Shift_Ins INS - T T HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chrX:76952093_76952094insT uc004ecp.3 - 5 573_574 c.341_342insA c.(340-342)AATfs p.N114fs ATRX_uc004ecq.3_Frame_Shift_Ins_p.N114fs|ATRX_uc004eco.3_Translation_Start_Site|ATRX_uc004ecr.2_Frame_Shift_Ins_p.N114fs|ATRX_uc010nlx.1_Frame_Shift_Ins_p.N114fs|ATRX_uc010nly.1_Frame_Shift_Ins_p.N59fs NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 114 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) TAGTAATATCATTTTCTGAATT 0.277 0.18 56 12 Unknown 0 broad.mit.edu 37 X 80185321 80185321 + Frame_Shift_Del DEL A - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chrX:80185321delA uc004eec.1 + 1 394 c.220delA c.(220-222)AAAfs p.K74fs SubName: Full=cDNA FLJ16670 fis, clone THYMU3001133, highly similar to Voltage-dependent anion-selective channel protein 1; SubName: Full=Voltage-dependent anion channel 1, isoform CRA_a; TAACACTGGGAAAAAAAATGC 0.483 0.48 69 64 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 23 JAK1 3716 broad.mit.edu 37 1 65325833 65325833 + Frame_Shift_Del DEL G - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr1:65325833delG uc001dbu.1 - 9 1538 c.1289delC c.(1288-1290)CCGfs p.P430fs JAK1_uc009wam.1_Frame_Shift_Del_p.P418fs NM_002227 NP_002218 P23458 JAK1_HUMAN janus kinase 1 430 interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway cytoskeleton|cytosol|endomembrane system|membrane|nucleus ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity p.P430fs*2(1) haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1) 61 BRCA - Breast invasive adenocarcinoma(111;0.0485) GACGATCAACGGGGGGGCCAC 0.542 0.50 5 5 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.43 190 141 LRP1B 53353 broad.mit.edu 37 2 141081572 141081572 + Frame_Shift_Del DEL T - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr2:141081572delT uc002tvj.1 - 81 13376 c.12404delA c.(12403-12405)AATfs p.N4135fs NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 4135 Extracellular (Potential). protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) AAATACACCATTTTTAGGTCC 0.299 0.40 52 35 TRPM8 79054 broad.mit.edu 37 2 234847688 234847688 + Frame_Shift_Del DEL T - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr2:234847688delT uc002vvh.2 + 5 435 c.395delT c.(394-396)CTGfs p.L132fs TRPM8_uc010fyj.2_5'UTR|TRPM8_uc002vvi.3_Frame_Shift_Del_p.L82fs|TRPM8_uc002vvj.3_Frame_Shift_Del_p.L55fs NM_024080 NP_076985 Q7Z2W7 TRPM8_HUMAN transient receptor potential cation channel, 132 Cytoplasmic (Potential). integral to membrane skin(4) 4 Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224) Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108) Menthol(DB00825) CTTTACGAGCTGCTGACCCAG 0.562 0.65 13 24 RPL14 9045 broad.mit.edu 37 3 40503495 40503496 + Frame_Shift_Ins INS - A A HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr3:40503495_40503496insA uc003ckg.2 + 6 471_472 c.420_421insA c.(418-423)CCCAAAfs p.P140fs RPL14_uc003ckh.2_Frame_Shift_Ins_p.P140fs|RPL14_uc003cki.2_Frame_Shift_Ins_p.P91fs NM_003973 NP_003964 P50914 RL14_HUMAN ribosomal protein L14 140_141 endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription cytosolic large ribosomal subunit protein binding|RNA binding|structural constituent of ribosome 0 KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065) AAGCTTCTCCCAAAAAAGCACC 0.337 0.68 6 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.35 34 18 INPP4B 8821 broad.mit.edu 37 4 143352347 143352348 + Frame_Shift_Ins INS - T T HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr4:143352347_143352348insT uc003iix.3 - 5 660_661 c.65_66insA c.(64-66)AATfs p.N22fs INPP4B_uc003iiw.3_Frame_Shift_Ins_p.N22fs|INPP4B_uc011chm.1_RNA|INPP4B_uc011cho.1_RNA|INPP4B_uc003iiz.2_RNA NM_003866 NP_003857 O15327 INP4B_HUMAN inositol polyphosphate-4-phosphatase, type II, 22 signal transduction phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity ovary(1)|lung(1) 2 all_hematologic(180;0.158) CCCCGGGATCATTGGCCTGGGC 0.416 0.45 38 31 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 18 39 MAP3K1 4214 broad.mit.edu 37 5 56178258 56178258 + Frame_Shift_Del DEL A - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr5:56178258delA uc003jqw.3 + 14 3732 c.3231delA c.(3229-3231)TCAfs p.S1077fs NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 1077 cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) GAGATCCCTCAAAAAATAGCA 0.443 0.44 141 109 CDKL3 51265 broad.mit.edu 37 5 133634349 133634349 + Frame_Shift_Del DEL A - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr5:133634349delA uc003kzf.3 - 13 1891 c.1772delT c.(1771-1773)TTCfs p.F591fs CDKL3_uc011cxm.1_Intron|CDKL3_uc011cxn.1_Intron|CDKL3_uc010jdw.2_Intron|CDKL3_uc011cxo.1_Intron|CDKL3_uc011cxp.1_Intron|CDKL3_uc011cxq.1_3'UTR NM_001113575 NP_001107047 Q8IVW4 CDKL3_HUMAN cyclin-dependent kinase-like 3 isoform 1 591 cytoplasm ATP binding|cyclin-dependent protein kinase activity breast(1) 1 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) ACACTACCAGAAAAAAAACCT 0.353 0.42 65 48 DEK 7913 broad.mit.edu 37 6 18258250 18258250 + Frame_Shift_Del DEL A - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr6:18258250delA uc003ncr.1 - 4 484 c.291delT c.(289-291)TTTfs p.F97fs DEK_uc011djf.1_Frame_Shift_Del_p.F63fs|DEK_uc011djg.1_RNA NM_003472 NP_003463 P35659 DEK_HUMAN DEK oncogene isoform 1 97 chromatin modification|regulation of transcription from RNA polymerase II promoter|signal transduction|transcription from RNA polymerase II promoter|viral genome replication nucleus DNA binding|histone binding kidney(1) 1 Ovarian(93;0.00769)|Breast(50;0.0495) all_hematologic(90;0.053) OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332) 0.000 0.14 604 96 NOS3 4846 broad.mit.edu 37 7 150698398 150698398 + Frame_Shift_Del DEL G - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr7:150698398delG uc003wif.2 + 11 1609 c.1313delG c.(1312-1314)AGGfs p.R438fs NOS3_uc011kuy.1_Frame_Shift_Del_p.R232fs|NOS3_uc011kuz.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kva.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kvb.1_Frame_Shift_Del_p.R438fs NM_000603 NP_000594 P29474 NOS3_HUMAN nitric oxide synthase 3 isoform 1 438 Interaction with NOSIP. anti-apoptosis|arginine catabolic process|blood vessel remodeling|endothelial cell migration|mitochondrion organization|negative regulation of muscle hyperplasia|negative regulation of platelet activation|nitric oxide biosynthetic process|platelet activation|positive regulation of angiogenesis|positive regulation of guanylate cyclase activity|positive regulation of vasodilation|regulation of blood vessel size|regulation of nitric-oxide synthase activity|regulation of systemic arterial blood pressure by endothelin|response to fluid shear stress|response to heat|smooth muscle hyperplasia caveola|cytoskeleton|cytosol|Golgi membrane actin monomer binding|arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding central_nervous_system(5)|large_intestine(2)|skin(1) 8 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) L-Arginine(DB00125)|L-Citrulline(DB00155)|Rosuvastatin(DB01098)|Tetrahydrobiopterin(DB00360) CAGAAGGCCAGGGGGGGCTGC 0.617 0.31 9 4 MLL3 58508 broad.mit.edu 37 7 151843774 151843775 + Frame_Shift_Ins INS - T T HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr7:151843774_151843775insT uc003wla.2 - 53 14159_14160 c.13940_13941insA c.(13939-13941)AAGfs p.K4647fs MLL3_uc003wkz.2_Frame_Shift_Ins_p.K3765fs|MLL3_uc003wkx.2_Frame_Shift_Ins_p.K805fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.K2211fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 4647 FYR C-terminal. intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) GCATTTCAGACTTTTTTCTCAC 0.426 0.19 122 29 ARFGEF1 10565 broad.mit.edu 37 8 68111217 68111217 + Frame_Shift_Del DEL A - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr8:68111217delA uc003xxo.1 - 39 5892 c.5502delT c.(5500-5502)TTTfs p.F1834fs ARFGEF1_uc003xxl.1_Intron|ARFGEF1_uc003xxm.1_Frame_Shift_Del_p.F237fs|ARFGEF1_uc003xxn.1_Frame_Shift_Del_p.F779fs|ARFGEF1_uc003xxp.1_3'UTR NM_006421 NP_006412 Q9Y6D6 BIG1_HUMAN brefeldin A-inhibited guanine 1834 exocytosis|regulation of ARF protein signal transduction cytoplasm ARF guanyl-nucleotide exchange factor activity|myosin binding ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1) 8 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206) GTGATATCTGAAAAACTACTC 0.363 0.26 114 40 TRPS1 7227 broad.mit.edu 37 8 116631783 116631784 + Frame_Shift_Del DEL TG - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr8:116631783_116631784delTG uc003ynz.2 - 2 961_962 c.502_503delCA c.(502-504)CAGfs p.Q168fs TRPS1_uc011lhy.1_Frame_Shift_Del_p.Q172fs|TRPS1_uc003yny.2_Frame_Shift_Del_p.Q181fs|TRPS1_uc010mcy.2_Frame_Shift_Del_p.Q168fs NM_014112 NP_054831 Q9UHF7 TRPS1_HUMAN zinc finger transcription factor TRPS1 168 negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) TTGACCACTCTGTGCTTGCCCT 0.495 0.52 42 46 ROR2 4920 broad.mit.edu 37 9 94486395 94486395 + Frame_Shift_Del DEL G - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr9:94486395delG uc004arj.1 - 9 2580 c.2381delC c.(2380-2382)CCGfs p.P794fs ROR2_uc004ari.1_Intron NM_004560 NP_004551 Q01974 ROR2_HUMAN receptor tyrosine kinase-like orphan receptor 2 794 Cytoplasmic (Potential).|Pro-rich. negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1) 20 TGGGAAGGGCGGGGCCTTCTG 0.672 0.26 20 7 CEP110 11064 broad.mit.edu 37 9 123924525 123924525 + Frame_Shift_Del DEL A - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr9:123924525delA uc004bkx.1 + 32 5430 c.5399delA c.(5398-5400)GAAfs p.E1800fs CEP110_uc004blb.1_Frame_Shift_Del_p.E469fs|CEP110_uc010mvp.1_Intron NM_007018 NP_008949 Q7Z7A1 CNTRL_HUMAN centrosomal protein 110kDa 1800 Potential. cell division|G2/M transition of mitotic cell cycle centrosome|cytosol protein binding 0 GACATTTGGGAAAAAAAGTTG 0.383 0.44 18 14 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.64 9 16 MLL 4297 broad.mit.edu 37 11 118307394 118307394 + Frame_Shift_Del DEL C - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr11:118307394delC uc001pta.2 + 1 190 c.167delC c.(166-168)TCCfs p.S56fs MLL_uc001ptb.2_Frame_Shift_Del_p.S56fs|uc001psy.2_5'Flank|MLL_uc001psz.1_Frame_Shift_Del_p.S56fs NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 56 Ala/Gly/Ser-rich. apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) 0.000 0.23 502 149 EP400 57634 broad.mit.edu 37 12 132547139 132547141 + In_Frame_Del DEL CAG - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr12:132547139_132547141delCAG uc001ujn.2 + 46 8262_8264 c.8227_8229delCAG c.(8227-8229)CAGdel p.Q2748del EP400_uc001ujl.2_In_Frame_Del_p.Q2747del|EP400_uc001ujm.2_In_Frame_Del_p.Q2667del|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784 Poly-Gln.|Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) gcagcagcaacagcagcagcagc 0.325 0.23 23 7 EDNRB 1910 broad.mit.edu 37 13 78475267 78475267 + Frame_Shift_Del DEL A - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr13:78475267delA uc001vko.2 - 4 1135 c.877delT c.(877-879)TATfs p.Y293fs EDNRB_uc001vkq.1_Frame_Shift_Del_p.Y293fs|uc001vkn.1_Intron|EDNRB_uc010aez.1_Frame_Shift_Del_p.Y293fs|EDNRB_uc001vkp.1_Frame_Shift_Del_p.Y376fs NM_001122659 NP_001116131 P24530 EDNRB_HUMAN endothelin receptor type B isoform 1 precursor 293 Helical; Name=5; (Potential). activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction integral to plasma membrane endothelin-B receptor activity|peptide hormone binding 0 Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037) GBM - Glioblastoma multiforme(99;0.0933) Bosentan(DB00559) ATTAGTGTATAAAAAAATGCA 0.343 0.36 103 58 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.36 9 5 SPRED1 161742 broad.mit.edu 37 15 38614463 38614463 + Frame_Shift_Del DEL A - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr15:38614463delA uc001zka.3 + 3 564 c.229delA c.(229-231)AAAfs p.K77fs NM_152594 NP_689807 Q7Z699 SPRE1_HUMAN sprouty-related protein 1 with EVH-1 domain 77 WH1. inactivation of MAPK activity|multicellular organismal development caveola|nucleus stem cell factor receptor binding ovary(2)|lung(2)|skin(1) 5 all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091) GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244) 0.000 0.67 65 130 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 18 224 COL1A1 1277 broad.mit.edu 37 17 48266157 48266158 + Splice_Site INS - A A rs67965462;rs72653171 HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr17:48266157_48266158insA uc002iqm.2 - 42 3172 c.3046_splice c.e42-1 p.G1016_splice NM_000088 NP_000079 P02452 CO1A1_HUMAN alpha 1 type I collagen preproprotein axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception collagen type I|extracellular space|plasma membrane identical protein binding|platelet-derived growth factor binding COL1A1/PDGFB(372) soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1) 382 Collagenase(DB00048)|Palifermin(DB00039) 0.000 0.16 1499 277 ATP8B1 5205 broad.mit.edu 37 18 55365039 55365040 + Frame_Shift_Ins INS - T T HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr18:55365039_55365040insT uc002lgw.2 - 6 614_615 c.614_615insA c.(613-615)AATfs p.N205fs uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 205 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) GAACAAAATCATTTTTTTTCAG 0.386 0.54 13 15 PKN1 5585 broad.mit.edu 37 19 14562741 14562741 + Frame_Shift_Del DEL C - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr19:14562741delC uc002myp.2 + 7 1239 c.1071delC c.(1069-1071)CGCfs p.R357fs PKN1_uc002myq.2_Frame_Shift_Del_p.R363fs NM_002741 NP_002732 Q16512 PKN1_HUMAN protein kinase N1 isoform 2 357 C2. activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent endosome|nucleus|plasma membrane androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1) 8 0.000 0.38 882 532 CPAMD8 27151 broad.mit.edu 37 19 17085999 17085999 + Frame_Shift_Del DEL A - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr19:17085999delA uc002nfb.2 - 17 2151 c.2119delT c.(2119-2121)TGGfs p.W707fs NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 660 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 0.000 0.33 1307 649 CRTC1 23373 broad.mit.edu 37 19 18887992 18887993 + Frame_Shift_Ins INS - C C HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr19:18887992_18887993insC uc002nkb.3 + 14 1793_1794 c.1705_1706insC c.(1705-1707)TCCfs p.S569fs CRTC1_uc010ebv.2_Frame_Shift_Ins_p.S585fs|CRTC1_uc010ebw.2_Frame_Shift_Ins_p.S405fs|CRTC1_uc002nkc.3_Frame_Shift_Ins_p.S267fs NM_015321 NP_056136 Q6UUV9 CRTC1_HUMAN mucoepidermoid carcinoma translocated 1 isoform 569 interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus|plasma membrane cAMP response element binding protein binding|protein binding CRTC1/MAML2(516) salivary_gland(474)|lung(35)|thyroid(4)|breast(3)|skin(2)|ovary(1) 519 GACAGGAGAGTCCCCCCCCAGC 0.614 0.33 18 9 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 156 762 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 6 53 DDX17 10521 broad.mit.edu 37 22 38897211 38897211 + Frame_Shift_Del DEL T - - HEC1B_ENDOMETRIUM NA HEC1B_ENDOMETRIUM NA g.chr22:38897211delT uc003avy.3 - 2 465 c.362delA c.(361-363)AAGfs p.K121fs DDX17_uc003avx.3_Frame_Shift_Del_p.K121fs|DDX17_uc011anu.1_Frame_Shift_Del_p.K34fs NM_001098504 NP_001091974 Q92841 DDX17_HUMAN DEAD box polypeptide 17 isoform 3 42 RNA processing nucleus ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity skin(3)|upper_aerodigestive_tract(1) 4 Melanoma(58;0.0286) 0.000 0.34 365 189 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 3 38 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 332 102 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.43 16 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 58 84 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.56 96 120 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 23 39 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.32 17 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 1 20 IFNA2 3440 broad.mit.edu 37 9 21385010 21385011 + Frame_Shift_Ins INS - T T HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr9:21385010_21385011insT uc003zpb.2 - 1 386_387 c.318_319insA c.(316-321)AAATTCfs p.K106fs NM_000605 NP_000596 P01563 IFNA2_HUMAN interferon, alpha 2 precursor 106_107 blood coagulation|cell-cell signaling|induction of apoptosis|inflammatory response|negative regulation of interleukin-13 secretion|negative regulation of interleukin-5 secretion|negative regulation of T cell differentiation|negative regulation of T-helper 2 cell cytokine production|negative regulation of transcription, DNA-dependent|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway extracellular space cytokine activity|interferon-alpha/beta receptor binding breast(1) 1 Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173) Interferon Alfa-2a, Recombinant(DB00034)|Interferon Alfa-2b, Recombinant(DB00105)|Interferon alfa-n1(DB00011)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022) TCAGTGTAGAATTTGTCTAGGA 0.510 0.45 59 48 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 269 95 CASP4 837 broad.mit.edu 37 11 104815501 104815502 + Frame_Shift_Ins INS - A A HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr11:104815501_104815502insA uc001pid.1 - 8 1185_1186 c.1112_1113insT c.(1111-1113)TTCfs p.F371fs CASP4_uc001pib.1_Frame_Shift_Ins_p.F315fs|CASP4_uc009yxg.1_Frame_Shift_Ins_p.F280fs NM_001225 NP_001216 P49662 CASP4_HUMAN caspase 4 isoform alpha precursor 371 apoptosis|induction of apoptosis|proteolysis intracellular cysteine-type endopeptidase activity|protein binding lung(2)|ovary(1)|skin(1) 4 Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047) BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357) GAAAGAGGTAGAAATATCTTGT 0.376 0.42 128 94 CNTN1 1272 broad.mit.edu 37 12 41410561 41410562 + Frame_Shift_Ins INS - A A HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr12:41410561_41410562insA uc001rmm.1 + 19 2375_2376 c.2262_2263insA c.(2260-2265)TGGAAAfs p.W754fs CNTN1_uc001rmn.1_Frame_Shift_Ins_p.W743fs NM_001843 NP_001834 Q12860 CNTN1_HUMAN contactin 1 isoform 1 precursor 754_755 Fibronectin type-III 2. axon guidance|cell adhesion|Notch signaling pathway anchored to membrane|membrane fraction|plasma membrane lung(4)|ovary(3)|large_intestine(1)|skin(1) 9 all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716) Lung NSC(34;0.0211)|all_lung(34;0.0294) GAGAAGAATGGAAAAAAGTCAC 0.366 0.26 61 21 ZMYM2 7750 broad.mit.edu 37 13 20638619 20638620 + Frame_Shift_Ins INS - T T HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr13:20638619_20638620insT uc001umr.2 + 20 3364_3365 c.3066_3067insT c.(3064-3069)GAATTTfs p.E1022fs ZMYM2_uc001ums.2_Frame_Shift_Ins_p.E1022fs|ZMYM2_uc001umt.2_Frame_Shift_Ins_p.E1022fs|ZMYM2_uc001umv.2_Frame_Shift_Ins_p.E402fs|ZMYM2_uc001umw.2_Frame_Shift_Ins_p.E475fs NM_003453 NP_003444 Q9UBW7 ZMYM2_HUMAN zinc finger protein 198 1022_1023 regulation of transcription, DNA-dependent|transcription, DNA-dependent PML body ubiquitin conjugating enzyme binding|zinc ion binding lung(3)|ovary(2)|prostate(1) 6 all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856) TGGAAAATGAATTTTTATTACC 0.347 0.39 79 50 ERCC5 2073 broad.mit.edu 37 13 103524567 103524568 + Frame_Shift_Ins INS - A A HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr13:103524567_103524568insA uc001vpw.2 + 13 3141_3142 c.2698_2699insA c.(2698-2700)CAAfs p.Q900fs ERCC5_uc001vpu.1_Frame_Shift_Ins_p.Q1354fs|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_Frame_Shift_Ins_p.Q732fs NM_000123 NP_000114 P28715 ERCC5_HUMAN XPG-complementing protein 900 negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection nucleoplasm bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding ovary(4)|lung(1)|central_nervous_system(1)|skin(1) 7 all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211) GCATGAAGCTCAAAAAAATCCA 0.371 0.45 18 15 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.31 9 4 CHRNA5 1138 broad.mit.edu 37 15 78882365 78882366 + Frame_Shift_Ins INS - T T HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr15:78882365_78882366insT uc002bdy.2 + 5 794_795 c.632_633insT c.(631-633)GATfs p.D211fs CHRNA5_uc002bdz.2_Intron NM_000745 NP_000736 P30532 ACHA5_HUMAN cholinergic receptor, nicotinic, alpha 5 211 Extracellular (Potential). behavioral response to nicotine cell junction|postsynaptic membrane acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity ovary(1)|central_nervous_system(1)|skin(1) 3 GACAAGAGAGATTTTTTTGATA 0.406 0.43 113 84 GRIN2A 2903 broad.mit.edu 37 16 10032381 10032382 + Frame_Shift_Ins INS - A A rs35898789 HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr16:10032381_10032382insA uc002czo.3 - 3 989_990 c.441_442insT c.(439-444)TTTGGAfs p.F147fs GRIN2A_uc010uym.1_Frame_Shift_Ins_p.F147fs|GRIN2A_uc010uyn.1_5'UTR|GRIN2A_uc002czr.3_Frame_Shift_Ins_p.F147fs NM_001134407 NP_001127879 Q12879 NMDE1_HUMAN N-methyl-D-aspartate receptor subunit 2A isoform 147_148 Extracellular (Potential). response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1) 45 Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043) ATGGACGCTCCAAACTGGAAGA 0.500 0.43 66 49 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HEC251_ENDOMETRIUM NA HEC251_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 261 630 FAM48B1 100130302 broad.mit.edu 37 X 24382400 24382401 + In_Frame_Ins INS - TAT TAT HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chrX:24382400_24382401insTAT uc011mjx.1 + 1 1523_1524 c.1523_1524insTAT c.(1522-1524)GCT>GCTATT p.508_509insI NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 gctgctgctgctgctgctgctg 0.149 0.38 41 25 NRK 203447 broad.mit.edu 37 X 105132386 105132386 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chrX:105132386delC uc004emd.2 + 5 655 c.352delC c.(352-354)CCCfs p.P118fs NRK_uc010npc.1_5'UTR NM_198465 NP_940867 Q7Z2Y5 NRK_HUMAN Nik related kinase 118 Protein kinase. ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1) 14 CAAGCTGAGTCCCCCTGGTCA 0.398 0.49 56 54 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 2 98 EPHA2 1969 broad.mit.edu 37 1 16462199 16462199 + Frame_Shift_Del DEL G - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr1:16462199delG uc001aya.1 - 6 1516 c.1379delC c.(1378-1380)CCGfs p.P460fs EPHA2_uc010oca.1_Frame_Shift_Del_p.P460fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 460 Extracellular (Potential).|Fibronectin type-III 2. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) 0.000 0.38 784 483 EPHA2 1969 broad.mit.edu 37 1 16474977 16474977 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr1:16474977delC uc001aya.1 - 3 856 c.719delG c.(718-720)GGTfs p.G240fs EPHA2_uc010oca.1_Frame_Shift_Del_p.G240fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 240 Extracellular (Potential).|Cys-rich. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) GGGCTCTTCACCCCCCGGTGG 0.667 0.42 49 35 ARID1A 8289 broad.mit.edu 37 1 27101117 27101117 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr1:27101117delC uc001bmv.1 + 18 4772 c.4399delC c.(4399-4401)CCCfs p.P1467fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.P1466fs|ARID1A_uc001bmu.1_Intron|ARID1A_uc001bmw.1_Frame_Shift_Del_p.P1084fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.P313fs|ARID1A_uc009vsm.1_Intron|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1467 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) TGTCTCTGCACCCCCTGGCAC 0.607 0.44 245 196 PLK3 1263 broad.mit.edu 37 1 45270026 45270026 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr1:45270026delC uc001cmn.2 + 12 1458 c.1358delC c.(1357-1359)GCCfs p.A453fs PLK3_uc001cmo.2_RNA NM_004073 NP_004064 Q9H4B4 PLK3_HUMAN polo-like kinase 3 453 membrane ATP binding|protein binding|protein serine/threonine kinase activity 0 Acute lymphoblastic leukemia(166;0.155) CAGAACCCGGCCCCCCTGGCC 0.617 0.17 191 39 MAST2 23139 broad.mit.edu 37 1 46499885 46499885 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr1:46499885delC uc001cov.2 + 28 4098 c.3815delC c.(3814-3816)TCCfs p.S1272fs MAST2_uc001cow.2_Frame_Shift_Del_p.S1271fs|MAST2_uc001cpa.2_RNA NM_015112 NP_055927 Q6P0Q8 MAST2_HUMAN microtubule associated serine/threonine kinase 1272 regulation of interleukin-12 biosynthetic process|spermatid differentiation cytoplasm|cytoskeleton|plasma membrane ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity ovary(5)|lung(3)|stomach(2)|breast(1) 11 Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184) CACAGCCTTTCCCCCCGATCT 0.607 0.47 285 248 DAB1 1600 broad.mit.edu 37 1 57491693 57491693 + Frame_Shift_Del DEL A - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr1:57491693delA uc001cys.1 - 12 1421 c.747delT c.(745-747)TTTfs p.F249fs DAB1_uc001cyt.1_Frame_Shift_Del_p.F247fs|DAB1_uc001cyq.1_Frame_Shift_Del_p.F247fs|DAB1_uc001cyr.1_Frame_Shift_Del_p.F163fs|DAB1_uc009vzw.1_Frame_Shift_Del_p.F231fs|DAB1_uc009vzx.1_Frame_Shift_Del_p.F249fs NM_021080 NP_066566 O75553 DAB1_HUMAN disabled homolog 1 282 cell differentiation|nervous system development skin(2)|ovary(1) 3 ACATGTCCCCAAAAAGTTCTA 0.463 0.47 111 98 RBM15 64783 broad.mit.edu 37 1 110882436 110882436 + Frame_Shift_Del DEL G - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr1:110882436delG uc001dzl.1 + 1 492 c.409delG c.(409-411)GGGfs p.G137fs RBM15_uc001dzm.1_Frame_Shift_Del_p.G137fs|uc001dzj.2_5'Flank NM_022768 NP_073605 Q96T37 RBM15_HUMAN RNA binding motif protein 15 137 Gly/Ser-rich. interspecies interaction between organisms nucleus nucleotide binding|protein binding|RNA binding ovary(3) 3 all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634) BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135) TTCTTCGGGCGGGGGCGAATC 0.667 0.27 70 26 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 309 82 HORMAD1 84072 broad.mit.edu 37 1 150680744 150680744 + Frame_Shift_Del DEL A - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr1:150680744delA uc001evk.1 - 9 641 c.535delT c.(535-537)TACfs p.Y179fs HORMAD1_uc001evl.1_Frame_Shift_Del_p.Y172fs|HORMAD1_uc001evm.1_Frame_Shift_Del_p.Y99fs NM_032132 NP_115508 Q86X24 HORM1_HUMAN HORMA domain containing 1 179 HORMA. blastocyst development|cell differentiation|meiotic DNA double-strand break formation|meiotic recombination checkpoint|meiotic sister chromatid cohesion|mitosis|oogenesis|regulation of homologous chromosome segregation|spermatogenesis|synaptonemal complex assembly chromosome|nucleus ovary(2)|central_nervous_system(1) 3 all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171) UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171) TCATCATAGTAAAAAAGTTTC 0.328 0.42 42 31 ABL2 27 broad.mit.edu 37 1 179078242 179078242 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr1:179078242delC uc001gmj.3 - 12 2447 c.2160delG c.(2158-2160)GGGfs p.G720fs ABL2_uc010pnf.1_Intron|ABL2_uc010png.1_Intron|ABL2_uc010pnh.1_Frame_Shift_Del_p.G699fs|ABL2_uc001gmg.3_Intron|ABL2_uc001gmi.3_Frame_Shift_Del_p.G705fs|ABL2_uc001gmh.3_Frame_Shift_Del_p.G684fs|ABL2_uc010pne.1_Intron NM_007314 NP_009298 P42684 ABL2_HUMAN arg tyrosine kinase isoform b 720 F-actin-binding (By similarity). axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction cytoskeleton|cytosol ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(8)|breast(3)|ovary(2)|central_nervous_system(1) 14 Adenosine triphosphate(DB00171)|Dasatinib(DB01254) GTGCAAAGCTCCCCCCATAGC 0.567 0.50 86 86 TTN 7273 broad.mit.edu 37 2 179647781 179647781 + Frame_Shift_Del DEL T - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr2:179647781delT uc010zfg.1 - 18 3076 c.2852delA c.(2851-2853)AATfs p.N951fs TTN_uc010zfh.1_Frame_Shift_Del_p.N905fs|TTN_uc010zfi.1_Frame_Shift_Del_p.N905fs|TTN_uc010zfj.1_Frame_Shift_Del_p.N905fs|TTN_uc002unb.2_Frame_Shift_Del_p.N951fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 951 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GACAGTCACATTTTTTAAGCC 0.393 0.46 62 53 IRS1 3667 broad.mit.edu 37 2 227660772 227660772 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr2:227660772delC uc002voh.3 - 1 2735 c.2683delG c.(2683-2685)GAAfs p.E895fs NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 895 fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) 0.000 0.15 343 59 PASK 23178 broad.mit.edu 37 2 242051701 242051701 + Frame_Shift_Del DEL A - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr2:242051701delA uc002wao.1 - 15 3579 c.3487delT c.(3487-3489)TGTfs p.C1163fs PASK_uc010zol.1_Frame_Shift_Del_p.C977fs|PASK_uc010zom.1_Frame_Shift_Del_p.C1128fs|PASK_uc010fzl.1_Frame_Shift_Del_p.C1170fs|PASK_uc010zon.1_Frame_Shift_Del_p.C944fs NM_015148 NP_055963 Q96RG2 PASK_HUMAN PAS domain containing serine/threonine kinase 1163 Protein kinase. regulation of transcription, DNA-dependent Golgi apparatus ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity ovary(4)|lung(1)|skin(1) 6 all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968) ATGGTCCCACAAAAAGTATAA 0.527 0.37 81 48 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.34 19 10 MLH1 4292 broad.mit.edu 37 3 37053348 37053348 + Frame_Shift_Del DEL A - - rs35847123 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr3:37053348delA uc003cgl.2 + 7 643 c.583delA c.(583-585)AAAfs p.K195fs MLH1_uc011aye.1_5'UTR|MLH1_uc011ayb.1_5'UTR|MLH1_uc010hge.2_Frame_Shift_Del_p.K195fs|MLH1_uc003cgn.3_5'UTR|MLH1_uc011ayc.1_Frame_Shift_Del_p.K97fs|MLH1_uc011ayd.1_5'UTR|MLH1_uc003cgo.2_5'UTR|MLH1_uc010hgg.1_5'Flank|MLH1_uc010hgh.1_5'Flank|MLH1_uc010hgi.1_5'Flank|MLH1_uc010hgj.1_5'Flank|MLH1_uc010hgk.2_5'Flank|MLH1_uc010hgl.1_5'Flank NM_000249 NP_000240 P40692 MLH1_HUMAN MutL protein homolog 1 195 mismatch repair|somatic hypermutation of immunoglobulin genes chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex ATP binding|ATPase activity|protein binding p.0?(1) large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1) 77 TTTCTCAGTTAAAAAAGTAAG 0.343 0.51 65 69 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.22 39 11 DVL3 1857 broad.mit.edu 37 3 183883913 183883914 + Splice_Site INS - A A HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr3:183883913_183883914insA uc003fms.2 + 8 904 c.764_splice c.e8-1 p.E255_splice DVL3_uc011bqw.1_Splice_Site_p.E255_splice|DVL3_uc003fmt.2_Splice_Site|DVL3_uc003fmu.2_Splice_Site_p.E87_splice NM_004423 NP_004414 Q92997 DVL3_HUMAN dishevelled 3 canonical Wnt receptor signaling pathway|intracellular signal transduction|positive regulation of JUN kinase activity|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent cytoplasm beta-catenin binding|frizzled binding|protease binding|protein heterodimerization activity|signal transducer activity ovary(1)|lung(1)|breast(1) 3 all_cancers(143;1.12e-10)|Ovarian(172;0.0339) Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22) ACTCTCTATAGAAAAATATAAC 0.460 0.33 8 4 EPHA5 2044 broad.mit.edu 37 4 66509084 66509085 + Frame_Shift_Ins INS - T T rs33932471 byFrequency;by1000genomes HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr4:66509084_66509085insT uc003hcy.2 - 2 435_436 c.242_243insA c.(241-243)AATfs p.N81fs EPHA5_uc003hcx.2_Frame_Shift_Ins_p.N12fs|EPHA5_uc003hcz.2_Frame_Shift_Ins_p.N81fs|EPHA5_uc011cah.1_Frame_Shift_Ins_p.N81fs|EPHA5_uc011cai.1_Frame_Shift_Ins_p.N81fs|EPHA5_uc003hda.2_Frame_Shift_Ins_p.N81fs NM_004439 NP_004430 P54756 EPHA5_HUMAN ephrin receptor EphA5 isoform a precursor 81 Extracellular (Potential). cAMP-mediated signaling|neuron development dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum ATP binding|transmembrane-ephrin receptor activity lung(19)|stomach(2)|ovary(2)|central_nervous_system(1) 24 AACTTACCCCATTTTTTGGAAA 0.342 0.56 17 22 CXCL9 4283 broad.mit.edu 37 4 76924806 76924806 + Frame_Shift_Del DEL T - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr4:76924806delT uc003hjh.1 - 4 362 c.323delA c.(322-324)AAGfs p.K108fs NM_002416 NP_002407 Q07325 CXCL9_HUMAN small inducible cytokine B9 precursor 108 cell-cell signaling|cellular defense response|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response extracellular space chemokine activity ovary(1) 1 Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934) CAGAACTTTCTTTTTTTGATG 0.333 0.39 68 44 BMP2K 55589 broad.mit.edu 37 4 79792137 79792145 + In_Frame_Del DEL CAGCAGCAG - - rs17855588 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr4:79792137_79792145delCAGCAGCAG uc003hlk.2 + 11 1598_1606 c.1432_1440delCAGCAGCAG c.(1432-1440)CAGCAGCAGdel p.QQQ484del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQ484del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 484_486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 gcaacagcaacagcagcagcagcagcagc 0.177 0.22 194 55 CFI 3426 broad.mit.edu 37 4 110687927 110687927 + Frame_Shift_Del DEL T - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr4:110687927delT uc003hzr.3 - 2 319 c.111delA c.(109-111)AAAfs p.K37fs CFI_uc011cft.1_Frame_Shift_Del_p.K37fs|CFI_uc003hzs.3_Frame_Shift_Del_p.K37fs NM_000204 NP_000195 P05156 CFAI_HUMAN complement factor I preproprotein 37 complement activation, classical pathway|innate immune response|proteolysis extracellular space|membrane scavenger receptor activity|serine-type endopeptidase activity 0 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.000331) GGTGAGTATATTTTTTTGCTA 0.398 0.36 82 46 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 138 254 NIPBL 25836 broad.mit.edu 37 5 36985605 36985605 + Frame_Shift_Del DEL A - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr5:36985605delA uc003jkl.3 + 10 2822 c.2323delA c.(2323-2325)AAAfs p.K775fs NIPBL_uc003jkk.3_Frame_Shift_Del_p.K775fs|NIPBL_uc003jkm.1_Frame_Shift_Del_p.K654fs NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 775 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) ATCTACAGAGAAAAAACCTGA 0.443 0.51 19 20 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 18 45 PIK3R1 5295 broad.mit.edu 37 5 67575467 67575468 + Frame_Shift_Ins INS - G G rs143572224 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr5:67575467_67575468insG uc003jva.2 + 5 1100_1101 c.540_541insG c.(538-543)CACGTTfs p.H180fs PIK3R1_uc003jvb.2_Frame_Shift_Ins_p.H180fs NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 180_181 Rho-GAP. epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.?(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) TCGATGTGCACGTTTTGGCTGA 0.391 0.41 127 90 PIK3R1 5295 broad.mit.edu 37 5 67591259 67591259 + Frame_Shift_Del DEL A - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr5:67591259delA uc003jva.2 + 14 2317 c.1757delA c.(1756-1758)CAAfs p.Q586fs PIK3R1_uc003jvb.2_Frame_Shift_Del_p.Q586fs|PIK3R1_uc003jvc.2_Frame_Shift_Del_p.Q286fs|PIK3R1_uc003jvd.2_Frame_Shift_Del_p.Q316fs|PIK3R1_uc003jve.2_Frame_Shift_Del_p.Q265fs|PIK3R1_uc011crb.1_Frame_Shift_Del_p.Q256fs NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 586 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.M582_D605>I(4)|p.Y580fs*1(1)|p.?(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) TGGTTGACTCAAAAAGGTGTT 0.358 0.53 28 32 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.20 293 71 CSNK1G3 1456 broad.mit.edu 37 5 122881495 122881495 + Frame_Shift_Del DEL A - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr5:122881495delA uc003ktm.2 + 2 857 c.138delA c.(136-138)GGAfs p.G46fs CSNK1G3_uc003ktl.2_Frame_Shift_Del_p.G46fs|CSNK1G3_uc003ktn.2_Frame_Shift_Del_p.G46fs|CSNK1G3_uc003kto.2_Frame_Shift_Del_p.G46fs|CSNK1G3_uc011cwr.1_Intron|CSNK1G3_uc011cws.1_Intron|CSNK1G3_uc010jda.2_Frame_Shift_Del_p.G46fs NM_004384 NP_004375 Q9Y6M4 KC1G3_HUMAN casein kinase 1, gamma 3 isoform 1 46 Protein kinase. Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity 0 all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245) KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229) OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176) TTAGAGTTGGAAAAAAAATTG 0.363 0.49 35 34 ALDH7A1 501 broad.mit.edu 37 5 125918645 125918645 + Frame_Shift_Del DEL T - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr5:125918645delT uc003ktx.2 - 5 607 c.415delA c.(415-417)ATCfs p.I139fs ALDH7A1_uc003kty.2_RNA|ALDH7A1_uc011cxa.1_Frame_Shift_Del_p.I166fs|ALDH7A1_uc003ktz.2_Frame_Shift_Del_p.I166fs NM_001182 NP_001173 P49419 AL7A1_HUMAN aldehyde dehydrogenase 7 family, member A1 139 cellular aldehyde metabolic process|lysine catabolic process|sensory perception of sound cytosol|mitochondrial matrix|nucleus aldehyde dehydrogenase (NAD) activity|betaine-aldehyde dehydrogenase activity|L-aminoadipate-semialdehyde dehydrogenase activity kidney(2)|ovary(1) 3 all_cancers(142;0.24)|Prostate(80;0.081) KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934) Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109) NADH(DB00157)|Pyridoxine(DB00165) TCCACTAAGATTTTCCCCATC 0.383 0.48 45 42 STK32A 202374 broad.mit.edu 37 5 146754725 146754725 + Frame_Shift_Del DEL A - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr5:146754725delA uc010jgn.1 + 11 1256 c.976delA c.(976-978)AAAfs p.K326fs STK32A_uc003lom.2_Frame_Shift_Del_p.K326fs|STK32A_uc011dbw.1_Frame_Shift_Del_p.K326fs NM_001112724 NP_001106195 Q8WU08 ST32A_HUMAN serine/threonine kinase 32A isoform 1 326 ATP binding|metal ion binding|protein serine/threonine kinase activity lung(2)|skin(1) 3 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TCTACATAAGAAAAAAAAGCG 0.453 0.62 6 10 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.54 6 7 HMMR 3161 broad.mit.edu 37 5 162917425 162917426 + Frame_Shift_Ins INS - A A HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr5:162917425_162917426insA uc003lzf.2 + 17 2171_2172 c.1989_1990insA c.(1987-1992)GCTAAAfs p.A663fs HMMR_uc003lzh.2_Frame_Shift_Ins_p.A664fs|HMMR_uc003lzg.2_Frame_Shift_Ins_p.A648fs|HMMR_uc011dem.1_Frame_Shift_Ins_p.A577fs|uc003lzi.2_Intron NM_012484 NP_036616 O75330 HMMR_HUMAN hyaluronan-mediated motility receptor isoform b 663_664 Hyaluronic acid-binding (Potential). cell surface|cytoplasm hyaluronic acid binding 0 Renal(175;0.000281) Medulloblastoma(196;0.00853)|all_neural(177;0.0408) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848) GTCAGCTTGCTAAAAAAAAACA 0.307 0.43 12 9 RANBP9 10048 broad.mit.edu 37 6 13632610 13632610 + Frame_Shift_Del DEL T - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr6:13632610delT uc003nbb.2 - 12 1998 c.1939delA c.(1939-1941)ATGfs p.M647fs RANBP9_uc003nba.2_Frame_Shift_Del_p.M306fs NM_005493 NP_005484 Q96S59 RANB9_HUMAN RAN binding protein 9 647 Interaction with FMR1. axon guidance|microtubule nucleation|protein complex assembly cytosol|microtubule associated complex|nucleus Ran GTPase binding lung(1)|skin(1) 2 Breast(50;0.00669)|Ovarian(93;0.0634) all_hematologic(90;0.117) Epithelial(50;0.223) ACCTTCAACATTTTTTTGTTT 0.378 0.48 94 88 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.22 54 15 CDKN1A 1026 broad.mit.edu 37 6 36652118 36652118 + Frame_Shift_Del DEL G - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr6:36652118delG uc003omm.3 + 2 362 c.240delG c.(238-240)ACGfs p.T80fs CDKN1A_uc011dtq.1_Frame_Shift_Del_p.T114fs|CDKN1A_uc003oml.2_Frame_Shift_Del_p.T80fs|CDKN1A_uc003omn.2_Frame_Shift_Del_p.T80fs NM_000389 NP_000380 P38936 CDN1A_HUMAN cyclin-dependent kinase inhibitor 1A 80 cell cycle arrest|cellular response to extracellular stimulus|cellular response to ionizing radiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|induction of apoptosis by intracellular signals|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of fibroblast proliferation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|S phase of mitotic cell cycle|stress-induced premature senescence cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleoplasm|PCNA-p21 complex cyclin-dependent protein kinase activating kinase activity|cyclin-dependent protein kinase inhibitor activity|metal ion binding ovary(1)|breast(1) 2 ACCTTCCCACGGGGCCCCGGC 0.657 0.65 6 11 HSP90AB1 3326 broad.mit.edu 37 6 44220917 44220917 + Frame_Shift_Del DEL A - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr6:44220917delA uc003oxa.1 + 11 1951 c.1867delA c.(1867-1869)AAAfs p.K623fs HSP90AB1_uc011dvr.1_Frame_Shift_Del_p.K613fs|HSP90AB1_uc003oxb.1_Frame_Shift_Del_p.K623fs|HSP90AB1_uc011dvs.1_Frame_Shift_Del_p.K443fs|HSP90AB1_uc003oxc.1_Frame_Shift_Del_p.K261fs NM_007355 NP_031381 P08238 HS90B_HUMAN heat shock 90kDa protein 1, beta 623 axon guidance|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of nitric oxide biosynthetic process|protein folding|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to unfolded protein cytosol|melanosome ATP binding|nitric-oxide synthase regulator activity|TPR domain binding|unfolded protein binding lung(3)|breast(1) 4 all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273) Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536) TATGATGGCCAAAAAGCACCT 0.552 0.47 85 74 PHF3 23469 broad.mit.edu 37 6 64401733 64401734 + Frame_Shift_Del DEL TG - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr6:64401733_64401734delTG uc003pep.1 + 4 2322_2323 c.2296_2297delTG c.(2296-2298)TGTfs p.C766fs PHF3_uc010kaf.1_Frame_Shift_Del_p.C766fs|PHF3_uc003pem.2_Frame_Shift_Del_p.C719fs|PHF3_uc010kag.1_Frame_Shift_Del_p.C678fs|PHF3_uc010kah.1_Frame_Shift_Del_p.C580fs|PHF3_uc003pen.2_Frame_Shift_Del_p.C678fs|PHF3_uc011dxs.1_Frame_Shift_Del_p.C35fs NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 766 PHD-type. multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) AGAATATGTCTGTGTAAAATGT 0.406 0.60 25 37 CYB5R4 51167 broad.mit.edu 37 6 84634230 84634231 + Frame_Shift_Ins INS - A A HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr6:84634230_84634231insA uc003pkf.2 + 10 865_866 c.733_734insA c.(733-735)CAAfs p.Q245fs NM_016230 NP_057314 Q7L1T6 NB5R4_HUMAN cytochrome b5 reductase 4 245 CS. cell development|detection of oxygen|generation of precursor metabolites and energy|glucose homeostasis|insulin secretion|response to antibiotic|superoxide metabolic process endoplasmic reticulum|perinuclear region of cytoplasm cytochrome-b5 reductase activity|heme binding|NAD(P)H oxidase activity breast(2) 2 all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128) BRCA - Breast invasive adenocarcinoma(397;0.0871) GATTGTTCTACAAAAAAAAGAG 0.337 0.40 68 45 HNRNPA2B1 3181 broad.mit.edu 37 7 26236953 26236953 + Frame_Shift_Del DEL T - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr7:26236953delT uc003sxr.3 - 4 498 c.282delA c.(280-282)AAAfs p.K94fs HNRNPA2B1_uc003sxs.3_Frame_Shift_Del_p.K82fs NM_031243 NP_112533 P22626 ROA2_HUMAN heterogeneous nuclear ribonucleoprotein A2/B1 94 RRM 1. RNA transport catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm nucleotide binding|protein binding|protein binding|RNA binding|single-stranded telomeric DNA binding ovary(1)|central_nervous_system(1)|skin(1) 3 CTACAGCACGTTTTGGCTCAA 0.418 0.46 96 82 GPR141 353345 broad.mit.edu 37 7 37780680 37780680 + Frame_Shift_Del DEL T - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr7:37780680delT uc003tfm.1 + 1 685 c.685delT c.(685-687)TTTfs p.F229fs uc003tfl.2_Intron NM_181791 NP_861456 Q7Z602 GP141_HUMAN G protein-coupled receptor 141 229 Helical; Name=6; (Potential). integral to membrane|plasma membrane G-protein coupled receptor activity ovary(3) 3 GAAAAACCTATTTTTTATAGG 0.433 0.49 161 153 RALA 5898 broad.mit.edu 37 7 39745786 39745787 + Frame_Shift_Ins INS - A A HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr7:39745786_39745787insA uc003thd.2 + 5 863_864 c.563_564insA c.(562-564)GGAfs p.G188fs NM_005402 NP_005393 P11233 RALA_HUMAN ras related v-ral simian leukemia viral oncogene 188 actin cytoskeleton reorganization|cell cycle|chemotaxis|cytokinesis|exocytosis|interspecies interaction between organisms|membrane raft localization|nerve growth factor receptor signaling pathway|positive regulation of filopodium assembly|Ras protein signal transduction|regulation of exocytosis cell surface|cleavage furrow|cytosol|midbody|plasma membrane Edg-2 lysophosphatidic acid receptor binding|GTP binding|GTPase activity lung(1)|skin(1) 2 0.000 0.38 173 104 SMO 6608 broad.mit.edu 37 7 128829075 128829075 + Frame_Shift_Del DEL G - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr7:128829075delG uc003vor.2 + 1 363 c.83delG c.(82-84)CGGfs p.R28fs NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 28 Extracellular (Potential). adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.32 691 320 SMO 6608 broad.mit.edu 37 7 128852004 128852004 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr7:128852004delC uc003vor.2 + 12 2356 c.2076delC c.(2074-2076)CACfs p.H692fs SMO_uc003vos.2_3'UTR NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 692 Cytoplasmic (Potential). adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 CTGAGCTTCACCCCCCTGCCC 0.592 0.59 15 22 BRAF 673 broad.mit.edu 37 7 140482927 140482927 + Frame_Shift_Del DEL G - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr7:140482927delG uc003vwc.3 - 10 1269 c.1208delC c.(1207-1209)CCTfs p.P403fs NM_004333 NP_004324 P15056 BRAF_HUMAN B-Raf 403 activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission cytosol|nucleus|plasma membrane ATP binding|metal ion binding KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2) thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1) 18290 Melanoma(164;0.00956) Sorafenib(DB00398) TAATGAGGCAGGGGGGGTAGC 0.428 0.27 118 44 EPHB6 2051 broad.mit.edu 37 7 142561447 142561448 + Frame_Shift_Ins INS - G G HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr7:142561447_142561448insG uc011kst.1 + 6 946_947 c.159_160insG c.(157-162)CCAGGGfs p.P53fs EPHB6_uc011ksu.1_Frame_Shift_Ins_p.P53fs|EPHB6_uc003wbs.2_Intron|EPHB6_uc003wbt.2_5'UTR|EPHB6_uc003wbu.2_Intron NM_004445 NP_004436 O15197 EPHB6_HUMAN ephrin receptor EphB6 precursor 53_54 Extracellular (Potential). extracellular region|integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1) 19 Melanoma(164;0.059) 0.000 0.36 277 153 EPHB6 2051 broad.mit.edu 37 7 142562398 142562398 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr7:142562398delC uc011kst.1 + 7 1627 c.840delC c.(838-840)AGCfs p.S280fs EPHB6_uc011ksu.1_Frame_Shift_Del_p.S280fs|EPHB6_uc003wbs.2_5'UTR|EPHB6_uc003wbt.2_5'UTR|EPHB6_uc003wbu.2_5'UTR|EPHB6_uc003wbv.2_5'Flank NM_004445 NP_004436 O15197 EPHB6_HUMAN ephrin receptor EphB6 precursor 280 Extracellular (Potential).|Cys-rich. extracellular region|integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1) 19 Melanoma(164;0.059) CAGGAGGCAGCCCCCCCAGGC 0.687 0.50 5 5 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.40 6 4 SGK223 157285 broad.mit.edu 37 8 8185549 8185550 + Frame_Shift_Ins INS - G G HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr8:8185549_8185550insG uc003wsh.3 - 4 2742_2743 c.2742_2743insC c.(2740-2745)CCCTCCfs p.P914fs NM_001080826 NP_001074295 Q86YV5 SG223_HUMAN pragmin 914_915 ATP binding|non-membrane spanning protein tyrosine kinase activity 0 GATGAGGCGGAGGGGGCCCCTT 0.658 0.47 86 75 WHSC1L1 54904 broad.mit.edu 37 8 38146925 38146926 + Frame_Shift_Ins INS - G G HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr8:38146925_38146926insG uc003xli.2 - 18 3734_3735 c.3216_3217insC c.(3214-3219)CCCTACfs p.P1072fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.P1072fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.P1023fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 1072_1073 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) ATGTGTTTGTAGGGAGGGGGTT 0.361 0.25 129 42 WHSC1L1 54904 broad.mit.edu 37 8 38205308 38205309 + Frame_Shift_Ins INS - T T HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr8:38205308_38205309insT uc003xli.2 - 2 899_900 c.381_382insA c.(379-384)AAACCTfs p.K127fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.K127fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.K127fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.K127fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 127_128 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) GGAGGGGAAGGTTTTTCCAGAA 0.421 0.46 156 131 RIMS2 9699 broad.mit.edu 37 8 104927733 104927734 + Frame_Shift_Ins INS - A A HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr8:104927733_104927734insA uc003yls.2 + 5 1398_1399 c.1157_1158insA c.(1156-1158)GGAfs p.G386fs RIMS2_uc003ylp.2_Frame_Shift_Ins_p.G608fs|RIMS2_uc003ylw.2_Frame_Shift_Ins_p.G416fs|RIMS2_uc003ylq.2_Frame_Shift_Ins_p.G416fs|RIMS2_uc003ylr.2_Frame_Shift_Ins_p.G463fs|RIMS2_uc003ylt.2_Frame_Shift_Ins_p.G9fs|RIMS2_uc003ylu.1_5'UTR|RIMS2_uc003ylv.1_5'UTR NM_014677 NP_055492 Q9UQ26 RIMS2_HUMAN regulating synaptic membrane exocytosis 2 686 PDZ. intracellular protein transport cell junction|presynaptic membrane metal ion binding|Rab GTPase binding ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1) 15 OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229) GTTGTAGGAGGAAAGATGACTG 0.351 0.44 61 48 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 58 WNK2 65268 broad.mit.edu 37 9 96021419 96021419 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr9:96021419delC uc004ati.1 + 11 2589 c.2589delC c.(2587-2589)CACfs p.H863fs WNK2_uc011lud.1_Frame_Shift_Del_p.H863fs|WNK2_uc004atj.2_Frame_Shift_Del_p.H863fs|WNK2_uc004atk.2_Frame_Shift_Del_p.H500fs|WNK2_uc010mrc.1_Frame_Shift_Del_p.H811fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 863 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 AGCTGCCCCACCCCCCTGGGG 0.697 0.40 223 151 WNK2 65268 broad.mit.edu 37 9 96051830 96051831 + Frame_Shift_Ins INS - G G HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr9:96051830_96051831insG uc004ati.1 + 20 4905_4906 c.4905_4906insG c.(4903-4908)TGCGGGfs p.C1635fs WNK2_uc011lud.1_Frame_Shift_Ins_p.C1598fs|WNK2_uc004atj.2_Frame_Shift_Ins_p.C1598fs|WNK2_uc004atk.2_Frame_Shift_Ins_p.C1235fs|WNK2_uc004atl.1_Frame_Shift_Ins_p.C193fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 1635_1636 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 CAGAGGTCTGCGGGGGGGACCT 0.683 0.33 32 16 CEP110 11064 broad.mit.edu 37 9 123912667 123912667 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr9:123912667delC uc004bkx.1 + 23 3900 c.3869delC c.(3868-3870)GCCfs p.A1290fs CEP110_uc004bky.1_Frame_Shift_Del_p.A894fs|CEP110_uc004bla.1_Frame_Shift_Del_p.A738fs|CEP110_uc010mvo.1_Intron|CEP110_uc004blb.1_5'Flank NM_007018 NP_008949 Q7Z7A1 CNTRL_HUMAN centrosomal protein 110kDa 1290 Pro-rich. cell division|G2/M transition of mitotic cell cycle centrosome|cytosol protein binding 0 CCTGCTGGGGCCCCCATGGTG 0.582 0.41 175 120 PTEN 5728 broad.mit.edu 37 10 89720803 89720804 + Frame_Shift_Ins INS - A A rs146650273 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr10:89720803_89720804insA uc001kfb.2 + 9 1985_1986 c.954_955insA c.(952-957)CTTACTfs p.L318fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 318_319 C2 tensin-type. Missing (in glioma; reduced tumor suppressor activity; fails to inactivate AKT/PKB). activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.L318fs*2(24)|p.T319fs*1(22)|p.T319fs*6(6)|p.V317fs*3(4)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.T319del(2)|p.V317fs*6(2)|p.T319_K332del(1)|p.G165_*404del(1)|p.L318fs*3(1)|p.G165_K342del(1)|p.L316fs*1(1)|p.T319fs*4(1)|p.W274_F341del(1)|p.V317_K322del(1)|p.L318F(1)|p.T318fs*2(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) ATCTAGTACTTACTTTAACAAA 0.327 0.94 6 96 SUFU 51684 broad.mit.edu 37 10 104309753 104309754 + Frame_Shift_Ins INS - T T HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr10:104309753_104309754insT uc001kvy.1 + 3 490_491 c.344_345insT c.(343-345)GGTfs p.G115fs SUFU_uc001kvw.1_Frame_Shift_Ins_p.G115fs|SUFU_uc001kvx.2_Frame_Shift_Ins_p.G115fs NM_016169 NP_057253 Q9UMX1 SUFU_HUMAN suppressor of fused 115 negative regulation of transcription from RNA polymerase II promoter|proteolysis|skeletal system development cytoplasm|nucleus identical protein binding|protein binding|signal transducer activity|transcription corepressor activity|transcription factor binding central_nervous_system(4)|skin(2)|breast(1) 7 Colorectal(252;0.207) Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242) GGACCTAGTGGTTTTGGCTTTG 0.446 0.46 152 127 LMO2 4005 broad.mit.edu 37 11 33886290 33886290 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr11:33886290delC uc001mve.2 - 2 554 c.115delG c.(115-117)GACfs p.D39fs LMO2_uc001mvc.2_Frame_Shift_Del_p.D32fs|LMO2_uc001mvd.2_Frame_Shift_Del_p.D32fs|LMO2_uc010rel.1_Frame_Shift_Del_p.D39fs|LMO2_uc010rem.1_Frame_Shift_Del_p.D108fs NM_001142316 NP_001135788 P25791 RBTN2_HUMAN LIM domain only 2 isoform 2 39 LIM zinc-binding 1. multicellular organismal development nucleus protein binding|zinc ion binding lung(1) 1 AAGTAGCGGTCCCCAATGTTC 0.642 0.60 27 40 SCYL1 57410 broad.mit.edu 37 11 65306004 65306004 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr11:65306004delC uc001oea.1 + 18 2471 c.2394delC c.(2392-2394)GGCfs p.G798fs SCYL1_uc009yqk.2_3'UTR|SCYL1_uc001oeb.1_Frame_Shift_Del_p.G781fs|SCYL1_uc001oec.1_Frame_Shift_Del_p.A786fs|SCYL1_uc001oed.1_Frame_Shift_Del_p.G655fs|SCYL1_uc001oee.1_Frame_Shift_Del_p.A424fs NM_020680 NP_065731 Q96KG9 NTKL_HUMAN SCY1-like 1 isoform A 798 Interaction with COPB1 (By similarity). regulation of transcription, DNA-dependent|retrograde vesicle-mediated transport, Golgi to ER|transcription, DNA-dependent cis-Golgi network|COPI vesicle coat|ER-Golgi intermediate compartment|microtubule organizing center|nucleus ATP binding|DNA binding|protein tyrosine kinase activity skin(1) 1 TGGCCAAGGGCCCCATGAAGC 0.652 0.60 6 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 1093 265 NCAPD3 23310 broad.mit.edu 37 11 134048586 134048586 + Frame_Shift_Del DEL G - - rs138442478 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr11:134048586delG uc001qhd.1 - 22 3331 c.2725delC c.(2725-2727)CAGfs p.Q909fs NCAPD3_uc010scm.1_RNA|NCAPD3_uc009zda.1_RNA NM_015261 NP_056076 P42695 CNDD3_HUMAN non-SMC condensin II complex, subunit D3 909 cell division|mitotic chromosome condensation nuclear centromeric heterochromatin|nuclear condensin complex methylated histone residue binding ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1) 5 all_hematologic(175;0.127) all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227) CCTCTGACCTGGGGGGGTGGC 0.522 0.54 17 20 WNK1 65125 broad.mit.edu 37 12 970296 970297 + Frame_Shift_Ins INS - A A HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr12:970296_970297insA uc001qio.3 + 7 2245_2246 c.1738_1739insA c.(1738-1740)GAAfs p.E580fs WNK1_uc001qip.3_Frame_Shift_Ins_p.E580fs|WNK1_uc001qir.3_Frame_Shift_Ins_p.E27fs NM_018979 NP_061852 Q9H4A3 WNK1_HUMAN WNK lysine deficient protein kinase 1 580 intracellular protein kinase cascade|ion transport|neuron development cytoplasm ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1) 23 all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632) Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197) GGAGGAGCAAGAAAAAAAAAAG 0.470 0.35 107 57 ATN1 1822 broad.mit.edu 37 12 7045892 7045894 + In_Frame_Del DEL CAG - - rs66756893;rs67074116 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr12:7045892_7045894delCAG uc001qrw.1 + 5 1699_1701 c.1462_1464delCAG c.(1462-1464)CAGdel p.Q502del ATN1_uc001qrx.1_In_Frame_Del_p.Q502del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagc 0.458 0.12 78 11 ITPR2 3709 broad.mit.edu 37 12 26808657 26808657 + Frame_Shift_Del DEL T - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr12:26808657delT uc001rhg.2 - 20 2990 c.2573delA c.(2572-2574)AATfs p.N858fs NM_002223 NP_002214 Q14571 ITPR2_HUMAN inositol 1,4,5-triphosphate receptor, type 2 858 Cytoplasmic (Potential). activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 14 Colorectal(261;0.0847) TGTCAGTTTATTTTTTTCTTT 0.318 0.57 29 39 LRRK2 120892 broad.mit.edu 37 12 40671946 40671946 + Frame_Shift_Del DEL A - - rs141585121 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr12:40671946delA uc001rmg.3 + 18 2245 c.2124delA c.(2122-2124)TTAfs p.L708fs LRRK2_uc001rmh.1_Frame_Shift_Del_p.L330fs NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 708 activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) ATGATTACTTAAAAAATGTGA 0.368 0.39 95 62 STAT6 6778 broad.mit.edu 37 12 57501425 57501425 + Frame_Shift_Del DEL T - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr12:57501425delT uc009zpe.2 - 3 469 c.218delA c.(217-219)GAGfs p.E73fs STAT6_uc009zpf.2_Frame_Shift_Del_p.E73fs|STAT6_uc001sna.2_Frame_Shift_Del_p.E73fs|STAT6_uc010srb.1_5'UTR|STAT6_uc010src.1_Intron|STAT6_uc010srd.1_Intron|STAT6_uc009zpg.2_Frame_Shift_Del_p.E122fs NM_003153 NP_003144 P42226 STAT6_HUMAN signal transducer and activator of transcription 73 regulation of transcription from RNA polymerase II promoter cytosol|nucleus calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity ovary(2)|lung(1)|skin(1) 4 GGTGCTCCCCTCCCCCTGCTC 0.617 0.13 218 34 DDIT3 1649 broad.mit.edu 37 12 57910960 57910963 + Frame_Shift_Del DEL CTTC - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr12:57910960_57910963delCTTC uc001soi.2 - 4 319_322 c.139_142delGAAG c.(139-144)GAAGAAfs p.E47fs MARS_uc001sof.1_Intron|DDIT3_uc009zps.2_Frame_Shift_Del_p.E70fs|DDIT3_uc009zpt.2_Frame_Shift_Del_p.E70fs NM_004083 NP_004074 P35638 DDIT3_HUMAN DNA-damage-inducible transcript 3 47_48 cell cycle arrest|cell redox homeostasis|mRNA transcription from RNA polymerase II promoter|negative regulation of determination of dorsal identity|regulation of DNA-dependent transcription in response to stress|response to DNA damage stimulus nucleus protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription factor binding FUS/DDIT3(623)|EWSR1/DDIT3(43) soft_tissue(666)|large_intestine(1)|central_nervous_system(1)|lung(1)|skin(1)|ovary(1) 671 ATTTTTGATTCTTCCTTCAAGGAA 0.471 0.43 67 51 PXN 5829 broad.mit.edu 37 12 120662041 120662042 + Frame_Shift_Ins INS - G G HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr12:120662041_120662042insG uc001txt.2 - 2 283_284 c.152_153insC c.(151-153)CCAfs p.P51fs PXN_uc001txv.2_5'UTR|PXN_uc001txx.2_5'UTR|PXN_uc001txy.2_Frame_Shift_Ins_p.P51fs|PXN_uc001txz.2_RNA NM_001080855 NP_001074324 P49023 PAXI_HUMAN paxillin isoform 1 51 Pro-rich. cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly cytoplasm|focal adhesion|lamellipodium|microtubule associated complex beta-catenin binding|vinculin binding|zinc ion binding ovary(1)|breast(1) 2 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) TGGACGGGGGTGGGGGGACGGG 0.619 0.65 23 42 ZMYM2 7750 broad.mit.edu 37 13 20657094 20657094 + Frame_Shift_Del DEL A - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr13:20657094delA uc001umr.2 + 24 4040 c.3742delA c.(3742-3744)AAAfs p.K1248fs ZMYM2_uc001ums.2_Frame_Shift_Del_p.K1248fs|ZMYM2_uc001umt.2_Frame_Shift_Del_p.K1248fs|ZMYM2_uc001umv.2_Frame_Shift_Del_p.K628fs|ZMYM2_uc001umw.2_Frame_Shift_Del_p.K701fs NM_003453 NP_003444 Q9UBW7 ZMYM2_HUMAN zinc finger protein 198 1248 regulation of transcription, DNA-dependent|transcription, DNA-dependent PML body ubiquitin conjugating enzyme binding|zinc ion binding lung(3)|ovary(2)|prostate(1) 6 all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856) TAGGCATTGGAAAAAAAATCC 0.363 0.46 56 48 NEK3 4752 broad.mit.edu 37 13 52725278 52725279 + Splice_Site INS - A A HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr13:52725278_52725279insA uc001vgi.2 - 7 783 c.548_splice c.e7+1 p.S183_splice NEK3_uc001vgg.2_Splice_Site_p.S177_splice|NEK3_uc001vgh.2_Splice_Site_p.S204_splice|NEK3_uc010tgx.1_Splice_Site|NEK3_uc010tgy.1_Splice_Site_p.S183_splice NM_152720 NP_689933 P51956 NEK3_HUMAN NIMA-related kinase 3 isoform a cell division|mitosis nucleus ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173) GBM - Glioblastoma multiforme(99;2.81e-08) ATGCAGCACTCACCTTTTATTG 0.421 0.40 78 53 MBIP 51562 broad.mit.edu 37 14 36784114 36784114 + Frame_Shift_Del DEL A - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr14:36784114delA uc001wtm.2 - 3 345 c.257delT c.(256-258)TTAfs p.L86fs MBIP_uc001wto.2_Frame_Shift_Del_p.L86fs|MBIP_uc010tpy.1_5'UTR|MBIP_uc001wtn.2_Frame_Shift_Del_p.L86fs NM_016586 NP_057670 Q9NS73 MBIP1_HUMAN MAP3K12 binding inhibitory protein 1 isoform 1 86 histone H3 acetylation|inactivation of MAPK activity involved in osmosensory signaling pathway Ada2/Gcn5/Ada3 transcription activator complex|cytoplasm|nucleolus identical protein binding|protein kinase inhibitor activity 0 all_cancers(3;1.55e-52)|all_epithelial(1;2.69e-62)|Breast(36;0.0505)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164) Lung(8;1.28e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.0303)|all cancers(34;0.0781) GBM - Glioblastoma multiforme(112;0.0191) AAGTTTTGCTAAAAAAGGCTG 0.323 0.33 59 29 MARK3 4140 broad.mit.edu 37 14 103969522 103969523 + Frame_Shift_Ins INS - A A HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr14:103969522_103969523insA uc001ymz.3 + 18 2886_2887 c.2220_2221insA c.(2218-2223)TTCAAAfs p.F740fs MARK3_uc001ymx.3_Frame_Shift_Ins_p.F731fs|MARK3_uc001ymw.3_Frame_Shift_Ins_p.F716fs|MARK3_uc001yna.3_Frame_Shift_Ins_p.F700fs|MARK3_uc001ymy.3_Frame_Shift_Ins_p.F646fs|MARK3_uc010awp.2_Frame_Shift_Ins_p.F739fs|MARK3_uc010tyb.1_Frame_Shift_Ins_p.F535fs|MARK3_uc010awq.2_Frame_Shift_Ins_p.F313fs|MARK3_uc001ynd.2_Frame_Shift_Ins_p.F148fs NM_001128918 NP_001122390 P27448 MARK3_HUMAN MAP/microtubule affinity-regulating kinase 3 740_741 KA1. ATP binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|ovary(1)|stomach(1) 4 Melanoma(154;0.155) Epithelial(46;0.241) 0.000 0.50 173 170 TTBK2 146057 broad.mit.edu 37 15 43044817 43044817 + Frame_Shift_Del DEL T - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr15:43044817delT uc001zqo.2 - 14 3066 c.2627delA c.(2626-2628)AATfs p.N876fs TTBK2_uc010bcy.2_Frame_Shift_Del_p.N807fs NM_173500 NP_775771 Q6IQ55 TTBK2_HUMAN tau tubulin kinase 2 876 cell death ATP binding|protein serine/threonine kinase activity p.N876fs*2(1) ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1) 7 all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216) GBM - Glioblastoma multiforme(94;3.23e-07) AGATATCTTATTTTTTTGCAT 0.408 0.51 135 140 NEIL1 79661 broad.mit.edu 37 15 75647130 75647132 + In_Frame_Del DEL GGA - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr15:75647130_75647132delGGA uc002bad.2 + 9 1579_1581 c.1073_1075delGGA c.(1072-1077)GGGAGG>GGG p.R360del NEIL1_uc002bae.2_In_Frame_Del_p.R446del|MIR631_hsa-mir-631|MI0003645_5'Flank NM_024608 NP_078884 Q96FI4 NEIL1_HUMAN nei endonuclease VIII-like 1 360 base-excision repair|negative regulation of nuclease activity|nucleotide-excision repair|response to oxidative stress cytoplasm|nucleus damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|protein C-terminus binding|zinc ion binding ovary(1) 1 0.000 0.26 533 185 ZFHX3 463 broad.mit.edu 37 16 72821889 72821890 + Frame_Shift_Ins INS - G G HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr16:72821889_72821890insG uc002fck.2 - 10 10958_10959 c.10285_10286insC c.(10285-10287)CGTfs p.R3429fs ZFHX3_uc002fcl.2_Frame_Shift_Ins_p.R2515fs NM_006885 NP_008816 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 isoform A 3429 muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation transcription factor complex enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding ovary(2)|skin(2) 4 Ovarian(137;0.13) GGACACCTCACGGGGGGTGTTT 0.569 0.31 11 5 ZFHX3 463 broad.mit.edu 37 16 72821959 72821960 + Frame_Shift_Ins INS - G G HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr16:72821959_72821960insG uc002fck.2 - 10 10888_10889 c.10215_10216insC c.(10213-10218)CCCGGGfs p.P3405fs ZFHX3_uc002fcl.2_Frame_Shift_Ins_p.P2491fs NM_006885 NP_008816 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 isoform A 3405_3406 muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation transcription factor complex enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding ovary(2)|skin(2) 4 Ovarian(137;0.13) GAAGGAGCCCCGGGGGGGACTG 0.416 0.43 40 30 MYH8 4626 broad.mit.edu 37 17 10314206 10314206 + Frame_Shift_Del DEL A - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr17:10314206delA uc002gmm.2 - 15 1570 c.1475delT c.(1474-1476)TTCfs p.F492fs uc002gml.1_Intron NM_002472 NP_002463 P13535 MYH8_HUMAN myosin, heavy chain 8, skeletal muscle, 492 Myosin head-like. muscle filament sliding cytosol|muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle skin(6)|ovary(3)|breast(2) 11 GTGGTGGTTGAAAAACTGTTG 0.443 0.35 76 41 COL1A1 1277 broad.mit.edu 37 17 48276671 48276672 + Frame_Shift_Ins INS - G G rs72667014 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr17:48276671_48276672insG uc002iqm.2 - 5 512_513 c.386_387insC c.(385-387)CCTfs p.P129fs NM_000088 NP_000079 P02452 CO1A1_HUMAN alpha 1 type I collagen preproprotein 129 axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception collagen type I|extracellular space|plasma membrane identical protein binding|platelet-derived growth factor binding COL1A1/PDGFB(372) soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1) 382 Collagenase(DB00048)|Palifermin(DB00039) 0.000 0.18 303 68 P4HB 5034 broad.mit.edu 37 17 79803763 79803764 + Frame_Shift_Ins INS - T T HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr17:79803763_79803764insT uc002kbn.1 - 8 1357_1358 c.1160_1161insA c.(1159-1161)AACfs p.N387fs P4HB_uc002kbl.1_Frame_Shift_Ins_p.N64fs|P4HB_uc002kbm.1_Frame_Shift_Ins_p.N64fs NM_000918 NP_000909 P07237 PDIA1_HUMAN prolyl 4-hydroxylase, beta subunit precursor 387 Thioredoxin 2. cell redox homeostasis|glycerol ether metabolic process|lipid metabolic process|lipoprotein metabolic process|peptidyl-proline hydroxylation to 4-hydroxy-L-proline cell surface|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|extracellular region|melanosome|plasma membrane electron carrier activity|procollagen-proline 4-dioxygenase activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity 0 all_neural(118;0.0878)|Ovarian(332;0.12) BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509) CCACAAAGACGTTTTTTTTCTC 0.559 0.37 252 150 YES1 7525 broad.mit.edu 37 18 745962 745963 + Frame_Shift_Del DEL CT - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr18:745962_745963delCT uc002kky.2 - 5 780_781 c.559_560delAG c.(559-561)AGTfs p.S187fs YES1_uc002kkz.2_Frame_Shift_Del_p.S187fs NM_005433 NP_005424 P07947 YES_HUMAN viral oncogene yes-1 homolog 1 187 SH2. blood coagulation|leukocyte migration|regulation of vascular permeability|T cell costimulation cytosol|plasma membrane ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity lung(2)|ovary(1) 3 Dasatinib(DB01254) AGTTGTTTCACTCTCTCTTACT 0.292 0.50 17 17 JUND 3727 broad.mit.edu 37 19 18392255 18392255 + Frame_Shift_Del DEL G - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr19:18392255delG uc002nip.2 - 1 178 c.40delC c.(40-42)CTGfs p.L14fs hsa-mir-3188|MI0014232_5'Flank NM_005354 NP_005345 P17535 JUND_HUMAN jun D proto-oncogene 14 regulation of transcription from RNA polymerase II promoter chromatin|nucleus protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding 0 0.000 0.42 74 53 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 129 98 REM1 28954 broad.mit.edu 37 20 30072099 30072099 + Frame_Shift_Del DEL C - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr20:30072099delC uc002wwa.2 + 5 1047 c.763delC c.(763-765)CCCfs p.P255fs NCRNA00028_uc010ztn.1_5'Flank NM_014012 NP_054731 O75628 REM1_HUMAN RAS-like GTP-binding protein REM 255 Arg-rich. small GTPase mediated signal transduction membrane calmodulin binding|GTP binding|GTPase activity lung(2)|pancreas(2) 4 all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198) Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347) GGCCAAGGAACCCCCAGCACC 0.726 0.48 62 57 RBL1 5933 broad.mit.edu 37 20 35663913 35663914 + Splice_Site INS - A A HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr20:35663913_35663914insA uc002xgi.2 - 15 1983 c.1904_splice c.e15-1 p.D635_splice RBL1_uc010zvt.1_Splice_Site|RBL1_uc002xgj.1_Splice_Site_p.D635_splice NM_002895 NP_002886 P28749 RBL1_HUMAN retinoblastoma-like protein 1 isoform a cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent transcription factor binding lung(5)|skin(3)|ovary(2) 10 Myeloproliferative disorder(115;0.00878) GTTGCATATCtaaaaaaaaata 0.282 0.36 49 28 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 108 13 ERG 2078 broad.mit.edu 37 21 39755554 39755554 + Frame_Shift_Del DEL G - - HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr21:39755554delG uc010gnw.2 - 12 1527 c.1232delC c.(1231-1233)CCGfs p.P411fs ERG_uc002yxa.2_Frame_Shift_Del_p.P404fs|ERG_uc011aek.1_Frame_Shift_Del_p.P312fs|ERG_uc010gnv.2_Frame_Shift_Del_p.P288fs|ERG_uc010gnx.2_Frame_Shift_Del_p.P387fs|ERG_uc011ael.1_Frame_Shift_Del_p.P411fs|ERG_uc002yxb.2_Frame_Shift_Del_p.P387fs NM_001136155 NP_001129627 P11308 ERG_HUMAN ets-related isoform 4 411 cell proliferation|multicellular organismal development|protein phosphorylation cytoplasm|nucleus|ribonucleoprotein complex protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162) prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1) 2828 Prostate(19;3.6e-06) AGATGACTCCGGGGGGTGGGG 0.587 0.44 150 118 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 123 545 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HEC265_ENDOMETRIUM NA HEC265_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 6 134 FOXO4 4303 broad.mit.edu 37 X 70321277 70321277 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chrX:70321277delG uc004dys.1 + 2 1550 c.1197delG c.(1195-1197)CTGfs p.L399fs FOXO4_uc010nkz.2_Intron|FOXO4_uc004dyt.1_Frame_Shift_Del_p.L344fs NM_005938 NP_005929 P98177 FOXO4_HUMAN forkhead box O4 399 cell cycle arrest|cell differentiation|embryo development|G1 phase of mitotic cell cycle|insulin receptor signaling pathway|mitotic cell cycle G2/M transition DNA damage checkpoint|muscle organ development|negative regulation of angiogenesis|negative regulation of cell proliferation|negative regulation of smooth muscle cell differentiation|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding central_nervous_system(2)|prostate(1) 3 Renal(35;0.156) TTCTGTTGCTGGGGGGGCTTC 0.632 0.57 107 142 KIAA2022 340533 broad.mit.edu 37 X 73962812 73962812 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chrX:73962812delT uc004eby.2 - 3 2197 c.1580delA c.(1579-1581)AAGfs p.K527fs NM_001008537 NP_001008537 Q5QGS0 K2022_HUMAN hypothetical protein LOC340533 527 base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle delta DNA polymerase complex 3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 TTTTCTTCTCTTTTTGGGACA 0.403 0.33 106 52 Unknown 0 broad.mit.edu 37 X 80185321 80185321 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chrX:80185321delA uc004eec.1 + 1 394 c.220delA c.(220-222)AAAfs p.K74fs SubName: Full=cDNA FLJ16670 fis, clone THYMU3001133, highly similar to Voltage-dependent anion-selective channel protein 1; SubName: Full=Voltage-dependent anion channel 1, isoform CRA_a; TAACACTGGGAAAAAAAATGC 0.483 0.28 162 64 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.85 10 56 ELF4 2000 broad.mit.edu 37 X 129203441 129203441 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chrX:129203441delG uc004evd.3 - 8 1406 c.1021delC c.(1021-1023)CAGfs p.Q341fs ELF4_uc004eve.3_Frame_Shift_Del_p.Q341fs NM_001421 NP_001412 Q99607 ELF4_HUMAN E74-like factor 4 341 natural killer cell proliferation|NK T cell proliferation|positive regulation of transcription from RNA polymerase II promoter PML body protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity ovary(1) 1 CCCTTGCCCTGGGGGGCAGAT 0.617 0.53 42 48 IRAK1 3654 broad.mit.edu 37 X 153278755 153278756 + Frame_Shift_Del DEL CA - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chrX:153278755_153278756delCA uc004fjs.1 - 12 1747_1748 c.1668_1669delTG c.(1666-1671)AGTGGGfs p.S556fs IRAK1_uc004fjr.1_Frame_Shift_Del_p.S526fs|IRAK1_uc004fjt.1_Frame_Shift_Del_p.S477fs|IRAK1_uc010nur.2_Intron NM_001569 NP_001560 P51617 IRAK1_HUMAN interleukin-1 receptor-associated kinase 1 556_557 activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|anti-apoptosis|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|lipopolysaccharide-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|protein autophosphorylation|protein oligomerization|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transmembrane receptor protein serine/threonine kinase signaling pathway cytosol|endosome membrane|interleukin-1 receptor complex ATP binding|NF-kappaB-inducing kinase activity|protein binding|protein heterodimerization activity|protein homodimerization activity|ubiquitin-protein ligase activity lung(5)|ovary(2)|breast(1)|central_nervous_system(1) 9 all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) 0.000 0.46 284 244 F8 2157 broad.mit.edu 37 X 154157686 154157686 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chrX:154157686delT uc004fmt.2 - 14 4550 c.4379delA c.(4378-4380)AATfs p.N1460fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1460 B. N -> K (in HEMA). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AGAAAGGTTATTTTTTTTGGC 0.413 0.24 141 44 F8 2157 broad.mit.edu 37 X 154159120 154159120 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chrX:154159120delT uc004fmt.2 - 14 3116 c.2945delA c.(2944-2946)AATfs p.N982fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 982 B. acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) TGACGATACATTTTTTCCCCA 0.373 0.30 69 29 DVL1 1855 broad.mit.edu 37 1 1271642 1271642 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:1271642delC uc001aer.3 - 15 1940 c.1893delG c.(1891-1893)GGGfs p.G631fs DVL1_uc002quu.2_Frame_Shift_Del_p.G373fs|DVL1_uc009vka.2_Frame_Shift_Del_p.G314fs|DVL1_uc001aeu.1_3'UTR NM_004421 NP_004412 O14640 DVL1_HUMAN dishevelled 1 656 canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome frizzled binding|identical protein binding|protein kinase binding|signal transducer activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145) 0.000 0.28 384 146 SPEN 23013 broad.mit.edu 37 1 16256321 16256321 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:16256321delA uc001axk.1 + 11 3790 c.3586delA c.(3586-3588)AAAfs p.K1196fs SPEN_uc010obp.1_Frame_Shift_Del_p.K1155fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 1196 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) TGGCAGTCCTAAAAAAGATGT 0.438 0.21 173 47 SPEN 23013 broad.mit.edu 37 1 16262632 16262633 + Frame_Shift_Ins INS - G G HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:16262632_16262633insG uc001axk.1 + 11 10101_10102 c.9897_9898insG c.(9895-9900)AGCGGGfs p.S3299fs SPEN_uc010obp.1_Frame_Shift_Ins_p.S3258fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 3299_3300 Pro-rich. interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) TGCACTCCAGCGGGGAGCTGTT 0.624 0.24 210 68 EPHA2 1969 broad.mit.edu 37 1 16462199 16462199 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:16462199delG uc001aya.1 - 6 1516 c.1379delC c.(1378-1380)CCGfs p.P460fs EPHA2_uc010oca.1_Frame_Shift_Del_p.P460fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 460 Extracellular (Potential).|Fibronectin type-III 2. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) 0.000 0.32 698 328 UBXN11 91544 broad.mit.edu 37 1 26608898 26608903 + In_Frame_Del DEL GGGACC - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:26608898_26608903delGGGACC uc001blw.2 - 16 1723_1728 c.1450_1455delGGTCCC c.(1450-1455)GGTCCCdel p.GP484del UBXN11_uc001blz.1_In_Frame_Del_p.GP451del|UBXN11_uc001blv.2_In_Frame_Del_p.GP446del|UBXN11_uc001bly.2_In_Frame_Del_p.GP364del|UBXN11_uc001blx.2_In_Frame_Del_p.GP242del|UBXN11_uc001bma.2_In_Frame_Del_p.GP451del|UBXN11_uc001bmb.1_In_Frame_Del_p.GP484del NM_183008 NP_892120 Q5T124 UBX11_HUMAN socius isoform 2 484_485 Pro-rich. cytoplasm|cytoskeleton ovary(1) 1 gaccgggacagggaccaggactgAAT 0.286 0.57 18 24 ARID1A 8289 broad.mit.edu 37 1 27106804 27106804 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:27106804delC uc001bmv.1 + 20 6788 c.6415delC c.(6415-6417)CCCfs p.P2139fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.P1922fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.P985fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.P467fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.P381fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 2139 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.F2141fs*59(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) TCTGGCCACACCCCCCTTCAG 0.587 0.20 266 66 TIE1 7075 broad.mit.edu 37 1 43778141 43778141 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:43778141delC uc001ciu.2 + 12 1875 c.1796delC c.(1795-1797)TCCfs p.S599fs TIE1_uc010okd.1_Frame_Shift_Del_p.S599fs|TIE1_uc010oke.1_Frame_Shift_Del_p.S554fs|TIE1_uc009vwq.2_Frame_Shift_Del_p.S555fs|TIE1_uc010okf.1_Frame_Shift_Del_p.S244fs|TIE1_uc010okg.1_Frame_Shift_Del_p.S244fs NM_005424 NP_005415 P35590 TIE1_HUMAN tyrosine kinase with immunoglobulin-like and 599 Fibronectin type-III 2.|Extracellular (Potential). mesoderm development integral to plasma membrane ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity lung(3)|stomach(1)|salivary_gland(1)|ovary(1)|skin(1) 7 Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0505) AACGTCTCATCCCCCCAGGCC 0.706 0.12 64 9 TIE1 7075 broad.mit.edu 37 1 43778242 43778242 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:43778242delC uc001ciu.2 + 12 1976 c.1897delC c.(1897-1899)CCCfs p.P633fs TIE1_uc010okd.1_Frame_Shift_Del_p.P633fs|TIE1_uc010oke.1_Frame_Shift_Del_p.P588fs|TIE1_uc009vwq.2_Frame_Shift_Del_p.P589fs|TIE1_uc010okf.1_Frame_Shift_Del_p.P278fs|TIE1_uc010okg.1_Frame_Shift_Del_p.P278fs NM_005424 NP_005415 P35590 TIE1_HUMAN tyrosine kinase with immunoglobulin-like and 633 Fibronectin type-III 2.|Extracellular (Potential). mesoderm development integral to plasma membrane ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity lung(3)|stomach(1)|salivary_gland(1)|ovary(1)|skin(1) 7 Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0505) CCCGGCCTCGCCCCCTGCACA 0.672 0.18 107 24 PTCH2 8643 broad.mit.edu 37 1 45288989 45288989 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:45288989delG uc010olf.1 - 20 3195 c.3183delC c.(3181-3183)CCCfs p.P1061fs PTCH2_uc010olg.1_Frame_Shift_Del_p.P759fs NM_003738 NP_003729 Q9Y6C5 PTC2_HUMAN patched 2 1061 Cytoplasmic (Potential). protein complex assembly|spermatogenesis integral to plasma membrane hedgehog receptor activity lung(6)|breast(6)|central_nervous_system(3)|skin(2)|ovary(1) 18 Acute lymphoblastic leukemia(166;0.155) CATCGGTCACGGGGGCAAATG 0.622 0.42 215 155 ROR1 4919 broad.mit.edu 37 1 64516359 64516359 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:64516359delC uc001dbj.2 + 4 852 c.453delC c.(451-453)GGCfs p.G151fs ROR1_uc001dbi.3_Frame_Shift_Del_p.G151fs NM_005012 NP_005003 Q01973 ROR1_HUMAN receptor tyrosine kinase-like orphan receptor 1 151 Extracellular (Potential). transmembrane receptor protein tyrosine kinase signaling pathway cytoplasm|integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1) 19 TTTCTTCAGGCCCCCCTCCCA 0.393 0.23 200 61 CDC7 8317 broad.mit.edu 37 1 91977476 91977476 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:91977476delA uc001doe.2 + 6 733 c.568delA c.(568-570)AAAfs p.K190fs CDC7_uc001dof.2_Frame_Shift_Del_p.K190fs|CDC7_uc010osw.1_Frame_Shift_Del_p.K162fs|CDC7_uc009wdc.2_Frame_Shift_Del_p.K190fs|CDC7_uc009wdd.2_5'Flank NM_003503 NP_003494 O00311 CDC7_HUMAN cell division cycle 7 190 Protein kinase. cell cycle checkpoint|cell division|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|positive regulation of cell proliferation|regulation of S phase cytoplasm|nucleoplasm ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity stomach(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 5 all_lung(203;0.0165)|Lung NSC(277;0.0562) all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124) TAGGCGCCTGAAAAAGTAAGT 0.234 0.24 72 23 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.27 343 130 ITGA10 8515 broad.mit.edu 37 1 145537735 145537736 + Splice_Site DEL AG - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:145537735_145537736delAG uc001eoa.2 + 21 2651 c.2575_splice c.e21-1 p.R859_splice NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Splice_Site_p.R728_splice|ITGA10_uc009wiw.2_Splice_Site_p.R716_splice|ITGA10_uc010oyw.1_Splice_Site_p.R804_splice NM_003637 NP_003628 O75578 ITA10_HUMAN integrin, alpha 10 precursor cell-matrix adhesion|integrin-mediated signaling pathway integrin complex collagen binding|receptor activity lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1) 8 all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786) CCCTGCCCTCAGAGAGAGAGCC 0.579 0.15 142 26 PIP5K1A 8394 broad.mit.edu 37 1 151206914 151206914 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:151206914delT uc001exj.2 + 8 1333 c.881delT c.(880-882)CTTfs p.L294fs PIP5K1A_uc001exi.2_Frame_Shift_Del_p.L281fs|PIP5K1A_uc010pcu.1_Frame_Shift_Del_p.L282fs|PIP5K1A_uc001exk.2_Frame_Shift_Del_p.L281fs|PIP5K1A_uc010pcv.1_Frame_Shift_Del_p.L51fs NM_001135638 NP_001129110 Q99755 PI51A_HUMAN phosphatidylinositol-4-phosphate 5-kinase, type 294 PIPK. phospholipid biosynthetic process|signal transduction endomembrane system|Golgi stack|lamellipodium|nuclear speck 1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|kinase binding ovary(1)|central_nervous_system(1)|skin(1) 3 Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.181) CCTGATGGTCTTTTTTTGGAT 0.438 0.25 103 35 RNASEL 6041 broad.mit.edu 37 1 182555365 182555365 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:182555365delC uc001gpj.1 - 1 744 c.577delG c.(577-579)GCAfs p.A193fs RNASEL_uc009wxz.1_Frame_Shift_Del_p.A193fs|RNASEL_uc001gpk.2_Frame_Shift_Del_p.A193fs|RNASEL_uc009wya.1_Frame_Shift_Del_p.A193fs NM_021133 NP_066956 Q05823 RN5A_HUMAN ribonuclease L 193 ANK 5. mRNA processing|response to virus|type I interferon-mediated signaling pathway mitochondrion ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding ovary(4)|stomach(1) 5 TTTACATCTGCCCCCATCTCA 0.517 0.22 204 56 RGL1 23179 broad.mit.edu 37 1 183881395 183881395 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:183881395delA uc001gqo.2 + 15 1899 c.1742delA c.(1741-1743)CAAfs p.Q581fs RGL1_uc010pof.1_Frame_Shift_Del_p.Q386fs|RGL1_uc001gqm.2_Frame_Shift_Del_p.Q616fs|RGL1_uc010pog.1_Frame_Shift_Del_p.Q579fs|RGL1_uc010poh.1_Frame_Shift_Del_p.Q579fs|RGL1_uc010poi.1_Frame_Shift_Del_p.Q552fs NM_015149 NP_055964 Q9NZL6 RGL1_HUMAN ral guanine nucleotide dissociation 581 Ser-rich. cellular lipid metabolic process|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction intracellular protein binding|Ral guanyl-nucleotide exchange factor activity breast(5)|ovary(4)|lung(2) 11 GATGAGCCTCAAAAAAAGGTA 0.488 0.17 91 18 PTPRC 5788 broad.mit.edu 37 1 198717301 198717301 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:198717301delA uc001gur.1 + 27 3085 c.2905delA c.(2905-2907)AAAfs p.K969fs PTPRC_uc001gus.1_Frame_Shift_Del_p.K921fs|PTPRC_uc001gut.1_Frame_Shift_Del_p.K808fs NM_002838 NP_002829 P08575 PTPRC_HUMAN protein tyrosine phosphatase, receptor type, C 969 Tyrosine-protein phosphatase 2.|Cytoplasmic (Potential). axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway focal adhesion|integral to plasma membrane|membrane raft protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1) 12 AAATAAAAGTAAAAACAGGAA 0.294 0.29 29 12 CDC42BPA 8476 broad.mit.edu 37 1 227333305 227333305 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:227333305delA uc001hqr.2 - 8 1971 c.1028delT c.(1027-1029)TTCfs p.F343fs CDC42BPA_uc001hqs.2_Frame_Shift_Del_p.F343fs|CDC42BPA_uc009xes.2_Frame_Shift_Del_p.F343fs|CDC42BPA_uc010pvs.1_Frame_Shift_Del_p.F343fs NM_003607 NP_003598 Q5VT25 MRCKA_HUMAN CDC42-binding protein kinase alpha isoform B 343 Protein kinase. actin cytoskeleton reorganization|intracellular signal transduction cell leading edge|cell-cell junction|cytoplasm ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1) 11 all_cancers(173;0.156)|Prostate(94;0.0792) AATTCCACTGAAAAATGGGTG 0.368 0.23 112 34 FMN2 56776 broad.mit.edu 37 1 240370419 240370419 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr1:240370419delC uc010pyd.1 + 5 2532 c.2307delC c.(2305-2307)TGCfs p.C769fs FMN2_uc010pye.1_Frame_Shift_Del_p.C773fs NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 769 Pro-rich.|FH1. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) GTCCTCCATGCCCCCCTGGGG 0.552 0.35 92 49 NCOA1 8648 broad.mit.edu 37 2 24952369 24952369 + Splice_Site DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr2:24952369delG uc002rfk.2 + 15 3145 c.2887_splice c.e15-1 p.G963_splice NCOA1_uc010eye.2_Splice_Site_p.G963_splice|NCOA1_uc002rfi.2_Splice_Site_p.G812_splice|NCOA1_uc002rfj.2_Splice_Site_p.G963_splice|NCOA1_uc002rfl.2_Splice_Site_p.G963_splice NM_003743 NP_003734 Q15788 NCOA1_HUMAN nuclear receptor coactivator 1 isoform 1 PAX3/NCOA1(8) soft_tissue(8)|ovary(1)|lung(1)|skin(1) 11 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) TTTTCTAACAGGGGGGTGGAT 0.373 0.64 34 60 NRBP1 29959 broad.mit.edu 37 2 27658018 27658018 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr2:27658018delC uc002rko.2 + 8 1417 c.585delC c.(583-585)GACfs p.D195fs NRBP1_uc002rkq.2_Frame_Shift_Del_p.D195fs|NRBP1_uc002rkp.2_Frame_Shift_Del_p.D195fs|NRBP1_uc002rkr.2_5'Flank NM_013392 NP_037524 Q9UHY1 NRBP_HUMAN nuclear receptor binding protein 195 Protein kinase. ER to Golgi vesicle-mediated transport|gene expression|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor cell cortex|endomembrane system|lamellipodium|membrane|nucleoplasm ATP binding|protein homodimerization activity|protein kinase activity ovary(2)|lung(1) 3 Acute lymphoblastic leukemia(172;0.155) ACTCCTGTGACCCCCCCATCA 0.587 0.68 89 188 MSH2 4436 broad.mit.edu 37 2 47690224 47690225 + Frame_Shift_Ins INS - TAAG TAAG HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr2:47690224_47690225insTAAG uc002rvy.1 + 9 1509_1510 c.1441_1442insTAAG c.(1441-1443)TTAfs p.L481fs MSH2_uc010yoh.1_Frame_Shift_Ins_p.L415fs|MSH2_uc002rvz.2_Frame_Shift_Ins_p.L481fs|MSH2_uc010fbg.2_Frame_Shift_Ins_p.L291fs|MSH2_uc010fbh.1_RNA|MSH2_uc010fbi.1_RNA NM_000251 NP_000242 P43246 MSH2_HUMAN mutS homolog 2 481 B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes MutSalpha complex|MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding p.?(2) large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1) 55 all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) TCTCAGTGAATTAAGAGAAATA 0.347 0.54 31 37 MSH6 2956 broad.mit.edu 37 2 48028089 48028089 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr2:48028089delT uc002rwd.3 + 4 3119 c.2967delT c.(2965-2967)AATfs p.N989fs MSH6_uc002rwc.2_Frame_Shift_Del_p.N989fs|MSH6_uc010fbj.2_Frame_Shift_Del_p.N687fs|MSH6_uc010yoi.1_Frame_Shift_Del_p.N859fs|MSH6_uc010yoj.1_Frame_Shift_Del_p.N687fs NM_000179 NP_000170 P52701 MSH6_HUMAN mutS homolog 6 989 determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes MutSalpha complex ATP binding|DNA-dependent ATPase activity|protein binding large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1) 168 Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) CCACTCGCAATTTGCCAGAAG 0.423 0.26 63 22 MERTK 10461 broad.mit.edu 37 2 112779892 112779892 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr2:112779892delG uc002thk.1 + 18 2529 c.2407delG c.(2407-2409)GGGfs p.G803fs MERTK_uc002thl.1_Frame_Shift_Del_p.G627fs NM_006343 NP_006334 Q12866 MERTK_HUMAN MER receptor tyrosine kinase precursor 803 Protein kinase.|Cytoplasmic (Potential). cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration integral to plasma membrane|soluble fraction ATP binding|transmembrane receptor protein tyrosine kinase activity lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1) 9 TCCCTATCCTGGGGTCCAGAA 0.522 0.19 192 46 IL1A 3552 broad.mit.edu 37 2 113532689 113532689 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr2:113532689delC uc002tig.2 - 7 1731 c.771delG c.(769-771)GGGfs p.G257fs NM_000575 NP_000566 P01583 IL1A_HUMAN interleukin 1, alpha proprotein 257 anti-apoptosis|apoptosis|cell proliferation|cellular response to heat|cytokine-mediated signaling pathway|fever generation|immune response|negative regulation of cell proliferation|positive regulation of angiogenesis|positive regulation of cell division|positive regulation of cytokine secretion|positive regulation of interleukin-2 biosynthetic process|positive regulation of mitosis|positive regulation vascular endothelial growth factor production|response to copper ion cytosol|extracellular space copper ion binding|cytokine activity|interleukin-1 receptor binding lung(1) 1 TAGAGGGTGGCCCCCCTGCCA 0.478 0.25 91 31 MYO3B 140469 broad.mit.edu 37 2 171242715 171242716 + Frame_Shift_Del DEL GA - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr2:171242715_171242716delGA uc002ufy.2 + 13 1450_1451 c.1307_1308delGA c.(1306-1308)GGAfs p.G436fs MYO3B_uc002ufv.2_Frame_Shift_Del_p.G423fs|MYO3B_uc010fqb.1_Frame_Shift_Del_p.G423fs|MYO3B_uc002ufz.2_Frame_Shift_Del_p.G436fs|MYO3B_uc002ufw.2_RNA|MYO3B_uc002ufx.2_RNA|MYO3B_uc002ugb.2_RNA NM_138995 NP_620482 Q8WXR4 MYO3B_HUMAN myosin IIIB isoform 2 436 Myosin head-like. response to stimulus|visual perception cytoplasm|myosin complex actin binding|ATP binding|motor activity|protein serine/threonine kinase activity lung(8)|ovary(6)|skin(4)|central_nervous_system(1) 19 GTCATCAGCGGAGAGAGTGGCT 0.406 0.20 222 57 TTN 7273 broad.mit.edu 37 2 179579063 179579063 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr2:179579063delT uc010zfg.1 - 88 22930 c.22706delA c.(22705-22707)AACfs p.N7569fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.N4230fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 8496 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CCCAGCATCGTTTTTGATCTG 0.418 0.20 145 36 PMS1 5378 broad.mit.edu 37 2 190682810 190682810 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr2:190682810delA uc002urh.3 + 5 1015 c.486delA c.(484-486)GCAfs p.A162fs PMS1_uc010zga.1_Frame_Shift_Del_p.A162fs|PMS1_uc010zgb.1_Frame_Shift_Del_p.A101fs|PMS1_uc002urk.3_Frame_Shift_Del_p.A162fs|PMS1_uc002uri.3_Frame_Shift_Del_p.A162fs|PMS1_uc010zgc.1_5'UTR|PMS1_uc010zgd.1_5'UTR|PMS1_uc002urj.2_RNA|PMS1_uc010fry.1_Frame_Shift_Del_p.A162fs|PMS1_uc010frz.2_Frame_Shift_Del_p.A162fs|PMS1_uc002url.2_5'UTR NM_000534 NP_000525 P54277 PMS1_HUMAN postmeiotic segregation 1 isoform a 162 mismatch repair|reciprocal meiotic recombination MutLalpha complex ATP binding|ATPase activity|mismatched DNA binding ovary(2)|kidney(1)|central_nervous_system(1) 4 OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751) ACTCAACTGCAAAAAAATGTA 0.328 0.67 7 14 HDAC4 9759 broad.mit.edu 37 2 240002823 240002823 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr2:240002823delG uc002vyk.3 - 22 3495 c.2703delC c.(2701-2703)CCCfs p.P901fs HDAC4_uc010fyy.2_Frame_Shift_Del_p.P858fs NM_006037 NP_006028 P56524 HDAC4_HUMAN histone deacetylase 4 901 Histone deacetylase. B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent histone deacetylase complex|transcriptional repressor complex activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding breast(3)|skin(2)|ovary(1) 6 all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159) Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04) CGTCTCCCATGGGGGGGTCCA 0.602 0.30 39 17 PASK 23178 broad.mit.edu 37 2 242066439 242066440 + Frame_Shift_Ins INS - T T HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr2:242066439_242066440insT uc002wao.1 - 10 1982_1983 c.1890_1891insA c.(1888-1893)CCCTCTfs p.P630fs PASK_uc010zol.1_Frame_Shift_Ins_p.P444fs|PASK_uc010zom.1_Frame_Shift_Ins_p.P595fs|PASK_uc010fzl.1_Frame_Shift_Ins_p.P630fs|PASK_uc010zon.1_Frame_Shift_Ins_p.P411fs|PASK_uc002wap.2_Frame_Shift_Ins_p.P173fs|PASK_uc002waq.2_Frame_Shift_Ins_p.P630fs NM_015148 NP_055963 Q96RG2 PASK_HUMAN PAS domain containing serine/threonine kinase 630_631 regulation of transcription, DNA-dependent Golgi apparatus ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity ovary(4)|lung(1)|skin(1) 6 all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968) GCCATCCCAGAGGGGCTGGGGG 0.614 0.64 21 38 IRAK2 3656 broad.mit.edu 37 3 10264349 10264349 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr3:10264349delC uc003bve.1 + 9 1119 c.1043delC c.(1042-1044)ACCfs p.T348fs NM_001570 NP_001561 O43187 IRAK2_HUMAN interleukin-1 receptor-associated kinase 2 348 Protein kinase. activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cell surface|cytosol|endosome membrane|plasma membrane ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity lung(5)|breast(3) 8 CAAAATCTCACCCCCAAACTT 0.478 0.24 109 34 NUP210 23225 broad.mit.edu 37 3 13429939 13429942 + Frame_Shift_Del DEL AAGA - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr3:13429939_13429942delAAGA uc003bxv.1 - 5 628_631 c.545_548delTCTT c.(544-549)TTCTTGfs p.F182fs NM_024923 NP_079199 Q8TEM1 PO210_HUMAN nucleoporin 210 precursor 182_183 Lumenal (Probable). carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction endoplasmic reticulum membrane|nuclear membrane|nuclear pore ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1) 11 all_neural(104;0.187) CGTAGACTCCAAGAAAGTGAGGAT 0.485 0.24 60 19 CCR1 1230 broad.mit.edu 37 3 46245051 46245051 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr3:46245051delA uc003cph.1 - 2 825 c.754delT c.(754-756)TGGfs p.W252fs CCR3_uc003cpg.1_Intron NM_001295 NP_001286 P32246 CCR1_HUMAN chemokine (C-C motif) receptor 1 252 Helical; Name=6; (Potential). cell adhesion|cell-cell signaling|cytokine-mediated signaling pathway|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cyclic nucleotide second messenger|immune response|inflammatory response integral to plasma membrane C-C chemokine receptor activity skin(2)|pancreas(1) 3 BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203) 0.000 0.17 741 154 CCR5 1234 broad.mit.edu 37 3 46414826 46414826 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr3:46414826delG uc003cpo.3 + 3 555 c.433delG c.(433-435)GGGfs p.G145fs CCR5_uc010hjd.2_Frame_Shift_Del_p.G145fs NM_001100168 NP_001093638 P51681 CCR5_HUMAN chemokine (C-C motif) receptor 5 145 Helical; Name=4; (Potential). cell-cell signaling|cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|immune response|inflammatory response|initiation of viral infection endosome|external side of plasma membrane|integral to plasma membrane actin binding|C-C chemokine receptor activity|coreceptor activity|phosphatidylinositol phospholipase C activity lung(4)|upper_aerodigestive_tract(1)|central_nervous_system(1) 6 BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02) Maraviroc(DB04835) GGTCACCTTTGGGGTGGTGAC 0.478 0.22 201 58 SEMA3B 7869 broad.mit.edu 37 3 50310793 50310795 + In_Frame_Del DEL CTT - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr3:50310793_50310795delCTT uc003cyu.2 + 9 971_973 c.729_731delCTT c.(727-732)TACTTC>TAC p.F246del SEMA3B_uc010hlh.1_RNA|SEMA3B_uc003cyt.2_In_Frame_Del_p.F246del|SEMA3B_uc003cyv.2_In_Frame_Del_p.F133del|SEMA3B_uc003cyw.2_5'UTR|SEMA3B_uc010hli.2_In_Frame_Del_p.F133del|SEMA3B_uc003cyx.2_In_Frame_Del_p.F133del|SEMA3B_uc003cyy.2_5'UTR|SEMA3B_uc011bdo.1_Intron NM_004636 NP_004627 Q13214 SEM3B_HUMAN semaphorin 3B isoform 1 precursor 246 Sema. axon guidance|cell-cell signaling endoplasmic reticulum|extracellular region|membrane receptor activity lung(2)|central_nervous_system(2)|kidney(1)|skin(1) 6 BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605) ACAAAATCTACTTCTTCTTTCGT 0.626 0.34 143 75 DOCK3 1795 broad.mit.edu 37 3 51417604 51417605 + Frame_Shift_Del DEL CC - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr3:51417604_51417605delCC uc011bds.1 + 52 5572_5573 c.5549_5550delCC c.(5548-5550)ACCfs p.T1850fs NM_004947 NP_004938 Q8IZD9 DOCK3_HUMAN dedicator of cytokinesis 3 1850 cytoplasm GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding 0 BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518) CTGGGTGATACCCCCCCAGCCC 0.599 0.21 248 65 TLR9 54106 broad.mit.edu 37 3 52257757 52257757 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr3:52257757delG uc003dda.1 - 2 1209 c.575delC c.(574-576)CCGfs p.P192fs TLR9_uc003ddb.2_Frame_Shift_Del_p.P289fs NM_017442 NP_059138 Q9NR96 TLR9_HUMAN toll-like receptor 9 isoform A precursor 192 Extracellular (Potential). defense response to bacterium|fibroblast growth factor receptor signaling pathway|I-kappaB phosphorylation|inflammatory response|innate immune response|insulin receptor signaling pathway|maintenance of gastrointestinal epithelium|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-beta production|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|response to molecule of bacterial origin apical plasma membrane|basolateral plasma membrane|early phagosome|endoplasmic reticulum membrane|endosome membrane|extracellular region|integral to membrane|lysosome interleukin-1 receptor binding|siRNA binding|transmembrane receptor activity large_intestine(2)|skin(2) 4 BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716) Chloroquine(DB00608) 0.000 0.21 452 122 ROBO1 6091 broad.mit.edu 37 3 78710235 78710235 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr3:78710235delA uc003dqe.2 - 16 2473 c.2265delT c.(2263-2265)TTTfs p.F755fs ROBO1_uc003dqb.2_Frame_Shift_Del_p.F716fs|ROBO1_uc003dqc.2_Frame_Shift_Del_p.F719fs|ROBO1_uc003dqd.2_Frame_Shift_Del_p.F719fs|ROBO1_uc010hoh.2_5'UTR|ROBO1_uc011bgl.1_Frame_Shift_Del_p.F327fs|ROBO1_uc003dqf.1_Frame_Shift_Del_p.F434fs NM_002941 NP_002932 Q9Y6N7 ROBO1_HUMAN roundabout 1 isoform a 755 Extracellular (Potential).|Fibronectin type-III 2. activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway cell surface|cytoplasm|integral to plasma membrane axon guidance receptor activity|identical protein binding|LRR domain binding large_intestine(2) 2 Lung SC(41;0.0257)|Lung NSC(201;0.0439) LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274) GAAATTCATTAAAAAAAGGGC 0.398 0.26 70 25 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.36 35 20 KALRN 8997 broad.mit.edu 37 3 124431855 124431855 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr3:124431855delA uc003ehg.2 + 58 8276 c.8149delA c.(8149-8151)AAAfs p.K2717fs KALRN_uc003ehk.2_Frame_Shift_Del_p.K1020fs NM_001024660 NP_001019831 O60229 KALRN_HUMAN kalirin, RhoGEF kinase isoform 1 2716 Protein kinase. apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport actin cytoskeleton|cytosol ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1) 6 ATTTGTTAGCAAAAAAATGAA 0.473 0.50 112 112 TOPBP1 11073 broad.mit.edu 37 3 133335731 133335731 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr3:133335731delT uc003eps.2 - 23 3930 c.3798delA c.(3796-3798)AAAfs p.K1266fs NM_007027 NP_008958 Q92547 TOPB1_HUMAN topoisomerase (DNA) II binding protein 1 1266 BRCT 7. DNA repair|response to ionizing radiation microtubule organizing center|PML body|spindle pole DNA binding|protein C-terminus binding ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1) 7 ATATGTACTGTTTTTTTAATT 0.284 0.19 62 15 EPHA5 2044 broad.mit.edu 37 4 66509085 66509085 + Frame_Shift_Del DEL T - - rs33932471 byFrequency;by1000genomes HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr4:66509085delT uc003hcy.2 - 2 435 c.242delA c.(241-243)AATfs p.N81fs EPHA5_uc003hcx.2_Frame_Shift_Del_p.N12fs|EPHA5_uc003hcz.2_Frame_Shift_Del_p.N81fs|EPHA5_uc011cah.1_Frame_Shift_Del_p.N81fs|EPHA5_uc011cai.1_Frame_Shift_Del_p.N81fs|EPHA5_uc003hda.2_Frame_Shift_Del_p.N81fs NM_004439 NP_004430 P54756 EPHA5_HUMAN ephrin receptor EphA5 isoform a precursor 81 Extracellular (Potential). cAMP-mediated signaling|neuron development dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum ATP binding|transmembrane-ephrin receptor activity lung(19)|stomach(2)|ovary(2)|central_nervous_system(1) 24 ACTTACCCCATTTTTTGGAAA 0.338 0.56 11 14 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 26 7 MAML3 55534 broad.mit.edu 37 4 140641185 140641186 + Frame_Shift_Ins INS - G G HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr4:140641185_140641186insG uc003ihz.1 - 7 3445_3446 c.2693_2694insC c.(2692-2694)CCTfs p.P898fs MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_Frame_Shift_Ins_p.P366fs NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 899 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) GCCCAGAGGCAGGTTGCCTCGG 0.530 0.11 395 49 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 82 134 RAPGEF2 9693 broad.mit.edu 37 4 160274729 160274729 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr4:160274729delG uc003iqg.3 + 22 4009 c.3699delG c.(3697-3699)CAGfs p.Q1233fs NM_014247 NP_055062 Q9Y4G8 RPGF2_HUMAN Rap guanine nucleotide exchange factor 2 1233 cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction integral to plasma membrane|intracellular calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity lung(2)|upper_aerodigestive_tract(1)|skin(1) 4 all_hematologic(180;0.24) COAD - Colon adenocarcinoma(41;0.0817) CCCAGGATCAGGGGGATCGCG 0.527 0.57 55 74 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) ccaccacgagcaccaccaccaccaccacc 0.526 0.38 8 5 NIPBL 25836 broad.mit.edu 37 5 37048716 37048716 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr5:37048716delA uc003jkl.3 + 39 7201 c.6702delA c.(6700-6702)TTAfs p.L2234fs NIPBL_uc003jkk.3_Frame_Shift_Del_p.L2234fs|NIPBL_uc003jkn.2_5'Flank NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 2234 HEAT 4. brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) TACAAGTGTTAAAAAACCTCC 0.313 0.45 11 9 PIK3R1 5295 broad.mit.edu 37 5 67589609 67589610 + Frame_Shift_Ins INS - A A HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr5:67589609_67589610insA uc003jva.2 + 11 1932_1933 c.1372_1373insA c.(1372-1374)GAAfs p.E458fs PIK3R1_uc003jvb.2_Frame_Shift_Ins_p.E458fs|PIK3R1_uc003jvc.2_Frame_Shift_Ins_p.E158fs|PIK3R1_uc003jvd.2_Frame_Shift_Ins_p.E188fs|PIK3R1_uc003jve.2_Frame_Shift_Ins_p.E137fs|PIK3R1_uc011crb.1_Frame_Shift_Ins_p.E128fs NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 458 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.D434_Q475del(2)|p.S460fs*5(1)|p.?(1)|p.F456_R461>S(1)|p.Q457_R461del(1)|p.F456_R461del(1)|p.T454_D464del(1)|p.K459del(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) 0.000 0.47 232 208 CHD1 1105 broad.mit.edu 37 5 98193966 98193966 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr5:98193966delT uc003knf.2 - 34 4853 c.4705delA c.(4705-4707)AGTfs p.S1569fs CHD1_uc010jbn.2_Frame_Shift_Del_p.S295fs NM_001270 NP_001261 O14646 CHD1_HUMAN chromodomain helicase DNA binding protein 1 1569 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117) COAD - Colon adenocarcinoma(37;0.0717) Epirubicin(DB00445) CTGGAATCACTTTTTTTGTAA 0.408 0.19 107 25 TSSK1B 83942 broad.mit.edu 37 5 112769462 112769462 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr5:112769462delG uc003kqm.2 - 1 1267 c.1075delC c.(1075-1077)CAAfs p.Q359fs MCC_uc003kql.3_Intron NM_032028 NP_114417 Q9BXA7 TSSK1_HUMAN testis-specific serine kinase 1 359 cell differentiation|multicellular organismal development|spermatogenesis ATP binding|magnesium ion binding|protein serine/threonine kinase activity ovary(2)|skin(2)|stomach(1) 5 all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156) Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449) 0.000 0.28 457 178 CSNK1G3 1456 broad.mit.edu 37 5 122926143 122926144 + Frame_Shift_Ins INS - T T HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr5:122926143_122926144insT uc003ktm.2 + 9 1600_1601 c.881_882insT c.(880-882)GATfs p.D294fs CSNK1G3_uc003ktl.2_Frame_Shift_Ins_p.D294fs|CSNK1G3_uc003ktn.2_Frame_Shift_Ins_p.D294fs|CSNK1G3_uc003kto.2_Frame_Shift_Ins_p.D294fs|CSNK1G3_uc011cwr.1_Frame_Shift_Ins_p.D219fs|CSNK1G3_uc011cws.1_Frame_Shift_Ins_p.D182fs|CSNK1G3_uc010jda.2_Frame_Shift_Ins_p.D295fs NM_004384 NP_004375 Q9Y6M4 KC1G3_HUMAN casein kinase 1, gamma 3 isoform 1 294 Protein kinase. Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity 0 all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245) KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229) OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176) AGAAGGCTAGATTTTTTTGAAA 0.262 0.62 25 40 FBN2 2201 broad.mit.edu 37 5 127599141 127599141 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr5:127599141delG uc003kuu.2 - 63 8607 c.8168delC c.(8167-8169)CCTfs p.P2723fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 2723 EGF-like 47; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) GTAATACCCAGGGGGGCAGCC 0.592 0.27 35 13 HSPA4 3308 broad.mit.edu 37 5 132403128 132403129 + Frame_Shift_Del DEL AC - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr5:132403128_132403129delAC uc003kyj.2 + 3 466_467 c.185_186delAC c.(184-186)AACfs p.N62fs NM_002154 NP_002145 P34932 HSP74_HUMAN heat shock 70kDa protein 4 62 cellular chaperone-mediated protein complex assembly|protein import into mitochondrial outer membrane|response to unfolded protein cytoplasm|nucleus ATP binding lung(1)|breast(1) 2 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) AATGCAAAGAACACAGTCCAAG 0.347 0.22 58 16 CSF1R 1436 broad.mit.edu 37 5 149441304 149441304 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr5:149441304delG uc003lrl.2 - 11 1930 c.1735delC c.(1735-1737)CGGfs p.R579fs CSF1R_uc011dcd.1_Frame_Shift_Del_p.R431fs|CSF1R_uc010jhc.2_RNA|CSF1R_uc003lrm.2_Frame_Shift_Del_p.R579fs NM_005211 NP_005202 P07333 CSF1R_HUMAN colony stimulating factor 1 receptor precursor 579 Cytoplasmic (Potential). cell proliferation|multicellular organismal development|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane|receptor complex ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity haematopoietic_and_lymphoid_tissue(38)|lung(6)|central_nervous_system(3)|liver(3)|breast(2)|endometrium(1)|ovary(1) 54 KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147) Imatinib(DB00619)|Sunitinib(DB01268) 0.000 0.26 651 231 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.60 4 6 PRPF4B 8899 broad.mit.edu 37 6 4031880 4031881 + Frame_Shift_Ins INS - A A HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr6:4031880_4031881insA uc003mvv.2 + 2 220_221 c.129_130insA c.(127-132)CACAAAfs p.H43fs PRPF4B_uc011dhv.1_RNA NM_003913 NP_003904 Q13523 PRP4B_HUMAN serine/threonine-protein kinase PRP4K 43_44 His-rich.|Arg/Lys-rich (basic). catalytic step 2 spliceosome ATP binding|protein binding|protein serine/threonine kinase activity breast(5) 5 Ovarian(93;0.0925) all_hematologic(90;0.0895) ACAGTCGTCACaaaaaaaagaa 0.168 0.38 8 5 DAXX 1616 broad.mit.edu 37 6 33287609 33287609 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr6:33287609delG uc003oec.2 - 6 1692 c.1488delC c.(1486-1488)CCCfs p.P496fs ZBTB22_uc003oeb.2_5'Flank|ZBTB22_uc010juu.2_5'Flank|DAXX_uc011drd.1_Frame_Shift_Del_p.P421fs|DAXX_uc011dre.1_Frame_Shift_Del_p.P508fs|DAXX_uc003oed.2_Frame_Shift_Del_p.P496fs NM_001350 NP_001341 Q9UER7 DAXX_HUMAN death-domain associated protein isoform a 496 Asp/Glu-rich (acidic).|Necessary for interaction with USP7. activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent chromosome, centromeric region|cytosol|nucleolus|PML body androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding pancreas(18)|ovary(2)|skin(2)|prostate(1) 23 GTGAGGACATGGGGCTCTTGT 0.488 0.32 160 75 FANCE 2178 broad.mit.edu 37 6 35423951 35423953 + In_Frame_Del DEL GAA - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr6:35423951_35423953delGAA uc003oko.1 + 2 861_863 c.676_678delGAA c.(676-678)GAAdel p.E227del FANCE_uc010jvw.1_In_Frame_Del_p.E227del NM_021922 NP_068741 Q9HB96 FANCE_HUMAN Fanconi anemia, complementation group E 227 Interaction with FANCC. DNA repair nucleoplasm protein binding ovary(1)|lung(1)|skin(1) 3 TTGGGAAGAGGAAGAAGATCATG 0.532 0.37 51 30 DST 667 broad.mit.edu 37 6 56434717 56434717 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr6:56434717delT uc003pdf.2 - 48 7486 c.7458delA c.(7456-7458)AAAfs p.K2486fs DST_uc003pcz.3_Frame_Shift_Del_p.K2308fs|DST_uc011dxj.1_Frame_Shift_Del_p.K2337fs|DST_uc011dxk.1_Frame_Shift_Del_p.K2348fs|DST_uc003pcy.3_Frame_Shift_Del_p.K1982fs NM_001144769 NP_001138241 Q03001 DYST_HUMAN dystonin isoform 2 4394 cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1) 14 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) CAATGGGAACTTTTTTTGTTG 0.328 0.64 43 78 DST 667 broad.mit.edu 37 6 56437610 56437610 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr6:56437610delT uc003pdf.2 - 46 7160 c.7132delA c.(7132-7134)ACTfs p.T2378fs DST_uc003pcz.3_Frame_Shift_Del_p.T2200fs|DST_uc011dxj.1_Frame_Shift_Del_p.T2229fs|DST_uc011dxk.1_Frame_Shift_Del_p.T2240fs|DST_uc003pcy.3_Frame_Shift_Del_p.T1874fs|DST_uc010kaa.1_RNA NM_001144769 NP_001138241 Q03001 DYST_HUMAN dystonin isoform 2 4286 cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1) 14 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) AGAGCCTGAGTTTTTGTTTCT 0.393 0.35 108 59 HOXA9 3205 broad.mit.edu 37 7 27204507 27204507 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr7:27204507delG uc003syt.2 - 1 643 c.570delC c.(568-570)CCCfs p.P190fs NM_152739 NP_689952 P31269 HXA9_HUMAN homeobox A9 190 protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity p.P190P(1) lung(1)|central_nervous_system(1) 2 TGGGATCGATGGGGGGCTTGT 0.587 0.40 6 4 AKAP9 10142 broad.mit.edu 37 7 91732039 91732039 + Frame_Shift_Del DEL G - - rs143306820 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr7:91732039delG uc003ulg.2 + 46 11454 c.11229delG c.(11227-11229)ATGfs p.M3743fs AKAP9_uc003ulf.2_Frame_Shift_Del_p.M3735fs|AKAP9_uc003uli.2_Frame_Shift_Del_p.M3366fs|AKAP9_uc003ulj.2_Frame_Shift_Del_p.M1513fs|AKAP9_uc003ull.2_Frame_Shift_Del_p.M639fs NM_005751 NP_005742 Q99996 AKAP9_HUMAN A-kinase anchor protein 9 isoform 2 3747 G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport centrosome|cytosol|Golgi apparatus receptor binding breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1) 26 all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) TTGCCCGGATGGGGGGGCAGC 0.537 0.34 190 96 LMTK2 22853 broad.mit.edu 37 7 97822844 97822844 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr7:97822844delC uc003upd.1 + 11 3360 c.3067delC c.(3067-3069)CCCfs p.P1023fs NM_014916 NP_055731 Q8IWU2 LMTK2_HUMAN lemur tyrosine kinase 2 precursor 1023 early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1) 16 all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125) GAAACTAGTGCCCCCCGATAA 0.592 0.19 166 38 GRM8 2918 broad.mit.edu 37 7 126173278 126173278 + Frame_Shift_Del DEL G - - rs77499554 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr7:126173278delG uc003vlr.2 - 8 2469 c.2158delC c.(2158-2160)CACfs p.H720fs GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Frame_Shift_Del_p.H720fs|GRM8_uc010lkz.1_RNA NM_000845 NP_000836 O00222 GRM8_HUMAN glutamate receptor, metabotropic 8 isoform a 720 Extracellular (Potential). negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception integral to plasma membrane lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1) 23 Prostate(267;0.186) L-Glutamic Acid(DB00142) 0.000 0.21 607 166 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 20 KCNH2 3757 broad.mit.edu 37 7 150656679 150656679 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr7:150656679delG uc003wic.2 - 3 466 c.453delC c.(451-453)CCCfs p.P151fs KCNH2_uc011kux.1_Frame_Shift_Del_p.P55fs|KCNH2_uc003wie.2_Frame_Shift_Del_p.P151fs NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 151 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) GCCAGCTGGTGGGGGGGCCCC 0.587 0.45 84 68 WRN 7486 broad.mit.edu 37 8 30945377 30945379 + In_Frame_Del DEL AAG - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr8:30945377_30945379delAAG uc003xio.3 + 12 2305_2307 c.1517_1519delAAG c.(1516-1521)AAAGAA>AAA p.E510del WRN_uc011lbe.1_In_Frame_Del_p.E38del|WRN_uc010lvk.2_5'UTR NM_000553 NP_000544 Q14191 WRN_HUMAN Werner syndrome protein 510 Poly-Glu. base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance centrosome|nucleolus|nucleoplasm 3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1) 7 Breast(100;0.195) KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192) CTTCCTACTAaagaagaagaaga 0.266 0.50 11 11 WHSC1L1 54904 broad.mit.edu 37 8 38133981 38133981 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr8:38133981delT uc003xli.2 - 23 4423 c.3905delA c.(3904-3906)AATfs p.N1302fs WHSC1L1_uc011lbm.1_Frame_Shift_Del_p.N1291fs|WHSC1L1_uc010lwe.2_Frame_Shift_Del_p.N1253fs|WHSC1L1_uc003xlh.2_Frame_Shift_Del_p.N81fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 1302 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TAACTTAGCATTTTTTGCCTT 0.423 0.19 157 37 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.13 220 34 TGS1 96764 broad.mit.edu 37 8 56711599 56711599 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr8:56711599delA uc003xsj.3 + 8 2056 c.1669delA c.(1669-1671)AAAfs p.K557fs TGS1_uc010lyh.2_Frame_Shift_Del_p.K461fs NM_024831 NP_079107 Q96RS0 TGS1_HUMAN trimethylguanosine synthase homolog 557 cellular lipid metabolic process|ncRNA metabolic process|regulation of transcription, DNA-dependent|RNA capping|spliceosomal snRNP assembly|transcription, DNA-dependent Cajal body|cytosol RNA trimethylguanosine synthase activity ovary(1)|lung(1)|breast(1) 3 all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147) Epithelial(17;0.00027)|all cancers(17;0.00251) CATGTCTGTTAAAAAAGGTGA 0.403 0.18 74 16 NBN 4683 broad.mit.edu 37 8 90967512 90967512 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr8:90967512delT uc003yej.1 - 10 1506 c.1396delA c.(1396-1398)AGGfs p.R466fs NBN_uc003yei.1_Frame_Shift_Del_p.R384fs|NBN_uc011lgb.1_Frame_Shift_Del_p.R466fs NM_002485 NP_002476 O60934 NBN_HUMAN nibrin 466 Nuclear localization signal. KR->AA: Blocks the association with KPNA2, and reduces nuclear foci formation in response to ionizing radiation. cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm protein N-terminus binding|transcription factor binding central_nervous_system(3)|kidney(3)|lung(1) 7 BRCA - Breast invasive adenocarcinoma(11;0.0344) AAAACAGACCTTTTTTTGGTA 0.338 0.15 105 18 NBN 4683 broad.mit.edu 37 8 90993676 90993676 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr8:90993676delT uc003yej.1 - 3 357 c.247delA c.(247-249)ATGfs p.M83fs NBN_uc003yei.1_Frame_Shift_Del_p.M1fs|NBN_uc011lgb.1_Frame_Shift_Del_p.M83fs NM_002485 NP_002476 O60934 NBN_HUMAN nibrin 83 FHA. cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm protein N-terminus binding|transcription factor binding central_nervous_system(3)|kidney(3)|lung(1) 7 BRCA - Breast invasive adenocarcinoma(11;0.0344) CCATTCTGCATTTTTTCCTCA 0.308 0.26 45 16 COL14A1 7373 broad.mit.edu 37 8 121219269 121219269 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr8:121219269delC uc003yox.2 + 10 1392 c.1127delC c.(1126-1128)GCCfs p.A376fs COL14A1_uc003yoy.2_Frame_Shift_Del_p.A54fs|COL14A1_uc010mde.1_Frame_Shift_Del_p.A54fs NM_021110 NP_066933 Q05707 COEA1_HUMAN collagen, type XIV, alpha 1 precursor 376 Fibronectin type-III 2. cell-cell adhesion|collagen fibril organization collagen type XIV|extracellular space collagen binding|extracellular matrix structural constituent|protein binding, bridging ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1) 12 Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503) TGGACTCATGCCCCAGGAAAT 0.428 0.16 100 19 MAPK15 225689 broad.mit.edu 37 8 144804319 144804319 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr8:144804319delG uc003yzj.2 + 14 1574 c.1533delG c.(1531-1533)CAGfs p.Q511fs NM_139021 NP_620590 Q8TD08 MK15_HUMAN mitogen-activated protein kinase 15 511 protein autophosphorylation extracellular region ATP binding|MAP kinase activity|SH3 domain binding lung(2) 2 all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146) AGGGTGCCCAGGGGGGTGCCA 0.662 0.33 8 4 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.89 6 48 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.22 87 25 MLLT3 4300 broad.mit.edu 37 9 20365694 20365699 + In_Frame_Del DEL AGCTGG - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr9:20365694_20365699delAGCTGG uc003zoe.2 - 6 1428_1433 c.1169_1174delCCAGCT c.(1168-1176)TCCAGCTTC>TTC p.SS390del MLLT3_uc011lne.1_In_Frame_Del_p.SS358del|MLLT3_uc011lnf.1_In_Frame_Del_p.SS387del|MLLT3_uc003zof.2_In_Frame_Del_p.SS191del NM_004529 NP_004520 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia 390_391 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding lung(2)|ovary(1) 3 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) GATGGTGTGAagctggagctggagct 0.301 0.17 224 45 TAF1L 138474 broad.mit.edu 37 9 32633025 32633025 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr9:32633025delT uc003zrg.1 - 1 2643 c.2553delA c.(2551-2553)AAAfs p.K851fs uc003zrh.1_5'Flank NM_153809 NP_722516 Q8IZX4 TAF1L_HUMAN TBP-associated factor RNA polymerase 1-like 851 male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent transcription factor TFIID complex DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1) 26 LUSC - Lung squamous cell carcinoma(29;0.0181) GBM - Glioblastoma multiforme(74;0.00301) AAGGAAAGGCTTTTTTTATAT 0.443 0.18 165 37 TLR4 7099 broad.mit.edu 37 9 120475590 120475591 + Frame_Shift_Ins INS - T T rs79802422 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr9:120475590_120475591insT uc004bjz.2 + 3 1475_1476 c.1184_1185insT c.(1183-1185)GATfs p.D395fs TLR4_uc004bka.2_Frame_Shift_Ins_p.D355fs|TLR4_uc004bkb.2_Frame_Shift_Ins_p.D195fs NM_138554 NP_612564 O00206 TLR4_HUMAN toll-like receptor 4 precursor 395 Extracellular (Potential). activation of MAPK activity|cellular response to mechanical stimulus|detection of fungus|detection of lipopolysaccharide|I-kappaB phosphorylation|innate immune response|intestinal epithelial structure maintenance|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of interleukin-23 production|negative regulation of interleukin-6 production|negative regulation of osteoclast differentiation|negative regulation of tumor necrosis factor production|positive regulation of chemokine production|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interferon-gamma production|positive regulation of interleukin-1 production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 biosynthetic process|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of platelet activation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor biosynthetic process|positive regulation of tumor necrosis factor production|T-helper 1 type immune response|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway external side of plasma membrane|integral to plasma membrane|lipopolysaccharide receptor complex|perinuclear region of cytoplasm lipopolysaccharide receptor activity|transmembrane receptor activity lung(10)|ovary(4)|breast(1)|skin(1) 16 TCTCAAAGTGATTTTGGGACAA 0.386 0.22 111 31 DIP2C 22982 broad.mit.edu 37 10 412273 412274 + Frame_Shift_Ins INS - CA CA HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr10:412273_412274insCA uc001ifp.2 - 19 2299_2300 c.2209_2210insTG c.(2209-2211)GCAfs p.A737fs DIP2C_uc009xhi.1_Frame_Shift_Ins_p.A123fs|DIP2C_uc010pzz.1_Frame_Shift_Ins_p.A58fs NM_014974 NP_055789 Q9Y2E4 DIP2C_HUMAN DIP2 disco-interacting protein 2 homolog C 737 nucleus catalytic activity|transcription factor binding breast(4)|ovary(2)|large_intestine(1) 7 all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235) OV - Ovarian serous cystadenocarcinoma(33;0.136) Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106) CGTCGCAACTGCACACACACAC 0.545 0.16 690 129 MYO3A 53904 broad.mit.edu 37 10 26462760 26462760 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr10:26462760delA uc001isn.2 + 30 3927 c.3567delA c.(3565-3567)CCAfs p.P1189fs MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron NM_017433 NP_059129 Q8NEV4 MYO3A_HUMAN myosin IIIA 1189 protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception cytoplasm|filamentous actin|filopodium|myosin complex actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 18 ATCAGACTCCAAAAAAAATGA 0.403 0.46 59 51 ABI1 10006 broad.mit.edu 37 10 27044652 27044652 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr10:27044652delG uc001isx.2 - 10 1264 c.1097delC c.(1096-1098)CCTfs p.P366fs ABI1_uc001ite.2_Intron|ABI1_uc010qdh.1_Intron|ABI1_uc010qdi.1_Intron|ABI1_uc001isy.2_Frame_Shift_Del_p.P339fs|ABI1_uc001ita.2_Intron|ABI1_uc001isz.2_Frame_Shift_Del_p.P334fs|ABI1_uc001itb.2_Intron|ABI1_uc001itc.2_Frame_Shift_Del_p.P338fs|ABI1_uc010qdj.1_Frame_Shift_Del_p.P280fs|ABI1_uc001itd.2_Intron|ABI1_uc010qdk.1_Intron|ABI1_uc010qdg.1_Intron NM_005470 NP_005461 Q8IZP0 ABI1_HUMAN abl-interactor 1 isoform a 366 Pro-rich. actin polymerization or depolymerization|cellular component movement|negative regulation of cell proliferation|peptidyl-tyrosine phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway cell junction|cytoskeleton|cytosol|endoplasmic reticulum|filopodium|growth cone|lamellipodium|nucleus|soluble fraction|synapse|synaptosome cytoskeletal protein binding central_nervous_system(1) 1 CATAGGGGGAGGGGGTGGAGC 0.453 0.33 165 82 MSMB 4477 broad.mit.edu 37 10 51562364 51562364 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr10:51562364delA uc001jiq.2 + 4 341 c.309delA c.(307-309)CCAfs p.P103fs PARG_uc001jih.2_Intron|uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|MSMB_uc001jir.2_Frame_Shift_Del_p.Q68fs|NCOA4_uc009xon.2_5'Flank|NCOA4_uc010qhd.1_5'Flank|NCOA4_uc001jis.3_5'Flank|NCOA4_uc010qhe.1_5'Flank|NCOA4_uc010qhf.1_5'Flank NM_002443 NP_002434 P08118 MSMB_HUMAN beta-microseminoprotein isoform a precursor 103 extracellular space|nucleus ovary(2) 2 AGAAGGACCCAAAAAAGACCT 0.463 0.21 165 44 TET1 80312 broad.mit.edu 37 10 70446426 70446427 + Frame_Shift_Ins INS - A A HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr10:70446426_70446427insA uc001jok.3 + 11 5871_5872 c.5366_5367insA c.(5365-5367)ACAfs p.T1789fs NM_030625 NP_085128 Q8NFU7 TET1_HUMAN CXXC finger 6 1789 DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding ovary(5)|lung(2)|prostate(1)|breast(1) 9 AACTCAACAACAACAAACAACA 0.446 0.23 55 16 PTEN 5728 broad.mit.edu 37 10 89717770 89717770 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr10:89717770delA uc001kfb.2 + 8 1826 c.795delA c.(793-795)CTAfs p.L265fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 265 C2 tensin-type. KMLKKDK->AAGAADA: Reduces the growth suppression activity and cells show anchorage-independent growth. Reduces binding to phospholipid membranes in vitro. Phosphatase activity towards PtdIns(3,4,5)P3 is not affected. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.K267fs*9(4)|p.R55fs*1(4)|p.N212fs*1(2)|p.Y27fs*1(2)|p.M264fs*8(2)|p.G165_*404del(1)|p.?(1)|p.G165_K342del(1)|p.D268fs*30(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) ACAAGATGCTAAAAAAGGTTT 0.348 0.36 95 53 FAS 355 broad.mit.edu 37 10 90768708 90768708 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr10:90768708delT uc001kfr.2 + 4 743 c.397delT c.(397-399)TTTfs p.F133fs FAS_uc010qna.1_RNA|FAS_uc001kfs.2_Frame_Shift_Del_p.F133fs|FAS_uc001kft.2_Frame_Shift_Del_p.F133fs|FAS_uc010qnb.1_Intron|FAS_uc010qnc.1_Intron|FAS_uc001kfw.2_Intron|FAS_uc010qnd.1_Intron|FAS_uc010qne.1_Intron|FAS_uc009xtp.2_RNA NM_000043 NP_000034 P25445 TNR6_HUMAN tumor necrosis factor receptor superfamily, 133 TNFR-Cys 3.|Extracellular (Potential). activation of caspase activity|activation of pro-apoptotic gene products|anti-apoptosis|cellular response to mechanical stimulus|positive regulation of necrotic cell death cytosol|extracellular region|integral to membrane|soluble fraction identical protein binding|kinase binding upper_aerodigestive_tract(1)|breast(1) 2 Colorectal(252;0.0161) Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193) TAAACCAAACTTTTTTTGTAA 0.368 0.90 21 199 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.31 9 4 NUMA1 4926 broad.mit.edu 37 11 71746965 71746965 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr11:71746965delC uc001orl.1 - 3 197 c.25delG c.(25-27)GCTfs p.A9fs NUMA1_uc001ork.1_Frame_Shift_Del_p.A9fs|NUMA1_uc001orm.1_Frame_Shift_Del_p.A9fs|NUMA1_uc009ysx.1_Frame_Shift_Del_p.A9fs|NUMA1_uc001oro.1_Frame_Shift_Del_p.A9fs|NUMA1_uc009ysy.1_Frame_Shift_Del_p.A9fs|NUMA1_uc001orp.2_Frame_Shift_Del_p.A9fs|NUMA1_uc001orq.2_Frame_Shift_Del_p.A9fs NM_006185 NP_006176 Q14980 NUMA1_HUMAN nuclear mitotic apparatus protein 1 9 G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole protein binding|structural molecule activity ovary(3)|lung(2)|skin(2)|central_nervous_system(1) 8 AGGAGTGCAGCCCCCCGGGTG 0.502 0.18 129 28 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 858 241 BIRC2 329 broad.mit.edu 37 11 102220760 102220760 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr11:102220760delG uc001pgy.2 + 2 1574 c.175delG c.(175-177)GGGfs p.G59fs BIRC2_uc010ruq.1_Frame_Shift_Del_p.G10fs|BIRC2_uc010rur.1_Frame_Shift_Del_p.G59fs NM_001166 NP_001157 Q13490 BIRC2_HUMAN baculoviral IAP repeat-containing protein 2 59 BIR 1. cell surface receptor linked signaling pathway|cellular component disassembly involved in apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteasomal ubiquitin-dependent protein catabolic process|protein polyubiquitination CD40 receptor complex|cytosol|internal side of plasma membrane protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding ovary(1)|lung(1)|breast(1) 3 all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227) Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093) Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151) BRCA - Breast invasive adenocarcinoma(274;0.0144) TTTCCCCGCCGGGGTGCCTGT 0.428 0.23 184 54 ANKK1 255239 broad.mit.edu 37 11 113265743 113265743 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr11:113265743delC uc001pny.2 + 3 667 c.573delC c.(571-573)ATCfs p.I191fs NM_178510 NP_848605 Q8NFD2 ANKK1_HUMAN ankyrin repeat and kinase domain containing 1 191 Protein kinase. ATP binding|protein serine/threonine kinase activity lung(5)|stomach(1)|ovary(1)|breast(1) 8 all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194) BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238) TCAGCTACATCCCCCCTGAGA 0.572 0.38 72 45 GRAMD1B 57476 broad.mit.edu 37 11 123484236 123484237 + Frame_Shift_Ins INS - A A HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr11:123484236_123484237insA uc001pyx.2 + 15 1997_1998 c.1668_1669insA c.(1666-1671)AGCAAGfs p.S556fs GRAMD1B_uc001pyw.2_Frame_Shift_Ins_p.S563fs|GRAMD1B_uc010rzw.1_Frame_Shift_Ins_p.S516fs|GRAMD1B_uc010rzx.1_Frame_Shift_Ins_p.S516fs|GRAMD1B_uc001pyy.2_Frame_Shift_Ins_p.S247fs NM_020716 NP_065767 Q3KR37 GRM1B_HUMAN GRAM domain containing 1B 556_557 integral to membrane ovary(1) 1 Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394) AGAAGGCCAGCAAGACTACAAC 0.569 0.43 49 37 NCAPD3 23310 broad.mit.edu 37 11 134048586 134048586 + Frame_Shift_Del DEL G - - rs138442478 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr11:134048586delG uc001qhd.1 - 22 3331 c.2725delC c.(2725-2727)CAGfs p.Q909fs NCAPD3_uc010scm.1_RNA|NCAPD3_uc009zda.1_RNA NM_015261 NP_056076 P42695 CNDD3_HUMAN non-SMC condensin II complex, subunit D3 909 cell division|mitotic chromosome condensation nuclear centromeric heterochromatin|nuclear condensin complex methylated histone residue binding ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1) 5 all_hematologic(175;0.127) all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227) CCTCTGACCTGGGGGGGTGGC 0.522 0.21 26 7 ZNF384 171017 broad.mit.edu 37 12 6777070 6777075 + In_Frame_Del DEL TGCTGC - - rs151322806;rs111332695;rs78573212;rs1052680 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr12:6777070_6777075delTGCTGC uc010sfh.1 - 11 1747_1752 c.1539_1544delGCAGCA c.(1537-1545)CAGCAGCAA>CAA p.513_515QQQ>Q ZNF384_uc001qpz.2_In_Frame_Del_p.452_454QQQ>Q|ZNF384_uc001qqa.2_In_Frame_Del_p.452_454QQQ>Q|ZNF384_uc001qqb.2_In_Frame_Del_p.436_438QQQ>Q|ZNF384_uc001qqc.2_In_Frame_Del_p.452_454QQQ>Q|ZNF384_uc001qqd.2_In_Frame_Del_p.397_399QQQ>Q|ZNF384_uc001qqe.2_In_Frame_Del_p.436_438QQQ>Q NM_001135734 NP_001129206 Q8TF68 ZN384_HUMAN nuclear matrix transcription factor 4 isoform d 513_515 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding EWSR1/ZNF384(4) haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1) 8 TGGTGgctgttgctgctgctgctgct 0.335 0.15 220 39 ARHGDIB 397 broad.mit.edu 37 12 15103547 15103548 + Frame_Shift_Ins INS - T T HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr12:15103547_15103548insT uc001rcq.1 - 2 203_204 c.99_100insA c.(97-102)AAAGAGfs p.K33fs ARHGDIB_uc001rcp.1_5'Flank NM_001175 NP_001166 P52566 GDIR2_HUMAN Rho GDP dissociation inhibitor (GDI) beta 33_34 actin cytoskeleton organization|cellular component movement|immune response|multicellular organismal development|negative regulation of cell adhesion|regulation of small GTPase mediated signal transduction|Rho protein signal transduction cytoplasmic membrane-bounded vesicle|cytoskeleton|cytosol GTPase activator activity|Rho GDP-dissociation inhibitor activity 0 TCCTGCAGCTCTTTCAGGGACT 0.470 0.22 422 120 WNT1 7471 broad.mit.edu 37 12 49374348 49374348 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr12:49374348delG uc001rsu.2 + 3 698 c.500delG c.(499-501)TGGfs p.W167fs NM_005430 NP_005421 P04628 WNT1_HUMAN wingless-type MMTV integration site family, 167 brain segmentation|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|central nervous system morphogenesis|cerebellum formation|dermatome development|diencephalon development|embryonic axis specification|forebrain anterior/posterior pattern formation|fourth ventricle development|hemopoietic stem cell proliferation|hepatocyte differentiation|inner ear morphogenesis|mesoderm morphogenesis|midbrain development|midbrain-hindbrain boundary maturation during brain development|negative regulation of cell-cell adhesion|negative regulation of cell-substrate adhesion|negative regulation of DNA damage checkpoint|negative regulation of fat cell differentiation|neuron fate determination|positive regulation of fibroblast proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of lamellipodium assembly|positive regulation of Notch signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to wounding|signal transduction in response to DNA damage|Spemann organizer formation|T cell differentiation in thymus|Wnt receptor signaling pathway, calcium modulating pathway early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix cytokine activity|frizzled-2 binding|transcription regulatory region DNA binding kidney(1) 1 BRCA - Breast invasive adenocarcinoma(357;0.244) 0.000 0.23 245 73 AMHR2 269 broad.mit.edu 37 12 53819645 53819645 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr12:53819645delG uc001scx.1 + 6 872 c.794delG c.(793-795)CGGfs p.R265fs AMHR2_uc009zmy.1_Frame_Shift_Del_p.R265fs NM_020547 NP_065434 Q16671 AMHR2_HUMAN anti-Mullerian hormone receptor, type II isoform 265 Cytoplasmic (Potential).|Protein kinase. Mullerian duct regression ATP binding|hormone binding|metal ion binding ovary(1)|skin(1) 2 Adenosine triphosphate(DB00171) ACTGCCAGCCGGGGGGGTCCT 0.512 0.22 254 73 ACACB 32 broad.mit.edu 37 12 109671600 109671600 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr12:109671600delC uc001tob.2 + 30 4306 c.4187delC c.(4186-4188)ACCfs p.T1396fs ACACB_uc001toc.2_Frame_Shift_Del_p.T1396fs|ACACB_uc010sxl.1_RNA|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Frame_Shift_Del_p.T62fs NM_001093 NP_001084 O00763 ACACB_HUMAN acetyl-Coenzyme A carboxylase beta 1396 acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation cytosol|endomembrane system|Golgi apparatus|membrane acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1) 8 Biotin(DB00121) CCCAAAGACACCCCCCTCTTC 0.612 0.59 86 122 CIT 11113 broad.mit.edu 37 12 120241183 120241183 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr12:120241183delG uc001txi.1 - 10 1175 c.1122delC c.(1120-1122)CCCfs p.P374fs CIT_uc001txh.1_5'UTR|CIT_uc001txj.1_Frame_Shift_Del_p.P374fs NM_007174 NP_009105 O14578 CTRO_HUMAN citron 374 AGC-kinase C-terminal. intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TGGGAACGAAGGGGGGAGGAG 0.498 0.13 89 13 XPO4 64328 broad.mit.edu 37 13 21362689 21362689 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr13:21362689delT uc001unq.3 - 20 3019 c.2983delA c.(2983-2985)ATAfs p.I995fs NM_022459 NP_071904 Q9C0E2 XPO4_HUMAN exportin 4 995 protein transport cytoplasm|nucleus protein binding large_intestine(1)|ovary(1)|kidney(1) 3 all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244) all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548) AGCTGTGGTATTTTTTCAGGA 0.318 0.47 47 41 SACS 26278 broad.mit.edu 37 13 23914685 23914685 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr13:23914685delA uc001uon.2 - 10 3919 c.3330delT c.(3328-3330)ATTfs p.I1110fs SACS_uc001uoo.2_Frame_Shift_Del_p.I963fs|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 1110 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) GTAAGGCTTCAATTTTTTTTG 0.378 0.23 160 47 ABCC4 10257 broad.mit.edu 37 13 95735432 95735432 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr13:95735432delA uc001vmd.3 - 21 2767 c.2648delT c.(2647-2649)TTGfs p.L883fs ABCC4_uc010afk.2_Frame_Shift_Del_p.L836fs NM_005845 NP_005836 O15439 MRP4_HUMAN ATP-binding cassette, sub-family C, member 4 883 ABC transmembrane type-1 2. platelet activation|platelet degranulation integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane 15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity central_nervous_system(3)|skin(1) 4 all_neural(89;0.0878)|Medulloblastoma(90;0.163) Cefazolin(DB01327) TGACGTTTCCAAAAAATATCG 0.443 0.20 80 20 ERCC5 2073 broad.mit.edu 37 13 103504578 103504578 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr13:103504578delT uc001vpw.2 + 2 642 c.199delT c.(199-201)TTTfs p.F67fs ERCC5_uc001vpu.1_Frame_Shift_Del_p.F521fs|ERCC5_uc010tjb.1_Frame_Shift_Del_p.F67fs|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_5'UTR NM_000123 NP_000114 P28715 ERCC5_HUMAN XPG-complementing protein 67 N-domain. negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection nucleoplasm bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding ovary(4)|lung(1)|central_nervous_system(1)|skin(1) 7 all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211) CAAACTCTTATTTTTTCGAAT 0.383 0.67 29 60 MYH7 4625 broad.mit.edu 37 14 23897778 23897780 + In_Frame_Del DEL CTT - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr14:23897778_23897780delCTT uc001wjx.2 - 15 1613_1615 c.1507_1509delAAG c.(1507-1509)AAGdel p.K503del NM_000257 NP_000248 P12883 MYH7_HUMAN myosin, heavy chain 7, cardiac muscle, beta 503 Myosin head-like. adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle ovary(3)|skin(1) 4 all_cancers(95;2.54e-05) GBM - Glioblastoma multiforme(265;0.00725) CGATGCCCTCCTTCTTGTACTCC 0.512 0.44 120 93 FSCB 84075 broad.mit.edu 37 14 44975901 44975901 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr14:44975901delT uc001wvn.2 - 1 599 c.290delA c.(289-291)AAGfs p.K97fs NM_032135 NP_115511 Q5H9T9 FSCB_HUMAN fibrous sheath CABYR binding protein 97 cilium lung(3)|breast(3)|ovary(2)|central_nervous_system(1) 9 GBM - Glioblastoma multiforme(112;0.128) ATCAGCTGACTTTTCTTCAGG 0.403 0.23 305 90 HIF1A 3091 broad.mit.edu 37 14 62187171 62187171 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr14:62187171delT uc001xfq.2 + 2 511 c.107delT c.(106-108)GTTfs p.V36fs HIF1A_uc010tsc.1_Intron|HIF1A_uc001xfr.2_Frame_Shift_Del_p.V36fs|HIF1A_uc001xfs.2_Frame_Shift_Del_p.V37fs NM_001530 NP_001521 Q16665 HIF1A_HUMAN hypoxia-inducible factor 1, alpha subunit 36 Interaction with TSGA10 (By similarity).|Helix-loop-helix motif. cellular response to hypoxia|collagen metabolic process|connective tissue replacement involved in inflammatory response wound healing|elastin metabolic process|epithelial to mesenchymal transition|oxygen homeostasis|positive regulation of chemokine production|positive regulation of epithelial cell migration|positive regulation of hormone biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|regulation of transforming growth factor-beta2 production cytoplasm|nucleolus|transcription factor complex histone acetyltransferase binding|Hsp90 protein binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding kidney(3)|lung(1) 4 OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189) GAATCTGAAGTTTTTTATGAG 0.423 0.23 239 73 RAGE 5891 broad.mit.edu 37 14 102718301 102718301 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr14:102718301delA uc001ylm.2 - 5 541 c.315delT c.(313-315)ATTfs p.I105fs RAGE_uc010txv.1_Frame_Shift_Del_p.I75fs|RAGE_uc001yln.2_5'UTR NM_014226 NP_055041 Q9UQ07 MOK_HUMAN MAPK/MAK/MRK overlapping kinase 105 Protein kinase. signal transduction Golgi apparatus ATP binding|cyclin-dependent protein kinase activity|protein binding ovary(2)|breast(1)|central_nervous_system(1) 4 TATAGTGCATAATTTTTTTTT 0.328 0.50 46 46 PAK6 56924 broad.mit.edu 37 15 40558460 40558460 + Frame_Shift_Del DEL C - - rs35501648 byFrequency;by1000genomes HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr15:40558460delC uc010bbl.2 + 5 1062 c.622delC c.(622-624)CCCfs p.P208fs PAK6_uc010bbm.2_Frame_Shift_Del_p.P208fs|PAK6_uc001zky.3_Frame_Shift_Del_p.P208fs|PAK6_uc010bbn.2_Frame_Shift_Del_p.P208fs|PAK6_uc001zlb.2_Frame_Shift_Del_p.P208fs NM_001128628 NP_001122100 Q9NQU5 PAK6_HUMAN p21-activated kinase 6 208 Linker. ATP binding|protein binding|protein serine/threonine kinase activity lung(5)|large_intestine(1)|ovary(1)|skin(1) 8 all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544) 0.000 0.24 797 253 TP53BP1 7158 broad.mit.edu 37 15 43730536 43730536 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr15:43730536delG uc001zrs.2 - 16 3310 c.3162delC c.(3160-3162)CCCfs p.P1054fs TP53BP1_uc010udp.1_Frame_Shift_Del_p.P1054fs|TP53BP1_uc001zrq.3_Frame_Shift_Del_p.P1059fs|TP53BP1_uc001zrr.3_Frame_Shift_Del_p.P1059fs|TP53BP1_uc010udq.1_Frame_Shift_Del_p.P1059fs NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 1054 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) TGGGTGTGGTGGGGGGATCCT 0.413 0.63 44 74 TCF12 6938 broad.mit.edu 37 15 57355977 57355978 + Frame_Shift_Ins INS - G G HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr15:57355977_57355978insG uc002aec.2 + 4 462_463 c.178_179insG c.(178-180)TGGfs p.W60fs TCF12_uc010ugm.1_Frame_Shift_Ins_p.W112fs|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Frame_Shift_Ins_p.W60fs|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Frame_Shift_Ins_p.W60fs|TCF12_uc002aed.2_Frame_Shift_Ins_p.W60fs NM_207038 NP_996921 Q99081 HTF4_HUMAN transcription factor 12 isoform b 60 immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity central_nervous_system(5)|ovary(2)|lung(1) 8 Colorectal(260;0.0907) all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239) TACAACATCTTGGGGAACAAGT 0.356 0.64 33 59 PML 5371 broad.mit.edu 37 15 74337203 74337203 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr15:74337203delC uc002awv.2 + 9 2643 c.2503delC c.(2503-2505)CCCfs p.P835fs PML_uc002awu.2_Frame_Shift_Del_p.P787fs|PML_uc010ule.1_Frame_Shift_Del_p.P396fs NM_033238 NP_150241 P29590 PML_HUMAN promyelocytic leukemia protein isoform 1 835 cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding central_nervous_system(2)|kidney(2)|breast(1) 5 CACCACGTTGCCCCCTGCCCA 0.637 0.59 142 205 LRRK1 79705 broad.mit.edu 37 15 101549221 101549221 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr15:101549221delG uc002bwr.2 + 7 1261 c.942delG c.(940-942)CTGfs p.L314fs LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA NM_024652 NP_078928 Q38SD2 LRRK1_HUMAN leucine-rich repeat kinase 1 314 LRR 2. small GTPase mediated signal transduction mitochondrion ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1) 12 Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094) OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23) ACAACCACCTGGGGGAGCTGC 0.637 0.25 145 49 PKMYT1 9088 broad.mit.edu 37 16 3025797 3025799 + In_Frame_Del DEL TCC - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr16:3025797_3025799delTCC uc002csn.2 - 4 836_838 c.393_395delGGA c.(391-396)GAGGAC>GAC p.E131del PKMYT1_uc010uwn.1_RNA|PKMYT1_uc002csm.2_In_Frame_Del_p.E131del|PKMYT1_uc002cso.2_In_Frame_Del_p.E62del|PKMYT1_uc002csp.2_In_Frame_Del_p.E122del|PKMYT1_uc002csq.2_In_Frame_Del_p.E122del|PKMYT1_uc010bsy.1_In_Frame_Del_p.E122del NM_004203 NP_004194 Q99640 PMYT1_HUMAN protein kinase Myt1 isoform 1 131 Protein kinase. G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis endoplasmic reticulum membrane|Golgi membrane|membrane fraction|nucleoplasm ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity stomach(1) 1 0.000 0.16 97 18 CREBBP 1387 broad.mit.edu 37 16 3779211 3779211 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr16:3779211delG uc002cvv.2 - 31 6041 c.5837delC c.(5836-5838)CCAfs p.P1946fs CREBBP_uc002cvw.2_Frame_Shift_Del_p.P1908fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1946 Poly-Pro. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding p.P1946fs*30(1) haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) GGCCGGGGGTGGGGGGGCCGG 0.701 0.32 30 14 CIITA 4261 broad.mit.edu 37 16 10992844 10992844 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr16:10992844delA uc002dai.3 + 5 554 c.421delA c.(421-423)AAAfs p.K141fs CIITA_uc002daj.3_Frame_Shift_Del_p.K142fs|CIITA_uc002dak.3_Frame_Shift_Del_p.K141fs|CIITA_uc002dag.2_Frame_Shift_Del_p.K141fs|CIITA_uc002dah.2_Frame_Shift_Del_p.K142fs|CIITA_uc010bup.1_Frame_Shift_Del_p.K141fs NM_000246 NP_000237 P33076 C2TA_HUMAN class II transactivator 141 interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent nucleus activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding central_nervous_system(1) 1 AGTTGGGCAGAAAAGTCAGAA 0.498 0.14 97 16 ADAMTS18 170692 broad.mit.edu 37 16 77356311 77356312 + Frame_Shift_Del DEL AA - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr16:77356311_77356312delAA uc002ffc.3 - 14 2503_2504 c.2084_2085delTT c.(2083-2085)TTTfs p.F695fs ADAMTS18_uc010chc.1_Frame_Shift_Del_p.F283fs|ADAMTS18_uc002ffe.1_Frame_Shift_Del_p.F391fs NM_199355 NP_955387 Q8TE60 ATS18_HUMAN ADAM metallopeptidase with thrombospondin type 1 695 Cys-rich. proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding p.A696fs*18(2) large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1) 18 CGGACATTGCAAAAAAAAATTC 0.401 0.20 127 32 PER1 5187 broad.mit.edu 37 17 8049759 8049761 + In_Frame_Del DEL AGG - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr17:8049759_8049761delAGG uc002gkd.2 - 16 2205_2207 c.1967_1969delCCT c.(1966-1971)TCCTAT>TAT p.S656del PER1_uc010vuq.1_RNA|PER1_uc010vur.1_In_Frame_Del_p.S640del NM_002616 NP_002607 O15534 PER1_HUMAN period 1 656 Poly-Ser.|CSNK1E binding domain (By similarity). circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus signal transducer activity lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1) 9 0.000 0.21 423 110 KSR1 8844 broad.mit.edu 37 17 25910033 25910034 + Frame_Shift_Ins INS - A A HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr17:25910033_25910034insA uc010crg.2 + 5 916_917 c.471_472insA c.(469-474)CGCAAGfs p.R157fs KSR1_uc002gzj.1_RNA NM_014238 NP_055053 Q8IVT5 KSR1_HUMAN kinase suppressor of ras 292_293 Ras protein signal transduction cytoplasm|membrane ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity lung(3)|central_nervous_system(1) 4 Lung NSC(42;0.00836) BRCA - Breast invasive adenocarcinoma(3;0.00122) UCEC - Uterine corpus endometrioid carcinoma (53;0.168) CACCCAGCCGCAAGGTCTTCCA 0.663 0.15 81 14 NF1 4763 broad.mit.edu 37 17 29557929 29557929 + Frame_Shift_Del DEL A - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr17:29557929delA uc002hgg.2 + 24 3516 c.3183delA c.(3181-3183)GTAfs p.V1061fs NF1_uc002hgh.2_Frame_Shift_Del_p.V1061fs|NF1_uc010csn.1_Frame_Shift_Del_p.V921fs|NF1_uc002hgi.1_Frame_Shift_Del_p.V94fs NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 1061 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) ATGATGATGTAAAATGTCTTA 0.343 0.51 44 46 MLLT6 4302 broad.mit.edu 37 17 36872704 36872704 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr17:36872704delC uc002hqi.3 + 10 1134 c.1121delC c.(1120-1122)GCCfs p.A374fs MLLT6_uc002hqj.2_Intron|MLLT6_uc002hqk.3_5'Flank NM_005937 NP_005928 P55198 AF17_HUMAN myeloid/lymphoid or mixed-lineage leukemia 374 regulation of transcription, DNA-dependent nucleus protein binding|zinc ion binding breast(3)|prostate(1)|lung(1)|skin(1) 6 Breast(7;4.43e-21) AAGCCCACAGCCCCCGCCCCT 0.617 0.36 48 27 PNMT 5409 broad.mit.edu 37 17 37826061 37826062 + Frame_Shift_Ins INS - A A HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr17:37826061_37826062insA uc002hsi.1 + 2 604_605 c.382_383insA c.(382-384)CAAfs p.Q128fs NM_002686 NP_002677 P11086 PNMT_HUMAN phenylethanolamine N-methyltransferase 128 catecholamine biosynthetic process|hormone biosynthetic process cytosol phenylethanolamine N-methyltransferase activity ovary(1) 1 all_cancers(6;6.59e-85)|all_epithelial(6;2.89e-103)|Breast(7;1.05e-86)|Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052) UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;3.87e-45)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171) 0.000 0.25 542 180 TOP2A 7153 broad.mit.edu 37 17 38552661 38552661 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr17:38552661delC uc002huq.2 - 28 3720 c.3594delG c.(3592-3594)GGGfs p.G1198fs NM_001067 NP_001058 P11388 TOP2A_HUMAN DNA topoisomerase II, alpha isozyme 1198 apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1) 7 Breast(137;0.00328) STAD - Stomach adenocarcinoma(5;0.00183) Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385) CCTTGGCCTTCCCCCCTTTCC 0.428 0.38 202 122 WNK4 65266 broad.mit.edu 37 17 40939870 40939870 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr17:40939870delG uc002ibj.2 + 8 1837 c.1816delG c.(1816-1818)GGGfs p.G606fs WNK4_uc010wgx.1_Frame_Shift_Del_p.G270fs|WNK4_uc002ibk.1_Frame_Shift_Del_p.G378fs|WNK4_uc010wgy.1_Intron NM_032387 NP_115763 Q96J92 WNK4_HUMAN WNK lysine deficient protein kinase 4 606 intracellular protein kinase cascade tight junction ATP binding|protein serine/threonine kinase activity ovary(3)|skin(3)|stomach(1) 7 Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.0749) TCAGCCCCCTGGGGGGGTGCC 0.637 0.19 108 26 BRCA1 672 broad.mit.edu 37 17 41244311 41244311 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr17:41244311delT uc002icq.2 - 10 3469 c.3237delA c.(3235-3237)AAAfs p.K1079fs BRCA1_uc010whp.1_Intron|BRCA1_uc010whl.1_Intron|BRCA1_uc010whm.1_Intron|BRCA1_uc002icp.3_Frame_Shift_Del_p.K1008fs|BRCA1_uc002icu.2_Intron|BRCA1_uc010cyx.2_Frame_Shift_Del_p.K1032fs|BRCA1_uc002ict.2_Frame_Shift_Del_p.K1079fs|BRCA1_uc010whn.1_Intron|BRCA1_uc010who.1_Intron|BRCA1_uc010whq.1_Intron|BRCA1_uc002idc.1_Intron|BRCA1_uc010whr.1_Intron|BRCA1_uc002idd.2_Frame_Shift_Del_p.K1079fs|BRCA1_uc002ide.1_Frame_Shift_Del_p.K910fs|BRCA1_uc010cyy.1_Frame_Shift_Del_p.K1079fs|BRCA1_uc010whs.1_Frame_Shift_Del_p.K1079fs|BRCA1_uc010cyz.2_Frame_Shift_Del_p.K1032fs|BRCA1_uc010cza.2_Frame_Shift_Del_p.K1053fs|BRCA1_uc010wht.1_Frame_Shift_Del_p.K783fs NM_007294 NP_009225 P38398 BRCA1_HUMAN breast cancer 1, early onset isoform 1 1079 androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding ovary(24)|breast(21)|lung(4)|central_nervous_system(1)|endometrium(1)|urinary_tract(1) 52 Breast(137;0.000717) BRCA - Breast invasive adenocarcinoma(366;0.126) TAGCATTCAATTTTGGCCCTC 0.373 0.27 174 64 SOST 50964 broad.mit.edu 37 17 41836007 41836007 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr17:41836007delC uc002iec.1 - 1 150 c.103delG c.(103-105)GAAfs p.E35fs NM_025237 NP_079513 Q9BQB4 SOST_HUMAN sclerostin precursor 35 negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of ossification|negative regulation of protein complex assembly|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway heparin binding|protein binding 0 Breast(137;0.00725) UCEC - Uterine corpus endometrioid carcinoma (308;0.177)|BRCA - Breast invasive adenocarcinoma(366;0.0741) GGGATGATTTCCGTGGCATCA 0.637 0.23 46 14 NGFR 4804 broad.mit.edu 37 17 47590264 47590265 + Frame_Shift_Ins INS - A A HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr17:47590264_47590265insA uc002ioz.3 + 6 1302_1303 c.1177_1178insA c.(1177-1179)CAGfs p.Q393fs NM_002507 NP_002498 P08138 TNR16_HUMAN nerve growth factor receptor precursor 393 Cytoplasmic (Potential).|Death. anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|membrane protein intracellular domain proteolysis|negative regulation of axonogenesis|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis cell surface|cytosol|endosome|extracellular region|integral to plasma membrane|nucleoplasm ovary(1)|lung(1) 2 all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17) CTGGGCCACCCAGGACAGCGCC 0.693 0.28 50 19 SMAD7 4092 broad.mit.edu 37 18 46474795 46474795 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr18:46474795delG uc002ldg.2 - 2 913 c.626delC c.(625-627)CCTfs p.P209fs SMAD7_uc010xde.1_5'UTR NM_005904 NP_005895 O15105 SMAD7_HUMAN SMAD family member 7 209 Poly-Pro.|PY-motif.|Important for interaction with SMURF2. Missing: Diminishes interaction with SMURF2. adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding 0 Colorectal(1;0.0518) GGAGTAAGGAGGGGGGGGAGA 0.388 0.58 10 14 ALPK2 115701 broad.mit.edu 37 18 56247435 56247436 + Frame_Shift_Ins INS - A A HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr18:56247435_56247436insA uc002lhj.3 - 4 786_787 c.572_573insT c.(571-573)TTGfs p.L191fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 191 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 CTTTAACACCCAAAGGATTTTC 0.436 0.34 67 35 CDC34 997 broad.mit.edu 37 19 531985 531985 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:531985delG uc002lov.2 + 1 253 c.54delG c.(52-54)AAGfs p.K18fs NM_004359 NP_004350 P49427 UB2R1_HUMAN ubiquitin-conjugating enzyme Cdc34 18 DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|negative regulation of cAMP-mediated signaling|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination cytoplasm|nucleus ATP binding|protein binding|ubiquitin-protein ligase activity 0 all_cancers(10;1.94e-35)|all_epithelial(18;5.94e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.21 245 65 SMARCA4 6597 broad.mit.edu 37 19 11097624 11097625 + Frame_Shift_Ins INS - C C HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:11097624_11097625insC uc002mqf.3 + 5 1088_1089 c.804_805insC c.(802-807)GTGCCCfs p.V268fs SMARCA4_uc010dxp.2_Frame_Shift_Ins_p.V268fs|SMARCA4_uc010dxo.2_Frame_Shift_Ins_p.V268fs|SMARCA4_uc002mqg.1_Frame_Shift_Ins_p.V268fs|SMARCA4_uc010dxq.2_Frame_Shift_Ins_p.V268fs|SMARCA4_uc010dxr.2_Frame_Shift_Ins_p.V268fs|SMARCA4_uc002mqj.3_Frame_Shift_Ins_p.V268fs|SMARCA4_uc010dxs.2_Frame_Shift_Ins_p.V268fs|SMARCA4_uc002mqe.2_Frame_Shift_Ins_p.V268fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 268_269 Necessary for interaction with SS18L1/CREST (By similarity). chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.P270fs*16(1)|p.M272fs*31(1)|p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) 0.000 0.45 404 328 JUNB 3726 broad.mit.edu 37 19 12903092 12903093 + Frame_Shift_Ins INS - G G HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:12903092_12903093insG uc002mvc.2 + 1 783_784 c.507_508insG c.(505-510)CCCGGGfs p.P169fs JUNB_uc002mvb.2_RNA NM_002229 NP_002220 P17275 JUNB_HUMAN jun B proto-oncogene 169_170 chromatin|nucleus protein dimerization activity|transcription coactivator activity|transcription corepressor activity lung(2)|central_nervous_system(1) 3 cggctgggcccgggggcgTCTA 0.564 0.11 65 8 PKN1 5585 broad.mit.edu 37 19 14561743 14561743 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:14561743delG uc002myp.2 + 6 960 c.792delG c.(790-792)CTGfs p.L264fs PKN1_uc002myq.2_Frame_Shift_Del_p.L270fs NM_002741 NP_002732 Q16512 PKN1_HUMAN protein kinase N1 isoform 2 264 REM 3. activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent endosome|nucleus|plasma membrane androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1) 8 0.000 0.18 365 79 NOTCH3 4854 broad.mit.edu 37 19 15271908 15271908 + Frame_Shift_Del DEL T - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:15271908delT uc002nan.2 - 33 6607 c.6531delA c.(6529-6531)CCAfs p.P2177fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 2177 Cytoplasmic (Potential). Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.17 488 99 NOTCH3 4854 broad.mit.edu 37 19 15271909 15271909 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:15271909delG uc002nan.2 - 33 6606 c.6530delC c.(6529-6531)CCAfs p.P2177fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 2177 Cytoplasmic (Potential). Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.41 347 241 CPAMD8 27151 broad.mit.edu 37 19 17039884 17039884 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:17039884delC uc002nfb.2 - 24 3185 c.3153delG c.(3151-3153)GGGfs p.G1051fs NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 1004 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 TGTTCTGATGCCCCCCCAGGA 0.587 0.40 145 98 CRTC1 23373 broad.mit.edu 37 19 18879554 18879554 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:18879554delC uc002nkb.3 + 10 1359 c.1271delC c.(1270-1272)TCCfs p.S424fs CRTC1_uc010ebv.2_Frame_Shift_Del_p.S440fs|CRTC1_uc010ebw.2_Frame_Shift_Del_p.S289fs|CRTC1_uc002nkc.3_Intron NM_015321 NP_056136 Q6UUV9 CRTC1_HUMAN mucoepidermoid carcinoma translocated 1 isoform 424 interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus|plasma membrane cAMP response element binding protein binding|protein binding CRTC1/MAML2(516) salivary_gland(474)|lung(35)|thyroid(4)|breast(3)|skin(2)|ovary(1) 519 CTCCCCCAGTCCCCCCCAGAG 0.652 0.33 28 14 MAP3K10 4294 broad.mit.edu 37 19 40718783 40718783 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:40718783delG uc002ona.2 + 7 1912 c.1624delG c.(1624-1626)GGGfs p.G542fs MAP3K10_uc002onb.2_5'UTR NM_002446 NP_002437 Q02779 M3K10_HUMAN mitogen-activated protein kinase kinase kinase 542 activation of JUN kinase activity|induction of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of JNK cascade|protein autophosphorylation|smoothened signaling pathway cytoplasm ATP binding|bHLH transcription factor binding|JUN kinase kinase kinase activity|protein homodimerization activity|transcription corepressor activity ovary(2)|lung(2)|skin(1)|pancreas(1) 6 0.000 0.16 926 182 HIPK4 147746 broad.mit.edu 37 19 40885532 40885532 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:40885532delC uc002onp.2 - 4 2098 c.1813delG c.(1813-1815)GCCfs p.A605fs NM_144685 NP_653286 Q8NE63 HIPK4_HUMAN homeodomain interacting protein kinase 4 605 cytoplasm ATP binding|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292) 0.000 0.19 257 59 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.32 187 88 AXL 558 broad.mit.edu 37 19 41743933 41743933 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:41743933delC uc010ehj.2 + 7 1058 c.868delC c.(868-870)CCCfs p.P290fs CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Frame_Shift_Del_p.P290fs|AXL_uc010ehk.2_Frame_Shift_Del_p.P290fs NM_021913 NP_068713 P30530 UFO_HUMAN AXL receptor tyrosine kinase isoform 1 290 Extracellular (Potential).|Fibronectin type-III 1. integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1) 13 AGCATCCGTGCCCCCCCATCA 0.647 0.17 195 39 LMTK3 114783 broad.mit.edu 37 19 49000732 49000732 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:49000732delG uc002pjk.2 - 12 3681 c.3681delC c.(3679-3681)CCCfs p.P1227fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.34 786 398 LMTK3 114783 broad.mit.edu 37 19 49002615 49002615 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:49002615delG uc002pjk.2 - 12 1798 c.1798delC c.(1798-1800)CAGfs p.Q600fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.36 430 238 KLK7 5650 broad.mit.edu 37 19 51483130 51483130 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr19:51483130delG uc002puo.2 - 5 622 c.520delC c.(520-522)CAGfs p.Q174fs KLK7_uc002pup.2_Frame_Shift_Del_p.Q174fs|KLK7_uc010yco.1_Frame_Shift_Del_p.Q48fs|KLK7_uc010eok.2_Frame_Shift_Del_p.Q102fs NM_139277 NP_644806 P49862 KLK7_HUMAN stratum corneum chymotryptic enzyme 174 Peptidase S1. epidermis development|proteolysis extracellular region serine-type endopeptidase activity 0 all_neural(266;0.026) OV - Ovarian serous cystadenocarcinoma(262;0.00382)|GBM - Glioblastoma multiforme(134;0.00895) GTGCAGTCCTGGGGGGAGATG 0.572 0.14 510 84 SULF2 55959 broad.mit.edu 37 20 46318931 46318931 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr20:46318931delG uc002xto.2 - 5 1006 c.676delC c.(676-678)CACfs p.H226fs SULF2_uc002xtr.2_Frame_Shift_Del_p.H226fs|SULF2_uc002xtq.2_Frame_Shift_Del_p.H226fs|SULF2_uc010ghv.1_Frame_Shift_Del_p.H226fs NM_018837 NP_061325 Q8IWU5 SULF2_HUMAN sulfatase 2 isoform a precursor 226 bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway cell surface|endoplasmic reticulum|extracellular space|Golgi stack arylsulfatase activity|calcium ion binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 TCAGGGCCGTGGGGGGCTGCA 0.572 0.56 15 19 SULF2 55959 broad.mit.edu 37 20 46331294 46331295 + Frame_Shift_Ins INS - C C HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr20:46331294_46331295insC uc002xto.2 - 4 865_866 c.535_536insG c.(535-537)GTGfs p.V179fs SULF2_uc002xtr.2_Frame_Shift_Ins_p.V179fs|SULF2_uc002xtq.2_Frame_Shift_Ins_p.V179fs|SULF2_uc010ghv.1_Frame_Shift_Ins_p.V179fs NM_018837 NP_061325 Q8IWU5 SULF2_HUMAN sulfatase 2 isoform a precursor 179 bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway cell surface|endoplasmic reticulum|extracellular space|Golgi stack arylsulfatase activity|calcium ion binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 CTTCTCTTTCACCCCGTTCCGA 0.446 0.26 99 34 COL18A1 80781 broad.mit.edu 37 21 46907379 46907379 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr21:46907379delG uc011afs.1 + 16 3118 c.3097delG c.(3097-3099)GGGfs p.G1033fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.G618fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.G798fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1033 Nonhelical region 4 (NC4). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.35 148 78 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 109 376 COL18A1 80781 broad.mit.edu 37 21 46925143 46925143 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr21:46925143delC uc011afs.1 + 35 4221 c.4200delC c.(4198-4200)GGCfs p.G1400fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.G985fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.G1165fs|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1403 Triple-helical region 9 (COL9). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.16 560 110 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 108 MN1 4330 broad.mit.edu 37 22 28193569 28193569 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr22:28193569delC uc003adj.2 - 1 3918 c.2963delG c.(2962-2964)GGAfs p.G988fs NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 988 binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 TGCGGAGCTTCCCCCGACGGC 0.706 0.31 61 27 MN1 4330 broad.mit.edu 37 22 28193623 28193623 + Frame_Shift_Del DEL C - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr22:28193623delC uc003adj.2 - 1 3864 c.2909delG c.(2908-2910)GGCfs p.G970fs NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 970 binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 CCCAGGTGCGCCCCCGCTGTC 0.716 0.16 46 9 ZNRF3 84133 broad.mit.edu 37 22 29445693 29445694 + Frame_Shift_Ins INS - T T HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr22:29445693_29445694insT uc003aeg.2 + 8 1389_1390 c.1224_1225insT c.(1222-1227)CTCTTCfs p.L408fs ZNRF3_uc003aeh.1_Frame_Shift_Ins_p.L408fs NM_032173 NP_115549 Q9ULT6 ZNRF3_HUMAN zinc and ring finger 3 508_509 Cytoplasmic (Potential). integral to membrane zinc ion binding ovary(1) 1 0.000 0.19 563 131 ZNRF3 84133 broad.mit.edu 37 22 29445695 29445696 + Frame_Shift_Ins INS - C C HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr22:29445695_29445696insC uc003aeg.2 + 8 1391_1392 c.1226_1227insC c.(1225-1227)TTCfs p.F409fs ZNRF3_uc003aeh.1_Frame_Shift_Ins_p.F409fs NM_032173 NP_115549 Q9ULT6 ZNRF3_HUMAN zinc and ring finger 3 509 Cytoplasmic (Potential). integral to membrane zinc ion binding ovary(1) 1 0.000 0.11 623 74 TIMP3 7078 broad.mit.edu 37 22 33255323 33255324 + Frame_Shift_Ins INS - C C HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr22:33255323_33255324insC uc003anb.2 + 5 1781_1782 c.595_596insC c.(595-597)GCCfs p.A199fs SYN3_uc003amx.2_Intron|SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron NM_000362 NP_000353 P35625 TIMP3_HUMAN tissue inhibitor of metalloproteinase 3 199 negative regulation of membrane protein ectodomain proteolysis|visual perception metal ion binding|metalloendopeptidase inhibitor activity|protein binding lung(1) 1 CCGAGGATGGGCCCCCCCGGAT 0.604 0.20 68 17 MYH9 4627 broad.mit.edu 37 22 36708257 36708257 + Frame_Shift_Del DEL G - - HEC59_ENDOMETRIUM NA HEC59_ENDOMETRIUM NA g.chr22:36708257delG uc003apg.2 - 14 1796 c.1565delC c.(1564-1566)CCGfs p.P522fs MYH9_uc003aph.1_Frame_Shift_Del_p.P386fs NM_002473 NP_002464 P35579 MYH9_HUMAN myosin, heavy polypeptide 9, non-muscle 522 Myosin head-like. actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1) 11 CAGAATGCCCGGGGGGCCTGC 0.642 0.14 249 41 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 4 40 B3GALT6 126792 broad.mit.edu 37 1 1168570 1168570 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:1168570delG uc001adk.2 + 1 942 c.912delG c.(910-912)GTGfs p.V304fs SDF4_uc001adh.3_5'Flank|SDF4_uc001adi.3_5'Flank|SDF4_uc009vjv.2_5'Flank|SDF4_uc009vjw.2_5'Flank NM_080605 NP_542172 Q96L58 B3GT6_HUMAN beta-1,3-galactosyltransferase 6 304 Lumenal (Potential). glycosaminoglycan biosynthetic process|protein glycosylation Golgi cisterna membrane|Golgi medial cisterna|integral to membrane galactosylxylosylprotein 3-beta-galactosyltransferase activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.22e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199) 0.000 0.30 507 220 CHD5 26038 broad.mit.edu 37 1 6219573 6219573 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:6219573delC uc001amb.1 - 3 310 c.210delG c.(208-210)GGGfs p.G70fs NM_015557 NP_056372 Q8TDI0 CHD5_HUMAN chromodomain helicase DNA binding protein 5 70 Lys-rich. chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1) 12 Ovarian(185;0.0634) all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15) Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193) CATCATTGCTCCCCTGGAAAA 0.507 0.18 185 41 SPEN 23013 broad.mit.edu 37 1 16255141 16255142 + Frame_Shift_Ins INS - GA GA HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:16255141_16255142insGA uc001axk.1 + 11 2610_2611 c.2406_2407insGA c.(2404-2409)GTGGAGfs p.V802fs SPEN_uc010obp.1_Frame_Shift_Ins_p.V761fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 802_803 Arg-rich. interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) CGGAGAGAGTGGAGAGAGAGAG 0.431 0.56 77 99 EPHA2 1969 broad.mit.edu 37 1 16462199 16462199 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:16462199delG uc001aya.1 - 6 1516 c.1379delC c.(1378-1380)CCGfs p.P460fs EPHA2_uc010oca.1_Frame_Shift_Del_p.P460fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 460 Extracellular (Potential).|Fibronectin type-III 2. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) 0.000 0.80 155 608 ARID1A 8289 broad.mit.edu 37 1 27024001 27024002 + Frame_Shift_Ins INS - G G HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:27024001_27024002insG uc001bmv.1 + 1 1480_1481 c.1107_1108insG c.(1105-1110)GGCGGGfs p.G369fs ARID1A_uc001bmt.1_Frame_Shift_Ins_p.G369fs|ARID1A_uc001bmu.1_Frame_Shift_Ins_p.G369fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 369_370 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.Q372fs*19(1)|p.Q372fs*28(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.60 63 95 ARID1A 8289 broad.mit.edu 37 1 27105931 27105931 + Frame_Shift_Del DEL G - - rs140055856 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:27105931delG uc001bmv.1 + 20 5915 c.5542delG c.(5542-5544)GGGfs p.G1848fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.G1631fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.G694fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.G176fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.G90fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1848 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.G1848fs*6(3) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GCGGATTGGTGGGGGGGACAC 0.582 0.85 22 127 SLC2A1 6513 broad.mit.edu 37 1 43395333 43395333 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:43395333delG uc001cik.2 - 6 1323 c.798delC c.(796-798)CCCfs p.P266fs NM_006516 NP_006507 P11166 GTR1_HUMAN solute carrier family 2 (facilitated glucose 266 Cytoplasmic (Potential). carbohydrate metabolic process|energy reserve metabolic process|regulation of insulin secretion|water-soluble vitamin metabolic process integral to membrane|melanosome|membrane fraction|midbody D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity central_nervous_system(2)|pancreas(2)|ovary(1) 5 Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0122) Etomidate(DB00292) 0.000 0.18 532 113 PLK3 1263 broad.mit.edu 37 1 45270026 45270026 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:45270026delC uc001cmn.2 + 12 1458 c.1358delC c.(1357-1359)GCCfs p.A453fs PLK3_uc001cmo.2_RNA NM_004073 NP_004064 Q9H4B4 PLK3_HUMAN polo-like kinase 3 453 membrane ATP binding|protein binding|protein serine/threonine kinase activity 0 Acute lymphoblastic leukemia(166;0.155) CAGAACCCGGCCCCCCTGGCC 0.617 0.67 31 64 DAB1 1600 broad.mit.edu 37 1 57537235 57537235 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:57537235delT uc001cys.1 - 8 1192 c.518delA c.(517-519)AAGfs p.K173fs DAB1_uc001cyt.1_Frame_Shift_Del_p.K173fs|DAB1_uc001cyq.1_Frame_Shift_Del_p.K173fs|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Frame_Shift_Del_p.K173fs|DAB1_uc009vzx.1_Frame_Shift_Del_p.K173fs NM_021080 NP_066566 O75553 DAB1_HUMAN disabled homolog 1 173 PID. cell differentiation|nervous system development skin(2)|ovary(1) 3 CTTTTGTGCCTTTTTTTCTAA 0.393 0.18 42 9 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.10 333 37 HORMAD1 84072 broad.mit.edu 37 1 150676776 150676776 + Frame_Shift_Del DEL T - - rs45439605 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:150676776delT uc001evk.1 - 11 954 c.848delA c.(847-849)AACfs p.N283fs HORMAD1_uc001evl.1_Frame_Shift_Del_p.N276fs|HORMAD1_uc001evm.1_Frame_Shift_Del_p.N203fs NM_032132 NP_115508 Q86X24 HORM1_HUMAN HORMA domain containing 1 283 blastocyst development|cell differentiation|meiotic DNA double-strand break formation|meiotic recombination checkpoint|meiotic sister chromatid cohesion|mitosis|oogenesis|regulation of homologous chromosome segregation|spermatogenesis|synaptonemal complex assembly chromosome|nucleus ovary(2)|central_nervous_system(1) 3 all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171) UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171) AGATGCAGGGTTTTTTTCCTG 0.289 0.11 202 24 FCRL4 83417 broad.mit.edu 37 1 157559183 157559184 + Frame_Shift_Del DEL CT - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:157559183_157559184delCT uc001fqw.2 - 3 253_254 c.117_118delAG c.(115-120)AGAGTGfs p.R39fs FCRL4_uc010phy.1_RNA NM_031282 NP_112572 Q96PJ5 FCRL4_HUMAN Fc receptor-like 4 precursor 39_40 Extracellular (Potential).|Ig-like C2-type 1. integral to membrane|plasma membrane receptor activity ovary(2)|kidney(1)|skin(1) 4 all_hematologic(112;0.0378)|Hepatocellular(266;0.178) Prostate(1639;0.245) GTCAGAGTCACTCTCTCTCCTT 0.475 0.28 169 67 PIK3C2B 5287 broad.mit.edu 37 1 204423858 204423858 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:204423858delG uc001haw.2 - 13 2484 c.2005delC c.(2005-2007)CTGfs p.L669fs PIK3C2B_uc010pqv.1_Frame_Shift_Del_p.L669fs|PIK3C2B_uc001hax.1_Frame_Shift_Del_p.L669fs|PIK3C2B_uc009xbd.1_RNA NM_002646 NP_002637 O00750 P3C2B_HUMAN phosphoinositide-3-kinase, class 2 beta 669 cell communication|phosphatidylinositol-mediated signaling endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1) 7 all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227) GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193) CGGGTCTGCAGGGGGCTGCAC 0.582 0.11 95 12 NUAK2 81788 broad.mit.edu 37 1 205273141 205273141 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:205273141delG uc001hce.2 - 7 1451 c.1324delC c.(1324-1326)CTGfs p.L442fs NM_030952 NP_112214 Q9H093 NUAK2_HUMAN NUAK family, SNF1-like kinase, 2 442 actin cytoskeleton organization|apoptosis|cellular response to glucose starvation|negative regulation of apoptosis ATP binding|magnesium ion binding|protein serine/threonine kinase activity ovary(3)|stomach(1)|breast(1) 5 Breast(84;0.186) BRCA - Breast invasive adenocarcinoma(75;0.117) TTGGGGAGCAGGGGGGCAGCC 0.632 0.16 205 39 NUAK2 81788 broad.mit.edu 37 1 205277809 205277809 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:205277809delC uc001hce.2 - 3 531 c.404delG c.(403-405)GGCfs p.G135fs NUAK2_uc009xbj.1_Frame_Shift_Del_p.G7fs NM_030952 NP_112214 Q9H093 NUAK2_HUMAN NUAK family, SNF1-like kinase, 2 135 Protein kinase. actin cytoskeleton organization|apoptosis|cellular response to glucose starvation|negative regulation of apoptosis ATP binding|magnesium ion binding|protein serine/threonine kinase activity ovary(3)|stomach(1)|breast(1) 5 Breast(84;0.186) BRCA - Breast invasive adenocarcinoma(75;0.117) ATAAAGGTCGCCCCGGCTGGC 0.572 0.46 155 130 MAPKAPK2 9261 broad.mit.edu 37 1 206904495 206904496 + Frame_Shift_Ins INS - C C HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:206904495_206904496insC uc001hem.1 + 7 1066_1067 c.780_781insC c.(778-783)TATCCCfs p.Y260fs MAPKAPK2_uc001hel.1_Frame_Shift_Ins_p.Y260fs NM_032960 NP_116584 P49137 MAPK2_HUMAN mitogen-activated protein kinase-activated 260_261 Protein kinase. activation of MAPK activity|hormone biosynthetic process|innate immune response|leukotriene biosynthetic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|prostanoid metabolic process|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|protein binding|protein serine/threonine kinase activity|signal transducer activity 0 Breast(84;0.183) BRCA - Breast invasive adenocarcinoma(75;0.211) TGTGTGGGTATCCCCCCTTCTA 0.540 0.55 55 68 TGFB2 7042 broad.mit.edu 37 1 218609371 218609371 + Frame_Shift_Del DEL A - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:218609371delA uc001hlm.2 + 5 1467 c.814delA c.(814-816)AAAfs p.K272fs TGFB2_uc001hln.2_Frame_Shift_Del_p.K300fs|TGFB2_uc010pue.1_Intron|TGFB2_uc001hlo.2_Intron NM_003238 NP_003229 P61812 TGFB2_HUMAN transforming growth factor, beta 2 isoform 2 272 activation of protein kinase activity|angiogenesis|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cardioblast differentiation|catagen|cell cycle arrest|cell death|cell growth|cell-cell junction organization|cell-cell signaling|collagen fibril organization|dopamine biosynthetic process|embryonic digestive tract development|eye development|glial cell migration|hair follicle morphogenesis|hemopoiesis|menstrual cycle phase|negative regulation of alkaline phosphatase activity|negative regulation of cell growth|negative regulation of epithelial cell proliferation|negative regulation of immune response|negative regulation of macrophage cytokine production|neuron development|neutrophil chemotaxis|odontogenesis|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of cardioblast differentiation|positive regulation of catagen|positive regulation of cell adhesion mediated by integrin|positive regulation of cell cycle|positive regulation of cell division|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of epithelial cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of heart contraction|positive regulation of immune response|positive regulation of integrin biosynthetic process|positive regulation of neuron apoptosis|positive regulation of ossification|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein secretion|positive regulation of stress-activated MAPK cascade|regulation of transforming growth factor-beta2 production|response to hypoxia|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein import into nucleus|somatic stem cell division|transforming growth factor beta receptor signaling pathway axon|extracellular matrix|extracellular space|neuronal cell body|platelet alpha granule lumen beta-amyloid binding|cytokine activity|growth factor activity|protein heterodimerization activity|protein homodimerization activity|receptor signaling protein serine/threonine kinase activity|type II transforming growth factor beta receptor binding 0 all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776) GTCCACTAGGAAAAAAAACAG 0.433 0.56 158 204 CDC42BPA 8476 broad.mit.edu 37 1 227261574 227261576 + In_Frame_Del DEL ATG - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:227261574_227261576delATG uc001hqr.2 - 19 3667_3669 c.2724_2726delCAT c.(2722-2727)ATCATA>ATA p.908_909II>I CDC42BPA_uc001hqq.2_In_Frame_Del_p.172_173II>I|CDC42BPA_uc001hqs.2_In_Frame_Del_p.827_828II>I|CDC42BPA_uc009xes.2_In_Frame_Del_p.908_909II>I|CDC42BPA_uc010pvs.1_In_Frame_Del_p.908_909II>I|CDC42BPA_uc001hqp.2_In_Frame_Del_p.64_65II>I|CDC42BPA_uc001hqu.1_In_Frame_Del_p.64_65II>I NM_003607 NP_003598 Q5VT25 MRCKA_HUMAN CDC42-binding protein kinase alpha isoform B 908_909 Potential. actin cytoskeleton reorganization|intracellular signal transduction cell leading edge|cell-cell junction|cytoplasm ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1) 11 all_cancers(173;0.156)|Prostate(94;0.0792) CCATTCTGTTATGATATTAGATG 0.355 0.14 186 30 KIAA1804 84451 broad.mit.edu 37 1 233514889 233514890 + Frame_Shift_Ins INS - C C HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr1:233514889_233514890insC uc001hvt.3 + 9 2398_2399 c.2137_2138insC c.(2137-2139)TCCfs p.S713fs KIAA1804_uc001hvu.3_Frame_Shift_Ins_p.S159fs NM_032435 NP_115811 Q5TCX8 M3KL4_HUMAN mixed lineage kinase 4 713 activation of JUN kinase activity|protein autophosphorylation ATP binding|MAP kinase kinase kinase activity|protein homodimerization activity lung(5)|central_nervous_system(2)|skin(1) 8 all_cancers(173;0.000405)|all_epithelial(177;0.0345)|Prostate(94;0.122) TCTGAGTAGATCCCCCCAGAGA 0.540 0.33 10 5 CYP1B1 1545 broad.mit.edu 37 2 38301673 38301673 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr2:38301673delC uc002rqo.2 - 3 1262 c.859delG c.(859-861)GCCfs p.A287fs NM_000104 NP_000095 Q16678 CP1B1_HUMAN cytochrome P450, family 1, subfamily B, 287 visual perception|xenobiotic metabolic process endoplasmic reticulum membrane|microsome aromatase activity|electron carrier activity|heme binding|oxygen binding|protein binding ovary(1)|central_nervous_system(1) 2 all_hematologic(82;0.21) Estrone(DB00655) cggggggcggccccgggccgA 0.512 0.38 10 6 BCL11A 53335 broad.mit.edu 37 2 60688969 60688969 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr2:60688969delG uc002sae.1 - 4 1306 c.1078delC c.(1078-1080)CTCfs p.L360fs BCL11A_uc002sab.2_Frame_Shift_Del_p.L360fs|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Frame_Shift_Del_p.L326fs|BCL11A_uc002sad.1_Frame_Shift_Del_p.L208fs|BCL11A_uc002saf.1_Frame_Shift_Del_p.L326fs NM_022893 NP_075044 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A isoform 1 360 Pro-rich. negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|cytoplasm|nucleus|nucleus nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding central_nervous_system(6)|breast(3)|ovary(2)|skin(2) 13 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) 0.000 0.68 118 253 BCL11A 53335 broad.mit.edu 37 2 60689254 60689254 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr2:60689254delG uc002sae.1 - 4 1021 c.793delC c.(793-795)CTGfs p.L265fs BCL11A_uc002sab.2_Frame_Shift_Del_p.L265fs|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Frame_Shift_Del_p.L231fs|BCL11A_uc002sad.1_Frame_Shift_Del_p.L113fs|BCL11A_uc002saf.1_Frame_Shift_Del_p.L231fs NM_022893 NP_075044 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A isoform 1 265 Pro-rich. negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|cytoplasm|nucleus|nucleus nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding central_nervous_system(6)|breast(3)|ovary(2)|skin(2) 13 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) 0.000 0.27 414 155 TTN 7273 broad.mit.edu 37 2 179432761 179432764 + Frame_Shift_Del DEL TTTC - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr2:179432761_179432764delTTTC uc010zfg.1 - 275 70615_70618 c.70391_70394delGAAA c.(70390-70395)AGAAACfs p.R23464fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.R17159fs|TTN_uc010zfi.1_Frame_Shift_Del_p.R17092fs|TTN_uc010zfj.1_Frame_Shift_Del_p.R16967fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 24391_24392 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CAAAATACTGTTTCTTTCTTTTCT 0.412 0.39 186 120 TTN 7273 broad.mit.edu 37 2 179604689 179604689 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr2:179604689delT uc010zfh.1 - 46 12982 c.12758delA c.(12757-12759)AAGfs p.K4253fs TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Frame_Shift_Del_p.K4186fs|TTN_uc010zfj.1_Frame_Shift_Del_p.K4061fs|TTN_uc002umz.1_Intron NM_133437 NP_597681 Q8WZ42 TITIN_HUMAN titin isoform novex-2 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GACCTCCACCTTTTCAATATT 0.473 0.46 129 109 TTN 7273 broad.mit.edu 37 2 179640485 179640486 + Frame_Shift_Ins INS - T T HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr2:179640485_179640486insT uc010zfg.1 - 28 6329_6330 c.6105_6106insA c.(6103-6108)AAAGATfs p.K2035fs TTN_uc010zfh.1_Frame_Shift_Ins_p.K1989fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.K1989fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.K1989fs|TTN_uc002unb.2_Frame_Shift_Ins_p.K2035fs|uc002unc.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 2035_2036 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AGAAGTTCATCTTTTGTCTTCC 0.436 0.41 222 154 STRADB 55437 broad.mit.edu 37 2 202339391 202339391 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr2:202339391delT uc002uyd.3 + 6 702 c.337delT c.(337-339)TTTfs p.F113fs NM_018571 NP_061041 Q9C0K7 STRAB_HUMAN STE20-related kinase adaptor beta 113 Protein kinase. activation of protein kinase activity|cell cycle arrest|insulin receptor signaling pathway|protein export from nucleus|regulation of fatty acid oxidation cytosol|nucleus ATP binding|protein binding|protein kinase activity skin(2)|stomach(1)|lung(1) 4 TCTATCCCACTTTTTCCGGCA 0.408 0.62 74 119 ERBB4 2066 broad.mit.edu 37 2 212530143 212530143 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr2:212530143delT uc002veg.1 - 15 1874 c.1776delA c.(1774-1776)AAAfs p.K592fs ERBB4_uc002veh.1_Frame_Shift_Del_p.K592fs|ERBB4_uc010zji.1_Frame_Shift_Del_p.K592fs|ERBB4_uc010zjj.1_Frame_Shift_Del_p.K592fs|ERBB4_uc010fut.1_Frame_Shift_Del_p.K592fs NM_005235 NP_005226 Q15303 ERBB4_HUMAN v-erb-a erythroblastic leukemia viral oncogene 592 Extracellular (Potential).|Cys-rich. cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway basolateral plasma membrane|cytoplasm|integral to membrane|nucleus ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 33 Renal(323;0.06)|Lung NSC(271;0.197) UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266) CATCTGGACATTTTTCCACAC 0.433 0.34 123 62 HDAC4 9759 broad.mit.edu 37 2 240024508 240024508 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr2:240024508delG uc002vyk.3 - 16 2974 c.2182delC c.(2182-2184)CTCfs p.L728fs HDAC4_uc010fyz.1_Frame_Shift_Del_p.L723fs|HDAC4_uc010zoa.1_Frame_Shift_Del_p.L728fs|HDAC4_uc010fza.2_Frame_Shift_Del_p.L733fs|HDAC4_uc010fyy.2_Frame_Shift_Del_p.L685fs|HDAC4_uc010znz.1_Frame_Shift_Del_p.L611fs NM_006037 NP_006028 P56524 HDAC4_HUMAN histone deacetylase 4 728 Histone deacetylase. B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent histone deacetylase complex|transcriptional repressor complex activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding breast(3)|skin(2)|ovary(1) 6 all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159) Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04) TGCCGGTTGAGGGGGTTCGTG 0.567 0.23 88 27 CCR4 1233 broad.mit.edu 37 3 32995598 32995599 + Frame_Shift_Ins INS - T T HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr3:32995598_32995599insT uc003cfg.1 + 2 852_853 c.684_685insT c.(682-687)ACCTTGfs p.T228fs NM_005508 NP_005499 P51679 CCR4_HUMAN chemokine (C-C motif) receptor 4 228_229 Cytoplasmic (Potential). chemotaxis|elevation of cytosolic calcium ion concentration|immune response|inflammatory response integral to plasma membrane lung(1) 1 TCATCAGGACCTTGCAGCATTG 0.480 0.10 157 17 MLH1 4292 broad.mit.edu 37 3 37053576 37053576 + Frame_Shift_Del DEL A - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr3:37053576delA uc003cgl.2 + 8 723 c.663delA c.(661-663)GGAfs p.G221fs MLH1_uc011aye.1_5'UTR|MLH1_uc011ayb.1_5'UTR|MLH1_uc010hge.2_Frame_Shift_Del_p.G221fs|MLH1_uc003cgn.3_5'UTR|MLH1_uc011ayc.1_Frame_Shift_Del_p.G123fs|MLH1_uc011ayd.1_5'UTR|MLH1_uc003cgo.2_5'UTR|MLH1_uc010hgg.1_5'UTR|MLH1_uc010hgh.1_5'UTR|MLH1_uc010hgi.1_5'UTR|MLH1_uc010hgj.1_5'UTR|MLH1_uc010hgk.2_5'UTR|MLH1_uc010hgl.1_5'Flank NM_000249 NP_000240 P40692 MLH1_HUMAN MutL protein homolog 1 221 mismatch repair|somatic hypermutation of immunoglobulin genes chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex ATP binding|ATPase activity|protein binding p.0?(1) large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1) 77 CCATCTTTGGAAATGCTGTTA 0.368 0.37 121 72 MLH1 4292 broad.mit.edu 37 3 37067184 37067184 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr3:37067184delT uc003cgl.2 + 12 1155 c.1095delT c.(1093-1095)AGTfs p.S365fs MLH1_uc011aye.1_Frame_Shift_Del_p.S124fs|MLH1_uc011ayb.1_Frame_Shift_Del_p.S124fs|MLH1_uc010hge.2_Frame_Shift_Del_p.S365fs|MLH1_uc003cgn.3_Frame_Shift_Del_p.S124fs|MLH1_uc011ayc.1_Frame_Shift_Del_p.S267fs|MLH1_uc011ayd.1_Frame_Shift_Del_p.S124fs|MLH1_uc003cgo.2_Frame_Shift_Del_p.S124fs|MLH1_uc010hgg.1_Frame_Shift_Del_p.S24fs|MLH1_uc010hgh.1_Frame_Shift_Del_p.S24fs|MLH1_uc010hgi.1_Frame_Shift_Del_p.S7fs|MLH1_uc010hgj.1_Frame_Shift_Del_p.S7fs|MLH1_uc010hgk.2_Frame_Shift_Del_p.S7fs|MLH1_uc010hgl.1_Intron|MLH1_uc010hgn.2_Frame_Shift_Del_p.S7fs|MLH1_uc010hgm.2_RNA|MLH1_uc010hgo.2_Frame_Shift_Del_p.S7fs NM_000249 NP_000240 P40692 MLH1_HUMAN MutL protein homolog 1 365 mismatch repair|somatic hypermutation of immunoglobulin genes chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex ATP binding|ATPase activity|protein binding p.0?(1) large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1) 77 CCACAACAAGTCTGACCTCGT 0.398 0.53 31 35 SMARCC1 6599 broad.mit.edu 37 3 47677558 47677559 + Frame_Shift_Ins INS - T T HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr3:47677558_47677559insT uc003crq.2 - 23 2562_2563 c.2444_2445insA c.(2443-2445)AATfs p.N815fs SMARCC1_uc011bbc.1_RNA|SMARCC1_uc011bbd.1_Frame_Shift_Ins_p.N706fs NM_003074 NP_003065 Q92922 SMRC1_HUMAN SWI/SNF-related matrix-associated 815 Glu-rich. chromatin remodeling|nervous system development|transcription, DNA-dependent nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex DNA binding|protein N-terminus binding|transcription coactivator activity skin(2)|lung(1) 3 BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01) 0.000 0.10 136 15 SEMA3B 7869 broad.mit.edu 37 3 50311902 50311902 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr3:50311902delG uc003cyu.2 + 13 1488 c.1246delG c.(1246-1248)GGGfs p.G416fs SEMA3B_uc003cyt.2_Frame_Shift_Del_p.G415fs|SEMA3B_uc003cyv.2_Frame_Shift_Del_p.G303fs|SEMA3B_uc003cyw.2_Frame_Shift_Del_p.G139fs|SEMA3B_uc010hli.2_Frame_Shift_Del_p.G308fs|SEMA3B_uc003cyx.2_Frame_Shift_Del_p.G302fs|SEMA3B_uc003cyy.2_Frame_Shift_Del_p.G73fs|SEMA3B_uc011bdo.1_Frame_Shift_Del_p.G73fs NM_004636 NP_004627 Q13214 SEM3B_HUMAN semaphorin 3B isoform 1 precursor 416 Sema. axon guidance|cell-cell signaling endoplasmic reticulum|extracellular region|membrane receptor activity lung(2)|central_nervous_system(2)|kidney(1)|skin(1) 6 BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605) CCTGCCCACTGGGGGGCGCCC 0.562 0.19 196 46 FLNB 2317 broad.mit.edu 37 3 58089788 58089788 + Frame_Shift_Del DEL G - - rs145086495 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr3:58089788delG uc003djj.2 + 10 1751 c.1586delG c.(1585-1587)TGGfs p.W529fs FLNB_uc010hne.2_Frame_Shift_Del_p.W529fs|FLNB_uc003djk.2_Frame_Shift_Del_p.W529fs|FLNB_uc010hnf.2_Frame_Shift_Del_p.W529fs|FLNB_uc003djl.2_Frame_Shift_Del_p.W360fs|FLNB_uc003djm.2_Frame_Shift_Del_p.W360fs NM_001457 NP_001448 O75369 FLNB_HUMAN filamin B isoform 2 529 Filamin 3. actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction cell cortex|integral to membrane|nucleus|sarcomere actin binding breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1) 19 BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898) 0.000 0.43 388 288 PXK 54899 broad.mit.edu 37 3 58395318 58395318 + Frame_Shift_Del DEL A - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr3:58395318delA uc003djz.1 + 15 1467 c.1368delA c.(1366-1368)AGAfs p.R456fs PXK_uc003djx.1_Frame_Shift_Del_p.R456fs|PXK_uc003djy.1_Frame_Shift_Del_p.R439fs|PXK_uc003dka.1_Frame_Shift_Del_p.R456fs|PXK_uc003dkb.1_Frame_Shift_Del_p.R373fs|PXK_uc003dkc.1_Frame_Shift_Del_p.R439fs|PXK_uc011bfe.1_Frame_Shift_Del_p.R423fs|PXK_uc010hnj.1_Frame_Shift_Del_p.R423fs|PXK_uc003dkd.1_Frame_Shift_Del_p.R319fs|PXK_uc010hnk.1_Frame_Shift_Del_p.R230fs NM_017771 NP_060241 Q7Z7A4 PXK_HUMAN PX domain containing serine/threonine kinase 456 Protein kinase. cell communication|inflammatory response|negative regulation of ATPase activity|negative regulation of ion transport|regulation of synaptic transmission centrosome|cytoplasm|nucleus|plasma membrane actin binding|ATP binding|phosphatidylinositol binding|phosphatidylinositol binding|protein C-terminus binding|protein kinase activity ovary(1) 1 BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22) AGGAGGAAAGAAAAAAAAGAA 0.418 0.31 96 43 ATR 545 broad.mit.edu 37 3 142211980 142211980 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr3:142211980delT uc003eux.3 - 35 6194 c.6072delA c.(6070-6072)AAAfs p.K2024fs NM_001184 NP_001175 Q13535 ATR_HUMAN ataxia telangiectasia and Rad3 related protein 2024 FAT. cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence PML body ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1) 20 TTGCCTTATATTTTTTCATAA 0.348 0.27 79 29 PIK3CA 5290 broad.mit.edu 37 3 178927980 178927985 + In_Frame_Del DEL TGTCCA - - rs121913272 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr3:178927980_178927985delTGTCCA uc003fjk.2 + 8 1415_1420 c.1258_1263delTGTCCA c.(1258-1263)TGTCCAdel p.CP420del NM_006218 NP_006209 P42336 PK3CA_HUMAN phosphoinositide-3-kinase, catalytic, alpha 420_421 C2 PI3K-type. epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity p.C420R(26) breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1) 3553 all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155) OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282) TAAGGAACACTGTCCATTGGCATGGG 0.325 0.40 87 58 BMP2K 55589 broad.mit.edu 37 4 79792137 79792145 + In_Frame_Del DEL CAGCAGCAG - - rs17855588 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr4:79792137_79792145delCAGCAGCAG uc003hlk.2 + 11 1598_1606 c.1432_1440delCAGCAGCAG c.(1432-1440)CAGCAGCAGdel p.QQQ484del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQ484del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 484_486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 gcaacagcaacagcagcagcagcagcagc 0.177 0.41 27 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 88 73 MAML3 55534 broad.mit.edu 37 4 140810639 140810641 + In_Frame_Del DEL GCT - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr4:140810639_140810641delGCT uc003ihz.1 - 3 2689_2691 c.1937_1939delAGC c.(1936-1941)CAGCCG>CCG p.Q646del MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 646 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) GGAGGTGGCGgctgctgctgctg 0.419 0.29 37 15 TRIO 7204 broad.mit.edu 37 5 14387555 14387556 + Frame_Shift_Del DEL AG - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr5:14387555_14387556delAG uc003jff.2 + 22 3585_3586 c.3579_3580delAG c.(3577-3582)AAAGAGfs p.K1193fs TRIO_uc003jfg.2_RNA|TRIO_uc011cna.1_Frame_Shift_Del_p.K1144fs|TRIO_uc003jfh.1_Frame_Shift_Del_p.K842fs NM_007118 NP_009049 O75962 TRIO_HUMAN triple functional domain (PTPRF interacting) 1193_1194 Spectrin 4. apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway cytosol ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1) 18 Lung NSC(4;0.000742) AGCAAACCAAAGAGAGAGTGAA 0.446 0.17 152 31 RICTOR 253260 broad.mit.edu 37 5 38950049 38950049 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr5:38950049delG uc003jlp.2 - 31 3925 c.3901delC c.(3901-3903)CAGfs p.Q1301fs RICTOR_uc003jlo.2_Frame_Shift_Del_p.Q1301fs|RICTOR_uc010ivf.2_Frame_Shift_Del_p.Q1016fs NM_152756 NP_689969 Q6R327 RICTR_HUMAN rapamycin-insensitive companion of mTOR 1301 actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation cytosol|TORC2 complex protein binding ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1) 10 all_lung(31;0.000396) TTAAGGGACTGTGCTCTTCTA 0.433 0.42 403 287 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 29 55 COL4A3BP 10087 broad.mit.edu 37 5 74696124 74696125 + Splice_Site INS - A A HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr5:74696124_74696125insA uc011csu.1 - 10 1440 c.1018_splice c.e10-1 p.S340_splice COL4A3BP_uc003kds.2_Splice_Site_p.S340_splice|COL4A3BP_uc003kdt.2_Splice_Site_p.S468_splice|COL4A3BP_uc003kdu.2_Splice_Site_p.S340_splice NM_005713 NP_005704 Q9Y5P4 C43BP_HUMAN alpha 3 type IV collagen binding protein isoform ER to Golgi ceramide transport|immune response cytosol|endoplasmic reticulum membrane|Golgi apparatus ceramide binding|phosphatidylinositol-4-phosphate binding|protein binding|protein kinase activity skin(1) 1 all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174) OV - Ovarian serous cystadenocarcinoma(47;1e-53) ACTCTGTGACTAAAAAAACATA 0.371 0.25 108 36 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.23 193 57 CSNK1G3 1456 broad.mit.edu 37 5 122881495 122881495 + Frame_Shift_Del DEL A - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr5:122881495delA uc003ktm.2 + 2 857 c.138delA c.(136-138)GGAfs p.G46fs CSNK1G3_uc003ktl.2_Frame_Shift_Del_p.G46fs|CSNK1G3_uc003ktn.2_Frame_Shift_Del_p.G46fs|CSNK1G3_uc003kto.2_Frame_Shift_Del_p.G46fs|CSNK1G3_uc011cwr.1_Intron|CSNK1G3_uc011cws.1_Intron|CSNK1G3_uc010jda.2_Frame_Shift_Del_p.G46fs NM_004384 NP_004375 Q9Y6M4 KC1G3_HUMAN casein kinase 1, gamma 3 isoform 1 46 Protein kinase. Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity 0 all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245) KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229) OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176) TTAGAGTTGGAAAAAAAATTG 0.363 0.64 56 98 FBN2 2201 broad.mit.edu 37 5 127610311 127610311 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr5:127610311delC uc003kuu.2 - 60 8098 c.7659delG c.(7657-7659)GGGfs p.G2553fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 2553 EGF-like 43; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) TACAGGTAAACCCCCCCAGGG 0.423 0.15 229 42 PKHD1 5314 broad.mit.edu 37 6 51882388 51882390 + In_Frame_Del DEL TCC - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr6:51882388_51882390delTCC uc003pah.1 - 34 5694_5696 c.5418_5420delGGA c.(5416-5421)GAGGAC>GAC p.E1806del PKHD1_uc003pai.2_In_Frame_Del_p.E1806del NM_138694 NP_619639 P08F94 PKHD1_HUMAN fibrocystin isoform 1 1806 Extracellular (Potential). E -> K (in a colorectal cancer sample; somatic mutation). cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body protein binding|receptor activity p.E1806K(1) lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1) 44 Lung NSC(77;0.0605) CTCACAGCTGTCCTCCTCACGCT 0.522 0.20 141 36 INHBA 3624 broad.mit.edu 37 7 41739907 41739907 + Frame_Shift_Del DEL G - - rs147747702 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr7:41739907delG uc003thq.2 - 1 301 c.66delC c.(64-66)CCCfs p.P22fs LOC285954_uc003tht.3_Intron|INHBA_uc003thr.2_Frame_Shift_Del_p.P22fs|LOC285954_uc003ths.2_Intron NM_002192 NP_002183 P08476 INHBA_HUMAN inhibin beta A precursor 22 cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway activin A complex|inhibin A complex cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity p.P22H(1) lung(5)|ovary(1) 6 ATCCTGGGGTGGGGGAACTCC 0.572 0.52 10 11 PIK3CG 5294 broad.mit.edu 37 7 106513176 106513176 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr7:106513176delT uc003vdv.3 + 4 2165 c.2080delT c.(2080-2082)TTTfs p.F694fs PIK3CG_uc003vdu.2_Frame_Shift_Del_p.F694fs|PIK3CG_uc003vdw.2_Frame_Shift_Del_p.F694fs NM_002649 NP_002640 P48736 PK3CG_HUMAN phosphoinositide-3-kinase, catalytic, gamma 694 G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation phosphatidylinositol 3-kinase complex 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1) 38 AATTGGTCACTTTTTGTTTTG 0.418 0.22 221 61 FOXP2 93986 broad.mit.edu 37 7 114269962 114269964 + In_Frame_Del DEL CAG - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr7:114269962_114269964delCAG uc003vhb.2 + 5 873_875 c.499_501delCAG c.(499-501)CAGdel p.Q191del FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_In_Frame_Del_p.Q216del|FOXP2_uc003vha.2_In_Frame_Del_p.Q99del|FOXP2_uc011kmu.1_In_Frame_Del_p.Q208del|FOXP2_uc011kmv.1_In_Frame_Del_p.Q191del|FOXP2_uc010ljz.1_In_Frame_Del_p.Q99del|FOXP2_uc003vgt.1_RNA|FOXP2_uc003vgv.1_In_Frame_Del_p.Q191del|FOXP2_uc003vgx.2_In_Frame_Del_p.Q191del|FOXP2_uc003vhd.2_In_Frame_Del_p.Q191del|FOXP2_uc003vhc.2_In_Frame_Del_p.Q216del NM_014491 NP_055306 O15409 FOXP2_HUMAN forkhead box P2 isoform I 191 Gln-rich. camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning cytoplasm|transcription factor complex chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1) 8 gcagcaacaacagcagcagcaac 0.158 0.20 35 9 KCNH2 3757 broad.mit.edu 37 7 150644883 150644884 + Frame_Shift_Ins INS - C C HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr7:150644883_150644884insC uc003wic.2 - 12 2788_2789 c.2775_2776insG c.(2773-2778)GGGCCGfs p.G925fs KCNH2_uc003wib.2_Frame_Shift_Ins_p.G585fs|KCNH2_uc011kux.1_Frame_Shift_Ins_p.G829fs NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 925_926 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) 0.000 0.11 655 79 SMARCD3 6604 broad.mit.edu 37 7 150939007 150939007 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr7:150939007delC uc003wjs.2 - 7 834 c.733delG c.(733-735)GACfs p.D245fs SMARCD3_uc003wjt.2_Frame_Shift_Del_p.D232fs|SMARCD3_uc003wju.2_Frame_Shift_Del_p.D232fs|SMARCD3_uc011kvh.1_Frame_Shift_Del_p.D245fs|SMARCD3_uc010lqa.1_Frame_Shift_Del_p.D245fs NM_001003801 NP_001003801 Q6STE5 SMRD3_HUMAN SWI/SNF related, matrix associated, actin 245 cellular lipid metabolic process|chromatin modification|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex nuclear hormone receptor binding|protein binding|transcription coactivator activity|transcription factor binding ovary(1)|lung(1) 2 OV - Ovarian serous cystadenocarcinoma(82;0.00448) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.12 624 88 MLL3 58508 broad.mit.edu 37 7 151902220 151902221 + Frame_Shift_Del DEL AT - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr7:151902220_151902221delAT uc003wla.2 - 25 4150_4151 c.3931_3932delAT c.(3931-3933)ATTfs p.I1311fs MLL3_uc003wkz.2_Frame_Shift_Del_p.I372fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 1311 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) CTGCTCGGAAATAGAGCCTGAG 0.361 0.40 78 53 SGK223 157285 broad.mit.edu 37 8 8175875 8175875 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr8:8175875delC uc003wsh.3 - 5 4010 c.4010delG c.(4009-4011)GGCfs p.G1337fs NM_001080826 NP_001074295 Q86YV5 SG223_HUMAN pragmin 1337 ATP binding|non-membrane spanning protein tyrosine kinase activity 0 CTCCGAGGTGCCCGGCTGCTG 0.672 1.00 0 10 SGK223 157285 broad.mit.edu 37 8 8185880 8185880 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr8:8185880delG uc003wsh.3 - 4 2412 c.2412delC c.(2410-2412)CCCfs p.P804fs NM_001080826 NP_001074295 Q86YV5 SG223_HUMAN pragmin 804 ATP binding|non-membrane spanning protein tyrosine kinase activity 0 GGGGGCCACTGGGGGACACGT 0.632 0.55 10 12 SGK3 23678 broad.mit.edu 37 8 67752239 67752239 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr8:67752239delT uc003xwr.2 + 11 1042 c.743delT c.(742-744)CTTfs p.L248fs SGK3_uc003xwp.2_Frame_Shift_Del_p.L242fs|SGK3_uc003xwt.2_Frame_Shift_Del_p.L248fs|SGK3_uc003xwu.2_Frame_Shift_Del_p.L248fs NM_001033578 NP_001028750 Q96BR1 SGK3_HUMAN serum/glucocorticoid regulated kinase 3 isoform 248 Protein kinase. cell communication|response to stress cytoplasmic membrane-bounded vesicle|early endosome ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity ovary(1)|large_intestine(1)|lung(1)|breast(1) 4 Breast(64;0.186) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206) ATTTGACAGCTTTTTTTCCAC 0.403 0.36 38 21 TRPS1 7227 broad.mit.edu 37 8 116631857 116631857 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr8:116631857delG uc003ynz.2 - 2 888 c.429delC c.(427-429)CCCfs p.P143fs TRPS1_uc011lhy.1_Frame_Shift_Del_p.P147fs|TRPS1_uc003yny.2_Frame_Shift_Del_p.P156fs|TRPS1_uc010mcy.2_Frame_Shift_Del_p.P143fs NM_014112 NP_054831 Q9UHF7 TRPS1_HUMAN zinc finger transcription factor TRPS1 143 negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) AGTCCCCTGAGGGGGTGCAGG 0.532 0.44 123 96 TRIB1 10221 broad.mit.edu 37 8 126443327 126443327 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr8:126443327delC uc003yrx.2 + 1 765 c.183delC c.(181-183)AGCfs p.S61fs TRIB1_uc011lis.1_5'Flank|TRIB1_uc010mdn.2_5'Flank NM_025195 NP_079471 Q96RU8 TRIB1_HUMAN G-protein-coupled receptor induced protein 61 Protein kinase. JNK cascade|negative regulation of lipopolysaccharide-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|regulation of MAP kinase activity|response to lipopolysaccharide cytoplasm|nucleus ATP binding|mitogen-activated protein kinase kinase binding|protein kinase activity|protein kinase inhibitor activity|transcription factor binding|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity lung(1) 1 all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108) STAD - Stomach adenocarcinoma(47;0.000918) 0.000 0.26 532 190 MAPK15 225689 broad.mit.edu 37 8 144803722 144803722 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr8:144803722delC uc003yzj.2 + 12 1249 c.1208delC c.(1207-1209)TCCfs p.S403fs NM_139021 NP_620590 Q8TD08 MK15_HUMAN mitogen-activated protein kinase 15 403 protein autophosphorylation extracellular region ATP binding|MAP kinase activity|SH3 domain binding lung(2) 2 all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146) 0.000 0.19 353 82 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.39 358 227 DAPK1 1612 broad.mit.edu 37 9 90321802 90321802 + Frame_Shift_Del DEL G - - rs56169226 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr9:90321802delG uc004apc.2 + 26 3954 c.3816delG c.(3814-3816)ATGfs p.M1272fs DAPK1_uc004apd.2_Frame_Shift_Del_p.M1272fs|DAPK1_uc011ltg.1_Frame_Shift_Del_p.M1206fs|DAPK1_uc011lth.1_Frame_Shift_Del_p.M1009fs|DAPK1_uc004apg.2_Frame_Shift_Del_p.M249fs NM_004938 NP_004929 P53355 DAPK1_HUMAN death-associated protein kinase 1 1272 apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade actin cytoskeleton|cytoplasm ATP binding|calmodulin binding|protein serine/threonine kinase activity ovary(1)|breast(1) 2 CCAACACCATGGGGGGGTACA 0.582 0.23 23 7 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.13 54 8 GRIN3A 116443 broad.mit.edu 37 9 104433234 104433234 + Frame_Shift_Del DEL C - - rs139560863 byFrequency;by1000genomes HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr9:104433234delC uc004bbp.1 - 3 2061 c.1460delG c.(1459-1461)GGAfs p.G487fs GRIN3A_uc004bbq.1_Frame_Shift_Del_p.G487fs NM_133445 NP_597702 Q8TCU5 NMD3A_HUMAN glutamate receptor, ionotropic, 487 Extracellular (Potential). response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1) 7 Acute lymphoblastic leukemia(62;0.0568) Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740) 0.000 0.39 282 183 SMC2 10592 broad.mit.edu 37 9 106862450 106862450 + Frame_Shift_Del DEL A - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr9:106862450delA uc004bbv.2 + 6 845 c.557delA c.(556-558)GAAfs p.E186fs SMC2_uc004bbu.1_Frame_Shift_Del_p.E186fs|SMC2_uc004bbw.2_Frame_Shift_Del_p.E186fs|SMC2_uc011lvl.1_Frame_Shift_Del_p.E186fs|SMC2_uc010mtg.1_Frame_Shift_Del_p.E41fs|SMC2_uc010mth.1_Frame_Shift_Del_p.E136fs|SMC2_uc004bbx.2_Frame_Shift_Del_p.E186fs NM_001042551 NP_001036016 O95347 SMC2_HUMAN structural maintenance of chromosomes 2 186 Potential. cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism condensin complex|cytoplasm|nuclear chromosome ATP binding|protein heterodimerization activity p.E186K(1) ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1) 9 AAAACTATAGAAAAAAAGGAG 0.299 0.35 13 7 PKN3 29941 broad.mit.edu 37 9 131482673 131482675 + In_Frame_Del DEL ACC - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr9:131482673_131482675delACC uc004bvw.2 + 22 2851_2853 c.2458_2460delACC c.(2458-2460)ACCdel p.T821del PKN3_uc010myh.2_In_Frame_Del_p.H806del|PKN3_uc011mbk.1_In_Frame_Del_p.T371del NM_013355 NP_037487 Q6P5Z2 PKN3_HUMAN protein kinase PKNbeta 821 AGC-kinase C-terminal. signal transduction Golgi apparatus|nucleus|perinuclear region of cytoplasm ATP binding|protein binding|protein kinase C activity stomach(2)|lung(2) 4 TTGCCCTCAGACCACCAACTGGC 0.665 0.92 3 33 MYST4 23522 broad.mit.edu 37 10 76744938 76744938 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr10:76744938delT uc001jwn.1 + 12 2967 c.2474delT c.(2473-2475)CTTfs p.L825fs MYST4_uc001jwm.1_Frame_Shift_Del_p.L533fs|MYST4_uc001jwo.1_Frame_Shift_Del_p.L533fs|MYST4_uc001jwp.1_Frame_Shift_Del_p.L642fs NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 825 Catalytic.|Interaction with BRPF1. histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) GAGCCATTCCTTTTTTATGTC 0.378 0.17 223 46 PTEN 5728 broad.mit.edu 37 10 89720712 89720712 + Frame_Shift_Del DEL A - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr10:89720712delA uc001kfb.2 + 9 1894 c.863delA c.(862-864)GAAfs p.E288fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 288 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.E288fs*3(6)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.E288*(2)|p.G165_*404del(1)|p.S287fs*1(1)|p.G165_K342del(1)|p.E288fs*8(1)|p.S287fs*8(1)|p.W274_F341del(1)|p.E288K(1)|p.E288fs*9(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GAAACCTCAGAAAAAGTAGAA 0.299 0.56 43 54 TNKS2 80351 broad.mit.edu 37 10 93604782 93604783 + Frame_Shift_Ins INS - G G rs145701051 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr10:93604782_93604783insG uc001khp.2 + 17 2463_2464 c.2166_2167insG c.(2164-2169)TACGGGfs p.Y722fs NM_025235 NP_079511 Q9H2K2 TNKS2_HUMAN tankyrase, TRF1-interacting ankyrin-related 722_723 ANK 14. positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm NAD+ ADP-ribosyltransferase activity|protein binding kidney(3)|skin(3)|ovary(1)|lung(1) 8 Colorectal(252;0.162) CAGCATCTTACGGGGTAAGTTC 0.317 0.67 47 95 NLRP6 171389 broad.mit.edu 37 11 280601 280601 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr11:280601delC uc010qvs.1 + 4 867 c.867delC c.(865-867)GGCfs p.G289fs NLRP6_uc010qvt.1_Frame_Shift_Del_p.G289fs NM_138329 NP_612202 P59044 NALP6_HUMAN NLR family, pyrin domain containing 6 289 NACHT. cytoplasm ATP binding upper_aerodigestive_tract(1)|skin(1) 2 all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122) 0.000 0.23 317 95 NUP98 4928 broad.mit.edu 37 11 3720492 3720492 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr11:3720492delG uc001lyh.2 - 25 4120 c.3829delC c.(3829-3831)CGTfs p.R1277fs NUP98_uc001lyi.2_Frame_Shift_Del_p.R1277fs|NUP98_uc001lyg.2_Frame_Shift_Del_p.R242fs NM_016320 NP_057404 P52948 NUP98_HUMAN nucleoporin 98kD isoform 1 1294 carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex protein binding|structural constituent of nuclear pore|transporter activity breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1) 12 Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227) BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199) ATGTATTCACGGGGTTCATTT 0.343 0.45 64 52 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.40 9 6 ANO1 55107 broad.mit.edu 37 11 70007346 70007346 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr11:70007346delC uc001opj.2 + 17 1963 c.1658delC c.(1657-1659)TCCfs p.S553fs ANO1_uc001opk.1_Frame_Shift_Del_p.S495fs|ANO1_uc001opl.1_RNA|ANO1_uc010rqk.1_Frame_Shift_Del_p.S262fs NM_018043 NP_060513 Q5XXA6 ANO1_HUMAN anoctamin 1, calcium activated chloride channel 553 Extracellular (Potential). multicellular organismal development chloride channel complex|cytoplasm|plasma membrane intracellular calcium activated chloride channel activity ovary(1)|pancreas(1) 2 0.000 0.39 449 291 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 211 35 MAML2 84441 broad.mit.edu 37 11 96075011 96075011 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr11:96075011delC uc001pfw.1 - 1 1334 c.49delG c.(49-51)GCCfs p.A17fs NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 17 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) GCCCCAGAGGCCCCCCCTAGC 0.677 0.42 23 17 ARHGEF12 23365 broad.mit.edu 37 11 120335991 120335991 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr11:120335991delT uc001pxl.1 + 28 2666 c.2659delT c.(2659-2661)TTTfs p.F887fs ARHGEF12_uc009zat.2_Frame_Shift_Del_p.F868fs|ARHGEF12_uc010rzn.1_Frame_Shift_Del_p.F784fs|ARHGEF12_uc009zau.1_Frame_Shift_Del_p.F784fs NM_015313 NP_056128 Q9NZN5 ARHGC_HUMAN Rho guanine nucleotide exchange factor (GEF) 12 887 DH. apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|membrane G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity lung(2)|breast(2)|skin(2)|ovary(1) 7 Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231) TGCTGCTACCTTTTGCAGTAA 0.428 0.25 74 25 ZNF384 171017 broad.mit.edu 37 12 6777070 6777078 + In_Frame_Del DEL TGCTGCTGC - - rs151322806;rs111332695;rs78573212;rs1052680;rs149757410 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr12:6777070_6777078delTGCTGCTGC uc010sfh.1 - 11 1744_1752 c.1536_1544delGCAGCAGCA c.(1534-1545)CAGCAGCAGCAA>CAA p.512_515QQQQ>Q ZNF384_uc001qpz.2_In_Frame_Del_p.451_454QQQQ>Q|ZNF384_uc001qqa.2_In_Frame_Del_p.451_454QQQQ>Q|ZNF384_uc001qqb.2_In_Frame_Del_p.435_438QQQQ>Q|ZNF384_uc001qqc.2_In_Frame_Del_p.451_454QQQQ>Q|ZNF384_uc001qqd.2_In_Frame_Del_p.396_399QQQQ>Q|ZNF384_uc001qqe.2_In_Frame_Del_p.435_438QQQQ>Q NM_001135734 NP_001129206 Q8TF68 ZN384_HUMAN nuclear matrix transcription factor 4 isoform d 512_515 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding EWSR1/ZNF384(4) haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1) 8 TGGTGgctgttgctgctgctgctgctgct 0.330 0.11 58 7 WNT1 7471 broad.mit.edu 37 12 49374348 49374348 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr12:49374348delG uc001rsu.2 + 3 698 c.500delG c.(499-501)TGGfs p.W167fs NM_005430 NP_005421 P04628 WNT1_HUMAN wingless-type MMTV integration site family, 167 brain segmentation|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|central nervous system morphogenesis|cerebellum formation|dermatome development|diencephalon development|embryonic axis specification|forebrain anterior/posterior pattern formation|fourth ventricle development|hemopoietic stem cell proliferation|hepatocyte differentiation|inner ear morphogenesis|mesoderm morphogenesis|midbrain development|midbrain-hindbrain boundary maturation during brain development|negative regulation of cell-cell adhesion|negative regulation of cell-substrate adhesion|negative regulation of DNA damage checkpoint|negative regulation of fat cell differentiation|neuron fate determination|positive regulation of fibroblast proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of lamellipodium assembly|positive regulation of Notch signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to wounding|signal transduction in response to DNA damage|Spemann organizer formation|T cell differentiation in thymus|Wnt receptor signaling pathway, calcium modulating pathway early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix cytokine activity|frizzled-2 binding|transcription regulatory region DNA binding kidney(1) 1 BRCA - Breast invasive adenocarcinoma(357;0.244) gACTGGCACTGGGGGGGCTGC 0.552 0.33 8 4 LRP1 4035 broad.mit.edu 37 12 57603940 57603940 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr12:57603940delC uc001snd.2 + 81 13034 c.12568delC c.(12568-12570)CCCfs p.P4190fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 4190 Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CTCTCCAACGCCCCCCCCAGA 0.637 0.28 39 15 NAV3 89795 broad.mit.edu 37 12 78594273 78594274 + Frame_Shift_Ins INS - G G HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr12:78594273_78594274insG uc001syp.2 + 38 6909_6910 c.6736_6737insG c.(6736-6738)TGCfs p.C2246fs NAV3_uc001syo.2_Frame_Shift_Ins_p.C2224fs|NAV3_uc010sub.1_Frame_Shift_Ins_p.C1703fs|NAV3_uc009zsf.2_Frame_Shift_Ins_p.C1055fs NM_014903 NP_055718 Q8IVL0 NAV3_HUMAN neuron navigator 3 2246 nuclear outer membrane ATP binding|nucleoside-triphosphatase activity large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 17 ATTCCTTCCTTGCCCCATGGAT 0.356 0.28 107 42 ACACB 32 broad.mit.edu 37 12 109671600 109671600 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr12:109671600delC uc001tob.2 + 30 4306 c.4187delC c.(4186-4188)ACCfs p.T1396fs ACACB_uc001toc.2_Frame_Shift_Del_p.T1396fs|ACACB_uc010sxl.1_RNA|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Frame_Shift_Del_p.T62fs NM_001093 NP_001084 O00763 ACACB_HUMAN acetyl-Coenzyme A carboxylase beta 1396 acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation cytosol|endomembrane system|Golgi apparatus|membrane acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1) 8 Biotin(DB00121) CCCAAAGACACCCCCCTCTTC 0.612 0.24 148 47 CIT 11113 broad.mit.edu 37 12 120220384 120220385 + Frame_Shift_Ins INS - T T HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr12:120220384_120220385insT uc001txi.1 - 13 1655_1656 c.1602_1603insA c.(1600-1605)AAAGCAfs p.K534fs CIT_uc001txh.1_Frame_Shift_Ins_p.K68fs|CIT_uc001txj.1_Frame_Shift_Ins_p.K534fs NM_007174 NP_009105 O14578 CTRO_HUMAN citron 534_535 Potential. intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) AGCTGCAGTGCTTTGTCATCCT 0.520 0.33 41 20 P2RX7 5027 broad.mit.edu 37 12 121600317 121600317 + Frame_Shift_Del DEL C - - rs61745024 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr12:121600317delC uc001tzm.2 + 5 623 c.527delC c.(526-528)GCCfs p.A176fs P2RX7_uc001tzn.2_Frame_Shift_Del_p.A86fs|P2RX7_uc001tzo.2_RNA|P2RX7_uc001tzp.2_5'UTR|P2RX7_uc001tzq.2_Intron NM_002562 NP_002553 Q99572 P2RX7_HUMAN purinergic receptor P2X7 176 integral to membrane ATP binding|ion channel activity|receptor activity large_intestine(2)|lung(1)|breast(1)|skin(1) 5 all_neural(191;0.0684)|Medulloblastoma(191;0.0922) GTGGAAGAGGCCCCCCGGTGA 0.612 0.68 25 52 POLE 5426 broad.mit.edu 37 12 133245024 133245024 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr12:133245024delG uc001uks.1 - 19 2135 c.2091delC c.(2089-2091)CCCfs p.P697fs POLE_uc010tbq.1_RNA|POLE_uc009zyu.1_Frame_Shift_Del_p.P670fs NM_006231 NP_006222 Q07864 DPOE1_HUMAN DNA-directed DNA polymerase epsilon 697 base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair nucleoplasm chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding ovary(3)|skin(3)|lung(1)|central_nervous_system(1) 8 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.0416) OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05) 0.000 0.37 290 167 FOXO1 2308 broad.mit.edu 37 13 41134007 41134007 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr13:41134007delG uc001uxl.3 - 2 2006 c.1621delC c.(1621-1623)CACfs p.H541fs FOXO1_uc010acc.1_Frame_Shift_Del_p.H356fs NM_002015 NP_002006 Q12778 FOXO1_HUMAN forkhead box O1 541 anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding PAX3/FOXO1(749)|PAX7/FOXO1(197) soft_tissue(946)|lung(1)|central_nervous_system(1) 948 Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194) all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815) CTTACCGTGTGGGGCAGGGGA 0.577 0.47 28 25 RCBTB2 1102 broad.mit.edu 37 13 49086154 49086154 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr13:49086154delC uc001vch.2 - 8 1044 c.673delG c.(673-675)GAGfs p.E225fs RCBTB2_uc010tgg.1_Frame_Shift_Del_p.E230fs|RCBTB2_uc001vci.2_Frame_Shift_Del_p.E201fs|RCBTB2_uc010tgh.1_5'UTR|RCBTB2_uc001vcj.2_Frame_Shift_Del_p.E229fs|RCBTB2_uc010acv.1_RNA|RCBTB2_uc010tgi.1_Frame_Shift_Del_p.E201fs NM_001268 NP_001259 O95199 RCBT2_HUMAN regulator of chromosome condensation and BTB 225 RCC1 4. Ran guanyl-nucleotide exchange factor activity ovary(2)|lung(2)|skin(1) 5 all_cancers(8;4.86e-71)|all_epithelial(8;2.11e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;2.3e-10)|Lung NSC(96;1.07e-07)|Breast(56;1.53e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.00826)|Myeloproliferative disorder(33;0.0179)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(99;1.8e-09)|LUSC - Lung squamous cell carcinoma(3;0.116) TTCCTTACCTCCCCCGTGTCT 0.468 0.40 86 58 DACH1 1602 broad.mit.edu 37 13 72440403 72440403 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr13:72440403delG uc010thn.1 - 2 922 c.499delC c.(499-501)CTCfs p.L167fs DACH1_uc010tho.1_Frame_Shift_Del_p.L167fs|DACH1_uc010thp.1_Frame_Shift_Del_p.L167fs NM_080759 NP_542937 Q9UI36 DACH1_HUMAN dachshund homolog 1 isoform a 167 multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus DNA binding|nucleotide binding|protein binding breast(1) 1 Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198) GBM - Glioblastoma multiforme(99;0.00032) TTCCCGGGGAGGGGGCCGCAg 0.348 0.38 18 11 EDNRB 1910 broad.mit.edu 37 13 78475267 78475267 + Frame_Shift_Del DEL A - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr13:78475267delA uc001vko.2 - 4 1135 c.877delT c.(877-879)TATfs p.Y293fs EDNRB_uc001vkq.1_Frame_Shift_Del_p.Y293fs|uc001vkn.1_Intron|EDNRB_uc010aez.1_Frame_Shift_Del_p.Y293fs|EDNRB_uc001vkp.1_Frame_Shift_Del_p.Y376fs NM_001122659 NP_001116131 P24530 EDNRB_HUMAN endothelin receptor type B isoform 1 precursor 293 Helical; Name=5; (Potential). activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction integral to plasma membrane endothelin-B receptor activity|peptide hormone binding 0 Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037) GBM - Glioblastoma multiforme(99;0.0933) Bosentan(DB00559) ATTAGTGTATAAAAAAATGCA 0.343 0.44 39 31 RASA3 22821 broad.mit.edu 37 13 114780718 114780720 + In_Frame_Del DEL AGA - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr13:114780718_114780720delAGA uc001vui.2 - 14 1501_1503 c.1370_1372delTCT c.(1369-1374)TTCTCC>TCC p.F457del RASA3_uc010tkk.1_In_Frame_Del_p.F425del|RASA3_uc001vuj.2_In_Frame_Del_p.F74del NM_007368 NP_031394 Q14644 RASA3_HUMAN RAS p21 protein activator 3 457 Ras-GAP. intracellular signal transduction|negative regulation of Ras protein signal transduction cytoplasm|intrinsic to internal side of plasma membrane calcium-release channel activity|metal ion binding|Ras GTPase activator activity lung(3)|skin(1) 4 Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218) all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188) BRCA - Breast invasive adenocarcinoma(86;0.128) TCCCGGAGGGAGAAGAAGATGTC 0.616 0.88 2 15 CHD8 57680 broad.mit.edu 37 14 21884030 21884031 + Frame_Shift_Ins INS - T T HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr14:21884030_21884031insT uc001was.1 - 6 1009_1010 c.915_916insA c.(913-918)AAATATfs p.K305fs CHD8_uc001war.1_Frame_Shift_Ins_p.K201fs NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 584_585 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) TCCTCTGTATATTTTTTTCGCT 0.396 0.19 166 40 NOVA1 4857 broad.mit.edu 37 14 27066542 27066542 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr14:27066542delG uc001wpy.2 - 1 419 c.101delC c.(100-102)CCTfs p.P34fs NOVA1_uc001wpz.2_Frame_Shift_Del_p.P34fs|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_Frame_Shift_Del_p.P34fs NM_002515 NP_002506 P51513 NOVA1_HUMAN neuro-oncological ventral antigen 1 isoform 1 34 Bipartite nuclear localization signal (Potential). locomotory behavior|RNA splicing|synaptic transmission nucleus RNA binding skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1) 5 GBM - Glioblastoma multiforme(265;0.0135) 0.000 0.81 153 643 NKX2-1 7080 broad.mit.edu 37 14 36988334 36988334 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr14:36988334delG uc001wtt.2 - 1 570 c.229delC c.(229-231)CAGfs p.Q77fs SFTA3_uc001wts.2_Intron|NKX2-1_uc001wtu.2_Frame_Shift_Del_p.Q107fs|NKX2-1_uc001wtv.2_Frame_Shift_Del_p.Q77fs|uc001wtw.1_5'Flank NM_003317 NP_003308 P43699 NKX21_HUMAN thyroid transcription factor 1 isoform 2 77 epithelial tube branching involved in lung morphogenesis|globus pallidus development|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|thyroid gland development protein binding|transcription regulatory region DNA binding skin(1) 1 all_cancers(3;4.47e-51)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.165) Lung(8;1.8e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.014)|all cancers(34;0.0366)|LUSC - Lung squamous cell carcinoma(13;0.132) GBM - Glioblastoma multiforme(112;0.0171) 0.000 0.50 216 217 NIN 51199 broad.mit.edu 37 14 51237236 51237236 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr14:51237236delT uc001wym.2 - 12 1495 c.1304delA c.(1303-1305)AATfs p.N435fs NIN_uc001wyi.2_Frame_Shift_Del_p.N435fs|NIN_uc001wyj.2_RNA|NIN_uc001wyk.2_Frame_Shift_Del_p.N435fs|NIN_uc010tqp.1_Frame_Shift_Del_p.N441fs|NIN_uc001wyo.2_Frame_Shift_Del_p.N435fs|NIN_uc001wyp.1_Frame_Shift_Del_p.N397fs NM_182946 NP_891991 Q8N4C6 NIN_HUMAN ninein isoform 5 435 Potential. centrosome localization centrosome|microtubule calcium ion binding|GTP binding|protein binding skin(3)|ovary(1)|kidney(1)|central_nervous_system(1) 6 all_epithelial(31;0.00244)|Breast(41;0.127) TCGGAGTTCATTTTTTAAGGC 0.438 0.67 189 384 TRIP11 9321 broad.mit.edu 37 14 92466331 92466331 + Frame_Shift_Del DEL T - - rs142039167 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr14:92466331delT uc001xzy.2 - 12 5467 c.4679delA c.(4678-4680)AATfs p.N1560fs TRIP11_uc010auf.1_Frame_Shift_Del_p.N1296fs NM_004239 NP_004230 Q15643 TRIPB_HUMAN thyroid hormone receptor interactor 11 1560 Potential. transcription from RNA polymerase II promoter cytoskeleton|Golgi apparatus|membrane|nucleus protein binding|transcription coactivator activity ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1) 13 COAD - Colon adenocarcinoma(157;0.223) TAGGGCAGTATTTTCCATTTG 0.343 0.22 222 63 TRIP11 9321 broad.mit.edu 37 14 92480823 92480823 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr14:92480823delT uc001xzy.2 - 7 1710 c.922delA c.(922-924)ATGfs p.M308fs TRIP11_uc010auf.1_Frame_Shift_Del_p.M73fs NM_004239 NP_004230 Q15643 TRIPB_HUMAN thyroid hormone receptor interactor 11 308 Potential. transcription from RNA polymerase II promoter cytoskeleton|Golgi apparatus|membrane|nucleus protein binding|transcription coactivator activity ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1) 13 COAD - Colon adenocarcinoma(157;0.223) AGTTGTTCCATTTTTTTGGTA 0.299 0.19 161 38 KIAA1409 57578 broad.mit.edu 37 14 94046589 94046589 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr14:94046589delG uc001ybv.1 + 16 2080 c.1997delG c.(1996-1998)TGGfs p.W666fs KIAA1409_uc001ybs.1_Frame_Shift_Del_p.W666fs NM_020818 NP_065869 Q9P2D8 UNC79_HUMAN hypothetical protein LOC57578 843 integral to membrane p.I654_H670del(1) ovary(10)|skin(4)|large_intestine(3) 17 all_cancers(154;0.0354)|all_epithelial(191;0.216) Epithelial(152;0.188) CAAGCCCCCTGGGGGGGATCC 0.448 0.16 281 52 HSP90AA1 3320 broad.mit.edu 37 14 102551161 102551163 + In_Frame_Del DEL TCT - - rs55793809 byFrequency;by1000genomes HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr14:102551161_102551163delTCT uc001yku.3 - 5 1026_1028 c.836_838delAGA c.(835-840)AAGATT>ATT p.K279del HSP90AA1_uc001ykv.3_In_Frame_Del_p.K401del|HSP90AA1_uc001ykw.1_In_Frame_Del_p.K100del|HSP90AA1_uc001ykx.1_In_Frame_Del_p.K268del NM_005348 NP_005339 P07900 HS90A_HUMAN heat shock 90kDa protein 1, alpha isoform 2 279 axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction cytosol|melanosome|plasma membrane ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding ovary(2)|central_nervous_system(2)|prostate(1)|lung(1)|breast(1) 7 Rifabutin(DB00615) ttttccttaatcttcttcttctt 0.256 0.11 443 57 ATP10A 57194 broad.mit.edu 37 15 25924712 25924712 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr15:25924712delG uc010ayu.2 - 21 4382 c.4276delC c.(4276-4278)CTGfs p.L1426fs NM_024490 NP_077816 O60312 AT10A_HUMAN ATPase, class V, type 10A 1426 Cytoplasmic (Potential). ATP biosynthetic process|regulation of cell shape integral to membrane|plasma membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity pancreas(2)|ovary(1)|breast(1)|liver(1) 5 all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125) all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244) AGGGAAGACAGGGGGGTCACC 0.622 0.22 29 8 HERC2 8924 broad.mit.edu 37 15 28361981 28361981 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr15:28361981delC uc001zbj.2 - 88 13545 c.13439delG c.(13438-13440)GGCfs p.G4480fs HERC2_uc001zbi.2_Frame_Shift_Del_p.G169fs NM_004667 NP_004658 O95714 HERC2_HUMAN hect domain and RLD 2 4480 HECT. DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process nucleus guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1) 13 all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227) all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199) GCTGTAGCCGCCCCCACAGTC 0.602 0.21 26 7 MGA 23269 broad.mit.edu 37 15 41961546 41961547 + Frame_Shift_Ins INS - TT TT HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr15:41961546_41961547insTT uc001zog.1 + 2 545_546 c.454_455insTT c.(454-456)GTTfs p.V152fs MGA_uc010ucy.1_Frame_Shift_Ins_p.V152fs|MGA_uc010ucz.1_Frame_Shift_Ins_p.V152fs NM_001080541 NP_001074010 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 2 152 T-box. MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) TGAACCTCATGTTTTGGGGAGG 0.401 0.28 298 114 FANCI 55215 broad.mit.edu 37 15 89850742 89850742 + Frame_Shift_Del DEL A - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr15:89850742delA uc010bnp.1 + 33 3663 c.3573delA c.(3571-3573)CCAfs p.P1191fs FANCI_uc002bnm.1_Frame_Shift_Del_p.P1131fs|FANCI_uc002bnn.1_RNA|FANCI_uc002bnp.1_Frame_Shift_Del_p.P951fs|FANCI_uc002bnq.1_Frame_Shift_Del_p.P604fs NM_001113378 NP_001106849 Q9NVI1 FANCI_HUMAN Fanconi anemia, complementation group I isoform 1191 cell cycle|DNA repair nucleoplasm protein binding ovary(2) 2 Lung NSC(78;0.0472)|all_lung(78;0.089) GAGGAATTCCAAAAAATATGG 0.423 0.32 54 25 FUS 2521 broad.mit.edu 37 16 31202376 31202376 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr16:31202376delG uc002ebf.2 + 14 1569 c.1486delG c.(1486-1488)GGGfs p.G496fs FUS_uc002ebh.2_Frame_Shift_Del_p.G495fs|FUS_uc002ebg.2_Frame_Shift_Del_p.G291fs|FUS_uc002ebi.2_Frame_Shift_Del_p.G497fs|FUS_uc002ebj.2_Frame_Shift_Del_p.G292fs NM_004960 NP_004951 P35637 FUS_HUMAN fusion (involved in t(12;16) in malignant 496 Arg/Gly-rich. cell death|nuclear mRNA splicing, via spliceosome nucleoplasm DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding FUS/DDIT3(623)|FUS/ERG(163)|FUS/CREB3L2(158)|FUS/CREB3L1(6)|FUS/ATF1(4)|FUS/FEV(2) soft_tissue(791)|haematopoietic_and_lymphoid_tissue(153)|bone(12)|breast(2) 958 Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121) GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209) AGGCTTCCGAGGGGGCCGGGG 0.592 0.41 16 11 CHD9 80205 broad.mit.edu 37 16 53190448 53190449 + Frame_Shift_Del DEL TA - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr16:53190448_53190449delTA uc002ehb.2 + 1 611_612 c.447_448delTA c.(445-450)TCTATGfs p.S149fs CHD9_uc002egy.2_Frame_Shift_Del_p.S149fs|CHD9_uc002egz.1_Frame_Shift_Del_p.S149fs|CHD9_uc002eha.1_Frame_Shift_Del_p.S149fs|CHD9_uc002ehc.2_Frame_Shift_Del_p.S149fs NM_025134 NP_079410 Q3L8U1 CHD9_HUMAN chromodomain helicase DNA binding protein 9 149_150 cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleoplasm ATP binding|DNA binding|helicase activity|protein binding lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1) 7 all_cancers(37;0.0212) ATTCACACTCTATGCATCAAAA 0.416 0.28 101 40 CHD9 80205 broad.mit.edu 37 16 53358641 53358643 + In_Frame_Del DEL AAG - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr16:53358641_53358643delAAG uc002ehb.2 + 38 8692_8694 c.8528_8530delAAG c.(8527-8532)AAAGAA>AAA p.E2845del CHD9_uc002egy.2_In_Frame_Del_p.E2829del|CHD9_uc002ehc.2_In_Frame_Del_p.E2830del|CHD9_uc002ehf.2_In_Frame_Del_p.E1943del|CHD9_uc010cbw.2_In_Frame_Del_p.E911del NM_025134 NP_079410 Q3L8U1 CHD9_HUMAN chromodomain helicase DNA binding protein 9 2845 cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleoplasm ATP binding|DNA binding|helicase activity|protein binding lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1) 7 all_cancers(37;0.0212) GTAGAAGTAAAAGAAGAAGATTC 0.399 0.39 51 33 GSG2 83903 broad.mit.edu 37 17 3628298 3628298 + Frame_Shift_Del DEL A - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr17:3628298delA uc002fwp.2 + 1 1102 c.1069delA c.(1069-1071)AAAfs p.K357fs ITGAE_uc002fwo.3_Intron|ITGAE_uc002fwn.3_5'Flank NM_031965 NP_114171 Q8TF76 HASP_HUMAN haspin 357 cell cycle|chromatin modification|intracellular protein kinase cascade nucleus ATP binding|protein serine/threonine kinase activity 0 CCACCGCTTTAAAAAGGGCCA 0.502 0.33 57 28 MYH10 4628 broad.mit.edu 37 17 8526464 8526464 + Frame_Shift_Del DEL T - - rs147363284 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr17:8526464delT uc002gll.2 - 2 197 c.101delA c.(100-102)AAGfs p.K34fs MYH10_uc002glm.2_Frame_Shift_Del_p.K34fs|MYH10_uc010cnx.2_Frame_Shift_Del_p.K34fs NM_005964 NP_005955 P35580 MYH10_HUMAN myosin, heavy polypeptide 10, non-muscle 34 Myosin head-like. actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape cell cortex|cleavage furrow|midbody|myosin complex|stress fiber actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity ovary(2) 2 CCACACTAGCTTTTTAGCTGT 0.488 0.34 224 115 SUZ12 23512 broad.mit.edu 37 17 30300238 30300239 + Frame_Shift_Ins INS - A A HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr17:30300238_30300239insA uc002hgs.2 + 6 801_802 c.579_580insA c.(577-582)CACAAAfs p.H193fs SUZ12_uc002hgt.2_Frame_Shift_Ins_p.H170fs NM_015355 NP_056170 Q15022 SUZ12_HUMAN joined to JAZF1 193_194 negative regulation of cell differentiation|transcription, DNA-dependent ESC/E(Z) complex histone methyltransferase activity|methylated histone residue binding|zinc ion binding JAZF1/SUZ12(131) soft_tissue(98)|endometrium(33) 131 Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231) AAGTTTGCCACAAAAAAAGAAA 0.282 0.50 5 5 WNK4 65266 broad.mit.edu 37 17 40939870 40939870 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr17:40939870delG uc002ibj.2 + 8 1837 c.1816delG c.(1816-1818)GGGfs p.G606fs WNK4_uc010wgx.1_Frame_Shift_Del_p.G270fs|WNK4_uc002ibk.1_Frame_Shift_Del_p.G378fs|WNK4_uc010wgy.1_Intron NM_032387 NP_115763 Q96J92 WNK4_HUMAN WNK lysine deficient protein kinase 4 606 intracellular protein kinase cascade tight junction ATP binding|protein serine/threonine kinase activity ovary(3)|skin(3)|stomach(1) 7 Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.0749) TCAGCCCCCTGGGGGGGTGCC 0.637 0.47 47 41 MYST2 11143 broad.mit.edu 37 17 47874140 47874141 + Frame_Shift_Del DEL TT - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr17:47874140_47874141delTT uc002ipm.2 + 3 318_319 c.192_193delTT c.(190-195)TCTTTTfs p.S64fs MYST2_uc002ipl.1_Frame_Shift_Del_p.S64fs|MYST2_uc010wma.1_Intron|MYST2_uc010wmb.1_Frame_Shift_Del_p.S64fs|MYST2_uc010wmc.1_Intron|MYST2_uc010wmd.1_5'UTR|MYST2_uc010wme.1_5'UTR NM_007067 NP_008998 O95251 MYST2_HUMAN MYST histone acetyltransferase 2 64_65 DNA replication|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation histone acetyltransferase complex histone acetyltransferase activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1)|lung(1)|skin(1) 3 ATCTGCAGTCTTTTGGCACTGA 0.421 0.20 163 40 PPM1D 8493 broad.mit.edu 37 17 58740623 58740624 + Frame_Shift_Ins INS - A A HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr17:58740623_58740624insA uc002iyt.1 + 6 1750_1751 c.1528_1529insA c.(1528-1530)CAAfs p.Q510fs PPM1D_uc010ddm.1_RNA NM_003620 NP_003611 O15297 PPM1D_HUMAN protein phosphatase 1D 510 negative regulation of cell proliferation|protein dephosphorylation|response to radiation nucleus|protein serine/threonine phosphatase complex metal ion binding|protein binding|protein serine/threonine phosphatase activity upper_aerodigestive_tract(1) 1 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) Epithelial(12;6.75e-12)|all cancers(12;1.96e-10) 0.000 0.34 390 201 ASPSCR1 79058 broad.mit.edu 37 17 79943427 79943428 + Frame_Shift_Del DEL CT - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr17:79943427_79943428delCT uc002kcx.2 + 4 415_416 c.318_319delCT c.(316-321)GACTCTfs p.D106fs ASPSCR1_uc002kcw.1_Frame_Shift_Del_p.D106fs|ASPSCR1_uc002kcy.2_Frame_Shift_Del_p.D106fs|ASPSCR1_uc002kcz.2_Frame_Shift_Del_p.D106fs|ASPSCR1_uc002kda.2_Frame_Shift_Del_p.D29fs|ASPSCR1_uc002kdb.1_Frame_Shift_Del_p.D29fs NM_024083 NP_076988 Q9BZE9 ASPC1_HUMAN alveolar soft part sarcoma chromosome region, 106_107 protein binding ASPSCR1/TFE3(161) soft_tissue(118)|kidney(43)|breast(1) 162 all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246) BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191) GGTTGCAGGACTCTTTCTGTTC 0.525 0.55 120 148 CSNK1D 1453 broad.mit.edu 37 17 80206876 80206876 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr17:80206876delG uc002kej.2 - 8 1388 c.1072delC c.(1072-1074)CGGfs p.R358fs SLC16A3_uc002kee.2_Intron|CSNK1D_uc002kef.2_Frame_Shift_Del_p.R358fs|CSNK1D_uc002kei.2_Frame_Shift_Del_p.R358fs|CSNK1D_uc010wvj.1_Frame_Shift_Del_p.R155fs|CSNK1D_uc010dil.2_RNA|CSNK1D_uc002keh.2_Frame_Shift_Del_p.R223fs NM_001893 NP_001884 P48730 KC1D_HUMAN casein kinase 1, delta isoform 1 358 circadian regulation of gene expression|DNA repair|G2/M transition of mitotic cell cycle|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|regulation of circadian rhythm|Wnt receptor signaling pathway centrosome|cytosol|nucleus ATP binding|protein binding|protein serine/threonine kinase activity breast(2) 2 Breast(20;0.00136)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227) OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0155) GAGACGGGCCGGGGGGAGGTG 0.652 0.50 8 8 KIAA0802 23255 broad.mit.edu 37 18 8783591 8783591 + Frame_Shift_Del DEL A - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr18:8783591delA uc002knr.2 + 6 623 c.481delA c.(481-483)AAAfs p.K161fs KIAA0802_uc002knq.2_Frame_Shift_Del_p.K161fs|KIAA0802_uc010dkw.1_5'UTR NM_015210 NP_056025 Q9Y4B5 CC165_HUMAN hypothetical protein LOC23255 512 Potential. 0 0.000 0.59 232 329 SMAD7 4092 broad.mit.edu 37 18 46474795 46474795 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr18:46474795delG uc002ldg.2 - 2 913 c.626delC c.(625-627)CCTfs p.P209fs SMAD7_uc010xde.1_5'UTR NM_005904 NP_005895 O15105 SMAD7_HUMAN SMAD family member 7 209 Poly-Pro.|PY-motif.|Important for interaction with SMURF2. Missing: Diminishes interaction with SMURF2. adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding 0 Colorectal(1;0.0518) GGAGTAAGGAGGGGGGGGAGA 0.388 0.36 36 20 ALPK2 115701 broad.mit.edu 37 18 56246440 56246440 + Frame_Shift_Del DEL T - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr18:56246440delT uc002lhj.3 - 4 1782 c.1568delA c.(1567-1569)AAGfs p.K523fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 523 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 CCATAAGTCCTTTCCCCCCAC 0.522 0.24 234 72 HIPK4 147746 broad.mit.edu 37 19 40889752 40889752 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr19:40889752delG uc002onp.2 - 2 1045 c.760delC c.(760-762)CACfs p.H254fs NM_144685 NP_653286 Q8NE63 HIPK4_HUMAN homeodomain interacting protein kinase 4 254 Protein kinase. cytoplasm ATP binding|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292) 0.000 0.23 429 125 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.62 10 16 AXL 558 broad.mit.edu 37 19 41743895 41743896 + Frame_Shift_Ins INS - C C HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr19:41743895_41743896insC uc010ehj.2 + 7 1020_1021 c.830_831insC c.(829-831)GACfs p.D277fs CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Frame_Shift_Ins_p.D277fs|AXL_uc010ehk.2_Frame_Shift_Ins_p.D277fs NM_021913 NP_068713 P30530 UFO_HUMAN AXL receptor tyrosine kinase isoform 1 277 Extracellular (Potential).|Fibronectin type-III 1. integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1) 13 GGAGAACCAGACCCCCCAGAGG 0.624 0.68 7 15 CIC 23152 broad.mit.edu 37 19 42791229 42791229 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr19:42791229delC uc002otf.1 + 3 329 c.289delC c.(289-291)CCCfs p.P97fs NM_015125 NP_055940 Q96RK0 CIC_HUMAN capicua homolog 97 Pro-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1) 11 Prostate(69;0.00682) 0.000 0.23 774 226 CIC 23152 broad.mit.edu 37 19 42799098 42799098 + Frame_Shift_Del DEL C - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr19:42799098delC uc002otf.1 + 20 4622 c.4582delC c.(4582-4584)CCCfs p.P1528fs NM_015125 NP_055940 Q96RK0 CIC_HUMAN capicua homolog 1528 Pro-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1) 11 Prostate(69;0.00682) CACGGAGCAGCCCCCTGGAGC 0.388 0.28 34 13 DMPK 1760 broad.mit.edu 37 19 46280835 46280836 + Frame_Shift_Del DEL AG - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr19:46280835_46280836delAG uc002pdd.1 - 7 1469_1470 c.925_926delCT c.(925-927)CTGfs p.L309fs DMPK_uc010xxs.1_Frame_Shift_Del_p.L210fs|DMPK_uc002pde.1_Frame_Shift_Del_p.L309fs|DMPK_uc002pdf.1_Frame_Shift_Del_p.L299fs|DMPK_uc002pdg.1_Frame_Shift_Del_p.L299fs|DMPK_uc002pdh.1_Frame_Shift_Del_p.L299fs|DMPK_uc002pdi.1_Frame_Shift_Del_p.L325fs|DMPK_uc010xxt.1_Frame_Shift_Del_p.L299fs NM_001081563 NP_001075032 Q09013 DMPK_HUMAN myotonic dystrophy protein kinase isoform 1 309 Protein kinase. regulation of heart contraction ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity lung(3) 3 Ovarian(192;0.0308)|all_neural(266;0.112) OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24) CACCAGCGGCAGAGAGAGGTGC 0.673 0.37 19 11 PTPRT 11122 broad.mit.edu 37 20 40739003 40739003 + Frame_Shift_Del DEL G - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr20:40739003delG uc002xkg.2 - 23 3408 c.3224delC c.(3223-3225)CCGfs p.P1075fs PTPRT_uc010ggj.2_Frame_Shift_Del_p.P1094fs|PTPRT_uc010ggi.2_Frame_Shift_Del_p.P278fs NM_007050 NP_008981 O14522 PTPRT_HUMAN protein tyrosine phosphatase, receptor type, T 1075 Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential). homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway cell surface|integral to membrane|plasma membrane alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity skin(8)|ovary(7)|lung(5) 20 Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783) 0.000 0.18 267 58 STK4 6789 broad.mit.edu 37 20 43615843 43615844 + Frame_Shift_Ins INS - A A HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr20:43615843_43615844insA uc002xnb.2 + 5 521_522 c.431_432insA c.(430-432)AGAfs p.R144fs STK4_uc010ggx.2_Frame_Shift_Ins_p.R144fs|STK4_uc010ggy.2_Intron|STK4_uc010ggw.1_Frame_Shift_Ins_p.R144fs NM_006282 NP_006273 Q13043 STK4_HUMAN serine/threonine kinase 4 144 Protein kinase. apoptosis|cell morphogenesis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of apoptosis|protein autophosphorylation cytoplasm|nucleus ATP binding|magnesium ion binding|protein homodimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity|transcription factor binding ovary(1)|skin(1) 2 Myeloproliferative disorder(115;0.0122) CATTTTATGAGAAAAATACACC 0.322 0.26 73 25 NCOA3 8202 broad.mit.edu 37 20 46264985 46264985 + Frame_Shift_Del DEL A - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr20:46264985delA uc002xtk.2 + 12 2060 c.1855delA c.(1855-1857)AAAfs p.K619fs NCOA3_uc010ght.1_Frame_Shift_Del_p.K629fs|NCOA3_uc002xtl.2_Frame_Shift_Del_p.K619fs|NCOA3_uc002xtm.2_Frame_Shift_Del_p.K619fs|NCOA3_uc002xtn.2_Frame_Shift_Del_p.K619fs|NCOA3_uc010zyc.1_Frame_Shift_Del_p.K414fs NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 619 Ser-rich. KK->QQ: Abolishes acetylation by CREBBP. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 CAAAGGTCATAAAAAATTACT 0.438 0.28 108 43 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.18 82 18 HUNK 30811 broad.mit.edu 37 21 33368102 33368103 + Frame_Shift_Ins INS - A A HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr21:33368102_33368103insA uc002yph.2 + 10 1687_1688 c.1327_1328insA c.(1327-1329)GAAfs p.E443fs NM_014586 NP_055401 P57058 HUNK_HUMAN hormonally upregulated Neu-associated kinase 443 multicellular organismal development|signal transduction ATP binding|protein serine/threonine kinase activity stomach(1)|skin(1) 2 CAAAGAACAAGAAAAAAGAGGG 0.421 0.57 20 26 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.23 269 81 COL18A1 80781 broad.mit.edu 37 21 46924428 46924437 + Splice_Site DEL CCCCCCAGGC - - rs28696990 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr21:46924428_46924437delCCCCCCAGGC uc011afs.1 + 34 4091 c.4070_splice c.e34-1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.67 116 231 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 4 49 EP300 2033 broad.mit.edu 37 22 41522009 41522009 + Frame_Shift_Del DEL A - - HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr22:41522009delA uc003azl.3 + 3 1266 c.871delA c.(871-873)AAAfs p.K291fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 291 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 TGCTATGGACAAAAAGGCAGT 0.408 0.20 144 37 EP300 2033 broad.mit.edu 37 22 41546147 41546148 + Frame_Shift_Ins INS - A A HEC6_ENDOMETRIUM NA HEC6_ENDOMETRIUM NA g.chr22:41546147_41546148insA uc003azl.3 + 14 3157_3158 c.2762_2763insA c.(2761-2763)GCAfs p.A921fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 921 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 CAGAGCACAGCAGCGTCTGTTC 0.545 0.27 124 45 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.83 3 15 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.12 302 43 CELF3 11189 broad.mit.edu 37 1 151678723 151678731 + In_Frame_Del DEL TGCTGCTGC - - HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:151678723_151678731delTGCTGCTGC uc001eys.1 - 10 1889_1897 c.1095_1103delGCAGCAGCA c.(1093-1104)CAGCAGCAGCAA>CAA p.365_368QQQQ>Q CELF3_uc010pdh.1_In_Frame_Del_p.151_154QQQQ>Q|CELF3_uc001eyr.2_In_Frame_Del_p.364_367QQQQ>Q|CELF3_uc009wmy.2_In_Frame_Del_p.315_318QQQQ>Q|CELF3_uc009wmx.1_In_Frame_Del_p.364_367QQQQ>Q NM_007185 NP_009116 Q5SZQ8 CELF3_HUMAN trinucleotide repeat containing 4 365_368 Gln-rich. nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome cytoplasm|nucleus mRNA binding|nucleotide binding ovary(1)|central_nervous_system(1) 2 ctgctgctgttgctgctgctgctgctgct 0.488 0.35 20 11 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.47 10 9 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.43 13 10 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.35 194 106 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.38 10 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 69 80 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.35 495 267 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.32 46 22 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 530 189 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.26 72 25 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.28 77 30 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 84 846 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 35 FAM48B1 100130302 broad.mit.edu 37 X 24382374 24382376 + In_Frame_Del DEL TGC - - HEP3B217_LIVER NA HEP3B217_LIVER NA g.chrX:24382374_24382376delTGC uc011mjx.1 + 1 1497_1499 c.1497_1499delTGC c.(1495-1500)ATTGCT>ATT p.A517del NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 ctgctgctattgctgctgctgct 0.202 0.25 27 9 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HEP3B217_LIVER NA HEP3B217_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 39 LOC642587 642587 broad.mit.edu 37 1 209605636 209605637 + In_Frame_Ins INS - AGC AGC rs146499758;rs3842530 by1000genomes HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr1:209605636_209605637insAGC uc009xcn.2 + 4 634_635 c.251_252insAGC c.(250-252)GTA>GTAGCA p.97_98insA NM_001104548 NP_001098018 hypothetical protein LOC642587 0 OV - Ovarian serous cystadenocarcinoma(81;0.0422) gccaccaccgTagcagcagcag 0.272 0.11 65 8 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.36 18 10 TPRXL 348825 broad.mit.edu 37 3 14106317 14106318 + In_Frame_Ins INS - CAGCAGTCCCAGCAC CAGCAGTCCCAGCAC HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr3:14106317_14106318insCAGCAGTCCCAGCAC uc011avd.1 + 3 1096_1097 c.641_642insCAGCAGTCCCAGCAC c.(640-642)ACC>ACCAGCAGTCCCAGCACC p.214_214T>TSSPST TPRXL_uc003byh.1_In_Frame_Ins_p.214_214T>TSSPST|TPRXL_uc003byg.2_In_Frame_Ins_p.214_214T>TSSPST NR_002223 RecName: Full=Putative protein TPRXL; 0 agctccagcaccagcagtccca 0.233 0.59 7 10 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.71 19 47 HTT 3064 broad.mit.edu 37 4 3076604 3076612 + In_Frame_Del DEL CAGCAGCAG - - rs10618869 HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr4:3076604_3076612delCAGCAGCAG uc011bvq.1 + 2 203_211 c.58_66delCAGCAGCAG c.(58-66)CAGCAGCAGdel p.QQQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagcagc 0.325 0.21 81 21 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.72 66 172 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.49 33 32 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 21 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.26 755 269 MYST4 23522 broad.mit.edu 37 10 76788653 76788654 + In_Frame_Ins INS - GAA GAA HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr10:76788653_76788654insGAA uc001jwn.1 + 18 4564_4565 c.4071_4072insGAA c.(4069-4074)insGAA p.1368_1369insE MYST4_uc001jwo.1_In_Frame_Ins_p.1076_1077insE|MYST4_uc001jwp.1_In_Frame_Ins_p.1185_1186insE NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1368_1369 Poly-Glu. histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) aagaggaggaggaggaggaaga 0.233 0.34 49 25 SLC3A2 6520 broad.mit.edu 37 11 62638220 62638221 + Frame_Shift_Ins INS - G G HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr11:62638220_62638221insG uc001nwd.2 + 2 340_341 c.116_117insG c.(115-117)TTGfs p.L39fs SLC3A2_uc001nwb.2_Frame_Shift_Ins_p.L39fs|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c 39 blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.31 67 30 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.81 6 26 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.48 383 360 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.64 48 84 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.39 121 77 MEF2A 4205 broad.mit.edu 37 15 100252709 100252710 + In_Frame_Ins INS - CAGCAG CAGCAG HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr15:100252709_100252710insCAGCAG uc010urw.1 + 11 1616_1617 c.1257_1258insCAGCAG c.(1255-1260)insCAGCAG p.429_430insQQ MEF2A_uc010urv.1_In_Frame_Ins_p.359_360insQQ|MEF2A_uc010bos.2_In_Frame_Ins_p.419_420insQQ|MEF2A_uc002bvf.2_In_Frame_Ins_p.421_422insQQ|MEF2A_uc002bve.2_In_Frame_Ins_p.427_428insQQ|MEF2A_uc002bvg.2_In_Frame_Ins_p.419_420insQQ|MEF2A_uc002bvi.2_In_Frame_Ins_p.419_420insQQ|MEF2A_uc010bot.2_In_Frame_Ins_p.351_352insQQ NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 429_430 Gln/Pro-rich. Missing (in Ref. 4; AAB17195/AAB17196). apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) CATCGGGCTTCcagcagcagca 0.485 0.28 48 19 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 35 396 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.11 775 97 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 31 151 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 260 36 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 141 750 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HEP3B217_LIVER NA HEP3B217_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 7 129 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HEYA8_OVARY NA HEYA8_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 5 172 NRD1 4898 broad.mit.edu 37 1 52306064 52306066 + In_Frame_Del DEL TCT - - rs145326984;rs72496486 HEYA8_OVARY NA HEYA8_OVARY NA g.chr1:52306064_52306066delTCT uc001ctc.3 - 2 784_786 c.462_464delAGA c.(460-465)GAAGAT>GAT p.E154del NRD1_uc009vzb.2_Translation_Start_Site|NRD1_uc001ctd.3_In_Frame_Del_p.E154del|NRD1_uc001cte.2_In_Frame_Del_p.E22del|NRD1_uc001ctf.2_In_Frame_Del_p.E154del|NRD1_uc010ong.1_RNA|NRD1_uc009vzc.1_In_Frame_Del_p.E22del|NRD1_uc001ctg.1_5'Flank NM_002525 NP_002516 O43847 NRDC_HUMAN nardilysin isoform a Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity cell surface|cytosol epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding 0 ttcatcatcatcttcttcttctt 0.158 0.50 5 5 CYP1B1 1545 broad.mit.edu 37 2 38302336 38302338 + In_Frame_Del DEL CCG - - HEYA8_OVARY NA HEYA8_OVARY NA g.chr2:38302336_38302338delCCG uc002rqo.2 - 3 597_599 c.194_196delCGG c.(193-198)GCGGTG>GTG p.A65del NM_000104 NP_000095 Q16678 CP1B1_HUMAN cytochrome P450, family 1, subfamily B, 65 visual perception|xenobiotic metabolic process endoplasmic reticulum membrane|microsome aromatase activity|electron carrier activity|heme binding|oxygen binding|protein binding ovary(1)|central_nervous_system(1) 2 all_hematologic(82;0.21) Estrone(DB00655) 0.000 0.48 426 393 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HEYA8_OVARY NA HEYA8_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.19 92 22 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HEYA8_OVARY NA HEYA8_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.28 120 46 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HEYA8_OVARY NA HEYA8_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 186 271 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HEYA8_OVARY NA HEYA8_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 54 131 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HEYA8_OVARY NA HEYA8_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 5 63 PAK1 5058 broad.mit.edu 37 11 77069989 77069990 + In_Frame_Ins INS - CAT CAT rs149665907 HEYA8_OVARY NA HEYA8_OVARY NA g.chr11:77069989_77069990insCAT uc001oyh.3 - 6 1083_1084 c.550_551insATG c.(550-552)GCT>GATGCT p.183_184insD PAK1_uc010rso.1_In_Frame_Ins_p.85_86insD|PAK1_uc001oyg.3_In_Frame_Ins_p.183_184insD|PAK1_uc001oyi.1_In_Frame_Ins_p.183_184insD|PAK1_uc010rsn.1_Translation_Start_Site NM_002576 NP_002567 Q13153 PAK1_HUMAN p21-activated kinase 1 isoform 2 183_184 Interaction with CRIPAK. apoptosis|axon guidance|cytoskeleton organization|ER-nucleus signaling pathway|positive regulation of JUN kinase activity|positive regulation of peptidyl-serine phosphorylation|protein autophosphorylation|T cell costimulation|T cell receptor signaling pathway cytosol|focal adhesion|Golgi apparatus ATP binding|collagen binding|protein binding|protein serine/threonine kinase activity skin(2)|stomach(1)|lung(1) 4 all_cancers(14;1.75e-18) TGGTGGGGTAGcatcatcatca 0.426 0.26 1224 439 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HEYA8_OVARY NA HEYA8_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 571 89 TP53BP1 7158 broad.mit.edu 37 15 43713344 43713345 + Frame_Shift_Ins INS - C C HEYA8_OVARY NA HEYA8_OVARY NA g.chr15:43713344_43713345insC uc001zrs.2 - 20 4261_4262 c.4113_4114insG c.(4111-4116)GGGACGfs p.G1371fs TP53BP1_uc010udp.1_Frame_Shift_Ins_p.G1371fs|TP53BP1_uc001zrq.3_Frame_Shift_Ins_p.G1376fs|TP53BP1_uc001zrr.3_Frame_Shift_Ins_p.G1376fs|TP53BP1_uc010udq.1_Frame_Shift_Ins_p.G1376fs NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 1371_1372 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) CACACTGGCGTCCCTGTCTGAC 0.569 0.63 75 126 ZFHX3 463 broad.mit.edu 37 16 72831358 72831363 + In_Frame_Del DEL TTGTTG - - HEYA8_OVARY NA HEYA8_OVARY NA g.chr16:72831358_72831363delTTGTTG uc002fck.2 - 9 5891_5896 c.5218_5223delCAACAA c.(5218-5223)CAACAAdel p.QQ1740del ZFHX3_uc002fcl.2_In_Frame_Del_p.QQ826del NM_006885 NP_008816 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 isoform A 1740_1741 Poly-Gln. muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation transcription factor complex enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding ovary(2)|skin(2) 4 Ovarian(137;0.13) GCGTTTGTGCttgttgttgttgttgt 0.413 0.46 7 6 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HEYA8_OVARY NA HEYA8_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 24 164 STAT3 6774 broad.mit.edu 37 17 40481792 40481793 + Frame_Shift_Del DEL TC - - HEYA8_OVARY NA HEYA8_OVARY NA g.chr17:40481792_40481793delTC uc002hzl.1 - 12 1351_1352 c.1111_1112delGA c.(1111-1113)GACfs p.D371fs STAT3_uc002hzk.1_Frame_Shift_Del_p.D371fs|STAT3_uc002hzm.1_Frame_Shift_Del_p.D371fs|STAT3_uc010wgh.1_Frame_Shift_Del_p.D273fs|STAT3_uc002hzn.1_Frame_Shift_Del_p.D371fs NM_139276 NP_644805 P40763 STAT3_HUMAN signal transducer and activator of transcription 371 cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis cytosol|nucleus|plasma membrane calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding ovary(1)|lung(1)|breast(1)|central_nervous_system(1) 4 all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135) BRCA - Breast invasive adenocarcinoma(366;0.139) GTCCCCAGAGTCTCTGTAAGAA 0.431 0.18 472 107 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HEYA8_OVARY NA HEYA8_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 51 144 LMTK3 114783 broad.mit.edu 37 19 49001791 49001792 + Frame_Shift_Ins INS - G G HEYA8_OVARY NA HEYA8_OVARY NA g.chr19:49001791_49001792insG uc002pjk.2 - 12 2621_2622 c.2621_2622insC c.(2620-2622)CCGfs p.P874fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) CCCGGGGCCCCGGGAGTGGGAG 0.718 0.14 70 11 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes HEYA8_OVARY NA HEYA8_OVARY NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.40 15 10 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HEYA8_OVARY NA HEYA8_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 97 386 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HEYA8_OVARY NA HEYA8_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 23 376 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HGC27_STOMACH NA HGC27_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 37 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HGC27_STOMACH NA HGC27_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.42 338 248 SHC1 6464 broad.mit.edu 37 1 154942637 154942637 + Frame_Shift_Del DEL A - - HGC27_STOMACH NA HGC27_STOMACH NA g.chr1:154942637delA uc001ffv.2 - 1 587 c.366delT c.(364-366)ACTfs p.T122fs SHC1_uc001ffz.1_5'Flank|SHC1_uc001ffw.2_Frame_Shift_Del_p.T122fs|SHC1_uc001ffx.2_Frame_Shift_Del_p.T12fs|SHC1_uc001ffy.2_Frame_Shift_Del_p.T12fs NM_183001 NP_892113 P29353 SHC1_HUMAN SHC-transforming protein 1 isoform 1 122 activation of MAPK activity|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|positive regulation of DNA replication|Ras protein signal transduction|regulation of epidermal growth factor receptor activity|regulation of growth cytosol|mitochondrial matrix|Shc-EGFR complex epidermal growth factor receptor binding|insulin receptor binding|insulin-like growth factor receptor binding|phospholipid binding|protein binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(1)|skin(1) 2 all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245) BRCA - Breast invasive adenocarcinoma(34;0.00034) CTTCCACCCGAGTCCTGCGCC 0.657 0.15 44 8 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HGC27_STOMACH NA HGC27_STOMACH NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.56 8 10 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HGC27_STOMACH NA HGC27_STOMACH NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.11 101 12 ATR 545 broad.mit.edu 37 3 142184033 142184033 + Frame_Shift_Del DEL C - - HGC27_STOMACH NA HGC27_STOMACH NA g.chr3:142184033delC uc003eux.3 - 41 7069 c.6947delG c.(6946-6948)GGCfs p.G2316fs ATR_uc003euy.1_Frame_Shift_Del_p.G202fs NM_001184 NP_001175 Q13535 ATR_HUMAN ataxia telangiectasia and Rad3 related protein 2316 cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence PML body ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1) 20 TCCATCTGAGCCTTTTAAAGA 0.338 0.46 79 68 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HGC27_STOMACH NA HGC27_STOMACH NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.47 16 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HGC27_STOMACH NA HGC27_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 35 54 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HGC27_STOMACH NA HGC27_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 25 47 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HGC27_STOMACH NA HGC27_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.82 3 14 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HGC27_STOMACH NA HGC27_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.31 24 11 CSPP1 79848 broad.mit.edu 37 8 68102870 68102883 + Splice_Site DEL TCGGGGTCCTCTTA - - HGC27_STOMACH NA HGC27_STOMACH NA g.chr8:68102870_68102883delTCGGGGTCCTCTTA uc003xxi.2 + 29 3342 c.3311_splice c.e29-2 p.G1104_splice ARFGEF1_uc003xxl.1_Intron|CSPP1_uc003xxj.2_Splice_Site_p.G1069_splice|CSPP1_uc003xxk.2_Splice_Site_p.G724_splice|CSPP1_uc010lyw.2_Splice_Site_p.G164_splice NM_001077204 NP_001070672 Q1MSJ5 CSPP1_HUMAN centrosome spindle pole associated protein 1 centrosome|microtubule|spindle ovary(3)|breast(2) 5 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153) CTTCTGCTTTTCGGGGTCCTCTTAGGGGCTTACG 0.463 0.96 1 24 VPS13B 157680 broad.mit.edu 37 8 100865996 100865997 + Frame_Shift_Del DEL AG - - HGC27_STOMACH NA HGC27_STOMACH NA g.chr8:100865996_100865997delAG uc003yiv.2 + 56 10565_10566 c.10454_10455delAG c.(10453-10455)CAGfs p.Q3485fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.Q3460fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 3485 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TCCAAAATGCAGAGTCTCCTCA 0.401 0.61 30 46 SMC2 10592 broad.mit.edu 37 9 106896718 106896718 + Frame_Shift_Del DEL T - - HGC27_STOMACH NA HGC27_STOMACH NA g.chr9:106896718delT uc004bbv.2 + 23 3419 c.3131delT c.(3130-3132)ATTfs p.I1044fs SMC2_uc004bbw.2_Frame_Shift_Del_p.I1044fs|SMC2_uc011lvl.1_Frame_Shift_Del_p.I1044fs|SMC2_uc004bbx.2_Frame_Shift_Del_p.I1044fs|SMC2_uc004bby.2_RNA NM_001042551 NP_001036016 O95347 SMC2_HUMAN structural maintenance of chromosomes 2 1044 cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism condensin complex|cytoplasm|nuclear chromosome ATP binding|protein heterodimerization activity ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1) 9 TTTGGGTCTATTTTTTCTACT 0.378 0.19 280 66 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HGC27_STOMACH NA HGC27_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 184 75 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HGC27_STOMACH NA HGC27_STOMACH NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 11 93 TP53 7157 broad.mit.edu 37 17 7578474 7578475 + Frame_Shift_Ins INS - G G HGC27_STOMACH NA HGC27_STOMACH NA g.chr17:7578474_7578475insG uc002gim.2 - 5 649_650 c.455_456insC c.(454-456)CCGfs p.P152fs TP53_uc002gig.1_Frame_Shift_Ins_p.P152fs|TP53_uc002gih.2_Frame_Shift_Ins_p.P152fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Ins_p.P20fs|TP53_uc010cng.1_Frame_Shift_Ins_p.P20fs|TP53_uc002gii.1_Frame_Shift_Ins_p.P20fs|TP53_uc010cnh.1_Frame_Shift_Ins_p.P152fs|TP53_uc010cni.1_Frame_Shift_Ins_p.P152fs|TP53_uc002gij.2_Frame_Shift_Ins_p.P152fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Ins_p.P59fs|TP53_uc002gio.2_Frame_Shift_Ins_p.P20fs|TP53_uc010vug.1_Frame_Shift_Ins_p.P113fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 152 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). P -> R (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|P -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> A (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.P152L(57)|p.P152S(21)|p.P152fs*18(17)|p.P153fs*28(8)|p.P152T(7)|p.0?(7)|p.P152fs*29(5)|p.P152P(5)|p.P152Q(4)|p.P152fs*14(4)|p.P152fs*28(3)|p.P152R(3)|p.T150fs*16(3)|p.P152A(2)|p.P153fs*16(1)|p.P151_V173del23(1)|p.P152_P153del(1)|p.G154fs*16(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.P153fs*20(1)|p.D148fs*23(1)|p.P152del(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.Q144_G154del11(1)|p.G154fs*27(1)|p.P152_P153insXXX(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGGTGCCGGGCGGGGGTGTGGA 0.614 0.87 6 41 SMARCA4 6597 broad.mit.edu 37 19 11118633 11118635 + In_Frame_Del DEL AGA - - HGC27_STOMACH NA HGC27_STOMACH NA g.chr19:11118633_11118635delAGA uc002mqf.3 + 14 2341_2343 c.2057_2059delAGA c.(2056-2061)GAGAAG>GAG p.K689del SMARCA4_uc010dxp.2_In_Frame_Del_p.K689del|SMARCA4_uc010dxo.2_In_Frame_Del_p.K689del|SMARCA4_uc002mqg.1_In_Frame_Del_p.K689del|SMARCA4_uc010dxq.2_In_Frame_Del_p.K689del|SMARCA4_uc010dxr.2_In_Frame_Del_p.K689del|SMARCA4_uc002mqj.3_In_Frame_Del_p.K689del|SMARCA4_uc010dxs.2_In_Frame_Del_p.K689del NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 689 chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.K687E(1)|p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) CCCGTGGAGGAGAAGAAGAAGAT 0.586 0.14 60 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HGC27_STOMACH NA HGC27_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.53 23 26 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HGC27_STOMACH NA HGC27_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 124 430 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HGC27_STOMACH NA HGC27_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 77 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.87 5 33 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 494 130 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 158 36 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.48 45 41 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 34 99 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 10 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.15 46 8 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.29 77 32 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.12 490 66 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 328 104 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 23 468 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 0.95 1 18 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.44 51 40 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 57 194 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 8 92 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 8 72 ABL2 27 broad.mit.edu 37 1 179077737 179077738 + Frame_Shift_Ins INS - G G HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:179077737_179077738insG uc001gmj.3 - 12 2951_2952 c.2664_2665insC c.(2662-2667)CCCAAGfs p.P888fs ABL2_uc010pnf.1_Frame_Shift_Ins_p.P785fs|ABL2_uc010png.1_Frame_Shift_Ins_p.P764fs|ABL2_uc010pnh.1_Frame_Shift_Ins_p.P867fs|ABL2_uc001gmg.3_Frame_Shift_Ins_p.P770fs|ABL2_uc001gmi.3_Frame_Shift_Ins_p.P873fs|ABL2_uc001gmh.3_Frame_Shift_Ins_p.P852fs|ABL2_uc010pne.1_Frame_Shift_Ins_p.P749fs NM_007314 NP_009298 P42684 ABL2_HUMAN arg tyrosine kinase isoform b 888_889 F-actin-binding (By similarity).|Pro-rich. axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction cytoskeleton|cytosol ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(8)|breast(3)|ovary(2)|central_nervous_system(1) 14 Adenosine triphosphate(DB00171)|Dasatinib(DB01254) TCTTTACCCTTGGGGGCAGCTG 0.619 0.10 274 32 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.36 34 19 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376116 + In_Frame_Del DEL TGCTGC - - rs143860374;rs62265537 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376116delTGCTGC uc003eam.2 - 7 4824_4829 c.4413_4418delGCAGCA c.(4411-4419)CAGCAGCAA>CAA p.1471_1473QQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1415_1417QQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1471_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgct 0.359 0.19 85 20 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.54 31 36 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.72 145 367 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 21 58 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.53 7 8 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.67 17 35 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.13 341 52 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 26 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.35 11 6 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 48 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.48 745 678 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.40 18 12 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.84 22 114 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.47 137 121 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.15 245 44 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 181 663 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 5 176 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HLFA_LUNG NA HLFA_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 48 ARID1A 8289 broad.mit.edu 37 1 27023909 27023923 + In_Frame_Del DEL GCTGCGGCGGCGGCA - - HLFA_LUNG NA HLFA_LUNG NA g.chr1:27023909_27023923delGCTGCGGCGGCGGCA uc001bmv.1 + 1 1388_1402 c.1015_1029delGCTGCGGCGGCGGCA c.(1015-1029)GCTGCGGCGGCGGCAdel p.AAAAA344del ARID1A_uc001bmt.1_In_Frame_Del_p.AAAAA344del|ARID1A_uc001bmu.1_In_Frame_Del_p.AAAAA344del NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 344_348 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.A339fs*24(1)|p.A344_A348del(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.43 55 42 ROR1 4919 broad.mit.edu 37 1 64643630 64643630 + Frame_Shift_Del DEL C - - HLFA_LUNG NA HLFA_LUNG NA g.chr1:64643630delC uc001dbj.2 + 9 2305 c.1906delC c.(1906-1908)CTTfs p.L636fs uc001dbm.2_5'Flank NM_005012 NP_005003 Q01973 ROR1_HUMAN receptor tyrosine kinase-like orphan receptor 1 636 Cytoplasmic (Potential).|Protein kinase. transmembrane receptor protein tyrosine kinase signaling pathway cytoplasm|integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1) 19 AGACTTGGGGCTTTCCAGAGA 0.458 0.17 90 19 DENND4B 9909 broad.mit.edu 37 1 153907278 153907279 + In_Frame_Ins INS - CTG CTG rs141373027 by1000genomes HLFA_LUNG NA HLFA_LUNG NA g.chr1:153907278_153907279insCTG uc001fdd.1 - 18 3131_3132 c.2730_2731insCAG c.(2728-2733)insCAG p.910_911insQ uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910_911 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) GACACctgctcctgctgctgct 0.455 0.17 38 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HLFA_LUNG NA HLFA_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.33 73 36 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HLFA_LUNG NA HLFA_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.31 43 19 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 HLFA_LUNG NA HLFA_LUNG NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.50 5 5 PTK7 5754 broad.mit.edu 37 6 43109757 43109758 + Frame_Shift_Ins INS - A A HLFA_LUNG NA HLFA_LUNG NA g.chr6:43109757_43109758insA uc003oub.1 + 12 2055_2056 c.1857_1858insA c.(1855-1860)CCCAAGfs p.P619fs PTK7_uc003ouc.1_Frame_Shift_Ins_p.P619fs|PTK7_uc003oud.1_Frame_Shift_Ins_p.P579fs|PTK7_uc003oue.1_Frame_Shift_Ins_p.P489fs|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Frame_Shift_Ins_p.P627fs|PTK7_uc010jyj.1_Intron NM_002821 NP_002812 Q13308 PTK7_HUMAN PTK7 protein tyrosine kinase 7 isoform a 619_620 Ig-like C2-type 7.|Extracellular (Potential). actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration cell-cell junction|integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ovary(2)|large_intestine(1) 3 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423) AGGGGGACCCCAAGCCGCTGAT 0.599 0.21 46 12 HOXA11 3207 broad.mit.edu 37 7 27224218 27224219 + In_Frame_Ins INS - GCC GCC rs13224700 HLFA_LUNG NA HLFA_LUNG NA g.chr7:27224218_27224219insGCC uc003syx.2 - 1 617_618 c.545_546insGGC c.(544-546)GCT>GCGGCT p.182_182A>AA HOXA11_uc003syy.2_RNA|HOXA11AS_uc003syz.1_5'Flank NM_005523 NP_005514 P31270 HXA11_HUMAN homeobox A11 182 Poly-Ala. branching involved in ureteric bud morphogenesis|cartilage development involved in endochondral bone morphogenesis|developmental growth|dorsal/ventral pattern formation|mesodermal cell fate specification|positive regulation of cell development|positive regulation of chondrocyte differentiation protein-DNA complex|transcription factor complex sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity lung(1)|breast(1) 2 0.000 0.24 680 210 POU5F1B 5462 broad.mit.edu 37 8 128429026 128429027 + Frame_Shift_Del DEL AG - - HLFA_LUNG NA HLFA_LUNG NA g.chr8:128429026_128429027delAG uc003ysf.2 + 1 1170_1171 c.915_916delAG c.(913-918)TCAGGGfs p.S305fs uc003ysc.1_Intron|uc003ysd.1_Intron|LOC727677_uc003yse.1_Intron|uc011liu.1_5'Flank NM_001159542 NP_001153014 Q06416 P5F1B_HUMAN POU class 5 homeobox 1B 305_306 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 CTCCTTTCTCAGGGGGACCAGT 0.589 0.56 34 43 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HLFA_LUNG NA HLFA_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 11 NLRP6 171389 broad.mit.edu 37 11 280794 280796 + In_Frame_Del DEL AAG - - HLFA_LUNG NA HLFA_LUNG NA g.chr11:280794_280796delAAG uc010qvs.1 + 4 1060_1062 c.1060_1062delAAG c.(1060-1062)AAGdel p.K356del NLRP6_uc010qvt.1_In_Frame_Del_p.K356del NM_138329 NP_612202 P59044 NALP6_HUMAN NLR family, pyrin domain containing 6 356 NACHT. cytoplasm ATP binding upper_aerodigestive_tract(1)|skin(1) 2 all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122) 0.000 0.31 656 296 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HLFA_LUNG NA HLFA_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.43 8 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HLFA_LUNG NA HLFA_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 140 23 SIK2 23235 broad.mit.edu 37 11 111571666 111571667 + Frame_Shift_Ins INS - G G HLFA_LUNG NA HLFA_LUNG NA g.chr11:111571666_111571667insG uc001plt.2 + 5 653_654 c.535_536insG c.(535-537)AGCfs p.S179fs NM_015191 NP_056006 Q9H0K1 SIK2_HUMAN SNF1-like kinase 2 179 Protein kinase. intracellular protein kinase cascade|regulation of insulin receptor signaling pathway Golgi apparatus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|skin(1) 3 ATGGTGTGGCAGCCCCCCTTAT 0.431 0.19 105 25 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HLFA_LUNG NA HLFA_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.22 25 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HLFA_LUNG NA HLFA_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 20 141 LAMA5 3911 broad.mit.edu 37 20 60928210 60928210 + Frame_Shift_Del DEL T - - HLFA_LUNG NA HLFA_LUNG NA g.chr20:60928210delT uc002ycq.2 - 3 615 c.548delA c.(547-549)CAGfs p.Q183fs NM_005560 NP_005551 O15230 LAMA5_HUMAN laminin alpha 5 precursor 183 Laminin N-terminal. angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex integrin binding ovary(1)|pancreas(1)|skin(1) 3 Breast(26;1.57e-08) BRCA - Breast invasive adenocarcinoma(19;4.36e-06) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) 0.000 0.91 2 20 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HLFA_LUNG NA HLFA_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.22 170 47 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HLFA_LUNG NA HLFA_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 125 494 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HLFA_LUNG NA HLFA_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.99 1 73 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HMC18_BREAST NA HMC18_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 1 19 XIAP 331 broad.mit.edu 37 X 123025155 123025157 + In_Frame_Del DEL GAG - - HMC18_BREAST NA HMC18_BREAST NA g.chrX:123025155_123025157delGAG uc010nqu.2 + 4 1171_1173 c.1045_1047delGAG c.(1045-1047)GAGdel p.E350del XIAP_uc004etx.2_In_Frame_Del_p.E350del|XIAP_uc010nqv.2_5'UTR NM_001167 NP_001158 P98170 XIAP_HUMAN baculoviral IAP repeat-containing protein 4 350 anti-apoptosis|apoptosis|induction of apoptosis by intracellular signals|response to DNA damage stimulus cytosol caspase inhibitor activity|ligase activity|protein binding|zinc ion binding ovary(1)|lung(1) 2 TCATTCACTTGAGGAGTGTCTGG 0.197 0.87 6 39 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HMC18_BREAST NA HMC18_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.41 268 189 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HMC18_BREAST NA HMC18_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.36 14 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HMC18_BREAST NA HMC18_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 58 65 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HMC18_BREAST NA HMC18_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 26 52 TRPS1 7227 broad.mit.edu 37 8 116599379 116599394 + Frame_Shift_Del DEL TGGGCGGCCTCCACAT - - HMC18_BREAST NA HMC18_BREAST NA g.chr8:116599379_116599394delTGGGCGGCCTCCACAT uc003ynz.2 - 4 2954_2969 c.2495_2510delATGTGGAGGCCGCCCA c.(2494-2511)AATGTGGAGGCCGCCCATfs p.N832fs TRPS1_uc011lhy.1_Frame_Shift_Del_p.N836fs|TRPS1_uc003yny.2_Frame_Shift_Del_p.N845fs|TRPS1_uc010mcy.2_Frame_Shift_Del_p.N832fs NM_014112 NP_054831 Q9UHF7 TRPS1_HUMAN zinc finger transcription factor TRPS1 832_837 negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) TCGCGCCAGATGGGCGGCCTCCACATTGGGACTATC 0.611 0.34 85 43 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HMC18_BREAST NA HMC18_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.88 2 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HMC18_BREAST NA HMC18_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.71 110 263 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HMC18_BREAST NA HMC18_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 265 125 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes HMC18_BREAST NA HMC18_BREAST NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.12 105 15 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HMC18_BREAST NA HMC18_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 36 412 TP53 7157 broad.mit.edu 37 17 7578475 7578475 + Frame_Shift_Del DEL G - - HMC18_BREAST NA HMC18_BREAST NA g.chr17:7578475delG uc002gim.2 - 5 649 c.455delC c.(454-456)CCGfs p.P152fs TP53_uc002gig.1_Frame_Shift_Del_p.P152fs|TP53_uc002gih.2_Frame_Shift_Del_p.P152fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.P20fs|TP53_uc010cng.1_Frame_Shift_Del_p.P20fs|TP53_uc002gii.1_Frame_Shift_Del_p.P20fs|TP53_uc010cnh.1_Frame_Shift_Del_p.P152fs|TP53_uc010cni.1_Frame_Shift_Del_p.P152fs|TP53_uc002gij.2_Frame_Shift_Del_p.P152fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.P59fs|TP53_uc002gio.2_Frame_Shift_Del_p.P20fs|TP53_uc010vug.1_Frame_Shift_Del_p.P113fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 152 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). P -> R (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|P -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> A (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.P152L(57)|p.P152S(21)|p.P152fs*18(17)|p.P152T(7)|p.0?(7)|p.P152fs*29(5)|p.P152P(5)|p.P152Q(4)|p.P153fs*28(4)|p.P152fs*14(4)|p.P152fs*28(3)|p.P152R(3)|p.T150fs*16(3)|p.P152A(2)|p.P153fs*16(1)|p.P151_V173del23(1)|p.P152_P153del(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.D148fs*23(1)|p.P152del(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.Q144_G154del11(1)|p.P152_P153insXXX(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGTGCCGGGCGGGGGTGTGGA 0.612 0.79 10 38 RAI1 10743 broad.mit.edu 37 17 17697094 17697102 + In_Frame_Del DEL CAGCAGCAG - - rs113303801;rs149882795;rs35068024;rs144872134;rs34083643 byFrequency HMC18_BREAST NA HMC18_BREAST NA g.chr17:17697094_17697102delCAGCAGCAG uc002grm.2 + 3 1301_1309 c.832_840delCAGCAGCAG c.(832-840)CAGCAGCAGdel p.QQQ287del RAI1_uc002grn.1_In_Frame_Del_p.QQQ287del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 287_289 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagcagcagc 0.507 0.36 9 5 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HMC18_BREAST NA HMC18_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.75 20 59 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HMC18_BREAST NA HMC18_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 81 299 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HMC18_BREAST NA HMC18_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 58 GPR112 139378 broad.mit.edu 37 X 135428002 135428002 + Frame_Shift_Del DEL G - - HOS_BONE NA HOS_BONE NA g.chrX:135428002delG uc004ezu.1 + 6 2428 c.2137delG c.(2137-2139)GGTfs p.G713fs GPR112_uc010nsb.1_Frame_Shift_Del_p.G508fs|GPR112_uc010nsc.1_Frame_Shift_Del_p.G480fs NM_153834 NP_722576 Q8IZF6 GP112_HUMAN G-protein coupled receptor 112 713 Extracellular (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1) 12 Acute lymphoblastic leukemia(192;0.000127) AGAGGGCAAAGGTACCACTGC 0.393 0.98 2 80 TTN 7273 broad.mit.edu 37 2 179542390 179542392 + In_Frame_Del DEL CTT - - HOS_BONE NA HOS_BONE NA g.chr2:179542390_179542392delCTT uc010zfg.1 - 143 30739_30741 c.30515_30517delAAG c.(30514-30519)GAAGTC>GTC p.E10172del TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Del_p.E6833del|TTN_uc010fre.1_Intron|TTN_uc002una.1_RNA|TTN_uc010frf.1_RNA NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 11099 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCTGGAAGGACTTCTTCTTCAGG 0.443 0.33 39 19 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HOS_BONE NA HOS_BONE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.25 21 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HOS_BONE NA HOS_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 48 33 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HOS_BONE NA HOS_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.58 20 28 ADAM18 8749 broad.mit.edu 37 8 39587420 39587429 + Frame_Shift_Del DEL TTCATCCGTT - - rs142507282 byFrequency HOS_BONE NA HOS_BONE NA g.chr8:39587420_39587429delTTCATCCGTT uc003xni.2 + 20 2181_2190 c.2181_2190delTTCATCCGTT c.(2179-2190)AATTCATCCGTTfs p.N727fs ADAM18_uc010lww.2_RNA|ADAM18_uc010lwx.2_Frame_Shift_Del_p.N703fs NM_014237 NP_055052 Q9Y3Q7 ADA18_HUMAN a disintegrin and metalloprotease domain 18 727_730 Cytoplasmic (Potential). cell differentiation|multicellular organismal development|proteolysis|spermatogenesis integral to membrane|membrane fraction metalloendopeptidase activity|zinc ion binding central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1) 6 all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112) LUSC - Lung squamous cell carcinoma(45;0.000199) ACTATAGTAATTCATCCGTTGTATCAGAAA 0.310 0.41 39 27 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HOS_BONE NA HOS_BONE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.33 16 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HOS_BONE NA HOS_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 109 22 OR4E2 26686 broad.mit.edu 37 14 22133493 22133493 + Frame_Shift_Del DEL T - - HOS_BONE NA HOS_BONE NA g.chr14:22133493delT uc010tmd.1 + 1 197 c.197delT c.(196-198)CTGfs p.L66fs NM_001001912 NP_001001912 Q8NGC2 OR4E2_HUMAN olfactory receptor, family 4, subfamily E, 66 Helical; Name=2; (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(2)|pancreas(1)|skin(1) 4 all_cancers(95;0.00113) Acute lymphoblastic leukemia(2;0.0279) GBM - Glioblastoma multiforme(265;0.0137) CTGAGCAATCTGTCCTTTATT 0.423 0.94 7 120 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HOS_BONE NA HOS_BONE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.61 7 11 Unknown 0 broad.mit.edu 37 15 20649659 20649661 + In_Frame_Del DEL GGA - - rs150988515 byFrequency HOS_BONE NA HOS_BONE NA g.chr15:20649659_20649661delGGA uc001ytg.2 - 18 2557_2559 c.1848_1850delTCC c.(1846-1851)CCTCCA>CCA p.616_617PP>P uc010tyx.1_RNA|uc001yth.3_In_Frame_Del_p.616_617PP>P|uc010tyy.1_In_Frame_Del_p.616_617PP>P RecName: Full=Putative HERC2-like protein 3; GCCTAGGCCTGGAGGAGGCCTAT 0.571 0.96 2 44 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HOS_BONE NA HOS_BONE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 20 192 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HOS_BONE NA HOS_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.29 29 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HOS_BONE NA HOS_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 117 391 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HOS_BONE NA HOS_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 5 54 KDM6A 7403 broad.mit.edu 37 X 44941946 44941958 + Splice_Site DEL GTCTCTTTTTTAA - - HPAC_PANCREAS NA HPAC_PANCREAS NA g.chrX:44941946_44941958delGTCTCTTTTTTAA uc004dge.3 + 22 3585 c.3210_splice c.e22-2 p.N1070_splice KDM6A_uc011mkz.1_Splice_Site_p.N1122_splice|KDM6A_uc011mla.1_Splice_Site_p.N1025_splice|KDM6A_uc011mlb.1_Splice_Site_p.N1077_splice|KDM6A_uc011mlc.1_Splice_Site_p.N774_splice|KDM6A_uc011mld.1_Splice_Site_p.N709_splice NM_021140 NP_066963 O15550 KDM6A_HUMAN ubiquitously transcribed tetratricopeptide histone H3-K4 methylation metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2) 84 CTAATACTGTGTCTCTTTTTTAAGTTCTGGGAG 0.333 0.72 23 59 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 39 ARID1A 8289 broad.mit.edu 37 1 27101611 27101612 + Frame_Shift_Ins INS - C C HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr1:27101611_27101612insC uc001bmv.1 + 18 5266_5267 c.4893_4894insC c.(4891-4896)CAGCCCfs p.Q1631fs ARID1A_uc001bmt.1_Frame_Shift_Ins_p.Q1630fs|ARID1A_uc001bmu.1_Frame_Shift_Ins_p.Q1414fs|ARID1A_uc001bmw.1_Frame_Shift_Ins_p.Q1248fs|ARID1A_uc001bmx.1_Frame_Shift_Ins_p.Q477fs|ARID1A_uc009vsm.1_Intron|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1631_1632 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CCCCTGTGCAGCCCCCCATGAT 0.574 0.58 95 129 EPHA6 285220 broad.mit.edu 37 3 97251249 97251250 + Frame_Shift_Del DEL AG - - HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr3:97251249_97251250delAG uc010how.1 + 11 2291_2292 c.2248_2249delAG c.(2248-2250)AGAfs p.R750fs EPHA6_uc011bgo.1_RNA|EPHA6_uc011bgp.1_Frame_Shift_Del_p.R116fs|EPHA6_uc003drs.3_Frame_Shift_Del_p.R142fs|EPHA6_uc003drr.3_Frame_Shift_Del_p.R142fs|EPHA6_uc003drt.2_Frame_Shift_Del_p.R142fs|EPHA6_uc010hox.1_RNA NM_001080448 NP_001073917 Q9UF33 EPHA6_HUMAN EPH receptor A6 isoform a 655 Protein kinase.|Cytoplasmic (Potential). integral to plasma membrane ATP binding|ephrin receptor activity stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1) 16 ACCAGGGAAAAGAGAGATCCCA 0.396 0.11 184 22 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 29 21 HTT 3064 broad.mit.edu 37 4 3076672 3076673 + In_Frame_Ins INS - CCGCCGCCG CCGCCGCCG rs76533208 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr4:3076672_3076673insCCGCCGCCG uc011bvq.1 + 2 271_272 c.126_127insCCGCCGCCG c.(124-129)insCCGCCGCCG p.51_52insPPP NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 49_50 establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) aacagccgccaccgccgccgcc 0.084 0.28 117 46 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.72 147 381 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 64 121 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.85 21 119 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.87 2 13 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.58 20 28 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.97 1 35 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.31 117 52 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 61 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.48 825 776 MEF2A 4205 broad.mit.edu 37 15 100252710 100252712 + In_Frame_Del DEL CAG - - HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr15:100252710_100252712delCAG uc010urw.1 + 11 1617_1619 c.1258_1260delCAG c.(1258-1260)CAGdel p.Q430del MEF2A_uc010urv.1_In_Frame_Del_p.Q360del|MEF2A_uc010bos.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvf.2_In_Frame_Del_p.Q422del|MEF2A_uc002bve.2_In_Frame_Del_p.Q428del|MEF2A_uc002bvg.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvi.2_In_Frame_Del_p.Q420del|MEF2A_uc010bot.2_In_Frame_Del_p.Q352del NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 430 Gln/Pro-rich. Missing (in Ref. 4; AAB17195/AAB17196). apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) ATCGGGCTTCcagcagcagcagc 0.493 0.33 33 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 30 445 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.11 76 9 SMAD4 4089 broad.mit.edu 37 18 48573563 48573564 + Frame_Shift_Ins INS - A A HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr18:48573563_48573564insA uc010xdp.1 + 2 685_686 c.147_148insA c.(145-150)GAGAAAfs p.E49fs SMAD4_uc010xdo.1_RNA NM_005359 NP_005350 Q13485 SMAD4_HUMAN mothers against decapentaplegic homolog 4 49_50 MH1. BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway activin responsive factor complex|centrosome|cytosol I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity p.0?(35)|p.?(5) pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1) 369 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155) AGCTGAAGGAGAAAAAAGATGA 0.376 0.89 28 235 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 65 307 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 32 200 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 9 183 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes HPAC_PANCREAS NA HPAC_PANCREAS NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.13 465 70 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HPAFII_PANCREAS NA HPAFII_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 46 TNNI3K 51086 broad.mit.edu 37 1 74808813 74808813 + Frame_Shift_Del DEL A - - HPAFII_PANCREAS NA HPAFII_PANCREAS NA g.chr1:74808813delA uc001dgf.1 + 9 933 c.882delA c.(880-882)GGAfs p.G294fs TNNI3K_uc001dgc.1_Frame_Shift_Del_p.G395fs|TNNI3K_uc001dgd.2_Frame_Shift_Del_p.G395fs|TNNI3K_uc001dge.1_Frame_Shift_Del_p.G395fs NM_015978 NP_057062 Q59H18 TNI3K_HUMAN TNNI3 interacting kinase isoform b 294 ANK 7. cytoplasm|nucleus ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1) 10 AAATATCAGGAACAGAAAGTC 0.338 0.65 38 72 FGF2 2247 broad.mit.edu 37 4 123748258 123748259 + Frame_Shift_Ins INS - G G HPAFII_PANCREAS NA HPAFII_PANCREAS NA g.chr4:123748258_123748259insG uc003iev.1 + 1 396_397 c.328_329insG c.(328-330)CGGfs p.R110fs NM_002006 NP_001997 P09038 FGF2_HUMAN fibroblast growth factor 2 110 activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing extracellular space fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity ovary(1)|lung(1)|central_nervous_system(1) 3 Pentosan Polysulfate(DB00686) 0.000 0.13 52 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HPAFII_PANCREAS NA HPAFII_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 76 66 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HPAFII_PANCREAS NA HPAFII_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 21 56 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HPAFII_PANCREAS NA HPAFII_PANCREAS NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.42 150 108 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HPAFII_PANCREAS NA HPAFII_PANCREAS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 11 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HPAFII_PANCREAS NA HPAFII_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 32 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HPAFII_PANCREAS NA HPAFII_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 358 91 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HPAFII_PANCREAS NA HPAFII_PANCREAS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.25 58 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HPAFII_PANCREAS NA HPAFII_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.59 134 189 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HPAFII_PANCREAS NA HPAFII_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 45 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes HPAFII_PANCREAS NA HPAFII_PANCREAS NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.11 202 25 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 35 F8 2157 broad.mit.edu 37 X 154157686 154157686 + Frame_Shift_Del DEL T - - HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:154157686delT uc004fmt.2 - 14 4550 c.4379delA c.(4378-4380)AATfs p.N1460fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1460 B. N -> K (in HEMA). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AGAAAGGTTATTTTTTTTGGC 0.413 0.84 19 97 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.20 265 68 BIRC6 57448 broad.mit.edu 37 2 32706514 32706514 + Frame_Shift_Del DEL T - - HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:32706514delT uc010ezu.2 + 38 7669 c.7535delT c.(7534-7536)GTTfs p.V2512fs NM_016252 NP_057336 Q9NR09 BIRC6_HUMAN baculoviral IAP repeat-containing 6 2512 anti-apoptosis|apoptosis intracellular acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1) 14 Acute lymphoblastic leukemia(172;0.155) GCAGCCAAGGTTTTTAAGGTA 0.239 0.23 27 8 STK25 10494 broad.mit.edu 37 2 242438541 242438541 + Frame_Shift_Del DEL C - - HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:242438541delC uc002wbm.2 - 6 905 c.634delG c.(634-636)GAGfs p.E212fs STK25_uc002wbk.2_Frame_Shift_Del_p.E31fs|STK25_uc002wbl.2_Frame_Shift_Del_p.E31fs|STK25_uc002wbn.2_Frame_Shift_Del_p.E212fs|STK25_uc002wbo.2_Frame_Shift_Del_p.E135fs|STK25_uc010zos.1_Frame_Shift_Del_p.E118fs|STK25_uc010zot.1_Frame_Shift_Del_p.E138fs|STK25_uc002wbp.2_Frame_Shift_Del_p.E212fs|STK25_uc010fzo.2_Frame_Shift_Del_p.E135fs|STK25_uc010zou.1_Frame_Shift_Del_p.E118fs|STK25_uc010zov.1_Frame_Shift_Del_p.E118fs NM_006374 NP_006365 O00506 STK25_HUMAN serine/threonine kinase 25 212 Protein kinase. response to oxidative stress|signal transduction Golgi apparatus ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity 0 all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2) Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839) TTTGGAGGCTCCCCCTTGGCC 0.617 0.20 234 60 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.33 20 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.17 38 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 94 166 INPP4B 8821 broad.mit.edu 37 4 143007332 143007332 + Frame_Shift_Del DEL T - - HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:143007332delT uc003iix.3 - 25 3047 c.2452delA c.(2452-2454)AGAfs p.R818fs INPP4B_uc003iiw.3_Frame_Shift_Del_p.R818fs|INPP4B_uc011chm.1_RNA|INPP4B_uc011chn.1_Frame_Shift_Del_p.R633fs|INPP4B_uc011cho.1_RNA NM_003866 NP_003857 O15327 INP4B_HUMAN inositol polyphosphate-4-phosphatase, type II, 818 signal transduction phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity ovary(1)|lung(1) 2 all_hematologic(180;0.158) ACATTCTTTCTTTTTTTGGAT 0.343 0.36 25 14 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 18 42 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.71 4 10 ATXN1 6310 broad.mit.edu 37 6 16327865 16327867 + In_Frame_Del DEL TGC - - HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:16327865_16327867delTGC uc003nbt.2 - 8 1646_1648 c.675_677delGCA c.(673-678)CAGCAC>CAC p.Q225del ATXN1_uc010jpi.2_In_Frame_Del_p.Q225del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCTGCTGAGGtgctgctgctgct 0.369 0.15 39 7 EPHB6 2051 broad.mit.edu 37 7 142561447 142561448 + Frame_Shift_Ins INS - G G HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:142561447_142561448insG uc011kst.1 + 6 946_947 c.159_160insG c.(157-162)CCAGGGfs p.P53fs EPHB6_uc011ksu.1_Frame_Shift_Ins_p.P53fs|EPHB6_uc003wbs.2_Intron|EPHB6_uc003wbt.2_5'UTR|EPHB6_uc003wbu.2_Intron NM_004445 NP_004436 O15197 EPHB6_HUMAN ephrin receptor EphB6 precursor 53_54 Extracellular (Potential). extracellular region|integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1) 19 Melanoma(164;0.059) 0.000 0.43 183 139 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.32 15 7 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 35 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 704 370 TMPO 7112 broad.mit.edu 37 12 98938122 98938122 + Frame_Shift_Del DEL A - - HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:98938122delA uc001tfj.2 + 5 1015 c.778delA c.(778-780)AAAfs p.K260fs TMPO_uc001tfk.2_Intron|TMPO_uc001tfl.2_Intron NM_001032283 NP_001027454 P42167 LAP2B_HUMAN thymopoietin isoform beta 260 Nucleoplasmic (Potential). integral to membrane|nuclear inner membrane DNA binding|lamin binding ovary(2) 2 AACTCCAAGGAAAAGGGTGAT 0.378 0.13 76 11 BCKDK 10295 broad.mit.edu 37 16 31122472 31122473 + Frame_Shift_Ins INS - G G HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:31122472_31122473insG uc002eaw.3 + 9 1093_1094 c.777_778insG c.(775-780)GCTGCCfs p.A259fs BCKDK_uc002eav.3_Frame_Shift_Ins_p.A259fs|BCKDK_uc010cah.2_RNA|BCKDK_uc010cai.2_Frame_Shift_Ins_p.A259fs NM_005881 NP_005872 O14874 BCKD_HUMAN branched chain ketoacid dehydrogenase kinase 259_260 Histidine kinase. branched chain family amino acid catabolic process|peptidyl-histidine phosphorylation mitochondrial alpha-ketoglutarate dehydrogenase complex [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity|ATP binding|protein binding|protein serine/threonine kinase activity|two-component sensor activity stomach(1)|breast(1) 2 GCCATGTGGCTGCCCGGTTCCC 0.624 0.14 44 7 CYLD 1540 broad.mit.edu 37 16 50784085 50784085 + Frame_Shift_Del DEL C - - HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:50784085delC uc002egp.1 + 4 891 c.476delC c.(475-477)TCCfs p.S159fs CYLD_uc002egn.1_Frame_Shift_Del_p.S159fs|CYLD_uc002ego.2_Frame_Shift_Del_p.S159fs|CYLD_uc010cbs.1_Frame_Shift_Del_p.S159fs|CYLD_uc002egq.1_Frame_Shift_Del_p.S159fs|CYLD_uc002egr.1_Frame_Shift_Del_p.S159fs|CYLD_uc002egs.1_Frame_Shift_Del_p.S159fs NM_015247 NP_056062 Q9NQC7 CYLD_HUMAN ubiquitin carboxyl-terminal hydrolase CYLD 159 CAP-Gly 1.|Interaction with TRIP. cell cycle|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K63-linked deubiquitination|regulation of microtubule cytoskeleton organization|regulation of mitotic cell cycle|translation|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway cytosol|extrinsic to internal side of plasma membrane|microtubule|perinuclear region of cytoplasm|ribosome proline-rich region binding|protein kinase binding|structural constituent of ribosome|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding skin(19)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|central_nervous_system(3) 28 all_cancers(37;0.0156) AGGACAGTCTCCGGAATATTC 0.428 0.94 2 34 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 79 1246 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 58 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 108 273 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 11 118 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS229T_LUNG NA HS229T_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 4 31 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HS229T_LUNG NA HS229T_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.55 160 192 FMN2 56776 broad.mit.edu 37 1 240370942 240370974 + In_Frame_Del DEL CCTCCGCCCCCTCTACCCGGAGCGGCAATACCC - - rs150891575;rs6143701;rs142725738;rs146070457;rs72444563;rs144739133;rs142178619 byFrequency;byFrequency;byFrequency;byFrequency HS229T_LUNG NA HS229T_LUNG NA g.chr1:240370942_240370974delCCTCCGCCCCCTCTACCCGGAGCGGCAATACCC uc010pyd.1 + 5 3055_3087 c.2830_2862delCCTCCGCCCCCTCTACCCGGAGCGGCAATACCC c.(2830-2862)CCTCCGCCCCCTCTACCCGGAGCGGCAATACCCdel p.PPPPLPGAAIP944del FMN2_uc010pye.1_In_Frame_Del_p.PPPPLPGAAIP948del NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 944_954 Pro-rich.|FH1. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) GGGAATACCTCCTCCGCCCCCTCTACCCGGAGCGGCAATACCCCCTCCGCCCC 0.700 0.33 27 13 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HS229T_LUNG NA HS229T_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.44 18 14 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 HS229T_LUNG NA HS229T_LUNG NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.45 12 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS229T_LUNG NA HS229T_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.12 58 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS229T_LUNG NA HS229T_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 81 121 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS229T_LUNG NA HS229T_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 26 38 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HS229T_LUNG NA HS229T_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.29 397 160 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HS229T_LUNG NA HS229T_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.19 46 11 POU3F2 5454 broad.mit.edu 37 6 99283172 99283173 + In_Frame_Ins INS - CAG CAG HS229T_LUNG NA HS229T_LUNG NA g.chr6:99283172_99283173insCAG uc003ppe.2 + 1 593_594 c.423_424insCAG c.(421-426)insCAG p.149_150insQ NM_005604 NP_005595 P20265 PO3F2_HUMAN POU domain, class 3, transcription factor 2 149_150 positive regulation of cell proliferation identical protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197) BRCA - Breast invasive adenocarcinoma(108;0.0355) aacagcagcaacagcagcagca 0.465 0.17 126 25 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HS229T_LUNG NA HS229T_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 2 37 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS229T_LUNG NA HS229T_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 824 298 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS229T_LUNG NA HS229T_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 5 31 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS229T_LUNG NA HS229T_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.79 46 176 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HS229T_LUNG NA HS229T_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 107 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS229T_LUNG NA HS229T_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 70 768 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS229T_LUNG NA HS229T_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 8 109 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS274T_BREAST NA HS274T_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 70 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT HS274T_BREAST NA HS274T_BREAST NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.34 199 104 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A HS274T_BREAST NA HS274T_BREAST NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 1.00 0 13 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HS274T_BREAST NA HS274T_BREAST NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.52 11 12 HTT 3064 broad.mit.edu 37 4 3076672 3076673 + In_Frame_Ins INS - CCG CCG rs76533208 HS274T_BREAST NA HS274T_BREAST NA g.chr4:3076672_3076673insCCG uc011bvq.1 + 2 271_272 c.126_127insCCG c.(124-129)insCCG p.51_52insP NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 49_50 establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) aacagccgccaccgccgccgcc 0.084 0.27 35 13 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS274T_BREAST NA HS274T_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.60 17 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS274T_BREAST NA HS274T_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.76 77 245 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS274T_BREAST NA HS274T_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 35 79 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HS274T_BREAST NA HS274T_BREAST NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.32 355 164 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 HS274T_BREAST NA HS274T_BREAST NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.50 6 6 ATXN1 6310 broad.mit.edu 37 6 16327907 16327909 + In_Frame_Del DEL TGA - - rs59310777 by1000genomes HS274T_BREAST NA HS274T_BREAST NA g.chr6:16327907_16327909delTGA uc003nbt.2 - 8 1604_1606 c.633_635delTCA c.(631-636)CATCAG>CAG p.H211del ATXN1_uc010jpi.2_In_Frame_Del_p.H211del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 211 Poly-Gln. H -> HQ (in Ref. 1; CAA55793). cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgctgatgctgatgct 0.384 0.24 121 39 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 HS274T_BREAST NA HS274T_BREAST NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.10 208 24 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT HS274T_BREAST NA HS274T_BREAST NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.17 1066 217 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HS274T_BREAST NA HS274T_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.84 4 21 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS274T_BREAST NA HS274T_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 21 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - HS274T_BREAST NA HS274T_BREAST NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.12 909 123 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS274T_BREAST NA HS274T_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.52 458 498 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 HS274T_BREAST NA HS274T_BREAST NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.68 6 13 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes HS274T_BREAST NA HS274T_BREAST NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.25 103 35 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS274T_BREAST NA HS274T_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 19 180 ILVBL 10994 broad.mit.edu 37 19 15226818 15226819 + Frame_Shift_Ins INS - C C HS274T_BREAST NA HS274T_BREAST NA g.chr19:15226818_15226819insC uc002nam.2 - 13 1656_1657 c.1535_1536insG c.(1534-1536)GATfs p.D512fs ILVBL_uc010xof.1_Frame_Shift_Ins_p.D153fs|ILVBL_uc010dzw.2_Frame_Shift_Ins_p.D405fs NM_006844 NP_006835 A1L0T0 ILVBL_HUMAN ilvB (bacterial acetolactate synthase)-like 512 Thiamine pyrophosphate binding (By similarity). integral to membrane magnesium ion binding|thiamine pyrophosphate binding|transferase activity ovary(2) 2 0.000 1.00 0 11 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HS274T_BREAST NA HS274T_BREAST NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 232 47 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS274T_BREAST NA HS274T_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 121 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS281T_BREAST NA HS281T_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 5 88 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HS281T_BREAST NA HS281T_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.36 9 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS281T_BREAST NA HS281T_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 104 141 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS281T_BREAST NA HS281T_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 39 69 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS281T_BREAST NA HS281T_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.89 2 17 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HS281T_BREAST NA HS281T_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.11 1295 153 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - HS281T_BREAST NA HS281T_BREAST NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.21 38 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS281T_BREAST NA HS281T_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 360 148 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS281T_BREAST NA HS281T_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 21 162 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS281T_BREAST NA HS281T_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.33 55 27 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HS281T_BREAST NA HS281T_BREAST NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 142 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS281T_BREAST NA HS281T_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 214 1486 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS281T_BREAST NA HS281T_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 105 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS578T_BREAST NA HS578T_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 49 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 HS578T_BREAST NA HS578T_BREAST NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.14 43 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS578T_BREAST NA HS578T_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.35 20 11 FGF2 2247 broad.mit.edu 37 4 123748258 123748259 + Frame_Shift_Ins INS - G G HS578T_BREAST NA HS578T_BREAST NA g.chr4:123748258_123748259insG uc003iev.1 + 1 396_397 c.328_329insG c.(328-330)CGGfs p.R110fs NM_002006 NP_001997 P09038 FGF2_HUMAN fibroblast growth factor 2 110 activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing extracellular space fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity ovary(1)|lung(1)|central_nervous_system(1) 3 Pentosan Polysulfate(DB00686) 0.000 0.10 614 65 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS578T_BREAST NA HS578T_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 123 143 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS578T_BREAST NA HS578T_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 30 61 PIK3R1 5295 broad.mit.edu 37 5 67589591 67589592 + In_Frame_Ins INS - ATA ATA HS578T_BREAST NA HS578T_BREAST NA g.chr5:67589591_67589592insATA uc003jva.2 + 11 1914_1915 c.1354_1355insATA c.(1354-1356)TAT>TATAAT p.453_454insN PIK3R1_uc003jvb.2_In_Frame_Ins_p.453_454insN|PIK3R1_uc003jvc.2_In_Frame_Ins_p.153_154insN|PIK3R1_uc003jvd.2_In_Frame_Ins_p.183_184insN|PIK3R1_uc003jve.2_In_Frame_Ins_p.132_133insN|PIK3R1_uc011crb.1_In_Frame_Ins_p.123_124insN NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 453_454 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.N453_T454insN(2)|p.D434_Q475del(2)|p.G446_Y452>VI(1)|p.?(1)|p.E451_Y452del(1)|p.Y452_Q455>SGGSRIK(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) 0.000 0.97 19 628 CYP3A7 1551 broad.mit.edu 37 7 99306707 99306709 + In_Frame_Del DEL GAA - - rs143401162 byFrequency HS578T_BREAST NA HS578T_BREAST NA g.chr7:99306707_99306709delGAA uc003uru.2 - 11 1307_1309 c.1202_1204delTTC c.(1201-1206)CTTCAT>CAT p.L401del ZNF498_uc003urn.2_Intron|CYP3A5_uc003urs.2_Intron|CYP3A5_uc010lgg.2_Intron NM_000765 NP_000756 P24462 CP3A7_HUMAN cytochrome P450, family 3, subfamily A, 401 xenobiotic metabolic process endoplasmic reticulum membrane|microsome aromatase activity|electron carrier activity|heme binding|oxygen binding ovary(1) 1 Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228) GGGTCATGATGAAGAACATAGCT 0.498 0.61 108 168 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HS578T_BREAST NA HS578T_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.12 57 8 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 HS578T_BREAST NA HS578T_BREAST NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.68 6 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS578T_BREAST NA HS578T_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 788 322 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS578T_BREAST NA HS578T_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 42 331 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS578T_BREAST NA HS578T_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.85 30 164 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HS578T_BREAST NA HS578T_BREAST NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.27 95 35 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS578T_BREAST NA HS578T_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.37 614 357 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS578T_BREAST NA HS578T_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 10 210 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS600T_SKIN NA HS600T_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.86 3 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS600T_SKIN NA HS600T_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 66 37 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS600T_SKIN NA HS600T_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 22 40 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HS600T_SKIN NA HS600T_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 2 12 MLL3 58508 broad.mit.edu 37 7 151859815 151859816 + In_Frame_Ins INS - CAT CAT HS600T_SKIN NA HS600T_SKIN NA g.chr7:151859815_151859816insCAT uc003wla.2 - 43 11065_11066 c.10846_10847insATG c.(10846-10848)GCA>GATGCA p.3615_3616insD MLL3_uc003wkz.2_In_Frame_Ins_p.2676_2677insD|MLL3_uc003wky.2_In_Frame_Ins_p.1124_1125insD NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 3615_3616 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) GGTGGATTCTGCATCAtcatct 0.381 0.34 107 56 TGFBR1 7046 broad.mit.edu 37 9 101867548 101867549 + Frame_Shift_Ins INS - T T HS600T_SKIN NA HS600T_SKIN NA g.chr9:101867548_101867549insT uc004azc.2 + 1 137_138 c.61_62insT c.(61-63)GCGfs p.A21fs TGFBR1_uc004azd.2_Frame_Shift_Ins_p.A21fs NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 21 activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.22 29 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS600T_SKIN NA HS600T_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 116 49 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS600T_SKIN NA HS600T_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 29 211 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS600T_SKIN NA HS600T_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.26 34 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS600T_SKIN NA HS600T_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 117 496 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS600T_SKIN NA HS600T_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 67 HEPH 9843 broad.mit.edu 37 X 65393494 65393495 + Frame_Shift_Ins INS - C C HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:65393494_65393495insC uc011moz.1 + 4 545_546 c.485_486insC c.(484-486)GGCfs p.G162fs HEPH_uc004dwn.2_Frame_Shift_Ins_p.G162fs|HEPH_uc004dwo.2_5'UTR|HEPH_uc010nkr.2_Frame_Shift_Ins_p.G162fs|HEPH_uc011mpa.1_Frame_Shift_Ins_p.G162fs NM_138737 NP_620074 Q9BQS7 HEPH_HUMAN hephaestin isoform a 159 Extracellular (Potential).|Plastocyanin-like 1. cellular iron ion homeostasis|copper ion transport|transmembrane transport integral to membrane|plasma membrane copper ion binding|oxidoreductase activity lung(5)|ovary(4) 9 CCCCCGGGGGGCAGCCATATCT 0.535 0.20 41 10 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 35 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.35 184 97 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.26 26 9 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 97 20 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.41 16 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.30 92 40 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 22 52 FLT4 2324 broad.mit.edu 37 5 180041154 180041155 + Frame_Shift_Ins INS - C C HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:180041154_180041155insC uc003mma.3 - 24 3323_3324 c.3244_3245insG c.(3244-3246)GCCfs p.A1082fs FLT4_uc003mlz.3_Frame_Shift_Ins_p.A1082fs NM_002020 NP_002011 P35916 VGFR3_HUMAN fms-related tyrosine kinase 4 isoform 2 1082 Cytoplasmic (Potential).|Protein kinase. positive regulation of cell proliferation integral to plasma membrane ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1) 15 all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114) all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) all cancers(165;0.134) Sorafenib(DB00398)|Sunitinib(DB01268) GCTTTCAGGGGCCATCCACTTC 0.614 0.12 50 7 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.31 46 21 VPS13B 157680 broad.mit.edu 37 8 100844595 100844596 + Splice_Site DEL AG - - rs74485751 HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:100844595_100844596delAG uc003yiv.2 + 52 9517 c.9406_splice c.e52-1 p.Y3136_splice VPS13B_uc003yiw.2_Splice_Site_p.Y3111_splice NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) ttttttttttAGTATTTTCGTG 0.347 0.12 69 9 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.31 400 183 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 146 17 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 12 113 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.50 19 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 108 311 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 55 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS606T_BREAST NA HS606T_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 6 86 MAMLD1 10046 broad.mit.edu 37 X 149639324 149639325 + In_Frame_Ins INS - CAG CAG HS606T_BREAST NA HS606T_BREAST NA g.chrX:149639324_149639325insCAG uc004fee.1 + 3 1555_1556 c.1479_1480insCAG c.(1477-1482)insCAG p.502_503insQ MAMLD1_uc011mxt.1_In_Frame_Ins_p.464_465insQ|MAMLD1_uc011mxu.1_In_Frame_Ins_p.477_478insQ|MAMLD1_uc011mxv.1_In_Frame_Ins_p.477_478insQ|MAMLD1_uc011mxw.1_In_Frame_Ins_p.429_430insQ NM_005491 NP_005482 Q13495 MAMD1_HUMAN mastermind-like domain containing 1 502_503 male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus 0 Acute lymphoblastic leukemia(192;6.56e-05) TAAGCcagcaacagcagcagca 0.441 0.39 11 7 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HS606T_BREAST NA HS606T_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 481 149 ROCK2 9475 broad.mit.edu 37 2 11342248 11342249 + Splice_Site INS - T T HS606T_BREAST NA HS606T_BREAST NA g.chr2:11342248_11342249insT uc002rbd.1 - 21 2999 c.2550_splice c.e21-1 p.K850_splice NM_004850 NP_004841 O75116 ROCK2_HUMAN Rho-associated, coiled-coil containing protein axon guidance|cytokinesis|intracellular signal transduction cytosol|plasma membrane ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity stomach(2)|skin(2) 4 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162) CTGACGTTCTCTGTGAGGACAA 0.277 0.49 176 167 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HS606T_BREAST NA HS606T_BREAST NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.32 17 8 HTT 3064 broad.mit.edu 37 4 3076604 3076606 + In_Frame_Del DEL CAG - - rs10618869 HS606T_BREAST NA HS606T_BREAST NA g.chr4:3076604_3076606delCAG uc011bvq.1 + 2 203_205 c.58_60delCAG c.(58-60)CAGdel p.Q40del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagc 0.335 0.14 82 13 HTT 3064 broad.mit.edu 37 4 3076672 3076673 + In_Frame_Ins INS - CCGCCGCCG CCGCCGCCG rs76533208 HS606T_BREAST NA HS606T_BREAST NA g.chr4:3076672_3076673insCCGCCGCCG uc011bvq.1 + 2 271_272 c.126_127insCCGCCGCCG c.(124-129)insCCGCCGCCG p.51_52insPPP NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 49_50 establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) aacagccgccaccgccgccgcc 0.084 0.15 74 13 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS606T_BREAST NA HS606T_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.19 55 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS606T_BREAST NA HS606T_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 108 251 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS606T_BREAST NA HS606T_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.43 69 52 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HS606T_BREAST NA HS606T_BREAST NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.43 8 6 ATXN1 6310 broad.mit.edu 37 6 16327865 16327867 + In_Frame_Del DEL TGC - - HS606T_BREAST NA HS606T_BREAST NA g.chr6:16327865_16327867delTGC uc003nbt.2 - 8 1646_1648 c.675_677delGCA c.(673-678)CAGCAC>CAC p.Q225del ATXN1_uc010jpi.2_In_Frame_Del_p.Q225del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCTGCTGAGGtgctgctgctgct 0.369 0.12 98 14 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HS606T_BREAST NA HS606T_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 22 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS606T_BREAST NA HS606T_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 28 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HS606T_BREAST NA HS606T_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.26 85 30 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - HS606T_BREAST NA HS606T_BREAST NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 64 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS606T_BREAST NA HS606T_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.50 489 489 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCAGCAGCA GCAGCAGCA rs3832799;rs72405287 HS606T_BREAST NA HS606T_BREAST NA g.chr12:103352171_103352172insGCAGCAGCA uc001tjr.3 + 1 720_721 c.149_150insGCAGCAGCA c.(148-150)GCG>GCGCAGCAGCAG p.62_63insQQQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.33 12 6 CDX2 1045 broad.mit.edu 37 13 28542791 28542802 + In_Frame_Del DEL TGGTGGTGCGGA - - rs145287912 HS606T_BREAST NA HS606T_BREAST NA g.chr13:28542791_28542802delTGGTGGTGCGGA uc001urv.2 - 1 516_527 c.342_353delTCCGCACCACCA c.(340-354)CATCCGCACCACCAC>CAC p.114_118HPHHH>H NM_001265 NP_001256 Q99626 CDX2_HUMAN caudal type homeobox 2 114_118 organ morphogenesis|transcription from RNA polymerase II promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity lung(1) 1 all_cancers(110;0.191)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155) Lung SC(185;0.0156) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199) 0.000 0.29 602 244 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS606T_BREAST NA HS606T_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 32 232 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS606T_BREAST NA HS606T_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 134 596 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS606T_BREAST NA HS606T_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 6 117 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 53 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.31 180 79 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 68 112 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 26 54 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 1 9 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.12 53 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 326 152 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 41 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 89 576 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 71 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.85 4 23 TTN 7273 broad.mit.edu 37 2 179463253 179463255 + In_Frame_Del DEL CTT - - HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179463253_179463255delCTT uc010zfg.1 - 241 49609_49611 c.49385_49387delAAG c.(49384-49389)GAAGGA>GGA p.E16462del uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.E10157del|TTN_uc010zfi.1_In_Frame_Del_p.E10090del|TTN_uc010zfj.1_In_Frame_Del_p.E9965del NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 17389 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCTTCTTTTCCTTCTTCTTTATA 0.369 0.42 96 69 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.46 7 6 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.14 42 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 70 58 MGC42105 167359 broad.mit.edu 37 5 43277325 43277326 + Frame_Shift_Ins INS - G G HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:43277325_43277326insG uc003jno.2 + 3 1340_1341 c.459_460insG c.(457-462)GCAGGGfs p.A153fs NM_153361 NP_699192 Q8IY84 NIM1_HUMAN serine/threonine-protein kinase NIM1 153_154 Protein kinase. ATP binding|magnesium ion binding|protein serine/threonine kinase activity lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1) 9 TGGAGTATGCAGGGGGTGGGGA 0.515 0.43 71 54 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 29 48 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.64 4 7 NUP153 9972 broad.mit.edu 37 6 17633077 17633078 + Splice_Site INS - AA AA rs36027788;rs147103527 HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:17633077_17633078insAA uc003ncd.1 - 17 2665 c.2465_splice c.e17-1 p.G822_splice NUP153_uc011dje.1_Splice_Site_p.G853_splice|NUP153_uc010jpl.1_Splice_Site_p.G780_splice NM_005124 NP_005115 P49790 NU153_HUMAN nucleoporin 153kDa carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm DNA binding|protein binding|transporter activity|zinc ion binding lung(4)|ovary(2)|breast(2)|skin(1) 9 Breast(50;0.0259)|Ovarian(93;0.0584) all_hematologic(90;0.125) all cancers(50;0.0981)|Epithelial(50;0.112) CTGAACTTCCTAAAAAAAAAAA 0.406 0.20 40 10 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.38 430 264 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.61 14 22 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.11 135 16 ATN1 1822 broad.mit.edu 37 12 7045883 7045891 + In_Frame_Del DEL CAACAGCAA - - rs150855426 byFrequency HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:7045883_7045891delCAACAGCAA uc001qrw.1 + 5 1690_1698 c.1453_1461delCAACAGCAA c.(1453-1461)CAACAGCAAdel p.QQQ500del ATN1_uc001qrx.1_In_Frame_Del_p.QQQ500del|ATN1_uc001qry.1_In_Frame_Del_p.QQQ484del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 500_502 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 TCACCACcagcaacagcaacagcagcagc 0.450 0.33 22 11 SOCS1 8651 broad.mit.edu 37 16 11349196 11349197 + In_Frame_Ins INS - CCGGGA CCGGGA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:11349196_11349197insCCGGGA uc002dar.1 - 2 293_294 c.139_140insTCCCGG c.(139-141)GCC>GTCCCGGCC p.46_47insVP C16orf75_uc002daq.1_Intron NM_003745 NP_003736 O15524 SOCS1_HUMAN suppressor of cytokine signaling 1 46_47 interferon-gamma-mediated signaling pathway|JAK-STAT cascade|negative regulation of insulin receptor signaling pathway|negative regulation of tyrosine phosphorylation of Stat3 protein|regulation of growth|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway cytosol insulin-like growth factor receptor binding|protein kinase binding|protein kinase inhibitor activity p.A37fs*27(2) haematopoietic_and_lymphoid_tissue(64)|lung(3)|breast(1)|central_nervous_system(1) 69 0.000 0.15 509 88 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 9 138 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 34 306 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS616T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 66 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS618T_LUNG NA HS618T_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 9 81 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HS618T_LUNG NA HS618T_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 265 74 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS618T_LUNG NA HS618T_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.42 151 109 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HS618T_LUNG NA HS618T_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.68 76 163 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HS618T_LUNG NA HS618T_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.27 27 10 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HS618T_LUNG NA HS618T_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 23 PAXIP1 22976 broad.mit.edu 37 7 154760540 154760541 + In_Frame_Ins INS - TGC TGC HS618T_LUNG NA HS618T_LUNG NA g.chr7:154760540_154760541insTGC uc003wlp.2 - 7 1413_1414 c.1370_1371insGCA c.(1369-1371)CAA>CAGCAA p.457_457Q>QQ PAXIP1_uc003wlq.1_In_Frame_Ins_p.423_423Q>QQ|PAXIP1_uc011kvs.1_In_Frame_Ins_p.421_421Q>QQ|PAXIP1_uc003wlr.1_In_Frame_Ins_p.366_366Q>QQ NM_007349 NP_031375 Q6ZW49 PAXI1_HUMAN PAX interacting protein 1 457 Gln-rich. DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent histone methyltransferase complex|nuclear matrix p.F457C(1) lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_neural(206;0.119) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.0296) UCEC - Uterine corpus endometrioid carcinoma (81;0.178) GCGGATGGGCTtgctgctgctg 0.203 0.37 48 28 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS618T_LUNG NA HS618T_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 41 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HS618T_LUNG NA HS618T_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.34 521 271 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - HS618T_LUNG NA HS618T_LUNG NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.42 102 75 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HS618T_LUNG NA HS618T_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.37 19 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS618T_LUNG NA HS618T_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 794 185 ATN1 1822 broad.mit.edu 37 12 7045892 7045894 + In_Frame_Del DEL CAG - - rs66756893;rs67074116 HS618T_LUNG NA HS618T_LUNG NA g.chr12:7045892_7045894delCAG uc001qrw.1 + 5 1699_1701 c.1462_1464delCAG c.(1462-1464)CAGdel p.Q502del ATN1_uc001qrx.1_In_Frame_Del_p.Q502del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagc 0.458 0.15 44 8 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HS618T_LUNG NA HS618T_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.28 33 13 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS618T_LUNG NA HS618T_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.78 42 145 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HS618T_LUNG NA HS618T_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 91 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS618T_LUNG NA HS618T_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 49 447 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS618T_LUNG NA HS618T_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 7 127 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS675T_LARGE_INTESTINE NA HS675T_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS675T_LARGE_INTESTINE NA HS675T_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.43 52 39 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS675T_LARGE_INTESTINE NA HS675T_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.56 15 19 CDKL3 51265 broad.mit.edu 37 5 133695604 133695605 + Frame_Shift_Ins INS - A A HS675T_LARGE_INTESTINE NA HS675T_LARGE_INTESTINE NA g.chr5:133695604_133695605insA uc003kzf.3 - 3 462_463 c.343_344insT c.(343-345)TATfs p.Y115fs CDKL3_uc011cxm.1_Intron|CDKL3_uc011cxn.1_Intron|CDKL3_uc010jdw.2_Intron|CDKL3_uc011cxo.1_Intron|CDKL3_uc011cxp.1_Intron|CDKL3_uc011cxq.1_5'UTR|CDKL3_uc003kzg.3_Frame_Shift_Ins_p.Y115fs|CDKL3_uc011cxr.1_Frame_Shift_Ins_p.Y115fs NM_001113575 NP_001107047 Q8IVW4 CDKL3_HUMAN cyclin-dependent kinase-like 3 isoform 1 115 Protein kinase. cytoplasm ATP binding|cyclin-dependent protein kinase activity breast(1) 1 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) ACTGTGAAGATAGTCAATTGCT 0.337 0.47 20 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS675T_LARGE_INTESTINE NA HS675T_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 114 19 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS675T_LARGE_INTESTINE NA HS675T_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 8 72 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS675T_LARGE_INTESTINE NA HS675T_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.29 41 17 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HS675T_LARGE_INTESTINE NA HS675T_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.10 72 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS675T_LARGE_INTESTINE NA HS675T_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 49 471 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS675T_LARGE_INTESTINE NA HS675T_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 2 29 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.53 24 27 PDE4DIP 9659 broad.mit.edu 37 1 144923716 144923716 + Frame_Shift_Del DEL T - - HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923716delT uc001elw.3 - 6 1033 c.742delA c.(742-744)ATCfs p.I248fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.I314fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.I248fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.I248fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.I411fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.I35fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 248 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) GTTTGCTGGATTTTTTCCTGG 0.453 0.27 419 155 MSH2 4436 broad.mit.edu 37 2 47641559 47641560 + Splice_Site DEL TA - - rs11309117 HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr2:47641559_47641560delTA uc002rvy.1 + 5 1010 c.942_splice c.e5+2 p.Q314_splice MSH2_uc010yoh.1_Splice_Site_p.Q248_splice|MSH2_uc002rvz.2_Splice_Site_p.Q314_splice|MSH2_uc010fbg.2_Intron NM_000251 NP_000242 P43246 MSH2_HUMAN mutS homolog 2 B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes MutSalpha complex|MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding p.?(1) large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1) 55 all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) CTTTTTCAGGTaaaaaaaaaaa 0.297 0.18 42 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 47 87 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.34 75 39 POU3F2 5454 broad.mit.edu 37 6 99283172 99283173 + In_Frame_Ins INS - CAG CAG HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr6:99283172_99283173insCAG uc003ppe.2 + 1 593_594 c.423_424insCAG c.(421-426)insCAG p.149_150insQ NM_005604 NP_005595 P20265 PO3F2_HUMAN POU domain, class 3, transcription factor 2 149_150 positive regulation of cell proliferation identical protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197) BRCA - Breast invasive adenocarcinoma(108;0.0355) aacagcagcaacagcagcagca 0.465 0.14 50 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 1 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 16 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 646 69 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.17 71 15 CSNK2A1P 283106 broad.mit.edu 37 11 11374466 11374468 + In_Frame_Del DEL AAC - - HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr11:11374466_11374468delAAC uc001mjp.2 - 1 437_439 c.199_201delGTT c.(199-201)GTTdel p.V67del GALNTL4_uc001mjo.2_Intron NM_177559 NP_808227 casein kinase II alpha 1 subunit isoform a 0 TGAGAATTTTAACAACAACTTTT 0.365 0.36 95 54 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 291 131 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.11 139 17 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 8 155 OLIG2 10215 broad.mit.edu 37 21 34399730 34399739 + Frame_Shift_Del DEL CGGCCTGCGG - - HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr21:34399730_34399739delCGGCCTGCGG uc002yqx.1 + 2 718_727 c.560_569delCGGCCTGCGG c.(559-570)TCGGCCTGCGGCfs p.S187fs NM_005806 NP_005797 Q13516 OLIG2_HUMAN oligodendrocyte lineage transcription factor 2 187_190 cytoplasm|nucleus|plasma membrane DNA binding central_nervous_system(2) 2 0.000 0.30 957 414 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 119 477 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS683_CENTRAL_NERVOUS_SYSTEM NA HS683_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 3 42 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS688AT_SKIN NA HS688AT_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.54 16 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS688AT_SKIN NA HS688AT_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.25 82 28 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS688AT_SKIN NA HS688AT_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 21 34 ZNF323 64288 broad.mit.edu 37 6 28294200 28294201 + Frame_Shift_Ins INS - T T HS688AT_SKIN NA HS688AT_SKIN NA g.chr6:28294200_28294201insT uc003nla.2 - 4 1363_1364 c.963_964insA c.(961-966)AAACCAfs p.K321fs ZNF323_uc003nld.2_Frame_Shift_Ins_p.K321fs|ZNF323_uc010jra.2_Frame_Shift_Ins_p.K321fs|ZNF323_uc003nlb.2_Frame_Shift_Ins_p.K162fs|ZNF323_uc010jrb.2_Frame_Shift_Ins_p.K162fs|ZNF323_uc003nlc.2_Frame_Shift_Ins_p.K321fs NM_001135216 NP_001128688 Q96LW9 ZN323_HUMAN zinc finger protein 323 321_322 viral reproduction nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1)|skin(1) 2 CATTCATATGGTTTTTCCCCTG 0.500 0.60 6 9 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HS688AT_SKIN NA HS688AT_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.37 34 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS688AT_SKIN NA HS688AT_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 1 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS688AT_SKIN NA HS688AT_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.23 24 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS688AT_SKIN NA HS688AT_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 38 449 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 3 33 ARID1A 8289 broad.mit.edu 37 1 27100181 27100182 + In_Frame_Ins INS - GCA GCA HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr1:27100181_27100182insGCA uc001bmv.1 + 16 4350_4351 c.3977_3978insGCA c.(3976-3978)CCG>CCGCAG p.1334_1335insQ ARID1A_uc001bmt.1_In_Frame_Ins_p.1333_1334insQ|ARID1A_uc001bmu.1_In_Frame_Ins_p.1334_1335insQ|ARID1A_uc001bmw.1_In_Frame_Ins_p.951_952insQ|ARID1A_uc001bmx.1_In_Frame_Ins_p.180_181insQ|ARID1A_uc009vsm.1_5'UTR|ARID1A_uc009vsn.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1334_1335 Gln-rich. androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.Q1334_R1335insQ(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CGCTACCCCCCgcagcagcagc 0.510 0.21 45 12 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.26 241 85 IL1R1 3554 broad.mit.edu 37 2 102793184 102793184 + Frame_Shift_Del DEL A - - HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr2:102793184delA uc002tbq.2 + 12 1993 c.1675delA c.(1675-1677)AAAfs p.K559fs IL1R1_uc010fix.2_Frame_Shift_Del_p.K528fs|IL1R1_uc002tbr.2_Frame_Shift_Del_p.K559fs NM_000877 NP_000868 P14778 IL1R1_HUMAN interleukin 1 receptor, type I precursor 559 Cytoplasmic (Potential). innate immune response integral to plasma membrane interleukin-1, Type I, activating receptor activity|platelet-derived growth factor receptor binding skin(1) 1 Anakinra(DB00026) CACTAAGGAGAAACTGCAAAG 0.512 0.52 93 101 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 0.92 1 12 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.22 69 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.25 80 26 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.42 42 30 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.45 6 5 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.45 40 33 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.34 847 431 TCERG1L 256536 broad.mit.edu 37 10 133107556 133107557 + Frame_Shift_Ins INS - C C rs145740488 by1000genomes HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr10:133107556_133107557insC uc001lkp.2 - 2 434_435 c.348_349insG c.(346-351)CTGTTTfs p.L116fs NM_174937 NP_777597 Q5VWI1 TCRGL_HUMAN transcription elongation regulator 1-like 116_117 large_intestine(2)|ovary(2) 4 all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09) all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276) TGGCCACCAAACAGCCACTGCA 0.530 0.35 39 21 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 125 31 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.56 7 9 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 18 108 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.20 39 10 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 113 465 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS698T_LARGE_INTESTINE NA HS698T_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 3 42 KDM5C 8242 broad.mit.edu 37 X 53243902 53243902 + Frame_Shift_Del DEL C - - HS706T_BONE NA HS706T_BONE NA g.chrX:53243902delC uc004drz.2 - 8 1624 c.1091delG c.(1090-1092)GGTfs p.G364fs KDM5C_uc011moc.1_RNA|KDM5C_uc011mod.1_Frame_Shift_Del_p.G297fs|KDM5C_uc004dsa.2_Frame_Shift_Del_p.G363fs NM_004187 NP_004178 P41229 KDM5C_HUMAN jumonji, AT rich interactive domain 1C isoform 364 PHD-type 1. chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1) 18 0.000 0.11 462 60 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS706T_BONE NA HS706T_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.65 43 79 MUTYH 4595 broad.mit.edu 37 1 45797418 45797418 + Frame_Shift_Del DEL G - - HS706T_BONE NA HS706T_BONE NA g.chr1:45797418delG uc001cnm.2 - 12 1308 c.1092delC c.(1090-1092)CCCfs p.P364fs MUTYH_uc009vxn.2_Frame_Shift_Del_p.P189fs|MUTYH_uc001cnf.2_Frame_Shift_Del_p.P339fs|MUTYH_uc009vxo.2_Frame_Shift_Del_p.P339fs|MUTYH_uc001cng.2_Frame_Shift_Del_p.P350fs|MUTYH_uc001cnj.2_Frame_Shift_Del_p.P247fs|MUTYH_uc001cni.2_Frame_Shift_Del_p.P339fs|MUTYH_uc001cnh.2_Frame_Shift_Del_p.P340fs|MUTYH_uc001cno.2_Frame_Shift_Del_p.P247fs|MUTYH_uc001cnk.2_Frame_Shift_Del_p.P224fs|MUTYH_uc010oll.1_Intron|MUTYH_uc001cnl.2_Frame_Shift_Del_p.P353fs|MUTYH_uc009vxp.2_Frame_Shift_Del_p.P367fs|MUTYH_uc001cnn.2_Frame_Shift_Del_p.P354fs NM_012222 NP_036354 Q9UIF7 MUTYH_HUMAN mutY homolog isoform 1 364 Nudix hydrolase. depurination|mismatch repair nucleoplasm 4 iron, 4 sulfur cluster binding|DNA N-glycosylase activity|endonuclease activity|metal ion binding|MutSalpha complex binding 0 Acute lymphoblastic leukemia(166;0.155) 0.000 0.19 64 15 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 HS706T_BONE NA HS706T_BONE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.40 9 6 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS706T_BONE NA HS706T_BONE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.34 19 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS706T_BONE NA HS706T_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 85 146 IL6ST 3572 broad.mit.edu 37 5 55251977 55251978 + Frame_Shift_Del DEL TG - - HS706T_BONE NA HS706T_BONE NA g.chr5:55251977_55251978delTG uc003jqq.2 - 10 1397_1398 c.1142_1143delCA c.(1141-1143)ACAfs p.T381fs IL6ST_uc010iwb.2_Frame_Shift_Del_p.T381fs|IL6ST_uc010iwc.2_Intron|IL6ST_uc010iwd.2_Intron|IL6ST_uc011cqk.1_Frame_Shift_Del_p.T92fs|IL6ST_uc003jqr.2_3'UTR NM_002184 NP_002175 P40189 IL6RB_HUMAN interleukin 6 signal transducer isoform 1 381 Extracellular (Potential).|Fibronectin type-III 3. interleukin-6-mediated signaling pathway|leukemia inhibitory factor signaling pathway|negative regulation of interleukin-6-mediated signaling pathway|positive regulation of anti-apoptosis|positive regulation of cardiac muscle hypertrophy|positive regulation of osteoblast differentiation|positive regulation of T cell proliferation|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation vascular endothelial growth factor production ciliary neurotrophic factor receptor complex|extracellular region|extracellular space|interleukin-6 receptor complex|oncostatin-M receptor complex ciliary neurotrophic factor receptor activity|ciliary neurotrophic factor receptor binding|growth factor binding|protein homodimerization activity large_intestine(1)|ovary(1) 2 Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223) TGGCATTAACTGTGTAATTTTG 0.342 0.30 194 83 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS706T_BONE NA HS706T_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 105 65 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HS706T_BONE NA HS706T_BONE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.77 3 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS706T_BONE NA HS706T_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 432 175 GPR84 53831 broad.mit.edu 37 12 54757504 54757505 + Frame_Shift_Del DEL GG - - HS706T_BONE NA HS706T_BONE NA g.chr12:54757504_54757505delGG uc001sfu.2 - 2 221_222 c.131_132delCC c.(130-132)GCCfs p.A44fs NM_020370 NP_065103 Q9NQS5 GPR84_HUMAN G protein-coupled receptor 84 44 Helical; Name=1; (Potential). integral to membrane|plasma membrane G-protein coupled receptor activity breast(2) 2 0.000 0.48 406 372 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS706T_BONE NA HS706T_BONE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 13 254 RNF43 54894 broad.mit.edu 37 17 56439928 56439928 + Frame_Shift_Del DEL A - - HS706T_BONE NA HS706T_BONE NA g.chr17:56439928delA uc002iwf.2 - 5 2620 c.664delT c.(664-666)TGCfs p.C222fs RNF43_uc010wnv.1_Frame_Shift_Del_p.C181fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.C222fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.C222fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.C95fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 222 Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.15 123 21 NOTCH3 4854 broad.mit.edu 37 19 15300088 15300089 + Frame_Shift_Del DEL AG - - HS706T_BONE NA HS706T_BONE NA g.chr19:15300088_15300089delAG uc002nan.2 - 7 1263_1264 c.1187_1188delCT c.(1186-1188)TCTfs p.S396fs NOTCH3_uc002nao.1_Frame_Shift_Del_p.S396fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 396 Extracellular (Potential).|EGF-like 10; calcium-binding (Potential). Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.13 235 35 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS706T_BONE NA HS706T_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.32 67 32 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS706T_BONE NA HS706T_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.60 89 132 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS706T_BONE NA HS706T_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 78 DDX17 10521 broad.mit.edu 37 22 38881965 38881967 + In_Frame_Del DEL GGA - - HS706T_BONE NA HS706T_BONE NA g.chr22:38881965_38881967delGGA uc003avy.3 - 13 2272_2274 c.2169_2171delTCC c.(2167-2172)CCTCCC>CCC p.723_724PP>P DDX17_uc003avw.3_In_Frame_Del_p.175_176PP>P|DDX17_uc010gxp.2_In_Frame_Del_p.173_174PP>P|DDX17_uc003avx.3_In_Frame_Del_p.721_722PP>P NM_001098504 NP_001091974 Q92841 DDX17_HUMAN DEAD box polypeptide 17 isoform 3 642_643 Poly-Pro. RNA processing nucleus ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity skin(3)|upper_aerodigestive_tract(1) 4 Melanoma(58;0.0286) 0.000 0.13 185 28 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 52 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.40 21 14 ULK4 54986 broad.mit.edu 37 3 41795861 41795871 + Frame_Shift_Del DEL GCAACTGAGCA - - HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr3:41795861_41795871delGCAACTGAGCA uc003ckv.3 - 22 2504_2514 c.2303_2313delTGCTCAGTTGC c.(2302-2313)CTGCTCAGTTGCfs p.L768fs NM_017886 NP_060356 Q96C45 ULK4_HUMAN unc-51-like kinase 4 768_771 ATP binding|protein serine/threonine kinase activity 0 KIRC - Kidney renal clear cell carcinoma(284;0.214) ACCTTGCTTGGCAACTGAGCAGCAACATCTC 0.393 0.40 9 6 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.54 21 25 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.22 28 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 101 164 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.41 99 69 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.39 11 7 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.32 179 84 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 3 57 PPP3R2 5535 broad.mit.edu 37 9 104357003 104357004 + Frame_Shift_Ins INS - AGGTT AGGTT HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr9:104357003_104357004insAGGTT uc004bbr.2 - 1 280_281 c.209_210insAACCT c.(208-210)GATfs p.D70fs GRIN3A_uc004bbp.1_Intron|GRIN3A_uc004bbq.1_Intron|PPP3R2_uc010mtf.1_Intron NM_147180 NP_671709 Q96LZ3 CANB2_HUMAN protein phosphatase 3 regulatory subunit B, beta 67 EF-hand 2.|2. calcium ion binding ovary(1)|skin(1) 2 Acute lymphoblastic leukemia(62;0.0527) Cyclosporine(DB00091) CCACTTCTCCATCACCGTCGGT 0.569 0.39 91 59 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.81 4 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 909 505 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.12 70 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.49 122 117 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.42 71 51 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 80 753 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS729_SOFT_TISSUE NA HS729_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 9 124 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS737T_BONE NA HS737T_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 52 AKR7A2 8574 broad.mit.edu 37 1 19630781 19630781 + Frame_Shift_Del DEL C - - HS737T_BONE NA HS737T_BONE NA g.chr1:19630781delC uc001bbw.2 - 7 1040 c.1018delG c.(1018-1020)GTGfs p.V340fs AKR7A2_uc001bbx.2_Frame_Shift_Del_p.V305fs NM_003689 NP_003680 O43488 ARK72_HUMAN aldo-keto reductase family 7, member A2 340 carbohydrate metabolic process|cellular aldehyde metabolic process Golgi apparatus alditol:NADP+ 1-oxidoreductase activity|electron carrier activity central_nervous_system(1) 1 Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.00461)|BRCA - Breast invasive adenocarcinoma(304;1.83e-05)|Kidney(64;0.000167)|GBM - Glioblastoma multiforme(114;0.00115)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649) 0.000 0.92 1 12 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A HS737T_BONE NA HS737T_BONE NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 1.00 0 32 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HS737T_BONE NA HS737T_BONE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 84 23 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS737T_BONE NA HS737T_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.33 64 32 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS737T_BONE NA HS737T_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 24 39 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HS737T_BONE NA HS737T_BONE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.38 300 182 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HS737T_BONE NA HS737T_BONE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.37 40 23 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS737T_BONE NA HS737T_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 152 27 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HS737T_BONE NA HS737T_BONE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.50 6 6 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS737T_BONE NA HS737T_BONE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 16 138 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - HS737T_BONE NA HS737T_BONE NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 0.95 2 35 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS737T_BONE NA HS737T_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.62 16 26 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS737T_BONE NA HS737T_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 148 1551 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS742T_BREAST NA HS742T_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 49 ULK4 54986 broad.mit.edu 37 3 41860984 41860985 + Frame_Shift_Ins INS - T T HS742T_BREAST NA HS742T_BREAST NA g.chr3:41860984_41860985insT uc003ckv.3 - 19 1979_1980 c.1778_1779insA c.(1777-1779)AAGfs p.K593fs ULK4_uc003ckw.2_Frame_Shift_Ins_p.K593fs NM_017886 NP_060356 Q96C45 ULK4_HUMAN unc-51-like kinase 4 593 ATP binding|protein serine/threonine kinase activity 0 KIRC - Kidney renal clear cell carcinoma(284;0.214) CTCTAGGGTTCTTTTTTTTTTC 0.450 0.10 90 10 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HS742T_BREAST NA HS742T_BREAST NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 92 17 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS742T_BREAST NA HS742T_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.41 16 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS742T_BREAST NA HS742T_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.38 89 54 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS742T_BREAST NA HS742T_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 24 45 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - HS742T_BREAST NA HS742T_BREAST NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.31 123 56 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HS742T_BREAST NA HS742T_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.13 68 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS742T_BREAST NA HS742T_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 13 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - HS742T_BREAST NA HS742T_BREAST NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.12 645 84 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HS742T_BREAST NA HS742T_BREAST NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.59 9 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS742T_BREAST NA HS742T_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.11 185 24 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HS742T_BREAST NA HS742T_BREAST NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.56 8 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS742T_BREAST NA HS742T_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 12 157 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS742T_BREAST NA HS742T_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.24 42 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS742T_BREAST NA HS742T_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 131 1380 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS742T_BREAST NA HS742T_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.99 1 74 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 6 44 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 220 64 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 104 24 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 82 94 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 21 63 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.31 296 135 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.23 23 7 SMARCA2 6595 broad.mit.edu 37 9 2039806 2039807 + In_Frame_Ins INS - CAA CAA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039806_2039807insCAA uc003zhc.2 + 4 795_796 c.696_697insCAA c.(694-699)insCAA p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.15 651 115 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.43 8 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 207 64 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 23 255 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 27 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 141 539 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 78 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.10 179 21 SHROOM4 57477 broad.mit.edu 37 X 50350711 50350713 + In_Frame_Del DEL TCC - - rs6614551 HS766T_PANCREAS NA HS766T_PANCREAS NA g.chrX:50350711_50350713delTCC uc004dpe.2 - 6 3455_3457 c.3429_3431delGGA c.(3427-3432)GAGGAA>GAA p.1143_1144EE>E SHROOM4_uc004dpd.3_RNA NM_020717 NP_065768 Q9ULL8 SHRM4_HUMAN shroom family member 4 1143_1144 Glu-rich. actin filament organization|brain development|cell morphogenesis|cognition apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus actin filament binding upper_aerodigestive_tract(1) 1 Ovarian(276;0.236) ctcttcctcttcctcttcttctt 0.212 0.39 11 7 HEPH 9843 broad.mit.edu 37 X 65393494 65393495 + Frame_Shift_Ins INS - C C HS766T_PANCREAS NA HS766T_PANCREAS NA g.chrX:65393494_65393495insC uc011moz.1 + 4 545_546 c.485_486insC c.(484-486)GGCfs p.G162fs HEPH_uc004dwn.2_Frame_Shift_Ins_p.G162fs|HEPH_uc004dwo.2_5'UTR|HEPH_uc010nkr.2_Frame_Shift_Ins_p.G162fs|HEPH_uc011mpa.1_Frame_Shift_Ins_p.G162fs NM_138737 NP_620074 Q9BQS7 HEPH_HUMAN hephaestin isoform a 159 Extracellular (Potential).|Plastocyanin-like 1. cellular iron ion homeostasis|copper ion transport|transmembrane transport integral to membrane|plasma membrane copper ion binding|oxidoreductase activity lung(5)|ovary(4) 9 CCCCCGGGGGGCAGCCATATCT 0.535 0.10 542 62 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS766T_PANCREAS NA HS766T_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 15 214 CASP9 842 broad.mit.edu 37 1 15834394 15834394 + Frame_Shift_Del DEL C - - HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr1:15834394delC uc001awn.2 - 3 522 c.427delG c.(427-429)GAGfs p.E143fs CASP9_uc001awm.1_Frame_Shift_Del_p.E143fs|CASP9_uc001awo.2_Intron|CASP9_uc001awp.2_5'UTR|CASP9_uc009voi.2_5'UTR|CASP9_uc010obm.1_Frame_Shift_Del_p.E60fs|CASP9_uc001awq.2_Frame_Shift_Del_p.E60fs NM_001229 NP_001220 P55211 CASP9_HUMAN caspase 9 isoform alpha preproprotein 143 activation of caspase activity by cytochrome c|induction of apoptosis by intracellular signals|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling cytosol cysteine-type endopeptidase activity|enzyme activator activity|protein binding central_nervous_system(1)|kidney(1) 2 Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655) CTCAAACTCTCAAGAGCACCT 0.547 0.64 370 645 MUC1 4582 broad.mit.edu 37 1 155160853 155160863 + Frame_Shift_Del DEL AGGGTGGTAGG - - HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr1:155160853_155160863delAGGGTGGTAGG uc009wqa.2 - 3 422_432 c.253_263delCCTACCACCCT c.(253-264)CCTACCACCCTTfs p.P85fs RAG1AP1_uc010pey.1_Intron|MUC1_uc001fhy.2_5'UTR|MUC1_uc001fhz.2_5'UTR|MUC1_uc010pfb.1_Intron|MUC1_uc010pfc.1_Intron|MUC1_uc009wph.2_Intron|MUC1_uc010pfd.1_Intron|MUC1_uc010pfe.1_Intron|MUC1_uc010pff.1_Intron|MUC1_uc009wpi.2_Intron|MUC1_uc010pfg.1_Intron|MUC1_uc010pfh.1_Intron|MUC1_uc010pfi.1_Intron|MUC1_uc010pfj.1_Intron|MUC1_uc010pfk.1_Intron|MUC1_uc010pfl.1_Intron|MUC1_uc001fin.2_Intron|MUC1_uc009wpk.2_Intron|MUC1_uc001fip.2_Intron|MUC1_uc009wqg.2_Intron|MUC1_uc009wpo.2_Intron|MUC1_uc009wps.2_Intron|MUC1_uc009wpt.2_Intron|MUC1_uc001fic.2_Intron|MUC1_uc009wpu.2_Intron|MUC1_uc009wpq.2_Intron|MUC1_uc009wpv.2_Intron|MUC1_uc001fim.2_Intron|MUC1_uc001fib.2_Intron|MUC1_uc009wpw.2_Intron|MUC1_uc001fie.2_Intron|MUC1_uc009wpr.2_Intron|MUC1_uc001fig.2_Intron|MUC1_uc001fif.2_Intron|MUC1_uc009wpx.2_Intron|MUC1_uc001fid.2_Intron|MUC1_uc009wpj.2_Intron|MUC1_uc001fij.2_Intron|MUC1_uc009wpy.2_Intron|MUC1_uc010pfm.1_5'UTR|MUC1_uc001fiq.2_5'UTR|MUC1_uc009wpz.2_Intron|MUC1_uc010pfn.1_Intron|MUC1_uc010pfo.1_Intron|MUC1_uc010pfp.1_Intron|MUC1_uc001fii.2_Intron|MUC1_uc001fih.2_Intron|MUC1_uc001fia.2_Intron|MUC1_uc009wqc.2_Intron|MUC1_uc009wqd.2_Intron|MUC1_uc009wqb.2_Intron|MUC1_uc010pfq.1_Intron|MUC1_uc010pfr.1_Intron|MUC1_uc001fit.2_Intron|MUC1_uc009wqe.2_Intron|MUC1_uc001fil.2_Intron|MUC1_uc009wpm.2_Intron|MUC1_uc009wpp.2_Intron|MUC1_uc010pfs.1_Intron|MUC1_uc001fik.2_Intron|MUC1_uc001fio.2_Intron|MUC1_uc009wqf.2_Intron|MUC1_uc009wpl.2_Intron|MUC1_uc009wpn.2_Intron|MUC1_uc001fis.1_Intron P15941 MUC1_HUMAN SubName: Full=Mucin 1, cell surface associated; 1002_1005 Extracellular (Potential).|48; approximate. apical plasma membrane|cell surface|cytoplasm|extracellular region|integral to plasma membrane|nucleus protein binding large_intestine(1)|pancreas(1)|breast(1)|skin(1) 4 all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) ATGGCTGGCAAGGGTGGTAGGAGTATCAGAG 0.555 0.33 66 32 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.30 102 43 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.16 188 35 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 272 333 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 100 144 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.12 76 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 33 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.54 13 15 HSP90AA1 3320 broad.mit.edu 37 14 102548663 102548680 + In_Frame_Del DEL ATTGTTGAGTTGTCTCTT - - HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr14:102548663_102548680delATTGTTGAGTTGTCTCTT uc001yku.3 - 10 2047_2064 c.1857_1874delAAGAGACAACTCAACAAT c.(1855-1875)CTAAGAGACAACTCAACAATG>CTG p.RDNSTM620del HSP90AA1_uc001ykv.3_In_Frame_Del_p.RDNSTM742del NM_005348 NP_005339 P07900 HS90A_HUMAN heat shock 90kDa protein 1, alpha isoform 2 620_625 axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction cytosol|melanosome|plasma membrane ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding ovary(2)|central_nervous_system(2)|prostate(1)|lung(1)|breast(1) 7 Rifabutin(DB00615) CATGTAACCCATTGTTGAGTTGTCTCTTAGGGCTTGAG 0.445 0.19 1358 314 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 3 34 MAP2K7 5609 broad.mit.edu 37 19 7974990 7974990 + Frame_Shift_Del DEL G - - HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr19:7974990delG uc002mit.2 + 3 374 c.309delG c.(307-309)ACGfs p.T103fs MAP2K7_uc002miv.2_Frame_Shift_Del_p.T103fs|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_Frame_Shift_Del_p.T103fs|MAP2K7_uc010dvv.2_5'UTR NM_145185 NP_660186 O14733 MP2K7_HUMAN mitogen-activated protein kinase kinase 7 103 activation of JUN kinase activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleus ATP binding|JUN kinase kinase activity|magnesium ion binding|protein binding|protein kinase binding|protein phosphatase binding|protein serine/threonine kinase activity|protein tyrosine kinase activity large_intestine(7)|central_nervous_system(2)|ovary(1)|lung(1) 11 Etoposide(DB00773) 0.000 0.51 580 600 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 59 170 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.27 400 148 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 44 377 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS766T_PANCREAS NA HS766T_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 44 555 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.79 8 31 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 276 110 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.42 14 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.44 146 113 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 27 56 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.23 24 7 POU3F2 5454 broad.mit.edu 37 6 99283172 99283173 + In_Frame_Ins INS - CAG CAG HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chr6:99283172_99283173insCAG uc003ppe.2 + 1 593_594 c.423_424insCAG c.(421-426)insCAG p.149_150insQ NM_005604 NP_005595 P20265 PO3F2_HUMAN POU domain, class 3, transcription factor 2 149_150 positive regulation of cell proliferation identical protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197) BRCA - Breast invasive adenocarcinoma(108;0.0355) aacagcagcaacagcagcagca 0.465 0.24 83 26 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.76 4 13 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.33 10 5 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 729 189 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 8 135 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.68 54 114 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 40 264 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS840T_UPPER_AERODIGESTIVE_TRACT NA HS840T_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 14 117 BTK 695 broad.mit.edu 37 X 100608908 100608909 + Frame_Shift_Ins INS - C C HS852T_SKIN NA HS852T_SKIN NA g.chrX:100608908_100608909insC uc004ehg.2 - 17 1892_1893 c.1699_1700insG c.(1699-1701)GAAfs p.E567fs BTK_uc004ehf.2_Frame_Shift_Ins_p.E67fs|BTK_uc010nnh.2_Intron|BTK_uc010nni.2_Intron|BTK_uc004ehe.2_RNA|BTK_uc010nnj.2_RNA|BTK_uc010nnk.2_RNA|BTK_uc010nnl.2_Frame_Shift_Ins_p.E43fs|BTK_uc010nnm.2_Frame_Shift_Ins_p.E137fs|BTK_uc010nnn.2_Frame_Shift_Ins_p.E391fs|BTK_uc010nno.2_Frame_Shift_Ins_p.E601fs|BTK_uc004ehh.1_RNA NM_000061 NP_000052 Q06187 BTK_HUMAN Bruton agammaglobulinemia tyrosine kinase 567 Protein kinase. E -> K (in XLA; severe). calcium-mediated signaling|induction of apoptosis by extracellular signals|mesoderm development cytosol|membrane raft|nucleus|plasma membrane ATP binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol-3,4,5-trisphosphate binding lung(3)|central_nervous_system(2)|ovary(1) 6 CATCAGGACTTCCGGTGGGGAC 0.441 0.10 182 20 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS852T_SKIN NA HS852T_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.46 31 26 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HS852T_SKIN NA HS852T_SKIN NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.34 395 205 TNS1 7145 broad.mit.edu 37 2 218712886 218712887 + In_Frame_Ins INS - GCT GCT rs61747065 HS852T_SKIN NA HS852T_SKIN NA g.chr2:218712886_218712887insGCT uc002vgt.2 - 17 2376_2377 c.1978_1979insAGC c.(1978-1980)CCT>CAGCCT p.659_660insQ TNS1_uc002vgr.2_In_Frame_Ins_p.659_660insQ|TNS1_uc002vgs.2_In_Frame_Ins_p.659_660insQ|TNS1_uc010zjv.1_In_Frame_Ins_p.659_660insQ|TNS1_uc010fvj.1_In_Frame_Ins_p.727_728insQ|TNS1_uc010fvk.1_In_Frame_Ins_p.784_785insQ|TNS1_uc010fvi.1_In_Frame_Ins_p.346_347insQ NM_022648 NP_072174 Q9HBL0 TENS1_HUMAN tensin 659_660 Gln-rich. cytoplasm|cytoskeleton|focal adhesion actin binding ovary(3)|breast(1) 4 Renal(207;0.0483)|Lung NSC(271;0.213) Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013) AGGTGGGCGAGgctgctgctgc 0.564 0.40 6 4 IRAK2 3656 broad.mit.edu 37 3 10283873 10283874 + Frame_Shift_Del DEL AG - - HS852T_SKIN NA HS852T_SKIN NA g.chr3:10283873_10283874delAG uc003bve.1 + 13 1915_1916 c.1839_1840delAG c.(1837-1842)AAAGAGfs p.K613fs NM_001570 NP_001561 O43187 IRAK2_HUMAN interleukin-1 receptor-associated kinase 2 613_614 activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cell surface|cytosol|endosome membrane|plasma membrane ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity lung(5)|breast(3) 8 TGCTCTACAAAGAGGAAAAAGT 0.436 0.48 147 134 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS852T_SKIN NA HS852T_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 65 96 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HS852T_SKIN NA HS852T_SKIN NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.50 27 27 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HS852T_SKIN NA HS852T_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.38 64 39 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS852T_SKIN NA HS852T_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 18 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HS852T_SKIN NA HS852T_SKIN NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.40 9 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS852T_SKIN NA HS852T_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 270 117 PHKG2 5261 broad.mit.edu 37 16 30764880 30764881 + Splice_Site INS - GA GA HS852T_SKIN NA HS852T_SKIN NA g.chr16:30764880_30764881insGA uc002dzk.1 + 6 649 c.556_splice c.e6+2 p.E186_splice PHKG2_uc002dzi.1_Splice_Site_p.E186_splice|PHKG2_uc002dzj.1_Splice_Site_p.E84_splice NM_000294 NP_000285 P15735 PHKG2_HUMAN phosphorylase kinase, gamma 2 (testis) glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process cytosol ATP binding|calmodulin binding|phosphorylase kinase activity ovary(1) 1 Colorectal(24;0.198) AGCTTCGAGGTGAGGGGATCTA 0.525 0.42 98 71 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - HS852T_SKIN NA HS852T_SKIN NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 0.92 1 12 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS852T_SKIN NA HS852T_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 38 24 SRMS 6725 broad.mit.edu 37 20 62172870 62172875 + In_Frame_Del DEL GTCCCG - - HS852T_SKIN NA HS852T_SKIN NA g.chr20:62172870_62172875delGTCCCG uc002yfi.1 - 6 1086_1091 c.1045_1050delCGGGAC c.(1045-1050)CGGGACdel p.RD349del NM_080823 NP_543013 Q9H3Y6 SRMS_HUMAN src-related kinase lacking C-terminal regulatory 349_350 Protein kinase. Proton acceptor (By similarity). ATP binding|non-membrane spanning protein tyrosine kinase activity stomach(1)|lung(1) 2 all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13) Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06) 0.000 0.41 472 333 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS852T_SKIN NA HS852T_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 93 270 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS852T_SKIN NA HS852T_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 3 50 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS863T_BONE NA HS863T_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 40 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HS863T_BONE NA HS863T_BONE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 223 65 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HS863T_BONE NA HS863T_BONE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 72 19 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS863T_BONE NA HS863T_BONE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.58 8 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS863T_BONE NA HS863T_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.38 58 36 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS863T_BONE NA HS863T_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 15 30 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS863T_BONE NA HS863T_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS863T_BONE NA HS863T_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 105 23 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS863T_BONE NA HS863T_BONE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 37 306 PPY 5539 broad.mit.edu 37 17 42018936 42018937 + Frame_Shift_Ins INS - C C HS863T_BONE NA HS863T_BONE NA g.chr17:42018936_42018937insC uc002iep.2 - 2 131_132 c.86_87insG c.(85-87)GGAfs p.G29fs NM_002722 NP_002713 P01298 PAHO_HUMAN pancreatic polypeptide preproprotein 29 digestion|protein secretion extracellular region hormone activity 0 Breast(137;0.00314)|Prostate(33;0.0724) BRCA - Breast invasive adenocarcinoma(366;0.113) 0.000 1.00 0 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS863T_BONE NA HS863T_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.32 26 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS863T_BONE NA HS863T_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 146 442 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS863T_BONE NA HS863T_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 54 FAM48B1 100130302 broad.mit.edu 37 X 24382374 24382376 + In_Frame_Del DEL TGC - - HS870T_BONE NA HS870T_BONE NA g.chrX:24382374_24382376delTGC uc011mjx.1 + 1 1497_1499 c.1497_1499delTGC c.(1495-1500)ATTGCT>ATT p.A517del NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 ctgctgctattgctgctgctgct 0.202 0.15 41 7 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS870T_BONE NA HS870T_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 4 34 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HS870T_BONE NA HS870T_BONE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.39 17 11 HTT 3064 broad.mit.edu 37 4 3076604 3076609 + In_Frame_Del DEL CAGCAG - - rs10618869 HS870T_BONE NA HS870T_BONE NA g.chr4:3076604_3076609delCAGCAG uc011bvq.1 + 2 203_208 c.58_63delCAGCAG c.(58-63)CAGCAGdel p.QQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagc 0.330 0.15 101 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS870T_BONE NA HS870T_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.73 96 257 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS870T_BONE NA HS870T_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 37 86 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HS870T_BONE NA HS870T_BONE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.70 3 7 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 HS870T_BONE NA HS870T_BONE NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.10 270 30 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HS870T_BONE NA HS870T_BONE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 31 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HS870T_BONE NA HS870T_BONE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.32 48 23 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS870T_BONE NA HS870T_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 2 36 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HS870T_BONE NA HS870T_BONE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.30 90 39 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS870T_BONE NA HS870T_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.48 558 519 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 HS870T_BONE NA HS870T_BONE NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.50 9 9 EP400 57634 broad.mit.edu 37 12 132547088 132547090 + In_Frame_Del DEL CAA - - rs60930033;rs7974276 by1000genomes HS870T_BONE NA HS870T_BONE NA g.chr12:132547088_132547090delCAA uc001ujn.2 + 46 8211_8213 c.8176_8178delCAA c.(8176-8178)CAAdel p.Q2748del EP400_uc001ujl.2_In_Frame_Del_p.Q2747del|EP400_uc001ujm.2_In_Frame_Del_p.Q2667del|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784 Poly-Gln.|Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) gcagcagcagcaacaacagcagc 0.286 0.10 231 26 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS870T_BONE NA HS870T_BONE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 32 315 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 HS870T_BONE NA HS870T_BONE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.48 23 21 STARD3 10948 broad.mit.edu 37 17 37815324 37815326 + In_Frame_Del DEL GAA - - HS870T_BONE NA HS870T_BONE NA g.chr17:37815324_37815326delGAA uc002hsd.2 + 8 791_793 c.667_669delGAA c.(667-669)GAAdel p.E224del STARD3_uc010weh.1_RNA|STARD3_uc002hse.2_In_Frame_Del_p.E206del|STARD3_uc010wei.1_In_Frame_Del_p.E224del|STARD3_uc002hsf.2_In_Frame_Del_p.E90del|STARD3_uc002hsg.2_In_Frame_Del_p.E57del NM_006804 NP_006795 Q14849 STAR3_HUMAN StAR-related lipid transfer (START) domain 224 Cytoplasmic (Potential). cholesterol metabolic process|mitochondrial transport|steroid biosynthetic process integral to membrane|late endosome membrane cholesterol binding|cholesterol transporter activity 0 Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052) UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171) TGAATCAGATGAAGAAGTTGCTG 0.557 0.48 220 200 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS870T_BONE NA HS870T_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.49 81 78 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS870T_BONE NA HS870T_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 116 452 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS870T_BONE NA HS870T_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 9 126 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS888T_BONE NA HS888T_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.60 12 18 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HS888T_BONE NA HS888T_BONE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.50 13 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS888T_BONE NA HS888T_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.66 89 172 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS888T_BONE NA HS888T_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.79 14 53 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HS888T_BONE NA HS888T_BONE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 2 16 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HS888T_BONE NA HS888T_BONE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.89 4 31 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS888T_BONE NA HS888T_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.99 1 70 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS888T_BONE NA HS888T_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 877 431 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HS888T_BONE NA HS888T_BONE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.30 112 48 IRS2 8660 broad.mit.edu 37 13 110436296 110436297 + In_Frame_Ins INS - CGG CGG rs34412495 HS888T_BONE NA HS888T_BONE NA g.chr13:110436296_110436297insCGG uc001vqv.2 - 1 2618_2619 c.2104_2105insCCG c.(2104-2106)GTG>GCCGTG p.701_702insA NM_003749 NP_003740 Q9Y4H2 IRS2_HUMAN insulin receptor substrate 2 701_702 fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus cytosol|plasma membrane insulin receptor binding|signal transducer activity large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|skin(1)|ovary(1)|kidney(1) 8 all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155) Breast(118;0.159) all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147) 0.000 0.25 1701 580 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS888T_BONE NA HS888T_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.33 108 52 PIGU 128869 broad.mit.edu 37 20 33169424 33169425 + Frame_Shift_Ins INS - A A HS888T_BONE NA HS888T_BONE NA g.chr20:33169424_33169425insA uc002xas.2 - 10 1178_1179 c.978_979insT c.(976-981)TTTAAGfs p.F326fs PIGU_uc010zul.1_Frame_Shift_Ins_p.F326fs|PIGU_uc002xat.2_Frame_Shift_Ins_p.F306fs NM_080476 NP_536724 Q9H490 PIGU_HUMAN phosphatidylinositol glycan anchor biosynthesis, 326_327 Helical; (Potential). attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade GPI-anchor transamidase complex|plasma membrane 0 GGGTAGGACTTAAAGATGGCGA 0.564 0.48 58 54 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HS888T_BONE NA HS888T_BONE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.52 27 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS888T_BONE NA HS888T_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 67 194 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS888T_BONE NA HS888T_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 72 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS934T_SKIN NA HS934T_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 50 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 HS934T_SKIN NA HS934T_SKIN NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.35 11 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS934T_SKIN NA HS934T_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.40 70 46 ADAM29 11086 broad.mit.edu 37 4 175898930 175898983 + In_Frame_Del DEL CCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAA - - rs111721161;rs139608576;rs149749808;rs146283611;rs139492823 byFrequency;byFrequency;byFrequency HS934T_SKIN NA HS934T_SKIN NA g.chr4:175898930_175898983delCCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAA uc003iuc.2 + 5 2924_2977 c.2254_2307delCCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAA c.(2254-2307)CCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAAdel p.PQVMPSQSQPPVTPSQSQ752del ADAM29_uc003iud.2_In_Frame_Del_p.PQVMPSQSQPPVTPSQSQ752del|ADAM29_uc010irr.2_In_Frame_Del_p.PQVMPSQSQPPVTPSQSQ752del|ADAM29_uc011cki.1_In_Frame_Del_p.PQVMPSQSQPPVTPSQSQ752del NM_014269 NP_055084 Q9UKF5 ADA29_HUMAN ADAM metallopeptidase domain 29 preproprotein 752_769 Cytoplasmic (Potential).|4.|9 X 9 AA approximate repeats. QPRVM -> HPQLT (in Ref. 1; AAF03777). proteolysis|spermatogenesis integral to plasma membrane metalloendopeptidase activity|zinc ion binding skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1) 16 Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164) all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286) CCAGAGTCATCCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAACCTCGGGTGA 0.559 0.47 165 144 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS934T_SKIN NA HS934T_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 26 46 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HS934T_SKIN NA HS934T_SKIN NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.50 5 5 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS934T_SKIN NA HS934T_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 159 42 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS934T_SKIN NA HS934T_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.82 12 55 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS934T_SKIN NA HS934T_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.65 14 26 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS934T_SKIN NA HS934T_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 65 467 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS934T_SKIN NA HS934T_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 6 67 ATRX 546 broad.mit.edu 37 X 76907782 76907784 + In_Frame_Del DEL TCC - - HS936T_SKIN NA HS936T_SKIN NA g.chrX:76907782_76907784delTCC uc004ecp.3 - 15 4609_4611 c.4377_4379delGGA c.(4375-4380)GAGGAA>GAA p.1459_1460EE>E ATRX_uc004ecq.3_In_Frame_Del_p.1421_1422EE>E|ATRX_uc004eco.3_In_Frame_Del_p.1244_1245EE>E NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 1459_1460 Poly-Glu. DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) ctcctcctcttcctcctcctcct 0.212 0.71 55 136 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS936T_SKIN NA HS936T_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.82 9 41 CTNNB1 1499 broad.mit.edu 37 3 41266034 41266035 + Frame_Shift_Ins INS - A A HS936T_SKIN NA HS936T_SKIN NA g.chr3:41266034_41266035insA uc010hia.1 + 4 187_188 c.31_32insA c.(31-33)GACfs p.D11fs CTNNB1_uc003ckp.2_Frame_Shift_Ins_p.D11fs|CTNNB1_uc003ckq.2_Frame_Shift_Ins_p.D11fs|CTNNB1_uc003ckr.2_Frame_Shift_Ins_p.D11fs|CTNNB1_uc011azf.1_Frame_Shift_Ins_p.D4fs|CTNNB1_uc011azg.1_Intron|uc010hib.1_Intron NM_001904 NP_001895 P35222 CTNB1_HUMAN beta-catenin 11 Interaction with VCL (By similarity). adherens junction assembly|androgen receptor signaling pathway|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell-cell adhesion|cell-matrix adhesion|cellular component disassembly involved in apoptosis|cellular response to growth factor stimulus|cellular response to indole-3-methanol|central nervous system vasculogenesis|cytoskeletal anchoring at plasma membrane|determination of dorsal/ventral asymmetry|dorsal/ventral axis specification|ectoderm development|embryonic axis specification|embryonic foregut morphogenesis|embryonic leg joint morphogenesis|endodermal cell fate commitment|endothelial tube morphogenesis|epithelial to mesenchymal transition|gastrulation with mouth forming second|glial cell fate determination|hair follicle morphogenesis|hair follicle placode formation|hindbrain development|liver development|lung cell differentiation|lung induction|lung-associated mesenchyme development|male genitalia development|mesenchymal cell proliferation involved in lung development|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of osteoclast differentiation|negative regulation of transcription from RNA polymerase II promoter|nephron tubule formation|odontogenesis of dentine-containing tooth|oocyte development|pancreas development|positive regulation of anti-apoptosis|positive regulation of apoptosis|positive regulation of branching involved in lung morphogenesis|positive regulation of epithelial cell proliferation involved in prostate gland development|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of muscle cell differentiation|positive regulation of osteoblast differentiation|positive regulation of transcription from RNA polymerase II promoter|protein localization at cell surface|proximal/distal pattern formation|regulation of angiogenesis|regulation of calcium ion import|regulation of centriole-centriole cohesion|regulation of centromeric sister chromatid cohesion|regulation of fibroblast proliferation|regulation of nephron tubule epithelial cell differentiation|regulation of protein localization at cell surface|regulation of smooth muscle cell proliferation|regulation of T cell proliferation|renal inner medulla development|renal outer medulla development|renal vesicle formation|response to drug|response to estradiol stimulus|Schwann cell proliferation|smooth muscle cell differentiation|synapse organization|synaptic vesicle transport|T cell differentiation in thymus|thymus development|trachea formation APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin-TCF7L2 complex|catenin complex|cell cortex|cell-substrate adherens junction|centrosome|dendritic shaft|desmosome|fascia adherens|internal side of plasma membrane|lamellipodium|lateral plasma membrane|microvillus membrane|perinuclear region of cytoplasm|protein-DNA complex|synapse|transcription factor complex|Z disc|zonula adherens alpha-catenin binding|androgen receptor binding|cadherin binding|estrogen receptor binding|I-SMAD binding|ion channel binding|protein binding|protein C-terminus binding|protein kinase binding|protein phosphatase binding|R-SMAD binding|RPTP-like protein binding|signal transducer activity|specific RNA polymerase II transcription factor activity|structural molecule activity|transcription coactivator activity|transcription regulatory region DNA binding p.A5_A80del(63)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.T3_A126del(2)|p.A5fs*7(2)|p.M5_N141>D(2)|p.?(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.D6_S29del(1)|p.A5_Q72del(1)|p.E9_S47del(1)|p.M8_G50del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.D6_A43del(1)|p.D11N(1)|p.A5_T42del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.A5_R90del(1)|p.A5_D144>D(1)|p.L7_I140del(1)|p.A5_T40del(1)|p.E9_A80del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.E9_I140del(1)|p.D6_I140del(1)|p.M1_T42del(1)|p.D6_K133del(1)|p.A5_I35del(1)|p.A5_G80>(1) CTNNB1/PLAG1(60) liver(806)|soft_tissue(609)|large_intestine(243)|endometrium(222)|kidney(172)|stomach(157)|central_nervous_system(139)|ovary(104)|skin(97)|pancreas(91)|adrenal_gland(85)|pituitary(81)|salivary_gland(62)|haematopoietic_and_lymphoid_tissue(57)|thyroid(55)|biliary_tract(41)|lung(38)|prostate(24)|bone(20)|small_intestine(17)|cervix(9)|parathyroid(9)|urinary_tract(8)|breast(7)|oesophagus(5)|NS(3)|pleura(2)|upper_aerodigestive_tract(2)|eye(1) 3166 KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294) Lithium(DB01356) GATGGAGTTGGACATGGCCATG 0.406 0.72 13 33 KDR 3791 broad.mit.edu 37 4 55979587 55979589 + In_Frame_Del DEL TTC - - HS936T_SKIN NA HS936T_SKIN NA g.chr4:55979587_55979589delTTC uc003has.2 - 7 1160_1162 c.858_860delGAA c.(856-861)AAGAAA>AAA p.286_287KK>K KDR_uc003hat.1_In_Frame_Del_p.286_287KK>K|KDR_uc011bzx.1_In_Frame_Del_p.286_287KK>K NM_002253 NP_002244 P35968 VGFR2_HUMAN kinase insert domain receptor precursor 286_287 Ig-like C2-type 3.|Extracellular (Potential). angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape integral to plasma membrane ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1) 33 all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101) Epithelial(7;0.189) Sorafenib(DB00398)|Sunitinib(DB01268) GCTCAAAAATTTCTTCATCTCAC 0.433 0.48 71 66 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS936T_SKIN NA HS936T_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 36 53 RICTOR 253260 broad.mit.edu 37 5 38953586 38953587 + Frame_Shift_Ins INS - T T HS936T_SKIN NA HS936T_SKIN NA g.chr5:38953586_38953587insT uc003jlp.2 - 28 2790_2791 c.2766_2767insA c.(2764-2769)AAACTGfs p.K922fs RICTOR_uc003jlo.2_Frame_Shift_Ins_p.K922fs|RICTOR_uc010ivf.2_Frame_Shift_Ins_p.K637fs NM_152756 NP_689969 Q6R327 RICTR_HUMAN rapamycin-insensitive companion of mTOR 922_923 actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation cytosol|TORC2 complex protein binding ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1) 10 all_lung(31;0.000396) GATGCTTTCAGTTTTTTAATTT 0.287 0.12 73 10 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS936T_SKIN NA HS936T_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 22 50 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HS936T_SKIN NA HS936T_SKIN NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.38 161 100 PAXIP1 22976 broad.mit.edu 37 7 154760669 154760670 + In_Frame_Ins INS - TGCTGC TGCTGC HS936T_SKIN NA HS936T_SKIN NA g.chr7:154760669_154760670insTGCTGC uc003wlp.2 - 7 1284_1285 c.1241_1242insGCAGCA c.(1240-1242)CAC>CAGCAGCAC p.413_414insQQ PAXIP1_uc003wlq.1_In_Frame_Ins_p.379_380insQQ|PAXIP1_uc011kvs.1_In_Frame_Ins_p.377_378insQQ|PAXIP1_uc003wlr.1_In_Frame_Ins_p.322_323insQQ NM_007349 NP_031375 Q6ZW49 PAXI1_HUMAN PAX interacting protein 1 413_414 Gln-rich. DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent histone methyltransferase complex|nuclear matrix lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_neural(206;0.119) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.0296) UCEC - Uterine corpus endometrioid carcinoma (81;0.178) GTAAAACCGGGtgctgctgctg 0.366 0.22 76 21 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HS936T_SKIN NA HS936T_SKIN NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.38 10 6 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HS936T_SKIN NA HS936T_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.35 17 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS936T_SKIN NA HS936T_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 24 CDKN2A 1029 broad.mit.edu 37 9 21974808 21974809 + Frame_Shift_Ins INS - C C HS936T_SKIN NA HS936T_SKIN NA g.chr9:21974808_21974809insC uc003zpk.2 - 1 230_231 c.18_19insG c.(16-21)GGGAGCfs p.G6fs MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_Frame_Shift_Ins_p.G6fs|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Intron NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 6_7 cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.?(23)|p.A4_P11del(12)|p.G6G(2)|p.P3_P11del(2)|p.S7_A19del(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) TCCATGCTGCTCCCCGCCGCCG 0.777 0.30 19 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS936T_SKIN NA HS936T_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 169 26 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS936T_SKIN NA HS936T_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 8 115 NF1 4763 broad.mit.edu 37 17 29579996 29579996 + Frame_Shift_Del DEL A - - HS936T_SKIN NA HS936T_SKIN NA g.chr17:29579996delA uc002hgg.2 + 31 4484 c.4151delA c.(4150-4152)GAAfs p.E1384fs NF1_uc002hgh.2_Intron|NF1_uc002hgi.1_Intron NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 1384 Ras-GAP. actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) 0.000 0.16 47 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS936T_SKIN NA HS936T_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.69 8 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS936T_SKIN NA HS936T_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 122 366 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS936T_SKIN NA HS936T_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 84 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS939T_SKIN NA HS939T_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 5 87 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A HS939T_SKIN NA HS939T_SKIN NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 0.92 1 12 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HS939T_SKIN NA HS939T_SKIN NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.62 8 13 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HS939T_SKIN NA HS939T_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.38 13 8 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS939T_SKIN NA HS939T_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.19 47 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS939T_SKIN NA HS939T_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.73 91 245 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS939T_SKIN NA HS939T_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.40 80 53 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HS939T_SKIN NA HS939T_SKIN NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.43 222 170 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HS939T_SKIN NA HS939T_SKIN NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.75 3 9 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HS939T_SKIN NA HS939T_SKIN NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.56 24 30 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 HS939T_SKIN NA HS939T_SKIN NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.10 341 40 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HS939T_SKIN NA HS939T_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 3 28 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HS939T_SKIN NA HS939T_SKIN NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.40 9 6 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HS939T_SKIN NA HS939T_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.44 36 28 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS939T_SKIN NA HS939T_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 43 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency HS939T_SKIN NA HS939T_SKIN NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) agcagcagcaacagcagcagca 0.267 0.21 120 32 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS939T_SKIN NA HS939T_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 836 275 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS939T_SKIN NA HS939T_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 44 426 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 HS939T_SKIN NA HS939T_SKIN NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.11 84 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS939T_SKIN NA HS939T_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 41 162 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS939T_SKIN NA HS939T_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 112 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS940T_SKIN NA HS940T_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 23 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS940T_SKIN NA HS940T_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.42 74 54 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS940T_SKIN NA HS940T_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 23 42 CYP3A4 1576 broad.mit.edu 37 7 99355806 99355807 + Frame_Shift_Ins INS - T T rs67666821 HS940T_SKIN NA HS940T_SKIN NA g.chr7:99355806_99355807insT uc003urv.1 - 13 1565_1566 c.1461_1462insA c.(1459-1464)AAACCCfs p.K487fs CYP3A4_uc003urw.1_Frame_Shift_Ins_p.K486fs|CYP3A4_uc011kiz.1_Frame_Shift_Ins_p.K446fs|CYP3A4_uc011kja.1_Frame_Shift_Ins_p.K438fs|CYP3A4_uc011kjb.1_Frame_Shift_Ins_p.K337fs NM_017460 NP_059488 P08684 CP3A4_HUMAN cytochrome P450, family 3, subfamily A, 487_488 alkaloid catabolic process|androgen metabolic process|exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid catabolic process|xenobiotic metabolic process cell surface|endoplasmic reticulum membrane|integral to membrane|microsome albendazole monooxygenase activity|caffeine oxidase activity|electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding|quinine 3-monooxygenase activity|steroid binding|taurochenodeoxycholate 6alpha-hydroxylase activity|testosterone 6-beta-hydroxylase activity|vitamin D 24-hydroxylase activity|vitamin D3 25-hydroxylase activity central_nervous_system(3)|ovary(1) 4 Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228) Albendazole(DB00518)|Alclometasone(DB00240)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Aliskiren(DB01258)|Almotriptan(DB00918)|Alosetron(DB00969)|Alprazolam(DB00404)|Amlodipine(DB00381)|Amprenavir(DB00701)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Benazepril(DB00542)|Bepridil(DB01244)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bortezomib(DB00188)|Bosentan(DB00559)|Bromocriptine(DB01200)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Buspirone(DB00490)|Busulfan(DB01008)|Carbamazepine(DB00564)|Cevimeline(DB00185)|Chlorpheniramine(DB01114)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cinacalcet(DB01012)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clindamycin(DB01190)|Clofibrate(DB00636)|Clonazepam(DB01068)|Clopidogrel(DB00758)|Cocaine(DB00907)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cyproterone(DB04839)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Delavirdine(DB00705)|Desogestrel(DB00304)|Dexamethasone(DB01234)|Diazepam(DB00829)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dofetilide(DB00204)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Doxorubicin(DB00997)|Drospirenone(DB01395)|Dutasteride(DB01126)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Epirubicin(DB00445)|Eplerenone(DB00700)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Exemestane(DB00990)|Felodipine(DB01023)|Fentanyl(DB00813)|Fexofenadine(DB00950)|Finasteride(DB01216)|Fluconazole(DB00196)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Fosamprenavir(DB01319)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Granisetron(DB00889)|Grepafloxacin(DB00365)|Halofantrine(DB01218)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Imatinib(DB00619)|Indinavir(DB00224)|Ipratropium(DB00332)|Irinotecan(DB00762)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levomethadyl Acetate(DB01227)|Levothyroxine(DB00451)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Maraviroc(DB04835)|Marinol(DB00470)|Mebendazole(DB00643)|Medroxyprogesterone(DB00603)|Methadone(DB00333)|Methylprednisolone(DB00959)|Metyrapone(DB01011)|Mibefradil(DB01388)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirtazapine(DB00370)|Modafinil(DB00745)|Mometasone(DB00764)|Montelukast(DB00471)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norgestrel(DB00506)|Nystatin(DB00646)|Ondansetron(DB00904)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paricalcitol(DB00910)|Phenmetrazine(DB00830)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prednisolone(DB00860)|Prednisone(DB00635)|Prochlorperazine(DB00433)|Quetiapine(DB01224)|Quinapril(DB00881)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranolazine(DB00243)|Reboxetine(DB00234)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampin(DB01045)|Rimonabant(DB06155)|Ritonavir(DB00503)|Rofecoxib(DB00533)|Roxithromycin(DB00778)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sertindole(DB06144)|Sibutramine(DB01105)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Terconazole(DB00251)|Terfenadine(DB00342)|Testosterone(DB00624)|Tiagabine(DB00906)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tiotropium(DB01409)|Tipranavir(DB00932)|Toremifene(DB00539)|Triazolam(DB00897)|Trimetrexate(DB01157)|Troglitazone(DB00197)|Valdecoxib(DB00580)|Vardenafil(DB00862)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Voriconazole(DB00582)|Zaleplon(DB00962)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909) AGAACAACGGGTTTTTCTGGTT 0.401 0.44 73 57 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HS940T_SKIN NA HS940T_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.37 51 30 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HS940T_SKIN NA HS940T_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HS940T_SKIN NA HS940T_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 129 28 TRIM29 23650 broad.mit.edu 37 11 120008680 120008681 + Frame_Shift_Ins INS - T T HS940T_SKIN NA HS940T_SKIN NA g.chr11:120008680_120008681insT uc001pwz.2 - 1 183_184 c.59_60insA c.(58-60)CGGfs p.R20fs TRIM29_uc001pxa.2_RNA NM_012101 NP_036233 Q14134 TRI29_HUMAN tripartite motif protein TRIM29 20 transcription from RNA polymerase II promoter cytoplasm protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1)|breast(1)|kidney(1)|skin(1) 4 Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;5.37e-06) 0.000 1.00 0 13 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS940T_SKIN NA HS940T_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 16 185 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS940T_SKIN NA HS940T_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.23 30 9 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HS940T_SKIN NA HS940T_SKIN NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.18 84 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS940T_SKIN NA HS940T_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 91 327 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HS940T_SKIN NA HS940T_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 63 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HS944T_SKIN NA HS944T_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 68 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HS944T_SKIN NA HS944T_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.26 87 30 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HS944T_SKIN NA HS944T_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.23 127 37 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HS944T_SKIN NA HS944T_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.54 61 71 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HS944T_SKIN NA HS944T_SKIN NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.56 145 183 PTEN 5728 broad.mit.edu 37 10 89693002 89693003 + Frame_Shift_Ins INS - A A HS944T_SKIN NA HS944T_SKIN NA g.chr10:89693002_89693003insA uc001kfb.2 + 6 1517_1518 c.486_487insA c.(484-489)GACAAAfs p.D162fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 162_163 Phosphatase tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R55fs*1(4)|p.?(2)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.D162G(1)|p.D162H(1)|p.D162V(1)|p.F56fs*2(1)|p.D162fs*8(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GGACCAGAGACAAAAAGGTAAG 0.332 0.82 83 381 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HS944T_SKIN NA HS944T_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 37 393 TP53 7157 broad.mit.edu 37 17 7572963 7572963 + Frame_Shift_Del DEL T - - HS944T_SKIN NA HS944T_SKIN NA g.chr17:7572963delT uc002gim.2 - 11 1340 c.1146delA c.(1144-1146)AAAfs p.K382fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Intron|TP53_uc010cne.1_RNA|TP53_uc010cnf.1_3'UTR|TP53_uc010cng.1_3'UTR|TP53_uc002gii.1_Frame_Shift_Del_p.K250fs|TP53_uc010cnh.1_3'UTR|TP53_uc010cni.1_3'UTR|TP53_uc002gij.2_Frame_Shift_Del_p.K382fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 382 Basic (repression of DNA-binding).|Interaction with CARM1. K->R: Abolishes monomethylation by SETD8.|K->A: Abolishes acetylation by CREBBP. activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.K382fs*40(3)|p.K382fs*13(2)|p.?(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.87 71 464 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HS944T_SKIN NA HS944T_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.56 12 15 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HS944T_SKIN NA HS944T_SKIN NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.24 207 64 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HS944T_SKIN NA HS944T_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.65 133 249 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 5 76 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.52 177 193 CASP8 841 broad.mit.edu 37 2 202151192 202151192 + Frame_Shift_Del DEL A - - HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr2:202151192delA uc002uxr.1 + 10 1524 c.1315delA c.(1315-1317)ATTfs p.I439fs CASP8_uc002uxp.1_Frame_Shift_Del_p.I456fs|CASP8_uc002uxq.1_Frame_Shift_Del_p.I424fs|CASP8_uc002uxt.1_Frame_Shift_Del_p.I498fs|CASP8_uc002uxu.1_RNA|CASP8_uc002uxw.1_Frame_Shift_Del_p.I424fs|CASP8_uc002uxy.1_Intron|CASP8_uc002uxx.1_Intron|CASP8_uc010ftf.2_Frame_Shift_Del_p.I355fs NM_033355 NP_203519 Q14790 CASP8_HUMAN caspase 8 isoform B precursor 439 activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor centrosome|cytosol|mitochondrial outer membrane cysteine-type endopeptidase activity|protein binding|protein binding upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1) 5 AGGCGATGATATTCTCACCAT 0.423 1.00 0 17 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.24 97 31 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.48 69 63 DDR1 780 broad.mit.edu 37 6 30860846 30860851 + In_Frame_Del DEL TGTGGT - - HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr6:30860846_30860851delTGTGGT uc003nrr.2 + 10 1360_1365 c.1101_1106delTGTGGT c.(1099-1107)GATGTGGTG>GAG p.367_369DVV>E DDR1_uc010jse.2_In_Frame_Del_p.367_369DVV>E|DDR1_uc003nrq.2_In_Frame_Del_p.367_369DVV>E|DDR1_uc003nrs.2_In_Frame_Del_p.367_369DVV>E|DDR1_uc003nrt.2_In_Frame_Del_p.367_369DVV>E|DDR1_uc011dms.1_In_Frame_Del_p.385_387DVV>E|DDR1_uc003nru.2_In_Frame_Del_p.367_369DVV>E|DDR1_uc003nrv.2_In_Frame_Del_p.367_369DVV>E|DDR1_uc003nrw.1_In_Frame_Del_p.166_168DVV>E|DDR1_uc003nry.1_5'Flank|DDR1_uc003nrx.1_5'Flank NM_013993 NP_054699 Q08345 DDR1_HUMAN discoidin domain receptor family, member 1 367_369 Extracellular (Potential). cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway extracellular region|integral to plasma membrane ATP binding|protein binding|protein binding|transmembrane receptor protein tyrosine kinase activity lung(4)|central_nervous_system(3)|large_intestine(1)|ovary(1) 9 Imatinib(DB00619) TCTCCCCAGATGTGGTGAACAATTCC 0.587 0.25 27 9 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.40 9 6 DST 667 broad.mit.edu 37 6 56505280 56505299 + Frame_Shift_Del DEL TAAACTTTGAGTGATTCCTG - - HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr6:56505280_56505299delTAAACTTTGAGTGATTCCTG uc003pdf.2 - 17 2061_2080 c.2033_2052delCAGGAATCACTCAAAGTTTA c.(2032-2052)TCAGGAATCACTCAAAGTTTAfs p.S678fs DST_uc003pcz.3_Frame_Shift_Del_p.S500fs|DST_uc011dxj.1_Frame_Shift_Del_p.S529fs|DST_uc011dxk.1_Frame_Shift_Del_p.S540fs|DST_uc011dxl.1_Frame_Shift_Del_p.S529fs|DST_uc003pcy.3_Frame_Shift_Del_p.S174fs|DST_uc003pdb.2_Frame_Shift_Del_p.S174fs|DST_uc003pdc.3_Frame_Shift_Del_p.S174fs|DST_uc003pdd.3_Frame_Shift_Del_p.S174fs|DST_uc003pde.2_Frame_Shift_Del_p.S616fs NM_001144769 NP_001138241 Q03001 DYST_HUMAN dystonin isoform 2 500_506 cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1) 14 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) ATCCTGAGTTTAAACTTTGAGTGATTCCTGATATCATGAG 0.445 0.45 118 95 MLL3 58508 broad.mit.edu 37 7 151845580 151845581 + Frame_Shift_Ins INS - A A HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr7:151845580_151845581insA uc003wla.2 - 52 13650_13651 c.13431_13432insT c.(13429-13434)TTTCGAfs p.F4477fs MLL3_uc003wkz.2_Frame_Shift_Ins_p.F3595fs|MLL3_uc003wkx.2_Frame_Shift_Ins_p.F635fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.F2041fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 4477_4478 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTGGTGCATCGAAATCTGTGGC 0.441 0.46 100 84 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 22 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 387 102 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 18 203 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.48 14 13 SULF2 55959 broad.mit.edu 37 20 46295012 46295012 + Frame_Shift_Del DEL C - - HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr20:46295012delC uc002xto.2 - 12 2127 c.1797delG c.(1795-1797)GTGfs p.V599fs SULF2_uc002xtr.2_Frame_Shift_Del_p.V599fs|SULF2_uc002xtq.2_Frame_Shift_Del_p.V599fs|SULF2_uc010zyd.1_5'Flank NM_018837 NP_061325 Q8IWU5 SULF2_HUMAN sulfatase 2 isoform a precursor 599 bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway cell surface|endoplasmic reticulum|extracellular space|Golgi stack arylsulfatase activity|calcium ion binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 ACCGATGTGTCACTTTAATGG 0.602 0.52 198 213 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 101 378 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HSC2_UPPER_AERODIGESTIVE_TRACT NA HSC2_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 7 81 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 4 29 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.40 42 28 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.56 533 665 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.71 10 25 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 12 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.67 406 832 MLLT3 4300 broad.mit.edu 37 9 20414311 20414313 + In_Frame_Del DEL CTG - - HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr9:20414311_20414313delCTG uc003zoe.2 - 5 790_792 c.531_533delCAG c.(529-534)AGCAGT>AGT p.177_178SS>S MLLT3_uc011lne.1_In_Frame_Del_p.145_146SS>S|MLLT3_uc011lnf.1_In_Frame_Del_p.174_175SS>S|MLLT3_uc003zof.2_5'UTR NM_004529 NP_004520 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia 177_178 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding lung(2)|ovary(1) 3 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) gctgctgctactgctgctgctgc 0.143 0.14 95 15 NOTCH1 4851 broad.mit.edu 37 9 139418207 139418208 + Frame_Shift_Ins INS - GCGTG GCGTG HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr9:139418207_139418208insGCGTG uc004chz.2 - 3 364_365 c.364_365insCACGC c.(364-366)CTGfs p.L122fs NM_017617 NP_060087 P46531 NOTC1_HUMAN notch1 preproprotein 122 Extracellular (Potential).|EGF-like 3. aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity p.L122fs*3(1) haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1) 856 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06) 0.000 0.21 1290 347 NOTCH1 4851 broad.mit.edu 37 9 139418208 139418209 + Frame_Shift_Ins INS - CGTGA CGTGA HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr9:139418208_139418209insCGTGA uc004chz.2 - 3 363_364 c.363_364insTCACG c.(361-366)ACGCTGfs p.T121fs NM_017617 NP_060087 P46531 NOTC1_HUMAN notch1 preproprotein 121_122 Extracellular (Potential).|EGF-like 3. aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity p.L122fs*3(1) haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1) 856 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06) 0.000 0.10 1473 169 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 102 19 ADAMTS20 80070 broad.mit.edu 37 12 43833806 43833807 + Frame_Shift_Del DEL TC - - HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr12:43833806_43833807delTC uc010skx.1 - 17 2356_2357 c.2356_2357delGA c.(2356-2358)GAAfs p.E786fs ADAMTS20_uc001rno.1_5'Flank|ADAMTS20_uc001rnp.1_5'Flank NM_025003 NP_079279 P59510 ATS20_HUMAN a disintegrin-like and metalloprotease with 786 Spacer. proteinaceous extracellular matrix zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1) 19 all_cancers(12;2.6e-05)|Lung SC(27;0.184) Lung NSC(34;0.0569)|all_lung(34;0.129) GBM - Glioblastoma multiforme(48;0.0473) CACATTGATTTCTTTTTTTGAC 0.302 0.25 110 36 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.21 38 10 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.39 14 9 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 21 215 TP53 7157 broad.mit.edu 37 17 7577022 7577023 + Frame_Shift_Ins INS - CTTA CTTA rs121913344 HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr17:7577022_7577023insCTTA uc002gim.2 - 8 1109_1110 c.915_916insTAAG c.(913-918)AAGCGAfs p.K305fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Frame_Shift_Ins_p.K305fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Ins_p.K173fs|TP53_uc010cng.1_Frame_Shift_Ins_p.K173fs|TP53_uc002gii.1_Frame_Shift_Ins_p.K173fs|TP53_uc010cnh.1_Frame_Shift_Ins_p.K305fs|TP53_uc010cni.1_Frame_Shift_Ins_p.K305fs|TP53_uc002gij.2_Frame_Shift_Ins_p.K305fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 305_306 Bipartite nuclear localization signal.|Interaction with HIPK1 (By similarity).|Interaction with CARM1. R -> Q (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.R306*(99)|p.K305*(14)|p.0?(7)|p.K305N(3)|p.?(3)|p.K305R(2)|p.R306fs*39(2)|p.K305K(1)|p.L265_K305del41(1)|p.K305fs*1(1)|p.K305E(1)|p.K305fs*32(1)|p.K305T(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) TGCTTACCTCGCTTAGTGCTCC 0.559 0.75 14 43 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.59 14 20 NCOA3 8202 broad.mit.edu 37 20 46279860 46279861 + In_Frame_Ins INS - CAA CAA rs151060280 byFrequency HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr20:46279860_46279861insCAA uc002xtk.2 + 20 3991_3992 c.3786_3787insCAA c.(3784-3789)insCAA p.1276_1277insQ NCOA3_uc010ght.1_In_Frame_Ins_p.1267_1268insQ|NCOA3_uc002xtl.2_In_Frame_Ins_p.1272_1273insQ|NCOA3_uc002xtm.2_In_Frame_Ins_p.1271_1272insQ|NCOA3_uc002xtn.2_In_Frame_Ins_p.1275_1276insQ|NCOA3_uc010zyc.1_In_Frame_Ins_p.1071_1072insQ NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 1276_1277 Poly-Gln.|Acetyltransferase. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 agcagcagcagcagcaacagca 0.307 0.43 60 46 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 93 394 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HSC3_UPPER_AERODIGESTIVE_TRACT NA HSC3_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 3 127 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 28 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.26 29 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 83 128 RICTOR 253260 broad.mit.edu 37 5 38950568 38950569 + Frame_Shift_Ins INS - G G rs139245892 HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chr5:38950568_38950569insG uc003jlp.2 - 31 3405_3406 c.3381_3382insC c.(3379-3384)AGCAACfs p.S1127fs RICTOR_uc003jlo.2_Frame_Shift_Ins_p.S1127fs|RICTOR_uc010ivf.2_Frame_Shift_Ins_p.S842fs NM_152756 NP_689969 Q6R327 RICTR_HUMAN rapamycin-insensitive companion of mTOR 1127_1128 actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation cytosol|TORC2 complex protein binding ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1) 10 all_lung(31;0.000396) ATTCGCCTGTTGCTTGTCTTAC 0.366 0.47 91 81 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.55 21 26 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 3 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 3 40 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.20 37 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 890 195 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.26 64 23 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 11 70 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.13 77 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 138 785 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HT1080_SOFT_TISSUE NA HT1080_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 13 98 FAM123B 139285 broad.mit.edu 37 X 63412383 63412384 + Frame_Shift_Ins INS - G G HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chrX:63412383_63412384insG uc004dvo.2 - 2 1056_1057 c.783_784insC c.(781-786)CCCATGfs p.P261fs NM_152424 NP_689637 Q5JTC6 F123B_HUMAN family with sequence similarity 123B 261_262 Wnt receptor signaling pathway cytoplasm|nucleus|plasma membrane p.0?(40) kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1) 112 0.000 0.30 83 36 FAM123B 139285 broad.mit.edu 37 X 63412386 63412387 + Frame_Shift_Ins INS - T T HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chrX:63412386_63412387insT uc004dvo.2 - 2 1053_1054 c.780_781insA c.(778-783)AAACCCfs p.K260fs NM_152424 NP_689637 Q5JTC6 F123B_HUMAN family with sequence similarity 123B 260_261 Wnt receptor signaling pathway cytoplasm|nucleus|plasma membrane p.0?(40) kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1) 112 0.000 0.26 87 31 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.48 23 21 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.20 322 81 IL1RAP 3556 broad.mit.edu 37 3 190366326 190366328 + In_Frame_Del DEL GAG - - HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr3:190366326_190366328delGAG uc003fsm.1 + 12 1751_1753 c.1545_1547delGAG c.(1543-1548)AAGAGG>AAG p.R516del IL1RAP_uc010hzg.1_In_Frame_Del_p.R516del|IL1RAP_uc003fsn.1_RNA|IL1RAP_uc003fso.1_In_Frame_Del_p.R516del|IL1RAP_uc003fsp.1_RNA|IL1RAP_uc003fsq.2_Intron NM_002182 NP_002173 Q9NPH3 IL1AP_HUMAN interleukin 1 receptor accessory protein isoform 516 Cytoplasmic (Potential).|TIR. inflammatory response|innate immune response|protein complex assembly extracellular region|integral to plasma membrane ovary(1) 1 all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21) Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06) GBM - Glioblastoma multiforme(93;0.00851) AAGAGCTGAAGAGGGCTAAGACG 0.498 0.52 29 31 PDGFRA 5156 broad.mit.edu 37 4 55151647 55151647 + Frame_Shift_Del DEL A - - HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr4:55151647delA uc003han.3 + 17 2764 c.2433delA c.(2431-2433)TCAfs p.S811fs PDGFRA_uc003haa.2_Frame_Shift_Del_p.S571fs NM_006206 NP_006197 P16234 PGFRA_HUMAN platelet-derived growth factor receptor alpha 811 Protein kinase.|Cytoplasmic (Potential). cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye cytoplasm|integral to plasma membrane|nucleus ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1) 674 all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08) GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256) Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268) TTTTGGCTTCAAAAAATGTAA 0.413 0.43 24 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 7 5 FGF2 2247 broad.mit.edu 37 4 123748258 123748259 + Frame_Shift_Ins INS - G G HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr4:123748258_123748259insG uc003iev.1 + 1 396_397 c.328_329insG c.(328-330)CGGfs p.R110fs NM_002006 NP_001997 P09038 FGF2_HUMAN fibroblast growth factor 2 110 activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing extracellular space fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity ovary(1)|lung(1)|central_nervous_system(1) 3 Pentosan Polysulfate(DB00686) 0.000 0.12 118 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.67 65 133 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.37 52 31 APC 324 broad.mit.edu 37 5 112175951 112175952 + Frame_Shift_Ins INS - A A HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr5:112175951_112175952insA uc010jby.2 + 16 5040_5041 c.4660_4661insA c.(4660-4662)GAAfs p.E1554fs APC_uc011cvt.1_Frame_Shift_Ins_p.E1536fs|APC_uc003kpz.3_Frame_Shift_Ins_p.E1554fs|APC_uc003kpy.3_Frame_Shift_Ins_p.E1554fs|APC_uc010jbz.2_Frame_Shift_Ins_p.E1271fs|APC_uc010jca.2_Frame_Shift_Ins_p.E854fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1554 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.T1556fs*3(35)|p.E1554fs*5(2)|p.E1554*(2)|p.?(1)|p.T1556fs*9(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1554fs*11(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GAAAGAGGCAGAAAAAACTATT 0.342 0.38 13 8 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.30 16 7 RANBP17 64901 broad.mit.edu 37 5 170343550 170343553 + Frame_Shift_Del DEL TTAA - - HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr5:170343550_170343553delTTAA uc003mba.2 + 9 932_935 c.916_919delTTAA c.(916-921)TTAATTfs p.L306fs RANBP17_uc003max.1_RNA|RANBP17_uc003may.1_RNA|RANBP17_uc003maz.1_RNA|RANBP17_uc010jjr.1_RNA NM_022897 NP_075048 Q9H2T7 RBP17_HUMAN RAN binding protein 17 306_307 mRNA transport|protein import into nucleus|transmembrane transport cytoplasm|nuclear pore GTP binding|protein transporter activity ovary(2)|central_nervous_system(1) 3 Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123) Medulloblastoma(196;0.0399)|all_neural(177;0.0966) Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516) CCTTGGTAATTTAATTAAGGGAGT 0.324 0.35 77 42 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.85 2 11 ARFGEF1 10565 broad.mit.edu 37 8 68111237 68111238 + Frame_Shift_Ins INS - A A HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr8:68111237_68111238insA uc003xxo.1 - 39 5871_5872 c.5481_5482insT c.(5479-5484)TTTCTGfs p.F1827fs ARFGEF1_uc003xxl.1_Intron|ARFGEF1_uc003xxm.1_Frame_Shift_Ins_p.F230fs|ARFGEF1_uc003xxn.1_Frame_Shift_Ins_p.F772fs|ARFGEF1_uc003xxp.1_3'UTR NM_006421 NP_006412 Q9Y6D6 BIG1_HUMAN brefeldin A-inhibited guanine 1827_1828 exocytosis|regulation of ARF protein signal transduction cytoplasm ARF guanyl-nucleotide exchange factor activity|myosin binding ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1) 8 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206) CCGATTCGCAGAAAAAATCTTC 0.356 0.35 62 33 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 31 PSIP1 11168 broad.mit.edu 37 9 15474111 15474112 + Frame_Shift_Ins INS - T T HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr9:15474111_15474112insT uc003zlv.3 - 9 1083_1084 c.753_754insA c.(751-756)AAAGAGfs p.K251fs PSIP1_uc003zlw.3_Frame_Shift_Ins_p.K251fs|PSIP1_uc003zlz.3_Frame_Shift_Ins_p.K251fs|PSIP1_uc003zma.3_Frame_Shift_Ins_p.K242fs|PSIP1_uc003zly.2_Frame_Shift_Ins_p.K251fs NM_033222 NP_150091 O75475 PSIP1_HUMAN PC4 and SFRS1 interacting protein 1 isoform 2 251_252 initiation of viral infection|interspecies interaction between organisms|nuclear mRNA 5'-splice site recognition|provirus integration|regulation of transcription, DNA-dependent|response to heat|response to oxidative stress|transcription, DNA-dependent cytosol|nuclear heterochromatin|nuclear periphery|nucleoplasm|nucleoplasm|transcriptionally active chromatin activating transcription factor binding|chromatin binding|DNA secondary structure binding|RNA polymerase II transcription coactivator activity breast(1) 1 GBM - Glioblastoma multiforme(50;2.38e-06) TTCTTCCCCTCTTTTTTATCCG 0.401 0.46 142 121 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.47 19 17 FADD 8772 broad.mit.edu 37 11 70049816 70049817 + Frame_Shift_Ins INS - G G HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr11:70049816_70049817insG uc001opm.2 + 1 548_549 c.251_252insG c.(250-252)GCGfs p.A84fs NM_003824 NP_003815 Q13158 FADD_HUMAN Fas-associated via death domain 84 activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction cytosol death receptor binding|identical protein binding ovary(1)|lung(1)|pancreas(1) 3 Esophageal squamous(2;1.19e-45) LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) 0.000 0.14 423 68 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 940 414 LTBR 4055 broad.mit.edu 37 12 6493608 6493610 + In_Frame_Del DEL GCA - - HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr12:6493608_6493610delGCA uc001qny.1 + 1 252_254 c.84_86delGCA c.(82-87)TCGCAG>TCG p.Q29del LTBR_uc010sfc.1_Intron|LTBR_uc001qnz.1_In_Frame_Del_p.Q29del NM_002342 NP_002333 P36941 TNR3_HUMAN lymphotoxin beta receptor precursor 29 apoptosis|cellular response to mechanical stimulus|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade integral to membrane protein binding|receptor activity lung(2) 2 0.000 0.26 157 55 LRRK2 120892 broad.mit.edu 37 12 40722224 40722225 + Frame_Shift_Ins INS - T T HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr12:40722224_40722225insT uc001rmg.3 + 39 5840_5841 c.5719_5720insT c.(5719-5721)ATTfs p.I1907fs LRRK2_uc009zjw.2_Frame_Shift_Ins_p.I745fs|LRRK2_uc001rmi.2_Frame_Shift_Ins_p.I740fs NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 1907 Protein kinase. activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) GGCTGTGAAGATTTTTAATAAA 0.312 0.28 55 21 NAV3 89795 broad.mit.edu 37 12 78400805 78400806 + Frame_Shift_Ins INS - A A HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr12:78400805_78400806insA uc001syp.2 + 8 1660_1661 c.1487_1488insA c.(1486-1488)CCAfs p.P496fs NAV3_uc001syo.2_Frame_Shift_Ins_p.P496fs NM_014903 NP_055718 Q8IVL0 NAV3_HUMAN neuron navigator 3 496 nuclear outer membrane ATP binding|nucleoside-triphosphatase activity large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 17 GAGATGGCTCCAAAAAAGACCT 0.416 0.16 48 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.60 85 129 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 17 74 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HT115_LARGE_INTESTINE NA HT115_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.87 4 26 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 4 103 MAP4K3 8491 broad.mit.edu 37 2 39553380 39553380 + Frame_Shift_Del DEL C - - HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr2:39553380delC uc002rro.2 - 9 660 c.569delG c.(568-570)GGTfs p.G190fs MAP4K3_uc002rrp.2_Frame_Shift_Del_p.G190fs|MAP4K3_uc010yns.1_5'Flank NM_003618 NP_003609 Q8IVH8 M4K3_HUMAN mitogen-activated protein kinase kinase kinase 190 Protein kinase. JNK cascade ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity ovary(3)|lung(3)|stomach(1)|pancreas(1) 8 all_hematologic(82;0.211) TTGATTGTAACCCCCCTTCCT 0.433 0.54 386 456 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.30 47 20 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 269 54 FGF2 2247 broad.mit.edu 37 4 123748258 123748259 + Frame_Shift_Ins INS - G G HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr4:123748258_123748259insG uc003iev.1 + 1 396_397 c.328_329insG c.(328-330)CGGfs p.R110fs NM_002006 NP_001997 P09038 FGF2_HUMAN fibroblast growth factor 2 110 activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing extracellular space fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity ovary(1)|lung(1)|central_nervous_system(1) 3 Pentosan Polysulfate(DB00686) 0.000 0.10 104 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.39 151 97 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 49 121 CDKN1A 1026 broad.mit.edu 37 6 36651934 36651935 + Frame_Shift_Ins INS - C C HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr6:36651934_36651935insC uc003omm.3 + 2 178_179 c.56_57insC c.(55-57)CGCfs p.R19fs CDKN1A_uc011dtq.1_Frame_Shift_Ins_p.R53fs|CDKN1A_uc003oml.2_Frame_Shift_Ins_p.R19fs|CDKN1A_uc003omn.2_Frame_Shift_Ins_p.R19fs NM_000389 NP_000380 P38936 CDN1A_HUMAN cyclin-dependent kinase inhibitor 1A 19 Required for binding cyclins.|C4-type (Potential). cell cycle arrest|cellular response to extracellular stimulus|cellular response to ionizing radiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|induction of apoptosis by intracellular signals|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of fibroblast proliferation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|S phase of mitotic cell cycle|stress-induced premature senescence cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleoplasm|PCNA-p21 complex cyclin-dependent protein kinase activating kinase activity|cyclin-dependent protein kinase inhibitor activity|metal ion binding ovary(1)|breast(1) 2 AAGGCCTGCCGCCGCCTCTTCG 0.653 0.64 15 27 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.29 175 73 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 2 26 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.65 17 31 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.49 202 194 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 129 363 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 52 458 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 HT1376_URINARY_TRACT NA HT1376_URINARY_TRACT NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.14 42 7 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HT144_SKIN NA HT144_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 32 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes HT144_SKIN NA HT144_SKIN NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.41 19 13 TPRXL 348825 broad.mit.edu 37 3 14106310 14106311 + In_Frame_Ins INS - CCAGCACCAGCAGTC CCAGCACCAGCAGTC HT144_SKIN NA HT144_SKIN NA g.chr3:14106310_14106311insCCAGCACCAGCAGTC uc011avd.1 + 3 1089_1090 c.634_635insCCAGCACCAGCAGTC c.(634-636)TCC>TCCAGCACCAGCAGTCCC p.217_218insSTSSP TPRXL_uc003byh.1_In_Frame_Ins_p.217_218insSTSSP|TPRXL_uc003byg.2_In_Frame_Ins_p.217_218insSTSSP NR_002223 RecName: Full=Putative protein TPRXL; 0 cagcagcagctccagcaccagc 0.213 0.42 11 8 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HT144_SKIN NA HT144_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.41 42 29 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HT144_SKIN NA HT144_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 134 174 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HT144_SKIN NA HT144_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 37 86 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HT144_SKIN NA HT144_SKIN NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.51 28 29 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HT144_SKIN NA HT144_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 60 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HT144_SKIN NA HT144_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 551 227 ATN1 1822 broad.mit.edu 37 12 7045892 7045894 + In_Frame_Del DEL CAG - - rs66756893;rs67074116 HT144_SKIN NA HT144_SKIN NA g.chr12:7045892_7045894delCAG uc001qrw.1 + 5 1699_1701 c.1462_1464delCAG c.(1462-1464)CAGdel p.Q502del ATN1_uc001qrx.1_In_Frame_Del_p.Q502del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagc 0.458 0.14 103 17 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HT144_SKIN NA HT144_SKIN NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.24 91 28 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HT144_SKIN NA HT144_SKIN NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.49 25 24 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HT144_SKIN NA HT144_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.97 5 138 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HT144_SKIN NA HT144_SKIN NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 78 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HT144_SKIN NA HT144_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 74 333 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HT144_SKIN NA HT144_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 3 165 AMOT 154796 broad.mit.edu 37 X 112058884 112058885 + Frame_Shift_Ins INS - C C HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chrX:112058884_112058885insC uc004epr.2 - 2 1093_1094 c.1093_1094insG c.(1093-1095)GATfs p.D365fs AMOT_uc004eps.2_5'UTR|AMOT_uc004ept.1_Frame_Shift_Ins_p.D365fs NM_001113490 NP_001106962 Q4VCS5 AMOT_HUMAN angiomotin isoform 1 365 actin cytoskeleton organization|cell-cell junction assembly|negative regulation of angiogenesis|negative regulation of vascular permeability|positive regulation of blood vessel endothelial cell migration|positive regulation of cell size|positive regulation of stress fiber assembly|regulation of cell migration actin filament|cell surface|cytoplasm|endocytic vesicle|external side of plasma membrane|integral to membrane|lamellipodium|ruffle|stress fiber|tight junction|tight junction angiostatin binding|protein binding|receptor activity ovary(1) 1 ACGGTAATGATCCCCCTGGTGA 0.391 0.23 60 18 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 18 300 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.40 9 6 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 124 91 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.25 189 64 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 322 466 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.19 217 51 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.16 210 41 APC 324 broad.mit.edu 37 5 112175951 112175952 + Frame_Shift_Ins INS - A A HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr5:112175951_112175952insA uc010jby.2 + 16 5040_5041 c.4660_4661insA c.(4660-4662)GAAfs p.E1554fs APC_uc011cvt.1_Frame_Shift_Ins_p.E1536fs|APC_uc003kpz.3_Frame_Shift_Ins_p.E1554fs|APC_uc003kpy.3_Frame_Shift_Ins_p.E1554fs|APC_uc010jbz.2_Frame_Shift_Ins_p.E1271fs|APC_uc010jca.2_Frame_Shift_Ins_p.E854fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1554 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.T1556fs*3(35)|p.E1554fs*5(2)|p.E1554*(2)|p.?(1)|p.T1556fs*9(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1554fs*11(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GAAAGAGGCAGAAAAAACTATT 0.342 0.59 119 168 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.69 4 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 3 44 CTSW 1521 broad.mit.edu 37 11 65648935 65648937 + In_Frame_Del DEL AGG - - HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr11:65648935_65648937delAGG uc001ogc.1 + 3 272_274 c.230_232delAGG c.(229-234)CAGGAG>CAG p.E79del CTSW_uc001ogb.1_In_Frame_Del_p.E79del NM_001335 NP_001326 P56202 CATW_HUMAN cathepsin W preproprotein 79 immune response|proteolysis cysteine-type endopeptidase activity central_nervous_system(1) 1 READ - Rectum adenocarcinoma(159;0.168) CAGAGGCTGCAGGAGGAGGACTT 0.576 0.20 775 197 Unknown 0 broad.mit.edu 37 12 63359550 63359555 + In_Frame_Del DEL CTGCTG - - HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr12:63359550_63359555delCTGCTG uc001srn.1 + 1 451_456 c.446_451delCTGCTG c.(445-453)ACTGCTGCT>ACT p.AA158del SubName: Full=Putative uncharacterized protein RPL14P1; ACTAAGGGTActgctgctgctgctgc 0.379 0.45 6 5 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.18 81 18 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.44 208 166 BRSK1 84446 broad.mit.edu 37 19 55820004 55820005 + Splice_Site INS - A A HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr19:55820004_55820005insA uc002qkg.2 + 18 2367 c.2090_splice c.e18-2 p.G697_splice BRSK1_uc002qkf.2_Splice_Site_p.G713_splice|BRSK1_uc002qkh.2_Splice_Site_p.G392_splice NM_032430 NP_115806 Q8TDC3 BRSK1_HUMAN BR serine/threonine kinase 1 establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV cell junction|cytoplasm|nucleus magnesium ion binding|protein serine/threonine kinase activity ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1) 6 Renal(1328;0.245) BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.0474) CCTGTGCCTCTAGGTCCCAGCC 0.599 0.27 40 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 68 315 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HT29_LARGE_INTESTINE NA HT29_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 59 752 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.60 23 34 ATIC 471 broad.mit.edu 37 2 216184408 216184408 + Frame_Shift_Del DEL C - - HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr2:216184408delC uc002vex.3 + 4 418 c.244delC c.(244-246)CCAfs p.P82fs ATIC_uc010zjo.1_Frame_Shift_Del_p.P23fs|ATIC_uc002vey.3_Frame_Shift_Del_p.P81fs NM_004044 NP_004035 P31939 PUR9_HUMAN 5-aminoimidazole-4-carboxamide ribonucleotide 82 IMP biosynthetic process|purine base metabolic process cytosol IMP cyclohydrolase activity|phosphoribosylaminoimidazolecarboxamide formyltransferase activity|protein homodimerization activity ATIC/ALK(24) haematopoietic_and_lymphoid_tissue(22)|ovary(2)|lung(2)|soft_tissue(2)|skin(1) 29 Renal(323;0.229) Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097) Tetrahydrofolic acid(DB00116) TCGTAATATTCCAGAAGATAA 0.313 0.41 17 12 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.35 20 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.74 16 46 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.87 4 27 POU3F2 5454 broad.mit.edu 37 6 99283172 99283173 + In_Frame_Ins INS - CAG CAG HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr6:99283172_99283173insCAG uc003ppe.2 + 1 593_594 c.423_424insCAG c.(421-426)insCAG p.149_150insQ NM_005604 NP_005595 P20265 PO3F2_HUMAN POU domain, class 3, transcription factor 2 149_150 positive regulation of cell proliferation identical protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197) BRCA - Breast invasive adenocarcinoma(108;0.0355) aacagcagcaacagcagcagca 0.465 0.20 28 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.64 4 7 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.88 3 23 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 1 14 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.70 3 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 172 85 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.31 43 19 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.33 41 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.64 10 18 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HT55_LARGE_INTESTINE NA HT55_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.80 2 8 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 34 SPEN 23013 broad.mit.edu 37 1 16256372 16256372 + Frame_Shift_Del DEL A - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:16256372delA uc001axk.1 + 11 3841 c.3637delA c.(3637-3639)AAAfs p.K1213fs SPEN_uc010obp.1_Frame_Shift_Del_p.K1172fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 1213 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) CGAGGTAGGCAAACCCCCTCA 0.433 0.56 100 127 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 503 147 INSRR 3645 broad.mit.edu 37 1 156814053 156814053 + Frame_Shift_Del DEL C - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:156814053delC uc010pht.1 - 15 3011 c.2757delG c.(2755-2757)GGGfs p.G919fs NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron NM_014215 NP_055030 P14616 INSRR_HUMAN insulin receptor-related receptor precursor 919 Extracellular (Potential). protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity lung(11)|ovary(5)|skin(2)|kidney(1)|central_nervous_system(1) 20 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) GGACATGCAGCCCCCCAGCAT 0.562 0.45 121 99 OBSCN 84033 broad.mit.edu 37 1 228479653 228479653 + Frame_Shift_Del DEL C - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:228479653delC uc009xez.1 + 39 10438 c.10394delC c.(10393-10395)GCCfs p.A3465fs OBSCN_uc001hsn.2_Frame_Shift_Del_p.A3465fs|OBSCN_uc001hsq.1_Frame_Shift_Del_p.A721fs NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 3465 Ig-like 35. apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) GTGGAAGGGGCCACAGCCATG 0.592 0.47 53 47 MSH2 4436 broad.mit.edu 37 2 47702220 47702222 + In_Frame_Del DEL GTC - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:47702220_47702222delGTC uc002rvy.1 + 12 1884_1886 c.1816_1818delGTC c.(1816-1818)GTCdel p.V606del MSH2_uc010yoh.1_In_Frame_Del_p.V540del|MSH2_uc002rvz.2_In_Frame_Del_p.V606del|MSH2_uc010fbg.2_In_Frame_Del_p.V416del|MSH2_uc010fbi.1_RNA NM_000251 NP_000242 P43246 MSH2_HUMAN mutS homolog 2 606 Interaction with EXO1. B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes MutSalpha complex|MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding p.?(2) large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1) 55 all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) AGATGCTGTTGTCAGCTTTGCTC 0.394 0.98 2 119 ATP13A5 344905 broad.mit.edu 37 3 193051570 193051570 + Frame_Shift_Del DEL A - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:193051570delA uc011bsq.1 - 11 1241 c.1241delT c.(1240-1242)TTCfs p.F414fs NM_198505 NP_940907 Q4VNC0 AT135_HUMAN ATPase type 13A5 414 Helical; (Potential). ATP biosynthetic process|cation transport integral to membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding ovary(5)|skin(4)|large_intestine(2) 11 all_cancers(143;1.08e-08)|Ovarian(172;0.0386) OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06) GBM - Glioblastoma multiforme(46;0.000307) TAGGGCATAGAAAAAACCCAT 0.463 0.42 54 39 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 95 104 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.36 60 34 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.41 165 113 TRRAP 8295 broad.mit.edu 37 7 98507728 98507728 + Frame_Shift_Del DEL T - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:98507728delT uc003upp.2 + 15 1609 c.1400delT c.(1399-1401)ATTfs p.I467fs TRRAP_uc011kis.1_Frame_Shift_Del_p.I467fs|TRRAP_uc003upr.2_Frame_Shift_Del_p.I159fs NM_003496 NP_003487 Q9Y4A5 TRRAP_HUMAN transformation/transcription domain-associated 467 histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1) 37 all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274) STAD - Stomach adenocarcinoma(171;0.215) CTCTCTGCCATTTTTAAGAAG 0.512 0.49 151 144 KIAA1549 57670 broad.mit.edu 37 7 138603524 138603524 + Frame_Shift_Del DEL A - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:138603524delA uc011kql.1 - 2 897 c.848delT c.(847-849)TTAfs p.L283fs KIAA1549_uc003vuk.3_Frame_Shift_Del_p.L233fs|KIAA1549_uc011kqj.1_Frame_Shift_Del_p.L283fs NM_020910 NP_065961 Q9HCM3 K1549_HUMAN hypothetical protein LOC57670 isoform 1 283 integral to membrane KIAA1549/BRAF(229) central_nervous_system(229)|pancreas(1) 230 CCGGGAGCTTAAAAAAAGGGT 0.517 0.36 50 28 TRPS1 7227 broad.mit.edu 37 8 116426270 116426270 + Frame_Shift_Del DEL T - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:116426270delT uc003ynz.2 - 6 4286 c.3827delA c.(3826-3828)AATfs p.N1276fs TRPS1_uc011lhy.1_Frame_Shift_Del_p.N1280fs|TRPS1_uc003yny.2_Frame_Shift_Del_p.N1289fs|TRPS1_uc010mcy.2_Frame_Shift_Del_p.N1276fs NM_014112 NP_054831 Q9UHF7 TRPS1_HUMAN zinc finger transcription factor TRPS1 1276 Transcriptional repressor domain (By similarity). negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) AGGTTTTCCATTTTTTTCCAC 0.383 0.44 27 21 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 22 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 695 74 GRIN3A 116443 broad.mit.edu 37 9 104499661 104499661 + Frame_Shift_Del DEL G - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:104499661delG uc004bbp.1 - 1 1202 c.601delC c.(601-603)CAGfs p.Q201fs GRIN3A_uc004bbq.1_Frame_Shift_Del_p.Q201fs NM_133445 NP_597702 Q8TCU5 NMD3A_HUMAN glutamate receptor, ionotropic, 201 Extracellular (Potential). response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1) 7 Acute lymphoblastic leukemia(62;0.0568) Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740) 0.000 0.52 320 343 ABI1 10006 broad.mit.edu 37 10 27057885 27057885 + Frame_Shift_Del DEL T - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:27057885delT uc001isx.2 - 6 782 c.615delA c.(613-615)AAAfs p.K205fs ABI1_uc001ite.2_Frame_Shift_Del_p.K200fs|ABI1_uc010qdh.1_Frame_Shift_Del_p.K200fs|ABI1_uc010qdi.1_Frame_Shift_Del_p.K141fs|ABI1_uc001isy.2_Frame_Shift_Del_p.K205fs|ABI1_uc001ita.2_Frame_Shift_Del_p.K205fs|ABI1_uc001isz.2_Frame_Shift_Del_p.K200fs|ABI1_uc001itb.2_Frame_Shift_Del_p.K222fs|ABI1_uc001itc.2_Frame_Shift_Del_p.K205fs|ABI1_uc010qdj.1_Frame_Shift_Del_p.K205fs|ABI1_uc001itd.2_Frame_Shift_Del_p.K205fs|ABI1_uc010qdk.1_Frame_Shift_Del_p.K205fs|ABI1_uc010qdg.1_Frame_Shift_Del_p.K71fs NM_005470 NP_005461 Q8IZP0 ABI1_HUMAN abl-interactor 1 isoform a 205 actin polymerization or depolymerization|cellular component movement|negative regulation of cell proliferation|peptidyl-tyrosine phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway cell junction|cytoskeleton|cytosol|endoplasmic reticulum|filopodium|growth cone|lamellipodium|nucleus|soluble fraction|synapse|synaptosome cytoskeletal protein binding central_nervous_system(1) 1 CTGTTGGGGGTTTAACAGGTT 0.398 0.46 215 181 TET1 80312 broad.mit.edu 37 10 70405700 70405701 + Frame_Shift_Ins INS - A A HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:70405700_70405701insA uc001jok.3 + 4 3719_3720 c.3214_3215insA c.(3214-3216)CAAfs p.Q1072fs NM_030625 NP_085128 Q8NFU7 TET1_HUMAN CXXC finger 6 1072 DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding ovary(5)|lung(2)|prostate(1)|breast(1) 9 AACCCATACCCAAATTGAGGAA 0.381 0.16 476 89 PTEN 5728 broad.mit.edu 37 10 89720648 89720649 + Splice_Site DEL TA - - rs34003473 HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:89720648_89720649delTA uc001kfb.2 + 9 1833 c.802_splice c.e9-2 p.D268_splice NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.?(7)|p.R55fs*1(4)|p.N212fs*1(2)|p.Y27fs*1(2)|p.M264fs*8(2)|p.G165_*404del(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) tttttttttttAGGACAAAATG 0.233 0.10 97 11 PTEN 5728 broad.mit.edu 37 10 89720649 89720649 + Splice_Site DEL A - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:89720649delA uc001kfb.2 + 9 1833 c.802_splice c.e9-2 p.D268_splice NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.?(4)|p.R55fs*1(4)|p.N212fs*1(2)|p.Y27fs*1(2)|p.M264fs*8(2)|p.G165_*404del(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) ttttttttttAGGACAAAATG 0.234 0.25 80 26 PDCD11 22984 broad.mit.edu 37 10 105176293 105176293 + Frame_Shift_Del DEL A - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:105176293delA uc001kwy.1 + 13 1651 c.1564delA c.(1564-1566)AAAfs p.K522fs NM_014976 NP_055791 Q14690 RRP5_HUMAN programmed cell death 11 522 S1 motif 5. mRNA processing|rRNA processing nucleolus RNA binding|transcription factor binding ovary(2)|breast(2)|skin(2)|central_nervous_system(1) 7 Colorectal(252;0.0747)|Breast(234;0.128) Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208) GATGACCCTGAAAAAAACCCT 0.483 0.48 118 107 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.52 13 14 GRM5 2915 broad.mit.edu 37 11 88338091 88338091 + Frame_Shift_Del DEL T - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:88338091delT uc001pcq.2 - 4 1389 c.1189delA c.(1189-1191)ATGfs p.M397fs GRM5_uc009yvm.2_Frame_Shift_Del_p.M397fs NM_001143831 NP_001137303 P41594 GRM5_HUMAN glutamate receptor, metabotropic 5 isoform a 397 Extracellular (Potential). activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission integral to plasma membrane G-protein coupled receptor activity|glutamate receptor activity central_nervous_system(4)|ovary(2)|lung(2)|breast(1) 9 Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834) Acamprosate(DB00659) 0.000 0.39 579 377 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 319 131 DACH1 1602 broad.mit.edu 37 13 72053363 72053363 + Frame_Shift_Del DEL A - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:72053363delA uc010thn.1 - 9 2231 c.1808delT c.(1807-1809)TTAfs p.L603fs DACH1_uc010tho.1_Frame_Shift_Del_p.L455fs|DACH1_uc010thp.1_Frame_Shift_Del_p.L401fs NM_080759 NP_542937 Q9UI36 DACH1_HUMAN dachshund homolog 1 isoform a 655 DACHbox-C.|Potential.|Interaction with SIN3A (By similarity). multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus DNA binding|nucleotide binding|protein binding breast(1) 1 Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198) GBM - Glioblastoma multiforme(99;0.00032) TCTTTCCCTTAAAAAATCCAT 0.373 0.50 160 162 ERCC5 2073 broad.mit.edu 37 13 103510739 103510741 + In_Frame_Del DEL AGA - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:103510739_103510741delAGA uc001vpw.2 + 6 1086_1088 c.643_645delAGA c.(643-645)AGAdel p.R216del ERCC5_uc001vpu.1_In_Frame_Del_p.R670del|ERCC5_uc010tjb.1_In_Frame_Del_p.R216del|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_In_Frame_Del_p.R48del NM_000123 NP_000114 P28715 ERCC5_HUMAN XPG-complementing protein 216 negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection nucleoplasm bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding ovary(4)|lung(1)|central_nervous_system(1)|skin(1) 7 all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211) CACCAAGCGCAGAAGAACATTAT 0.379 0.42 95 69 PAK6 56924 broad.mit.edu 37 15 40558254 40558255 + Frame_Shift_Ins INS - C C rs143850903 HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:40558254_40558255insC uc010bbl.2 + 5 856_857 c.416_417insC c.(415-417)GACfs p.D139fs PAK6_uc010bbm.2_Frame_Shift_Ins_p.D139fs|PAK6_uc001zky.3_Frame_Shift_Ins_p.D139fs|PAK6_uc010bbn.2_Frame_Shift_Ins_p.D139fs|PAK6_uc001zlb.2_Frame_Shift_Ins_p.D139fs NM_001128628 NP_001122100 Q9NQU5 PAK6_HUMAN p21-activated kinase 6 139 Linker. ATP binding|protein binding|protein serine/threonine kinase activity lung(5)|large_intestine(1)|ovary(1)|skin(1) 8 all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544) GAGCGCACTGACCCCCACGGCC 0.698 0.19 29 7 MAF 4094 broad.mit.edu 37 16 79633068 79633069 + Frame_Shift_Ins INS - C C HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:79633068_79633069insC uc002ffn.2 - 1 1554_1555 c.731_732insG c.(730-732)GGCfs p.G244fs MAF_uc002ffm.2_Frame_Shift_Ins_p.G244fs NM_001031804 NP_001026974 O75444 MAF_HUMAN v-maf musculoaponeurotic fibrosarcoma oncogene 244 Represses ARE-mediated transcription.|Ala-rich.|Gly-rich. transcription from RNA polymerase II promoter chromatin|nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity lung(1) 1 all_epithelial(2;0.139)|Lung NSC(2;0.186)|Melanoma(2;0.211) UCEC - Uterine corpus endometrioid carcinoma (2;0.0178) GGTGCAGGGCGccccccgcccc 0.376 0.35 15 8 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 1.00 0 10 FANCA 2175 broad.mit.edu 37 16 89869675 89869675 + Frame_Shift_Del DEL T - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:89869675delT uc002fou.1 - 8 826 c.784delA c.(784-786)ATGfs p.M262fs FANCA_uc010vpn.1_Frame_Shift_Del_p.M262fs|FANCA_uc002fov.1_Frame_Shift_Del_p.M245fs|FANCA_uc002fow.1_Frame_Shift_Del_p.M262fs|FANCA_uc002fox.1_Frame_Shift_Del_p.M262fs|FANCA_uc010ciu.1_Frame_Shift_Del_p.M230fs|FANCA_uc002foy.2_Frame_Shift_Del_p.M262fs NM_000135 NP_000126 O15360 FANCA_HUMAN Fanconi anemia, complementation group A isoform 262 DNA repair|protein complex assembly cytoplasm|nucleoplasm protein binding ovary(2)|breast(2)|central_nervous_system(1)|skin(1) 6 Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194) BRCA - Breast invasive adenocarcinoma(80;0.028) ACCTGCGGCATTTTTTCAGGC 0.368 0.43 114 85 TOP2A 7153 broad.mit.edu 37 17 38546381 38546381 + Frame_Shift_Del DEL T - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:38546381delT uc002huq.2 - 34 4429 c.4303delA c.(4303-4305)AGGfs p.R1435fs NM_001067 NP_001058 P11388 TOP2A_HUMAN DNA topoisomerase II, alpha isozyme 1435 apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1) 7 Breast(137;0.00328) STAD - Stomach adenocarcinoma(5;0.00183) Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385) GGGGCAGCCCTTTTTTTGGCA 0.413 0.44 149 119 KIAA0802 23255 broad.mit.edu 37 18 8784101 8784101 + Frame_Shift_Del DEL G - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr18:8784101delG uc002knr.2 + 6 1133 c.991delG c.(991-993)GGGfs p.G331fs KIAA0802_uc002knq.2_Frame_Shift_Del_p.G331fs|KIAA0802_uc010dkw.1_Frame_Shift_Del_p.G169fs NM_015210 NP_056025 Q9Y4B5 CC165_HUMAN hypothetical protein LOC23255 682 Potential. 0 0.000 0.48 622 564 SMAD7 4092 broad.mit.edu 37 18 46474795 46474795 + Frame_Shift_Del DEL G - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr18:46474795delG uc002ldg.2 - 2 913 c.626delC c.(625-627)CCTfs p.P209fs SMAD7_uc010xde.1_5'UTR NM_005904 NP_005895 O15105 SMAD7_HUMAN SMAD family member 7 209 Poly-Pro.|PY-motif.|Important for interaction with SMURF2. Missing: Diminishes interaction with SMURF2. adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding 0 Colorectal(1;0.0518) GGAGTAAGGAGGGGGGGGAGA 0.388 0.33 49 24 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 16 79 TGFB1 7040 broad.mit.edu 37 19 41847823 41847823 + Frame_Shift_Del DEL C - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41847823delC uc002oqh.1 - 5 1692 c.825delG c.(823-825)CGGfs p.R275fs CYP2F1_uc010xvw.1_Intron NM_000660 NP_000651 P01137 TGFB1_HUMAN transforming growth factor, beta 1 precursor 275 active induction of host immune response by virus|ATP biosynthetic process|cell cycle arrest|cell growth|cell-cell junction organization|chondrocyte differentiation|connective tissue replacement involved in inflammatory response wound healing|epidermal growth factor receptor signaling pathway|evasion of host defenses by virus|hemopoietic progenitor cell differentiation|induction of apoptosis|lymph node development|mitotic cell cycle G1/S transition checkpoint|negative regulation of blood vessel endothelial cell migration|negative regulation of cell growth|negative regulation of cell-cell adhesion|negative regulation of DNA replication|negative regulation of epithelial cell proliferation|negative regulation of fat cell differentiation|negative regulation of macrophage cytokine production|negative regulation of mitotic cell cycle|negative regulation of protein phosphorylation|ossification involved in bone remodeling|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of blood vessel endothelial cell migration|positive regulation of bone mineralization|positive regulation of cell division|positive regulation of chemotaxis|positive regulation of collagen biosynthetic process|positive regulation of epithelial to mesenchymal transition|positive regulation of fibroblast migration|positive regulation of interleukin-17 production|positive regulation of isotype switching to IgA isotypes|positive regulation of MAP kinase activity|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of protein dephosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein secretion|positive regulation of SMAD protein import into nucleus|protein export from nucleus|protein import into nucleus, translocation|receptor catabolic process|regulation of DNA binding|regulation of striated muscle tissue development|regulation of transforming growth factor beta receptor signaling pathway|response to cholesterol|response to estradiol stimulus|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway|viral infectious cycle extracellular space|Golgi lumen|nucleus|platelet alpha granule lumen|proteinaceous extracellular matrix growth factor activity|type II transforming growth factor beta receptor binding 0 Hyaluronidase(DB00070) CTCGGCGGTGCCGGGAGCTTT 0.637 0.29 27 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 58 426 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 5 70 DDX17 10521 broad.mit.edu 37 22 38895475 38895477 + In_Frame_Del DEL CTT - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:38895475_38895477delCTT uc003avy.3 - 3 569_571 c.466_468delAAG c.(466-468)AAGdel p.K156del DDX17_uc003avx.3_In_Frame_Del_p.K156del|DDX17_uc011anu.1_In_Frame_Del_p.K69del NM_001098504 NP_001091974 Q92841 DDX17_HUMAN DEAD box polypeptide 17 isoform 3 77 RNA processing nucleus ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity skin(3)|upper_aerodigestive_tract(1) 4 Melanoma(58;0.0286) 0.000 0.45 316 257 EP300 2033 broad.mit.edu 37 22 41569645 41569645 + Frame_Shift_Del DEL A - - HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:41569645delA uc003azl.3 + 29 5031 c.4636delA c.(4636-4638)AAAfs p.K1546fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1546 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding p.N1547fs*17(1) haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 GGGAGACAGCAAAAATGCTAA 0.398 0.50 7 7 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 7 124 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.14 457 74 FMO4 2329 broad.mit.edu 37 1 171293417 171293417 + Frame_Shift_Del DEL T - - HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr1:171293417delT uc001gho.2 + 5 679 c.462delT c.(460-462)CATfs p.H154fs NM_002022 NP_002013 P31512 FMO4_HUMAN flavin containing monooxygenase 4 154 xenobiotic metabolic process integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding kidney(2)|skin(1) 3 all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181) TGAATCCCCATTTACCTTTGG 0.433 0.44 200 159 CDK18 5129 broad.mit.edu 37 1 205497280 205497291 + In_Frame_Del DEL ACCCCCATTGAT - - HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr1:205497280_205497291delACCCCCATTGAT uc001hcr.2 + 10 1267_1278 c.1048_1059delACCCCCATTGAT c.(1048-1059)ACCCCCATTGATdel p.TPID350del CDK18_uc001hcp.2_In_Frame_Del_p.TPID320del|CDK18_uc001hcq.2_In_Frame_Del_p.TPID320del|CDK18_uc010prj.1_In_Frame_Del_p.TPID231del|CDK18_uc001hcs.2_In_Frame_Del_p.TPID231del|CDK18_uc009xbm.1_In_Frame_Del_p.TPID245del|CDK18_uc001hct.2_5'Flank NM_212503 NP_997668 Q07002 CDK18_HUMAN PCTAIRE protein kinase 3 isoform a 318_321 Protein kinase. D -> A (in Ref. 6; CAA47005). ATP binding|cyclin-dependent protein kinase activity|protein binding|signal transducer activity stomach(2) 2 AGAGTACTCCACCCCCATTGATATGTGGTGAG 0.608 0.31 150 67 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.43 13 10 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.39 20 13 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.14 127 21 PLD1 5337 broad.mit.edu 37 3 171406579 171406587 + In_Frame_Del DEL AGGCCACCG - - HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr3:171406579_171406587delAGGCCACCG uc003fhs.2 - 14 1534_1542 c.1418_1426delCGGTGGCCT c.(1417-1428)TCGGTGGCCTTT>TTT p.SVA473del PLD1_uc003fht.2_In_Frame_Del_p.SVA473del NM_002662 NP_002653 Q13393 PLD1_HUMAN phospholipase D1 isoform a 473_475 PLD phosphodiesterase 1.|Catalytic. cell communication|chemotaxis|Ras protein signal transduction endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity ovary(2)|lung(1) 3 all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186) LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14) Choline(DB00122) CCTCCCACAAAGGCCACCGATTGGTCAAT 0.536 0.11 207 25 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 143 207 CLPTM1L 81037 broad.mit.edu 37 5 1318538 1318538 + Frame_Shift_Del DEL G - - HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr5:1318538delG uc003jch.2 - 17 1609 c.1563delC c.(1561-1563)AACfs p.N521fs CLPTM1L_uc003jcg.2_Frame_Shift_Del_p.N352fs NM_030782 NP_110409 Q96KA5 CLP1L_HUMAN CLPTM1-like 521 Cytoplasmic (Potential). apoptosis integral to membrane breast(1)|central_nervous_system(1) 2 Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09) Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181) KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208) CCCCAAACTCGTTCACTCTGC 0.557 0.54 92 109 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.32 98 47 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.87 2 13 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 21 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.23 30 9 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.25 83 27 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.57 42 55 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 5 51 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 57 697 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HUCCT1_BILIARY_TRACT NA HUCCT1_BILIARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 90 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HUH1_LIVER NA HUH1_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 49 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HUH1_LIVER NA HUH1_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 550 211 YSK4 80122 broad.mit.edu 37 2 135779321 135779322 + Frame_Shift_Ins INS - T T HUH1_LIVER NA HUH1_LIVER NA g.chr2:135779321_135779322insT uc002tue.1 - 2 132_133 c.101_102insA c.(100-102)AATfs p.N34fs YSK4_uc010fne.1_Frame_Shift_Ins_p.N6fs|YSK4_uc002tuf.1_Frame_Shift_Ins_p.N34fs|YSK4_uc010fnc.1_Frame_Shift_Ins_p.N34fs|YSK4_uc010fnd.1_Frame_Shift_Ins_p.N34fs|YSK4_uc010zbg.1_Frame_Shift_Ins_p.N34fs|YSK4_uc002tui.3_Frame_Shift_Ins_p.N51fs NM_025052 NP_079328 Q56UN5 YSK4_HUMAN Yeast Sps1/Ste20-related kinase 4 isoform 1 34 ATP binding|protein serine/threonine kinase activity stomach(2)|urinary_tract(1)|ovary(1)|breast(1) 5 BRCA - Breast invasive adenocarcinoma(221;0.112) TGATGTTTTGATTTTTGGTAAC 0.371 0.35 129 69 TWF2 11344 broad.mit.edu 37 3 52266034 52266045 + In_Frame_Del DEL GCAGGTAGCAGG - - HUH1_LIVER NA HUH1_LIVER NA g.chr3:52266034_52266045delGCAGGTAGCAGG uc003ddd.2 - 3 348_359 c.197_208delCCTGCTACCTGC c.(196-210)CCCTGCTACCTGCTC>CTC p.PCYL66del TLR9_uc003ddb.2_5'Flank|TLR9_uc003ddc.1_5'Flank|TWF2_uc010hmc.2_In_Frame_Del_p.PCYL66del NM_007284 NP_009215 Q6IBS0 TWF2_HUMAN twinfilin-like protein 66_69 ADF-H 1. cytoskeleton|perinuclear region of cytoplasm actin binding|ATP binding stomach(1)|ovary(1)|lung(1) 3 BRCA - Breast invasive adenocarcinoma(193;2.43e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716) AGGCGGTAGAGCAGGTAGCAGGGCTGCTGGGC 0.646 0.22 121 35 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HUH1_LIVER NA HUH1_LIVER NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.45 21 17 HTT 3064 broad.mit.edu 37 4 3076604 3076606 + In_Frame_Del DEL CAG - - rs10618869 HUH1_LIVER NA HUH1_LIVER NA g.chr4:3076604_3076606delCAG uc011bvq.1 + 2 203_205 c.58_60delCAG c.(58-60)CAGdel p.Q40del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagc 0.335 0.37 29 17 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HUH1_LIVER NA HUH1_LIVER NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.41 24 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HUH1_LIVER NA HUH1_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.69 71 159 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HUH1_LIVER NA HUH1_LIVER NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.76 35 109 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC HUH1_LIVER NA HUH1_LIVER NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.33 89 43 BRD2 6046 broad.mit.edu 37 6 32942326 32942327 + Frame_Shift_Ins INS - TA TA HUH1_LIVER NA HUH1_LIVER NA g.chr6:32942326_32942327insTA uc003ocn.3 + 3 1818_1819 c.117_118insTA c.(115-120)TTGTATfs p.L39fs BRD2_uc003oco.2_RNA|BRD2_uc003ocq.3_Frame_Shift_Ins_p.L39fs|BRD2_uc003ocp.3_5'UTR|BRD2_uc010juh.2_Frame_Shift_Ins_p.L39fs NM_005104 NP_005095 P25440 BRD2_HUMAN bromodomain containing 2 39_40 spermatogenesis nucleus protein serine/threonine kinase activity central_nervous_system(3)|stomach(2) 5 CCTCTCTCTTGTATGAGGGCTT 0.589 0.17 115 23 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HUH1_LIVER NA HUH1_LIVER NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HUH1_LIVER NA HUH1_LIVER NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 32 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HUH1_LIVER NA HUH1_LIVER NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.35 22 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HUH1_LIVER NA HUH1_LIVER NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.51 469 489 FOXO1 2308 broad.mit.edu 37 13 41240050 41240051 + In_Frame_Ins INS - GCG GCG HUH1_LIVER NA HUH1_LIVER NA g.chr13:41240050_41240051insGCG uc001uxl.3 - 1 684_685 c.299_300insCGC c.(298-300)GCG>GCCGCG p.100_100A>AA NM_002015 NP_002006 Q12778 FOXO1_HUMAN forkhead box O1 100 Poly-Ala. anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding PAX3/FOXO1(749)|PAX7/FOXO1(197) soft_tissue(946)|lung(1)|central_nervous_system(1) 948 Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194) all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815) 0.000 0.29 22 9 Unknown 0 broad.mit.edu 37 14 23574096 23574098 + In_Frame_Del DEL GCA - - HUH1_LIVER NA HUH1_LIVER NA g.chr14:23574096_23574098delGCA uc010aki.1 - 1 80_82 c.32_34delTGC c.(31-36)CTGCCG>CCG p.L11del Homo sapiens cDNA clone IMAGE:40134016. ACTAGTGgcggcagcagcagcag 0.448 0.36 7 4 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HUH1_LIVER NA HUH1_LIVER NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 23 205 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HUH1_LIVER NA HUH1_LIVER NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 41 163 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HUH1_LIVER NA HUH1_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 123 465 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HUH1_LIVER NA HUH1_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 90 MED15 51586 broad.mit.edu 37 22 20918915 20918916 + In_Frame_Ins INS - CAG CAG HUH1_LIVER NA HUH1_LIVER NA g.chr22:20918915_20918916insCAG uc002zsp.2 + 6 710_711 c.630_631insCAG c.(628-633)insCAG p.218_219insQ MED15_uc002zsn.1_In_Frame_Ins_p.137_138insQ|MED15_uc002zso.2_In_Frame_Ins_p.147_148insQ|MED15_uc002zsq.2_In_Frame_Ins_p.218_219insQ|MED15_uc010gso.2_In_Frame_Ins_p.218_219insQ|MED15_uc002zsr.2_In_Frame_Ins_p.192_193insQ|MED15_uc011ahs.1_In_Frame_Ins_p.192_193insQ|MED15_uc011aht.1_In_Frame_Ins_p.192_193insQ|MED15_uc002zss.2_In_Frame_Ins_p.137_138insQ|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 218_219 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) agcagcagctccagcagcagca 0.178 0.33 40 20 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HUH28_BILIARY_TRACT NA HUH28_BILIARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 54 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HUH28_BILIARY_TRACT NA HUH28_BILIARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.48 150 136 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HUH28_BILIARY_TRACT NA HUH28_BILIARY_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 70 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 HUH28_BILIARY_TRACT NA HUH28_BILIARY_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.50 15 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HUH28_BILIARY_TRACT NA HUH28_BILIARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.31 43 19 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HUH28_BILIARY_TRACT NA HUH28_BILIARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.47 39 35 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HUH28_BILIARY_TRACT NA HUH28_BILIARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 89 14 NIN 51199 broad.mit.edu 37 14 51226613 51226614 + Frame_Shift_Del DEL CT - - HUH28_BILIARY_TRACT NA HUH28_BILIARY_TRACT NA g.chr14:51226613_51226614delCT uc001wym.2 - 17 2551_2552 c.2360_2361delAG c.(2359-2361)GAGfs p.E787fs NIN_uc001wyi.2_Frame_Shift_Del_p.E787fs|NIN_uc001wyj.2_RNA|NIN_uc001wyk.2_Frame_Shift_Del_p.E787fs|NIN_uc010tqp.1_Frame_Shift_Del_p.E793fs|NIN_uc001wyo.2_Frame_Shift_Del_p.E787fs NM_182946 NP_891991 Q8N4C6 NIN_HUMAN ninein isoform 5 787 Potential. centrosome localization centrosome|microtubule calcium ion binding|GTP binding|protein binding skin(3)|ovary(1)|kidney(1)|central_nervous_system(1) 6 all_epithelial(31;0.00244)|Breast(41;0.127) TTTCCAAGAGCTCTTTTCTTAA 0.505 0.96 5 113 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HUH28_BILIARY_TRACT NA HUH28_BILIARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.66 17 33 NCOA3 8202 broad.mit.edu 37 20 46279831 46279836 + In_Frame_Del DEL CAGCAA - - rs147879509 by1000genomes HUH28_BILIARY_TRACT NA HUH28_BILIARY_TRACT NA g.chr20:46279831_46279836delCAGCAA uc002xtk.2 + 20 3962_3967 c.3757_3762delCAGCAA c.(3757-3762)CAGCAAdel p.QQ1275del NCOA3_uc010ght.1_In_Frame_Del_p.QQ1266del|NCOA3_uc002xtl.2_In_Frame_Del_p.QQ1271del|NCOA3_uc002xtm.2_In_Frame_Del_p.QQ1270del|NCOA3_uc002xtn.2_In_Frame_Del_p.QQ1274del|NCOA3_uc010zyc.1_In_Frame_Del_p.QQ1070del NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 1275_1276 Poly-Gln.|Acetyltransferase. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 gcagcagcagcagcaacagcagcagc 0.291 0.32 59 28 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HUH28_BILIARY_TRACT NA HUH28_BILIARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 54 250 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HUH28_BILIARY_TRACT NA HUH28_BILIARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 48 MYH9 4627 broad.mit.edu 37 22 36685266 36685268 + In_Frame_Del DEL CTT - - HUH28_BILIARY_TRACT NA HUH28_BILIARY_TRACT NA g.chr22:36685266_36685268delCTT uc003apg.2 - 32 4651_4653 c.4420_4422delAAG c.(4420-4422)AAGdel p.K1474del NM_002473 NP_002464 P35579 MYH9_HUMAN myosin, heavy polypeptide 9, non-muscle 1474 Potential. actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1) 11 CCTTGGTCTCCTTCTCTCGGGCC 0.650 0.55 22 27 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HUH6_LIVER NA HUH6_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 2 24 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HUH6_LIVER NA HUH6_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.45 184 149 CCNA2 890 broad.mit.edu 37 4 122743803 122743804 + Splice_Site INS - A A HUH6_LIVER NA HUH6_LIVER NA g.chr4:122743803_122743804insA uc003iec.3 - 2 519 c.214_splice c.e2-1 p.V72_splice NM_001237 NP_001228 P20248 CCNA2_HUMAN cyclin A cell division|mitosis|mitotic cell cycle G2/M transition DNA damage checkpoint|Ras protein signal transduction|regulation of cyclin-dependent protein kinase activity cytoplasm|nucleoplasm protein kinase binding ovary(1) 1 GGGTGCAACCTAAAAAAAAATT 0.406 0.16 70 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HUH6_LIVER NA HUH6_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.35 61 33 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HUH6_LIVER NA HUH6_LIVER NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.41 33 23 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HUH6_LIVER NA HUH6_LIVER NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.93 2 26 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 HUH6_LIVER NA HUH6_LIVER NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.66 20 38 CSPP1 79848 broad.mit.edu 37 8 68071295 68071296 + In_Frame_Ins INS - AAG AAG HUH6_LIVER NA HUH6_LIVER NA g.chr8:68071295_68071296insAAG uc003xxi.2 + 21 2582_2583 c.2551_2552insAAG c.(2551-2553)AAA>AAAGAA p.855_856insE CSPP1_uc003xxh.1_RNA|CSPP1_uc003xxj.2_In_Frame_Ins_p.820_821insE|CSPP1_uc003xxk.2_In_Frame_Ins_p.475_476insE NM_001077204 NP_001070672 Q1MSJ5 CSPP1_HUMAN centrosome spindle pole associated protein 1 855_856 centrosome|microtubule|spindle ovary(3)|breast(2) 5 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153) aagaaagaagaaagaagaagaa 0.248 0.22 39 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HUH6_LIVER NA HUH6_LIVER NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 102 18 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HUH6_LIVER NA HUH6_LIVER NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.21 26 7 CSH2 1443 broad.mit.edu 37 17 61950602 61950602 + Frame_Shift_Del DEL A - - HUH6_LIVER NA HUH6_LIVER NA g.chr17:61950602delA uc002jch.2 - 2 223 c.108delT c.(106-108)TTTfs p.F36fs CSH2_uc002jcg.2_Frame_Shift_Del_p.F36fs|CSH2_uc002jci.2_Frame_Shift_Del_p.F36fs|GH2_uc002jcj.2_Intron|CSH2_uc002jck.2_Frame_Shift_Del_p.F36fs NM_020991 NP_066271 P01243 CSH_HUMAN chorionic somatomammotropin hormone 2 isoform 1 36 female pregnancy|signal transduction extracellular region hormone activity|metal ion binding 0 0.000 0.38 26 16 SERPINB4 6318 broad.mit.edu 37 18 61328072 61328073 + Frame_Shift_Ins INS - T T HUH6_LIVER NA HUH6_LIVER NA g.chr18:61328072_61328073insT uc002ljg.2 - 2 209_210 c.183_184insA c.(181-186)CAAGTCfs p.Q61fs SERPINB3_uc002lji.2_Frame_Shift_Ins_p.Q61fs|SERPINB3_uc010dqa.2_Frame_Shift_Ins_p.Q61fs|SERPINB3_uc010dqb.2_Frame_Shift_Ins_p.Q61fs|SERPINB3_uc010dqc.2_Frame_Shift_Ins_p.Q61fs P48594 SPB4_HUMAN SubName: Full=Squamous cell carcinoma antigen 2; 61_62 immune response|regulation of proteolysis cytoplasm|extracellular region protein binding|serine-type endopeptidase inhibitor activity ovary(2)|lung(1) 3 TTCTCTGTGACTTGATCAAAGT 0.436 0.38 23 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HUH6_LIVER NA HUH6_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.67 169 336 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HUH6_LIVER NA HUH6_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 3 51 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.79 8 30 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.57 10 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 100 171 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.46 36 31 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.64 4 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 48 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.36 481 266 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 792 342 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 35 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 88 325 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 6 79 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.11 181 23 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 4 46 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 326 88 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.54 11 13 TPRXL 348825 broad.mit.edu 37 3 14106310 14106311 + In_Frame_Ins INS - CCAGCACCAGCAGTC CCAGCACCAGCAGTC HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr3:14106310_14106311insCCAGCACCAGCAGTC uc011avd.1 + 3 1089_1090 c.634_635insCCAGCACCAGCAGTC c.(634-636)TCC>TCCAGCACCAGCAGTCCC p.217_218insSTSSP TPRXL_uc003byh.1_In_Frame_Ins_p.217_218insSTSSP|TPRXL_uc003byg.2_In_Frame_Ins_p.217_218insSTSSP NR_002223 RecName: Full=Putative protein TPRXL; 0 cagcagcagctccagcaccagc 0.213 0.33 8 4 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.35 11 6 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.11 70 9 BMP2K 55589 broad.mit.edu 37 4 79792137 79792139 + In_Frame_Del DEL CAG - - rs17855588 HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr4:79792137_79792139delCAG uc003hlk.2 + 11 1598_1600 c.1432_1434delCAG c.(1432-1434)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 gcaacagcaacagcagcagcagc 0.167 0.17 118 25 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 124 169 NIPBL 25836 broad.mit.edu 37 5 37014818 37014819 + In_Frame_Ins INS - ATA ATA HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr5:37014818_37014819insATA uc003jkl.3 + 22 5093_5094 c.4594_4595insATA c.(4594-4596)GAA>GATAAA p.1532_1532E>DK NIPBL_uc003jkk.3_In_Frame_Ins_p.1532_1532E>DK NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 1532 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) TAACTCTTATGAAACAGCTATG 0.317 0.46 36 31 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.20 53 13 RASA1 5921 broad.mit.edu 37 5 86564685 86564686 + Frame_Shift_Ins INS - C C HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr5:86564685_86564686insC uc003kiw.2 + 1 535_536 c.417_418insC c.(415-420)CCTCCCfs p.P139fs RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_5'Flank|RASA1_uc011ctv.1_5'Flank|RASA1_uc011ctw.1_5'Flank|RASA1_uc010jaw.2_5'Flank|RASA1_uc011ctu.1_Frame_Shift_Ins_p.P139fs NM_002890 NP_002881 P20936 RASA1_HUMAN RAS p21 protein activator 1 isoform 1 139_140 Poly-Pro. cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis cytosol|intrinsic to internal side of plasma membrane glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding upper_aerodigestive_tract(3)|ovary(1)|lung(1) 5 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) CTCTGCCCCCTCCCCCTTACCT 0.594 0.23 23 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 19 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 52 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.18 36 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 306 143 NCOR2 9612 broad.mit.edu 37 12 124887059 124887067 + In_Frame_Del DEL GCTGCTGCT - - rs67031864 HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr12:124887059_124887067delGCTGCTGCT uc010tba.1 - 14 1640_1648 c.1523_1531delAGCAGCAGC c.(1522-1533)CAGCAGCAGCCC>CCC p.QQQ508del NCOR2_uc010tay.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010taz.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010tbb.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010tbc.1_In_Frame_Del_p.QQQ507del|NCOR2_uc001ugj.1_In_Frame_Del_p.QQQ508del NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 508_510 Poly-Gln. cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) CGGGGCATGGgctgctgctgctgctgctg 0.316 0.48 49 46 WBP4 11193 broad.mit.edu 37 13 41642791 41642791 + Frame_Shift_Del DEL A - - HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr13:41642791delA uc001uxt.2 + 5 470 c.357delA c.(355-357)AGAfs p.R119fs WBP4_uc010tfd.1_Frame_Shift_Del_p.R98fs NM_007187 NP_009118 O75554 WBP4_HUMAN WW domain-containing binding protein 4 119 Lys-rich. nuclear mRNA cis splicing, via spliceosome nuclear speck|spliceosomal complex nucleic acid binding|proline-rich region binding|zinc ion binding breast(2)|kidney(1) 3 Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114) all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07) agaagaaaagaaaaaaagaTC 0.343 0.37 52 30 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 13 114 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 19 83 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 156 575 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HUPT3_PANCREAS NA HUPT3_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 5 69 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 1 18 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 253 56 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.33 14 7 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 87 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.51 42 43 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.20 36 9 DNAH8 1769 broad.mit.edu 37 6 38749088 38749089 + Frame_Shift_Ins INS - A A rs148035646 HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr6:38749088_38749089insA uc003ooe.1 + 14 2147_2148 c.1547_1548insA c.(1546-1548)GGAfs p.G516fs NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 CCTATAGCAGGAAAAATACTCT 0.381 0.44 89 71 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.87 2 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 27 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 288 79 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.58 5 7 TNFRSF13B 23495 broad.mit.edu 37 17 16843038 16843039 + Frame_Shift_Del DEL AG - - HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr17:16843038_16843039delAG uc002gqs.1 - 5 717_718 c.704_705delCT c.(703-705)CCTfs p.P235fs TNFRSF13B_uc010vwt.1_RNA|TNFRSF13B_uc002gqt.1_Frame_Shift_Del_p.P189fs NM_012452 NP_036584 O14836 TR13B_HUMAN tumor necrosis factor receptor 13B 235 Cytoplasmic (Potential). cell surface receptor linked signaling pathway integral to plasma membrane protein binding|receptor activity kidney(2) 2 0.000 0.54 672 788 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.23 27 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 59 296 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HUPT4_PANCREAS NA HUPT4_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 45 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 50 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.26 404 140 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.48 25 23 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.29 29 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 176 247 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 28 59 MAP3K1 4214 broad.mit.edu 37 5 56178577 56178579 + In_Frame_Del DEL GAA - - HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56178577_56178579delGAA uc003jqw.3 + 14 4051_4053 c.3550_3552delGAA c.(3550-3552)GAAdel p.E1187del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 1187 Poly-Glu. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) GATGGAAGCTGAAGAAGAAGAAG 0.429 0.28 71 27 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.40 249 167 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.13 106 16 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.37 36 21 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 3 29 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 911 214 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.29 30 12 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.23 123 36 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 46 454 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.78 53 185 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.18 102 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 173 615 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 10 171 HNRNPH2 3188 broad.mit.edu 37 X 100668132 100668132 + Frame_Shift_Del DEL G - - IALM_LUNG NA IALM_LUNG NA g.chrX:100668132delG uc004ehm.2 + 2 1326 c.1156delG c.(1156-1158)GGGfs p.G386fs HNRNPH2_uc004ehn.2_Frame_Shift_Del_p.G386fs NM_019597 NP_062543 P55795 HNRH2_HUMAN heterogeneous nuclear ribonucleoprotein H2 386 2 X 16 AA Gly-rich approximate repeats.|2 X 19 AA perfect repeats.|2-2. nuclear mRNA splicing, via spliceosome actin cytoskeleton|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm nucleotide binding|protein binding|RNA binding 0 TTCTACAGCAGGGGCAAGTGG 0.488 0.94 1 15 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 IALM_LUNG NA IALM_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.68 18 38 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - IALM_LUNG NA IALM_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.19 274 65 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes IALM_LUNG NA IALM_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.58 5 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 IALM_LUNG NA IALM_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.44 9 7 CCNA2 890 broad.mit.edu 37 4 122743803 122743804 + Splice_Site INS - A A IALM_LUNG NA IALM_LUNG NA g.chr4:122743803_122743804insA uc003iec.3 - 2 519 c.214_splice c.e2-1 p.V72_splice NM_001237 NP_001228 P20248 CCNA2_HUMAN cyclin A cell division|mitosis|mitotic cell cycle G2/M transition DNA damage checkpoint|Ras protein signal transduction|regulation of cyclin-dependent protein kinase activity cytoplasm|nucleoplasm protein kinase binding ovary(1) 1 GGGTGCAACCTAAAAAAAAATT 0.406 0.55 26 32 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 IALM_LUNG NA IALM_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.66 38 74 TRIO 7204 broad.mit.edu 37 5 14480033 14480033 + Frame_Shift_Del DEL A - - IALM_LUNG NA IALM_LUNG NA g.chr5:14480033delA uc003jff.2 + 43 6255 c.6249delA c.(6247-6249)TTAfs p.L2083fs TRIO_uc003jfg.2_RNA|TRIO_uc003jfh.1_Frame_Shift_Del_p.L1732fs NM_007118 NP_009049 O75962 TRIO_HUMAN triple functional domain (PTPRF interacting) 2083 DH 2. apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway cytosol ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1) 18 Lung NSC(4;0.000742) TGTAGGACTTAAAGCAGCGTC 0.423 0.24 38 12 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 IALM_LUNG NA IALM_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.50 24 24 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - IALM_LUNG NA IALM_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.91 2 21 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 IALM_LUNG NA IALM_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.46 13 11 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 IALM_LUNG NA IALM_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 46 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency IALM_LUNG NA IALM_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.56 197 252 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 IALM_LUNG NA IALM_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 340 135 RARA 5914 broad.mit.edu 37 17 38504639 38504640 + Frame_Shift_Ins INS - T T IALM_LUNG NA IALM_LUNG NA g.chr17:38504639_38504640insT uc002huk.1 + 3 705_706 c.250_251insT c.(250-252)ATCfs p.I84fs RARA_uc002hul.3_Frame_Shift_Ins_p.I84fs|RARA_uc010wfe.1_Intron|RARA_uc002hun.1_Frame_Shift_Ins_p.I79fs NM_000964 NP_000955 P10276 RARA_HUMAN retinoic acid receptor, alpha isoform 1 84 Modulating. apoptotic cell clearance|cellular response to estrogen stimulus|cellular response to retinoic acid|estrogen receptor signaling pathway|negative regulation of granulocyte differentiation|negative regulation of interferon-gamma production|negative regulation of tumor necrosis factor production|positive regulation of binding|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of interleukin-13 production|positive regulation of interleukin-4 production|positive regulation of interleukin-5 production|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus cytoplasm|nucleoplasm chromatin DNA binding|enzyme binding|protein domain specific binding|protein heterodimerization activity|receptor binding|retinoic acid binding|retinoic acid receptor activity|retinoic acid-responsive element binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding ovary(1)|lung(1)|breast(1) 3 Breast(137;0.00328) STAD - Stomach adenocarcinoma(5;0.00143) Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799) TCTACCCCGCATCTACAAGCCT 0.574 0.29 75 31 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 IALM_LUNG NA IALM_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.67 27 54 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 IALM_LUNG NA IALM_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.40 30 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 IALM_LUNG NA IALM_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 130 367 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 IALM_LUNG NA IALM_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 2 38 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 IGR37_SKIN NA IGR37_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 57 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - IGR37_SKIN NA IGR37_SKIN NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 356 103 THBS3 7059 broad.mit.edu 37 1 155172174 155172175 + Frame_Shift_Del DEL AG - - IGR37_SKIN NA IGR37_SKIN NA g.chr1:155172174_155172175delAG uc001fix.2 - 9 998_999 c.975_976delCT c.(973-978)CCCTGTfs p.P325fs RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Frame_Shift_Del_p.P316fs|THBS3_uc001fiz.2_Frame_Shift_Del_p.P325fs|THBS3_uc001fiy.2_5'UTR|THBS3_uc010pfu.1_Frame_Shift_Del_p.P205fs|THBS3_uc010pfv.1_RNA|THBS3_uc001fja.2_RNA NM_007112 NP_009043 P49746 TSP3_HUMAN thrombospondin 3 precursor 325_326 EGF-like 2; calcium-binding (Potential). cell-matrix adhesion extracellular region|perinuclear region of cytoplasm calcium ion binding|heparin binding|structural molecule activity breast(3)|ovary(2) 5 all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) CCCGGGAAACAGGGGTCAGCGT 0.614 0.39 61 39 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes IGR37_SKIN NA IGR37_SKIN NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.56 23 29 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 IGR37_SKIN NA IGR37_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 42 19 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 IGR37_SKIN NA IGR37_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.31 20 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 IGR37_SKIN NA IGR37_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 98 111 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 IGR37_SKIN NA IGR37_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 24 34 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes IGR37_SKIN NA IGR37_SKIN NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.68 6 13 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC IGR37_SKIN NA IGR37_SKIN NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.19 56 13 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 IGR37_SKIN NA IGR37_SKIN NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.38 20 12 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes IGR37_SKIN NA IGR37_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 26 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - IGR37_SKIN NA IGR37_SKIN NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.12 105 14 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes IGR37_SKIN NA IGR37_SKIN NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.11 88 11 NIN 51199 broad.mit.edu 37 14 51190283 51190285 + In_Frame_Del DEL CTC - - IGR37_SKIN NA IGR37_SKIN NA g.chr14:51190283_51190285delCTC uc001wyi.2 - 31 6489_6491 c.6298_6300delGAG c.(6298-6300)GAGdel p.E2100del NIN_uc001wyj.2_RNA NM_020921 NP_065972 Q8N4C6 NIN_HUMAN ninein isoform 2 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment centrosome localization centrosome|microtubule calcium ion binding|GTP binding|protein binding skin(3)|ovary(1)|kidney(1)|central_nervous_system(1) 6 all_epithelial(31;0.00244)|Breast(41;0.127) AATTTTTCTTCTCTGCTGTTTTC 0.448 0.36 119 68 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 IGR37_SKIN NA IGR37_SKIN NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.55 14 17 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes IGR37_SKIN NA IGR37_SKIN NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.18 93 21 TP53 7157 broad.mit.edu 37 17 7577594 7577595 + Frame_Shift_Del DEL AC - - IGR37_SKIN NA IGR37_SKIN NA g.chr17:7577594_7577595delAC uc002gim.2 - 7 880_881 c.686_687delGT c.(685-687)TGTfs p.C229fs TP53_uc002gig.1_Frame_Shift_Del_p.C229fs|TP53_uc002gih.2_Frame_Shift_Del_p.C229fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.C97fs|TP53_uc010cng.1_Frame_Shift_Del_p.C97fs|TP53_uc002gii.1_Frame_Shift_Del_p.C97fs|TP53_uc010cnh.1_Frame_Shift_Del_p.C229fs|TP53_uc010cni.1_Frame_Shift_Del_p.C229fs|TP53_uc002gij.2_Frame_Shift_Del_p.C229fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.C136fs|TP53_uc002gio.2_Frame_Shift_Del_p.C97fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 229 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). C -> Y (in sporadic cancers; somatic mutation).|C -> G (in a sporadic cancer; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> S (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.C229fs*10(10)|p.0?(7)|p.C229*(3)|p.C229S(2)|p.C229R(2)|p.C229Y(2)|p.C229_H233delCTTIH(2)|p.T230fs*9(1)|p.C229fs*1(1)|p.C229fs*18(1)|p.C229_T230insX(1)|p.C229C(1)|p.V225fs*23(1)|p.D228fs*12(1)|p.C229G(1)|p.C229_I232del(1)|p.S227_I232delSDCTTI(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGATGGTGGTACAGTCAGAGCC 0.525 0.91 11 110 COL1A1 1277 broad.mit.edu 37 17 48266756 48266757 + Frame_Shift_Ins INS - G G IGR37_SKIN NA IGR37_SKIN NA g.chr17:48266756_48266757insG uc002iqm.2 - 39 2936_2937 c.2810_2811insC c.(2809-2811)CCTfs p.P937fs NM_000088 NP_000079 P02452 CO1A1_HUMAN alpha 1 type I collagen preproprotein 937 Triple-helical region. axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception collagen type I|extracellular space|plasma membrane identical protein binding|platelet-derived growth factor binding COL1A1/PDGFB(372) soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1) 382 Collagenase(DB00048)|Palifermin(DB00039) 0.000 0.12 244 32 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 IGR37_SKIN NA IGR37_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 150 111 ID1 3397 broad.mit.edu 37 20 30193544 30193545 + Frame_Shift_Ins INS - G G rs11545371 IGR37_SKIN NA IGR37_SKIN NA g.chr20:30193544_30193545insG uc002wwg.1 + 1 453_454 c.354_355insG c.(352-357)CCCGGGfs p.P118fs ID1_uc002wwh.1_Frame_Shift_Ins_p.P118fs|hsa-mir-3193|MI0014238_5'Flank NM_002165 NP_002156 P41134 ID1_HUMAN inhibitor of DNA binding 1 isoform a 118_119 angiogenesis|blood vessel endothelial cell migration|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by transcription factor localization|transforming growth factor beta receptor signaling pathway cytoplasm protein binding ovary(1) 1 all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198) Epithelial(4;1.99e-05)|all cancers(5;0.000169)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264) TTGGAACCCCCGGGGGCCGAGG 0.614 0.12 51 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 IGR37_SKIN NA IGR37_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 68 451 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 IGR37_SKIN NA IGR37_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 8 135 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 IGR39_SKIN NA IGR39_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.84 6 31 THBS3 7059 broad.mit.edu 37 1 155172174 155172175 + Frame_Shift_Del DEL AG - - IGR39_SKIN NA IGR39_SKIN NA g.chr1:155172174_155172175delAG uc001fix.2 - 9 998_999 c.975_976delCT c.(973-978)CCCTGTfs p.P325fs RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Frame_Shift_Del_p.P316fs|THBS3_uc001fiz.2_Frame_Shift_Del_p.P325fs|THBS3_uc001fiy.2_5'UTR|THBS3_uc010pfu.1_Frame_Shift_Del_p.P205fs|THBS3_uc010pfv.1_RNA|THBS3_uc001fja.2_RNA NM_007112 NP_009043 P49746 TSP3_HUMAN thrombospondin 3 precursor 325_326 EGF-like 2; calcium-binding (Potential). cell-matrix adhesion extracellular region|perinuclear region of cytoplasm calcium ion binding|heparin binding|structural molecule activity breast(3)|ovary(2) 5 all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) CCCGGGAAACAGGGGTCAGCGT 0.614 0.15 82 15 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes IGR39_SKIN NA IGR39_SKIN NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.62 11 18 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 IGR39_SKIN NA IGR39_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.30 28 12 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 IGR39_SKIN NA IGR39_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.38 16 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 IGR39_SKIN NA IGR39_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 70 75 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 IGR39_SKIN NA IGR39_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.57 46 61 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes IGR39_SKIN NA IGR39_SKIN NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.56 8 10 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 IGR39_SKIN NA IGR39_SKIN NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.36 16 9 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes IGR39_SKIN NA IGR39_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 3 25 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 IGR39_SKIN NA IGR39_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 4 41 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - IGR39_SKIN NA IGR39_SKIN NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.11 322 38 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes IGR39_SKIN NA IGR39_SKIN NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.12 73 10 TAOK3 51347 broad.mit.edu 37 12 118675915 118675918 + Frame_Shift_Del DEL CATG - - rs140022569 IGR39_SKIN NA IGR39_SKIN NA g.chr12:118675915_118675918delCATG uc001twx.2 - 7 692_695 c.397_400delCATG c.(397-402)CATGGAfs p.H133fs TAOK3_uc001tww.2_5'UTR|TAOK3_uc001twy.3_Frame_Shift_Del_p.H133fs NM_016281 NP_057365 Q9H2K8 TAOK3_HUMAN TAO kinase 3 133_134 Protein kinase. MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation mitochondrion|plasma membrane ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity lung(5)|central_nervous_system(1) 6 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) TAGGCTAGTCCATGCAAGGCTCCA 0.397 0.24 31 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C IGR39_SKIN NA IGR39_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.85 3 17 TP53 7157 broad.mit.edu 37 17 7577594 7577595 + Frame_Shift_Del DEL AC - - IGR39_SKIN NA IGR39_SKIN NA g.chr17:7577594_7577595delAC uc002gim.2 - 7 880_881 c.686_687delGT c.(685-687)TGTfs p.C229fs TP53_uc002gig.1_Frame_Shift_Del_p.C229fs|TP53_uc002gih.2_Frame_Shift_Del_p.C229fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.C97fs|TP53_uc010cng.1_Frame_Shift_Del_p.C97fs|TP53_uc002gii.1_Frame_Shift_Del_p.C97fs|TP53_uc010cnh.1_Frame_Shift_Del_p.C229fs|TP53_uc010cni.1_Frame_Shift_Del_p.C229fs|TP53_uc002gij.2_Frame_Shift_Del_p.C229fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.C136fs|TP53_uc002gio.2_Frame_Shift_Del_p.C97fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 229 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). C -> Y (in sporadic cancers; somatic mutation).|C -> G (in a sporadic cancer; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> S (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.C229fs*10(10)|p.0?(7)|p.C229*(3)|p.C229S(2)|p.C229R(2)|p.C229Y(2)|p.C229_H233delCTTIH(2)|p.T230fs*9(1)|p.C229fs*1(1)|p.C229fs*18(1)|p.C229_T230insX(1)|p.C229C(1)|p.V225fs*23(1)|p.D228fs*12(1)|p.C229G(1)|p.C229_I232del(1)|p.S227_I232delSDCTTI(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGATGGTGGTACAGTCAGAGCC 0.525 0.93 10 139 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 IGR39_SKIN NA IGR39_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.54 102 121 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 IGR39_SKIN NA IGR39_SKIN NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.28 58 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 IGR39_SKIN NA IGR39_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 51 452 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 IGR39_SKIN NA IGR39_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 8 135 ARAF 369 broad.mit.edu 37 X 47426094 47426094 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chrX:47426094delC uc011mlq.1 + 7 747 c.614delC c.(613-615)GCCfs p.A205fs ARAF_uc011mln.1_Intron|ARAF_uc011mlo.1_Frame_Shift_Del_p.A71fs|ARAF_uc011mlp.1_Frame_Shift_Del_p.A205fs|ARAF_uc004dic.1_5'UTR NM_001654 NP_001645 P10398 ARAF_HUMAN v-raf murine sarcoma 3611 viral oncogene 205 intracellular signal transduction|negative regulation of apoptosis|positive regulation of peptidyl-serine phosphorylation ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity large_intestine(3)|lung(2)|ovary(1)|skin(1) 7 Adenosine triphosphate(DB00171) CCAGCCAATGCCCCCCTACAG 0.632 0.27 191 69 RPS6KA6 27330 broad.mit.edu 37 X 83403062 83403063 + Frame_Shift_Ins INS - T T IGROV1_OVARY NA IGROV1_OVARY NA g.chrX:83403062_83403063insT uc004eej.1 - 4 404_405 c.327_328insA c.(325-330)AAAGCCfs p.K109fs RPS6KA6_uc011mqt.1_Frame_Shift_Ins_p.K109fs|RPS6KA6_uc011mqu.1_Frame_Shift_Ins_p.K6fs|RPS6KA6_uc010nmo.1_RNA NM_014496 NP_055311 Q9UK32 KS6A6_HUMAN ribosomal protein S6 kinase polypeptide 6 109_110 Protein kinase 1. axon guidance|central nervous system development|intracellular protein kinase cascade|synaptic transmission cytosol|nucleoplasm ATP binding|magnesium ion binding|protein serine/threonine kinase activity lung(5)|stomach(1)|central_nervous_system(1)|skin(1) 8 TTTAAAGAGGCTTTTTTTAACA 0.302 0.51 26 27 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 IGROV1_OVARY NA IGROV1_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.99 2 166 EPHA2 1969 broad.mit.edu 37 1 16462199 16462199 + Frame_Shift_Del DEL G - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr1:16462199delG uc001aya.1 - 6 1516 c.1379delC c.(1378-1380)CCGfs p.P460fs EPHA2_uc010oca.1_Frame_Shift_Del_p.P460fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 460 Extracellular (Potential).|Fibronectin type-III 2. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) 0.000 0.41 685 478 EPHA2 1969 broad.mit.edu 37 1 16474977 16474977 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr1:16474977delC uc001aya.1 - 3 856 c.719delG c.(718-720)GGTfs p.G240fs EPHA2_uc010oca.1_Frame_Shift_Del_p.G240fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 240 Extracellular (Potential).|Cys-rich. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) GGGCTCTTCACCCCCCGGTGG 0.667 0.39 75 48 JAK1 3716 broad.mit.edu 37 1 65325833 65325833 + Frame_Shift_Del DEL G - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr1:65325833delG uc001dbu.1 - 9 1538 c.1289delC c.(1288-1290)CCGfs p.P430fs JAK1_uc009wam.1_Frame_Shift_Del_p.P418fs NM_002227 NP_002218 P23458 JAK1_HUMAN janus kinase 1 430 interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway cytoskeleton|cytosol|endomembrane system|membrane|nucleus ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity p.P430fs*2(1) haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1) 61 BRCA - Breast invasive adenocarcinoma(111;0.0485) GACGATCAACGGGGGGGCCAC 0.542 0.10 82 9 PTPN22 26191 broad.mit.edu 37 1 114377581 114377582 + Frame_Shift_Ins INS - G G IGROV1_OVARY NA IGROV1_OVARY NA g.chr1:114377581_114377582insG uc001eds.2 - 14 1974_1975 c.1844_1845insC c.(1843-1845)CCTfs p.P615fs PTPN22_uc009wgq.2_Frame_Shift_Ins_p.P560fs|PTPN22_uc010owo.1_Frame_Shift_Ins_p.P371fs|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Frame_Shift_Ins_p.P615fs|PTPN22_uc009wgs.2_Frame_Shift_Ins_p.P488fs|PTPN22_uc001edu.2_Frame_Shift_Ins_p.P615fs NM_015967 NP_057051 Q9Y2R2 PTN22_HUMAN protein tyrosine phosphatase, non-receptor type 615 negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation internal side of plasma membrane|nucleus|perinuclear region of cytoplasm kinase binding|protein tyrosine phosphatase activity|SH3 domain binding kidney(2)|lung(1)|skin(1) 4 Lung SC(450;0.184) all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06) Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133) CAGGAAGTGGAGGGGGGATTTC 0.332 0.12 319 44 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 667 193 NCOA1 8648 broad.mit.edu 37 2 24952369 24952369 + Splice_Site DEL G - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr2:24952369delG uc002rfk.2 + 15 3145 c.2887_splice c.e15-1 p.G963_splice NCOA1_uc010eye.2_Splice_Site_p.G963_splice|NCOA1_uc002rfi.2_Splice_Site_p.G812_splice|NCOA1_uc002rfj.2_Splice_Site_p.G963_splice|NCOA1_uc002rfl.2_Splice_Site_p.G963_splice NM_003743 NP_003734 Q15788 NCOA1_HUMAN nuclear receptor coactivator 1 isoform 1 PAX3/NCOA1(8) soft_tissue(8)|ovary(1)|lung(1)|skin(1) 11 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) TTTTCTAACAGGGGGGTGGAT 0.373 0.47 115 104 EPAS1 2034 broad.mit.edu 37 2 46607487 46607487 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr2:46607487delC uc002ruv.2 + 12 2164 c.1676delC c.(1675-1677)ACCfs p.T559fs EPAS1_uc002ruw.2_Frame_Shift_Del_p.T25fs NM_001430 NP_001421 Q99814 EPAS1_HUMAN endothelial PAS domain protein 1 559 angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia transcription factor complex histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding ovary(1)|skin(1) 2 all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18) LUSC - Lung squamous cell carcinoma(58;0.151) 0.000 0.46 538 451 LRP2 4036 broad.mit.edu 37 2 169997025 169997025 + Frame_Shift_Del DEL G - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr2:169997025delG uc002ues.2 - 72 13352 c.13139delC c.(13138-13140)CCAfs p.P4380fs NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 4380 EGF-like 17.|Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) 0.000 0.32 130 60 CASP8 841 broad.mit.edu 37 2 202149799 202149799 + Frame_Shift_Del DEL T - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr2:202149799delT uc002uxr.1 + 9 1272 c.1063delT c.(1063-1065)TTTfs p.F355fs CASP8_uc002uxp.1_Frame_Shift_Del_p.F372fs|CASP8_uc002uxq.1_Frame_Shift_Del_p.F340fs|CASP8_uc002uxt.1_Frame_Shift_Del_p.F414fs|CASP8_uc002uxu.1_RNA|CASP8_uc002uxw.1_Frame_Shift_Del_p.F340fs|CASP8_uc002uxy.1_Intron|CASP8_uc002uxx.1_Intron|CASP8_uc010ftf.2_Frame_Shift_Del_p.F271fs NM_033355 NP_203519 Q14790 CASP8_HUMAN caspase 8 isoform B precursor 355 activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor centrosome|cytosol|mitochondrial outer membrane cysteine-type endopeptidase activity|protein binding|protein binding p.S355F(1) upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1) 5 ACCCAAAGTGTTTTTTATTCA 0.453 0.44 337 261 IRS1 3667 broad.mit.edu 37 2 227662352 227662352 + Frame_Shift_Del DEL G - - rs13306467 IGROV1_OVARY NA IGROV1_OVARY NA g.chr2:227662352delG uc002voh.3 - 1 1155 c.1103delC c.(1102-1104)CCGfs p.P368fs NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 368 Ser-rich. fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) 0.000 0.43 372 285 CHL1 10752 broad.mit.edu 37 3 405019 405019 + Frame_Shift_Del DEL A - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr3:405019delA uc003bou.2 + 13 1761 c.1490delA c.(1489-1491)GAAfs p.E497fs CHL1_uc003bot.2_Frame_Shift_Del_p.E513fs|CHL1_uc003bow.1_Frame_Shift_Del_p.E497fs|CHL1_uc011asi.1_Frame_Shift_Del_p.E513fs NM_006614 NP_006605 O00533 CHL1_HUMAN cell adhesion molecule with homology to L1CAM 497 Ig-like C2-type 5.|Extracellular (Potential). axon guidance|cell adhesion|signal transduction integral to membrane|plasma membrane|proteinaceous extracellular matrix skin(5)|central_nervous_system(4)|large_intestine(2)|ovary(1) 12 all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201) Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198) TGTTGGGTAGAAAATGCTATA 0.408 0.21 31 8 MLH1 4292 broad.mit.edu 37 3 37070378 37070378 + Frame_Shift_Del DEL A - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr3:37070378delA uc003cgl.2 + 13 1573 c.1513delA c.(1513-1515)AGTfs p.S505fs MLH1_uc011aye.1_Frame_Shift_Del_p.S264fs|MLH1_uc011ayb.1_Frame_Shift_Del_p.S264fs|MLH1_uc010hge.2_Frame_Shift_Del_p.S505fs|MLH1_uc003cgn.3_Frame_Shift_Del_p.S264fs|MLH1_uc011ayc.1_Frame_Shift_Del_p.S407fs|MLH1_uc011ayd.1_Frame_Shift_Del_p.S264fs|MLH1_uc003cgo.2_Frame_Shift_Del_p.S264fs|MLH1_uc010hgi.1_Frame_Shift_Del_p.S147fs|MLH1_uc010hgj.1_Frame_Shift_Del_p.S147fs|MLH1_uc010hgk.2_Frame_Shift_Del_p.S147fs|MLH1_uc010hgl.1_Frame_Shift_Del_p.S80fs|MLH1_uc010hgn.2_Frame_Shift_Del_p.S147fs|MLH1_uc010hgm.2_RNA|MLH1_uc010hgo.2_Frame_Shift_Del_p.S147fs NM_000249 NP_000240 P40692 MLH1_HUMAN MutL protein homolog 1 505 Interaction with EXO1. mismatch repair|somatic hypermutation of immunoglobulin genes chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex ATP binding|ATPase activity|protein binding p.S505fs*3(2)|p.0?(1) large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1) 77 TAACCTCACTAGTGTTTTGAG 0.493 1.00 1 222 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 IGROV1_OVARY NA IGROV1_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.14 57 9 PIK3CB 5291 broad.mit.edu 37 3 138413710 138413710 + Frame_Shift_Del DEL G - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr3:138413710delG uc011bmq.1 - 12 1810 c.1810delC c.(1810-1812)CGGfs p.R604fs PIK3CB_uc011bmn.1_Frame_Shift_Del_p.R116fs|PIK3CB_uc011bmo.1_Frame_Shift_Del_p.R50fs|PIK3CB_uc011bmp.1_Frame_Shift_Del_p.R191fs NM_006219 NP_006210 P42338 PK3CB_HUMAN catalytic phosphatidylinositol 3-kinase beta 604 PI3K helical. activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway phosphatidylinositol 3-kinase complex 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity breast(2)|ovary(1)|lung(1)|skin(1) 5 AGGGCCTCCCGGGGGGGCAGT 0.468 0.39 165 105 DGKG 1608 broad.mit.edu 37 3 186006602 186006602 + Frame_Shift_Del DEL G - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr3:186006602delG uc003fqa.2 - 6 978 c.441delC c.(439-441)CCCfs p.P147fs DGKG_uc003fqb.2_Frame_Shift_Del_p.P147fs|DGKG_uc003fqc.2_Frame_Shift_Del_p.P147fs|DGKG_uc011brx.1_Frame_Shift_Del_p.P147fs NM_001346 NP_001337 P49619 DGKG_HUMAN diacylglycerol kinase gamma isoform 1 147 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation cytoplasm|plasma membrane ATP binding|calcium ion binding|diacylglycerol kinase activity breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1) 5 all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247) OV - Ovarian serous cystadenocarcinoma(80;1.93e-20) GBM - Glioblastoma multiforme(93;0.0657) Phosphatidylserine(DB00144) ACCGAGGGACGGGGGGTTCCA 0.552 0.32 111 52 EPHA5 2044 broad.mit.edu 37 4 66361174 66361175 + Frame_Shift_Ins INS - A A IGROV1_OVARY NA IGROV1_OVARY NA g.chr4:66361174_66361175insA uc003hcy.2 - 4 1190_1191 c.997_998insT c.(997-999)TCAfs p.S333fs EPHA5_uc003hcx.2_Frame_Shift_Ins_p.S264fs|EPHA5_uc003hcz.2_Frame_Shift_Ins_p.S333fs|EPHA5_uc011cah.1_Frame_Shift_Ins_p.S333fs|EPHA5_uc011cai.1_Frame_Shift_Ins_p.S333fs|EPHA5_uc003hda.2_Frame_Shift_Ins_p.S333fs NM_004439 NP_004430 P54756 EPHA5_HUMAN ephrin receptor EphA5 isoform a precursor 333 Extracellular (Potential).|Cys-rich. cAMP-mediated signaling|neuron development dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum ATP binding|transmembrane-ephrin receptor activity lung(19)|stomach(2)|ovary(2)|central_nervous_system(1) 24 ACAAGAGGTTGAAGCTTCCTCA 0.470 0.38 276 167 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 IGROV1_OVARY NA IGROV1_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.16 83 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 IGROV1_OVARY NA IGROV1_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 235 200 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 IGROV1_OVARY NA IGROV1_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.57 41 54 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 IGROV1_OVARY NA IGROV1_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.22 189 54 RASA1 5921 broad.mit.edu 37 5 86675571 86675571 + Frame_Shift_Del DEL A - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr5:86675571delA uc003kiw.2 + 19 2625 c.2507delA c.(2506-2508)GAAfs p.E836fs RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_Frame_Shift_Del_p.E659fs|RASA1_uc011ctv.1_Frame_Shift_Del_p.E669fs|RASA1_uc011ctw.1_Frame_Shift_Del_p.E670fs|RASA1_uc010jaw.2_Frame_Shift_Del_p.E658fs NM_002890 NP_002881 P20936 RASA1_HUMAN RAS p21 protein activator 1 isoform 1 836 Ras-GAP. cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis cytosol|intrinsic to internal side of plasma membrane glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding upper_aerodigestive_tract(3)|ovary(1)|lung(1) 5 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) TCAAAGTTAGAAAAAAATGAA 0.308 0.44 61 47 CHD1 1105 broad.mit.edu 37 5 98236745 98236745 + Frame_Shift_Del DEL T - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr5:98236745delT uc003knf.2 - 6 777 c.629delA c.(628-630)AAGfs p.K210fs NM_001270 NP_001261 O14646 CHD1_HUMAN chromodomain helicase DNA binding protein 1 210 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117) COAD - Colon adenocarcinoma(37;0.0717) Epirubicin(DB00445) AATCTGTCTCTTTTTTTGTCC 0.313 0.48 147 135 CSNK1G3 1456 broad.mit.edu 37 5 122881495 122881495 + Frame_Shift_Del DEL A - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr5:122881495delA uc003ktm.2 + 2 857 c.138delA c.(136-138)GGAfs p.G46fs CSNK1G3_uc003ktl.2_Frame_Shift_Del_p.G46fs|CSNK1G3_uc003ktn.2_Frame_Shift_Del_p.G46fs|CSNK1G3_uc003kto.2_Frame_Shift_Del_p.G46fs|CSNK1G3_uc011cwr.1_Intron|CSNK1G3_uc011cws.1_Intron|CSNK1G3_uc010jda.2_Frame_Shift_Del_p.G46fs NM_004384 NP_004375 Q9Y6M4 KC1G3_HUMAN casein kinase 1, gamma 3 isoform 1 46 Protein kinase. Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity 0 all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245) KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229) OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176) TTAGAGTTGGAAAAAAAATTG 0.363 0.55 96 117 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes IGROV1_OVARY NA IGROV1_OVARY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.42 7 5 PIP5K1P1 206426 broad.mit.edu 37 6 7987611 7987611 + Frame_Shift_Del DEL T - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr6:7987611delT uc003mxx.3 + 1 1277 c.842delT c.(841-843)CTTfs p.L281fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCTGATGGTCTTTTTTTGGAT 0.478 0.12 231 32 PTK7 5754 broad.mit.edu 37 6 43099754 43099754 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr6:43099754delC uc003oub.1 + 6 1011 c.813delC c.(811-813)CGCfs p.R271fs PTK7_uc003ouc.1_Frame_Shift_Del_p.R271fs|PTK7_uc003oud.1_Frame_Shift_Del_p.R271fs|PTK7_uc003oue.1_Frame_Shift_Del_p.R271fs|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Frame_Shift_Del_p.R279fs|PTK7_uc010jyj.1_5'Flank|PTK7_uc003oua.2_Frame_Shift_Del_p.R271fs NM_002821 NP_002812 Q13308 PTK7_HUMAN PTK7 protein tyrosine kinase 7 isoform a 271 Ig-like C2-type 3.|Extracellular (Potential). actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration cell-cell junction|integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ovary(2)|large_intestine(1) 3 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423) CCCTCTGCAGCCCCCCACACC 0.572 0.56 37 48 DST 667 broad.mit.edu 37 6 56434717 56434717 + Frame_Shift_Del DEL T - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr6:56434717delT uc003pdf.2 - 48 7486 c.7458delA c.(7456-7458)AAAfs p.K2486fs DST_uc003pcz.3_Frame_Shift_Del_p.K2308fs|DST_uc011dxj.1_Frame_Shift_Del_p.K2337fs|DST_uc011dxk.1_Frame_Shift_Del_p.K2348fs|DST_uc003pcy.3_Frame_Shift_Del_p.K1982fs NM_001144769 NP_001138241 Q03001 DYST_HUMAN dystonin isoform 2 4394 cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1) 14 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) CAATGGGAACTTTTTTTGTTG 0.328 0.48 143 134 MCHR2 84539 broad.mit.edu 37 6 100382358 100382359 + Frame_Shift_Del DEL AA - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr6:100382358_100382359delAA uc003pqh.1 - 5 937_938 c.622_623delTT c.(622-624)TTCfs p.F208fs MCHR2_uc003pqi.1_Frame_Shift_Del_p.F208fs NM_001040179 NP_001035269 Q969V1 MCHR2_HUMAN melanin-concentrating hormone receptor 2 208 Helical; Name=5; (Potential). integral to membrane|plasma membrane G-protein coupled receptor activity lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|skin(1) 8 all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069) BRCA - Breast invasive adenocarcinoma(108;0.0429) 0.000 0.40 72 48 AIM1 202 broad.mit.edu 37 6 106968795 106968796 + Frame_Shift_Ins INS - A A IGROV1_OVARY NA IGROV1_OVARY NA g.chr6:106968795_106968796insA uc003prh.2 + 2 2975_2976 c.2488_2489insA c.(2488-2490)GAAfs p.E830fs NM_001624 NP_001615 Q9Y4K1 AIM1_HUMAN absent in melanoma 1 830 sugar binding breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1) 9 Breast(9;0.0138)|all_epithelial(6;0.169) all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473) Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305) all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858) ATCGAGACTAGAAAAAAGTGCA 0.426 0.48 148 134 AKAP12 9590 broad.mit.edu 37 6 151670524 151670524 + Frame_Shift_Del DEL A - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr6:151670524delA uc011eep.1 + 4 1238 c.998delA c.(997-999)GAAfs p.E333fs AKAP12_uc003qoe.2_Frame_Shift_Del_p.E333fs|AKAP12_uc003qof.2_Frame_Shift_Del_p.E235fs|AKAP12_uc010kim.2_Intron|AKAP12_uc003qog.2_Frame_Shift_Del_p.E228fs NM_005100 NP_005091 Q02952 AKA12_HUMAN A kinase (PRKA) anchor protein 12 isoform 1 333 Involved in PKC-binding (Probable). G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting cell cortex|cytoskeleton|plasma membrane adenylate cyclase binding|protein kinase A binding large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1) 8 Ovarian(120;0.125) BRCA - Breast invasive adenocarcinoma(37;0.175) OV - Ovarian serous cystadenocarcinoma(155;2.98e-11) CAAGAGCCAGAAAAAGTAGAC 0.542 0.42 29 21 C6orf97 80129 broad.mit.edu 37 6 151936775 151936775 + Frame_Shift_Del DEL A - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr6:151936775delA uc003qol.2 + 10 1997 c.1908delA c.(1906-1908)CTAfs p.L636fs NM_025059 NP_079335 Q8IYT3 CF097_HUMAN hypothetical protein LOC80129 636 Potential. 0 Ovarian(120;0.126) BRCA - Breast invasive adenocarcinoma(37;0.111) OV - Ovarian serous cystadenocarcinoma(155;1.48e-10) TGAAGACACTAAAAAAATCTC 0.403 0.70 3 7 ARID1B 57492 broad.mit.edu 37 6 157099313 157099333 + In_Frame_Del DEL CACCACCACCACCACCATGCC - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr6:157099313_157099333delCACCACCACCACCACCATGCC uc003qqn.2 + 1 228_248 c.76_96delCACCACCACCACCACCATGCC c.(76-96)CACCACCACCACCACCATGCCdel p.HHHHHHA33del ARID1B_uc003qqo.2_In_Frame_Del_p.HHHHHHA33del|ARID1B_uc003qqp.2_In_Frame_Del_p.HHHHHHA33del NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 91_97 His-rich. chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) ccaccagcagcaccaccaccaccaccatgcccaccaccacc 0.357 0.24 52 16 AKAP9 10142 broad.mit.edu 37 7 91714947 91714951 + Frame_Shift_Del DEL ATCTC - - rs149341527 byFrequency IGROV1_OVARY NA IGROV1_OVARY NA g.chr7:91714947_91714951delATCTC uc003ulg.2 + 36 9196_9200 c.8971_8975delATCTC c.(8971-8976)ATCTCAfs p.I2991fs AKAP9_uc003ulf.2_Frame_Shift_Del_p.I2983fs|AKAP9_uc003uli.2_Frame_Shift_Del_p.I2614fs|AKAP9_uc003ulj.2_Frame_Shift_Del_p.I761fs|AKAP9_uc003ulk.2_Frame_Shift_Del_p.I266fs NM_005751 NP_005742 Q99996 AKAP9_HUMAN A-kinase anchor protein 9 isoform 2 2995_2996 G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport centrosome|cytosol|Golgi apparatus receptor binding breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1) 26 all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) CATCAATACAATCTCATCTCTAAAG 0.341 0.21 104 27 CYP3A4 1576 broad.mit.edu 37 7 99366000 99366000 + Frame_Shift_Del DEL A - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr7:99366000delA uc003urv.1 - 7 751 c.647delT c.(646-648)TTGfs p.L216fs CYP3A4_uc003urw.1_Frame_Shift_Del_p.L216fs|CYP3A4_uc011kiz.1_Frame_Shift_Del_p.L175fs|CYP3A4_uc011kja.1_Frame_Shift_Del_p.L167fs|CYP3A4_uc011kjb.1_Frame_Shift_Del_p.L66fs NM_017460 NP_059488 P08684 CP3A4_HUMAN cytochrome P450, family 3, subfamily A, 216 alkaloid catabolic process|androgen metabolic process|exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid catabolic process|xenobiotic metabolic process cell surface|endoplasmic reticulum membrane|integral to membrane|microsome albendazole monooxygenase activity|caffeine oxidase activity|electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding|quinine 3-monooxygenase activity|steroid binding|taurochenodeoxycholate 6alpha-hydroxylase activity|testosterone 6-beta-hydroxylase activity|vitamin D 24-hydroxylase activity|vitamin D3 25-hydroxylase activity central_nervous_system(3)|ovary(1) 4 Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228) Albendazole(DB00518)|Alclometasone(DB00240)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Aliskiren(DB01258)|Almotriptan(DB00918)|Alosetron(DB00969)|Alprazolam(DB00404)|Amlodipine(DB00381)|Amprenavir(DB00701)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Benazepril(DB00542)|Bepridil(DB01244)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bortezomib(DB00188)|Bosentan(DB00559)|Bromocriptine(DB01200)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Buspirone(DB00490)|Busulfan(DB01008)|Carbamazepine(DB00564)|Cevimeline(DB00185)|Chlorpheniramine(DB01114)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cinacalcet(DB01012)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clindamycin(DB01190)|Clofibrate(DB00636)|Clonazepam(DB01068)|Clopidogrel(DB00758)|Cocaine(DB00907)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cyproterone(DB04839)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Delavirdine(DB00705)|Desogestrel(DB00304)|Dexamethasone(DB01234)|Diazepam(DB00829)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dofetilide(DB00204)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Doxorubicin(DB00997)|Drospirenone(DB01395)|Dutasteride(DB01126)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Epirubicin(DB00445)|Eplerenone(DB00700)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Exemestane(DB00990)|Felodipine(DB01023)|Fentanyl(DB00813)|Fexofenadine(DB00950)|Finasteride(DB01216)|Fluconazole(DB00196)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Fosamprenavir(DB01319)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Granisetron(DB00889)|Grepafloxacin(DB00365)|Halofantrine(DB01218)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Imatinib(DB00619)|Indinavir(DB00224)|Ipratropium(DB00332)|Irinotecan(DB00762)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levomethadyl Acetate(DB01227)|Levothyroxine(DB00451)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Maraviroc(DB04835)|Marinol(DB00470)|Mebendazole(DB00643)|Medroxyprogesterone(DB00603)|Methadone(DB00333)|Methylprednisolone(DB00959)|Metyrapone(DB01011)|Mibefradil(DB01388)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirtazapine(DB00370)|Modafinil(DB00745)|Mometasone(DB00764)|Montelukast(DB00471)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norgestrel(DB00506)|Nystatin(DB00646)|Ondansetron(DB00904)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paricalcitol(DB00910)|Phenmetrazine(DB00830)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prednisolone(DB00860)|Prednisone(DB00635)|Prochlorperazine(DB00433)|Quetiapine(DB01224)|Quinapril(DB00881)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranolazine(DB00243)|Reboxetine(DB00234)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampin(DB01045)|Rimonabant(DB06155)|Ritonavir(DB00503)|Rofecoxib(DB00533)|Roxithromycin(DB00778)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sertindole(DB06144)|Sibutramine(DB01105)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Terconazole(DB00251)|Terfenadine(DB00342)|Testosterone(DB00624)|Tiagabine(DB00906)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tiotropium(DB01409)|Tipranavir(DB00932)|Toremifene(DB00539)|Triazolam(DB00897)|Trimetrexate(DB01157)|Troglitazone(DB00197)|Valdecoxib(DB00580)|Vardenafil(DB00862)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Voriconazole(DB00582)|Zaleplon(DB00962)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909) GAATGGATCCAAAAAATCAAA 0.294 0.32 125 58 GRM8 2918 broad.mit.edu 37 7 126544156 126544156 + Frame_Shift_Del DEL T - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr7:126544156delT uc003vlr.2 - 4 1199 c.888delA c.(886-888)AAAfs p.K296fs GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Frame_Shift_Del_p.K296fs|GRM8_uc010lkz.1_RNA|GRM8_uc003vlu.1_Frame_Shift_Del_p.K17fs NM_000845 NP_000836 O00222 GRM8_HUMAN glutamate receptor, metabotropic 8 isoform a 296 Extracellular (Potential). negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception integral to plasma membrane lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1) 23 Prostate(267;0.186) L-Glutamic Acid(DB00142) 0.000 0.45 321 260 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes IGROV1_OVARY NA IGROV1_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 3 30 FASTK 10922 broad.mit.edu 37 7 150774416 150774417 + Frame_Shift_Del DEL CA - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr7:150774416_150774417delCA uc003wix.1 - 7 1369_1370 c.1271_1272delTG c.(1270-1272)GTGfs p.V424fs uc011kvf.1_5'Flank|FASTK_uc003wiw.1_Frame_Shift_Del_p.V185fs|FASTK_uc003wiy.1_Frame_Shift_Del_p.V283fs|FASTK_uc003wiz.1_Frame_Shift_Del_p.V397fs|FASTK_uc003wja.1_3'UTR NM_006712 NP_006703 Q14296 FASTK_HUMAN Fas-activated serine/threonine kinase isoform 1 424 V -> L (in a lung adenocarcinoma sample; somatic mutation). apoptosis|induction of apoptosis by extracellular signals|regulation of RNA splicing ATP binding|Fas-activated serine/threonine kinase activity|protein binding p.V424L(2) lung(2)|stomach(2) 4 OV - Ovarian serous cystadenocarcinoma(82;0.00989) UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138) AGCCTGGAGGCACAGTCAGGTC 0.559 0.41 74 52 MLL3 58508 broad.mit.edu 37 7 151874148 151874149 + Frame_Shift_Del DEL TT - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr7:151874148_151874149delTT uc003wla.2 - 38 8608_8609 c.8389_8390delAA c.(8389-8391)AAGfs p.K2797fs MLL3_uc003wkz.2_Frame_Shift_Del_p.K1858fs|MLL3_uc003wky.2_Frame_Shift_Del_p.K306fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 2797 K -> R (in Ref. 1; AAK00583). intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding p.K2797fs*26(18) large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTCTTGTTCCTTTTTTTTTGGT 0.347 0.87 38 248 ADAM32 203102 broad.mit.edu 37 8 39080617 39080617 + Frame_Shift_Del DEL A - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr8:39080617delA uc003xmt.3 + 14 1630 c.1385delA c.(1384-1386)GAAfs p.E462fs ADAM32_uc011lch.1_Frame_Shift_Del_p.E363fs|ADAM32_uc003xmu.3_Frame_Shift_Del_p.E356fs|ADAM32_uc003xmv.2_5'UTR NM_145004 NP_659441 Q8TC27 ADA32_HUMAN a disintegrin and metalloprotease domain 32 462 Disintegrin.|Extracellular (Potential). proteolysis integral to membrane metalloendopeptidase activity|zinc ion binding ovary(1)|lung(1)|kidney(1) 3 all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503) LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146) GACATCGCTGAAAATTGTAAT 0.348 0.50 166 165 TRIB1 10221 broad.mit.edu 37 8 126443327 126443327 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr8:126443327delC uc003yrx.2 + 1 765 c.183delC c.(181-183)AGCfs p.S61fs TRIB1_uc011lis.1_5'Flank|TRIB1_uc010mdn.2_5'Flank NM_025195 NP_079471 Q96RU8 TRIB1_HUMAN G-protein-coupled receptor induced protein 61 Protein kinase. JNK cascade|negative regulation of lipopolysaccharide-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|regulation of MAP kinase activity|response to lipopolysaccharide cytoplasm|nucleus ATP binding|mitogen-activated protein kinase kinase binding|protein kinase activity|protein kinase inhibitor activity|transcription factor binding|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity lung(1) 1 all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108) STAD - Stomach adenocarcinoma(47;0.000918) 0.000 0.45 480 391 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency IGROV1_OVARY NA IGROV1_OVARY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.14 89 15 TEK 7010 broad.mit.edu 37 9 27185545 27185545 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr9:27185545delC uc003zqi.3 + 9 1687 c.1245delC c.(1243-1245)CTCfs p.L415fs TEK_uc011lno.1_Frame_Shift_Del_p.L372fs|TEK_uc011lnp.1_Frame_Shift_Del_p.L268fs|TEK_uc003zqj.1_Frame_Shift_Del_p.L349fs NM_000459 NP_000450 Q02763 TIE2_HUMAN TEK tyrosine kinase, endothelial precursor 415 Extracellular (Potential).|Ig-like C2-type 2. angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1) 12 all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255) Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027) ACCGGATCCTCCCCCCTGACT 0.433 0.40 355 238 WNK2 65268 broad.mit.edu 37 9 96019304 96019305 + Frame_Shift_Ins INS - C C IGROV1_OVARY NA IGROV1_OVARY NA g.chr9:96019304_96019305insC uc004ati.1 + 10 2265_2266 c.2265_2266insC c.(2263-2268)GTTCCCfs p.V755fs WNK2_uc011lud.1_Frame_Shift_Ins_p.V755fs|WNK2_uc004atj.2_Frame_Shift_Ins_p.V755fs|WNK2_uc004atk.2_Frame_Shift_Ins_p.V392fs|WNK2_uc010mrc.1_Frame_Shift_Ins_p.V703fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 755_756 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 TCCAGCCGGTTCCCCCCCACCT 0.728 0.24 26 8 WNK2 65268 broad.mit.edu 37 9 96021419 96021419 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr9:96021419delC uc004ati.1 + 11 2589 c.2589delC c.(2587-2589)CACfs p.H863fs WNK2_uc011lud.1_Frame_Shift_Del_p.H863fs|WNK2_uc004atj.2_Frame_Shift_Del_p.H863fs|WNK2_uc004atk.2_Frame_Shift_Del_p.H500fs|WNK2_uc010mrc.1_Frame_Shift_Del_p.H811fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 863 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 AGCTGCCCCACCCCCCTGGGG 0.697 0.46 169 143 ABL1 25 broad.mit.edu 37 9 133760024 133760024 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr9:133760024delC uc004bzw.2 + 11 2350 c.2347delC c.(2347-2349)CCCfs p.P783fs ABL1_uc004bzv.2_Frame_Shift_Del_p.P802fs NM_005157 NP_005148 P00519 ABL1_HUMAN c-abl oncogene 1, receptor tyrosine kinase 783 Pro-rich. actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1) 817 all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204) OV - Ovarian serous cystadenocarcinoma(145;5.4e-05) Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619) AGTAACGCCTCCCCCCAGGCT 0.587 0.34 19 10 NOTCH1 4851 broad.mit.edu 37 9 139412632 139412637 + In_Frame_Del DEL GTACCC - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr9:139412632_139412637delGTACCC uc004chz.2 - 7 1207_1212 c.1207_1212delGGGTAC c.(1207-1212)GGGTACdel p.GY403del NM_017617 NP_060087 P46531 NOTC1_HUMAN notch1 preproprotein 403_404 Extracellular (Potential).|EGF-like 10. aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1) 856 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06) CCGGGCCCGTGTACCCCGAGGGGCAG 0.670 0.45 6 5 MYO3A 53904 broad.mit.edu 37 10 26462760 26462760 + Frame_Shift_Del DEL A - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr10:26462760delA uc001isn.2 + 30 3927 c.3567delA c.(3565-3567)CCAfs p.P1189fs MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron NM_017433 NP_059129 Q8NEV4 MYO3A_HUMAN myosin IIIA 1189 protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception cytoplasm|filamentous actin|filopodium|myosin complex actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 18 ATCAGACTCCAAAAAAAATGA 0.403 0.14 246 39 MYST4 23522 broad.mit.edu 37 10 76781905 76781906 + In_Frame_Ins INS - GAA GAA rs138589645;rs111976843 by1000genomes IGROV1_OVARY NA IGROV1_OVARY NA g.chr10:76781905_76781906insGAA uc001jwn.1 + 16 3781_3782 c.3288_3289insGAA c.(3286-3291)insGAA p.1104_1105insE MYST4_uc001jwm.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwo.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwp.1_In_Frame_Ins_p.921_922insE NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1104_1105 histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) aggaagaagaggaagaagaaga 0.203 0.27 180 68 PTEN 5728 broad.mit.edu 37 10 89720799 89720802 + Frame_Shift_Del DEL TACT - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr10:89720799_89720802delTACT uc001kfb.2 + 9 1981_1984 c.950_953delTACT c.(949-954)GTACTTfs p.V317fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 317_318 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.L318fs*2(17)|p.V317fs*3(16)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.V317fs*6(2)|p.G165_*404del(1)|p.G165_K342del(1)|p.L316fs*1(1)|p.W274_F341del(1)|p.V317_K322del(1)|p.L318F(1)|p.T318fs*2(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GAATATCTAGTACTTACTTTAACA 0.333 0.36 149 83 NLRP6 171389 broad.mit.edu 37 11 280723 280723 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr11:280723delC uc010qvs.1 + 4 989 c.989delC c.(988-990)GCCfs p.A330fs NLRP6_uc010qvt.1_Frame_Shift_Del_p.A330fs NM_138329 NP_612202 P59044 NALP6_HUMAN NLR family, pyrin domain containing 6 330 NACHT. cytoplasm ATP binding upper_aerodigestive_tract(1)|skin(1) 2 all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122) CGCGCCGCCGCCCCCGGGAGG 0.701 0.44 18 14 ILK 3611 broad.mit.edu 37 11 6629392 6629392 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr11:6629392delC uc001mee.2 + 3 341 c.206delC c.(205-207)ACCfs p.T69fs ILK_uc001mef.2_Frame_Shift_Del_p.T69fs|ILK_uc010rap.1_Intron|ILK_uc010raq.1_Frame_Shift_Del_p.T69fs|ILK_uc001meg.2_5'UTR|ILK_uc001meh.2_Frame_Shift_Del_p.T69fs|ILK_uc001mei.2_5'Flank NM_001014794 NP_001014794 Q13418 ILK_HUMAN integrin-linked kinase 69 Interaction with LIMS1.|ANK 3. cell junction assembly|cell proliferation|cell-matrix adhesion|integrin-mediated signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of transcription, DNA-dependent cytosol|focal adhesion ATP binding|protein serine/threonine kinase activity central_nervous_system(1) 1 Breast(177;7.61e-05)|Medulloblastoma(188;0.00263)|all_neural(188;0.026)|all_lung(207;0.152) Epithelial(150;5.49e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00012)|Lung(200;0.00942)|LUSC - Lung squamous cell carcinoma(625;0.0163) GGGGATGACACCCCCCTGCAT 0.557 0.28 18 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 IGROV1_OVARY NA IGROV1_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 738 179 SIK2 23235 broad.mit.edu 37 11 111491121 111491121 + Frame_Shift_Del DEL T - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr11:111491121delT uc001plt.2 + 3 429 c.311delT c.(310-312)ATTfs p.I104fs NM_015191 NP_056006 Q9H0K1 SIK2_HUMAN SNF1-like kinase 2 104 Protein kinase. intracellular protein kinase cascade|regulation of insulin receptor signaling pathway Golgi apparatus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|skin(1) 3 AATGGAGAAATTTTTGGTAAG 0.284 0.45 69 57 PCSK7 9159 broad.mit.edu 37 11 117100518 117100518 + Frame_Shift_Del DEL G - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr11:117100518delG uc001pqr.2 - 3 244 c.43delC c.(43-45)CTGfs p.L15fs RNF214_uc001pqt.2_5'Flank|RNF214_uc001pqu.2_5'Flank|RNF214_uc010rxf.1_5'Flank NM_004716 NP_004707 Q16549 PCSK7_HUMAN proprotein convertase subtilisin/kexin type 7 15 peptide hormone processing integral to Golgi membrane serine-type endopeptidase activity 0 all_hematologic(175;0.0487) Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234) BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537) GGCAGGCCCAGGGGGGCATCC 0.587 0.43 46 35 PIK3C2G 5288 broad.mit.edu 37 12 18747475 18747478 + Frame_Shift_Del DEL AGTT - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr12:18747475_18747478delAGTT uc001rdt.2 + 29 4052_4055 c.3936_3939delAGTT c.(3934-3939)ACAGTTfs p.T1312fs PIK3C2G_uc010sia.1_RNA|PIK3C2G_uc010sib.1_Frame_Shift_Del_p.T1353fs|PIK3C2G_uc010sic.1_Frame_Shift_Del_p.T1131fs NM_004570 NP_004561 O75747 P3C2G_HUMAN phosphoinositide-3-kinase, class 2 gamma 1312_1313 cell communication|phosphatidylinositol-mediated signaling membrane|phosphatidylinositol 3-kinase complex 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2) 21 Hepatocellular(102;0.194) TGCAACAAACAGTTGAAGAATCAT 0.294 0.34 131 67 AGAP2 116986 broad.mit.edu 37 12 58130989 58130989 + Frame_Shift_Del DEL A - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr12:58130989delA uc001spq.2 - 1 1041 c.1041delT c.(1039-1041)TTTfs p.F347fs AGAP2_uc001spp.2_Frame_Shift_Del_p.F347fs|AGAP2_uc001spr.2_Intron NM_001122772 NP_001116244 Q99490 AGAP2_HUMAN centaurin, gamma 1 isoform PIKE-L 347 Interaction with PLCG1 (By similarity). axon guidance|negative regulation of neuron apoptosis|negative regulation of protein catabolic process|protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction mitochondrion|nucleolus ARF GTPase activator activity|GTP binding|zinc ion binding central_nervous_system(3)|breast(2) 5 TGCCGCTGATAAACTTGAGCA 0.672 0.55 5 6 ACACB 32 broad.mit.edu 37 12 109671600 109671600 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr12:109671600delC uc001tob.2 + 30 4306 c.4187delC c.(4186-4188)ACCfs p.T1396fs ACACB_uc001toc.2_Frame_Shift_Del_p.T1396fs|ACACB_uc010sxl.1_RNA|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Frame_Shift_Del_p.T62fs NM_001093 NP_001084 O00763 ACACB_HUMAN acetyl-Coenzyme A carboxylase beta 1396 acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation cytosol|endomembrane system|Golgi apparatus|membrane acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1) 8 Biotin(DB00121) CCCAAAGACACCCCCCTCTTC 0.612 0.44 313 241 NCOR2 9612 broad.mit.edu 37 12 124887058 124887059 + In_Frame_Ins INS - GCTGCT GCTGCT rs35831183;rs67031864 IGROV1_OVARY NA IGROV1_OVARY NA g.chr12:124887058_124887059insGCTGCT uc010tba.1 - 14 1648_1649 c.1531_1532insAGCAGC c.(1531-1533)CCC>CAGCAGCCC p.510_511insQQ NCOR2_uc010tay.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010taz.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbb.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbc.1_In_Frame_Ins_p.509_510insQQ|NCOR2_uc001ugj.1_In_Frame_Ins_p.510_511insQQ NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 510_511 cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) GCGGGGCATGGgctgctgctgc 0.312 0.17 84 17 CDX2 1045 broad.mit.edu 37 13 28537278 28537278 + Frame_Shift_Del DEL C - - rs142861632 IGROV1_OVARY NA IGROV1_OVARY NA g.chr13:28537278delC uc001urv.2 - 3 1090 c.916delG c.(916-918)GTGfs p.V306fs NM_001265 NP_001256 Q99626 CDX2_HUMAN caudal type homeobox 2 306 organ morphogenesis|transcription from RNA polymerase II promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity lung(1) 1 all_cancers(110;0.191)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155) Lung SC(185;0.0156) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199) GGGTTTAGCACCCCCCCAGTT 0.627 0.47 51 46 BRCA2 675 broad.mit.edu 37 13 32954204 32954204 + Frame_Shift_Del DEL T - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr13:32954204delT uc001uub.1 + 24 9405 c.9178delT c.(9178-9180)TTTfs p.F3060fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 3060 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) CTTCAGCAAATTTTTAGATCC 0.358 0.10 303 33 NOVA1 4857 broad.mit.edu 37 14 27066542 27066542 + Frame_Shift_Del DEL G - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr14:27066542delG uc001wpy.2 - 1 419 c.101delC c.(100-102)CCTfs p.P34fs NOVA1_uc001wpz.2_Frame_Shift_Del_p.P34fs|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_Frame_Shift_Del_p.P34fs NM_002515 NP_002506 P51513 NOVA1_HUMAN neuro-oncological ventral antigen 1 isoform 1 34 Bipartite nuclear localization signal (Potential). locomotory behavior|RNA splicing|synaptic transmission nucleus RNA binding skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1) 5 GBM - Glioblastoma multiforme(265;0.0135) 0.000 0.46 610 522 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 IGROV1_OVARY NA IGROV1_OVARY NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.41 44 30 DICER1 23405 broad.mit.edu 37 14 95562651 95562652 + Frame_Shift_Del DEL CA - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr14:95562651_95562652delCA uc001ydw.2 - 24 4787_4788 c.4605_4606delTG c.(4603-4608)TGTGGTfs p.C1535fs DICER1_uc010avh.1_Frame_Shift_Del_p.C433fs|DICER1_uc001ydv.2_Frame_Shift_Del_p.C1525fs|DICER1_uc001ydx.2_Frame_Shift_Del_p.C1535fs|DICER1_uc001ydy.1_Frame_Shift_Del_p.C387fs NM_030621 NP_085124 Q9UPY3 DICER_HUMAN dicer1 1535_1536 negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference cytosol|RNA-induced silencing complex ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity skin(2)|ovary(1)|pancreas(1)|lung(1) 5 all_cancers(154;0.0621)|all_epithelial(191;0.223) Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215) GTGTCAACACCACAGTTTTCTT 0.485 0.44 172 136 MKRN3 7681 broad.mit.edu 37 15 23811096 23811096 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr15:23811096delC uc001ywh.3 + 1 643 c.167delC c.(166-168)GCCfs p.A56fs MKRN3_uc001ywi.2_Frame_Shift_Del_p.A56fs|MKRN3_uc010ayi.1_Frame_Shift_Del_p.A56fs NM_005664 NP_005655 Q13064 MKRN3_HUMAN makorin ring finger protein 3 56 ribonucleoprotein complex ligase activity|nucleic acid binding|zinc ion binding lung(6)|large_intestine(2)|ovary(2) 10 all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14) all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012) AGGGGCTGGGCCCCCTTCCCT 0.687 0.46 64 54 MKRN3 7681 broad.mit.edu 37 15 23811405 23811405 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr15:23811405delC uc001ywh.3 + 1 952 c.476delC c.(475-477)GCCfs p.A159fs MKRN3_uc001ywi.2_Intron|MKRN3_uc010ayi.1_Frame_Shift_Del_p.A159fs NM_005664 NP_005655 Q13064 MKRN3_HUMAN makorin ring finger protein 3 159 ribonucleoprotein complex ligase activity|nucleic acid binding|zinc ion binding lung(6)|large_intestine(2)|ovary(2) 10 all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14) all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012) GTGGCGGAAGCCCCCCCGGCT 0.642 0.32 106 51 SRP14 6727 broad.mit.edu 37 15 40328597 40328599 + In_Frame_Del DEL TGC - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr15:40328597_40328599delTGC uc001zkq.2 - 5 418_420 c.346_348delGCA c.(346-348)GCAdel p.A116del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgcggcaggtgctgctgctgct 0.227 0.19 114 26 MGA 23269 broad.mit.edu 37 15 42021442 42021442 + Frame_Shift_Del DEL A - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr15:42021442delA uc010ucy.1 + 11 3919 c.3738delA c.(3736-3738)CGAfs p.R1246fs MGA_uc010ucz.1_Frame_Shift_Del_p.R1246fs NM_001164273 NP_001157745 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 1 1246 MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) TATATGAGCGAAAAAAAGAGG 0.413 0.48 183 168 CHRNB4 1143 broad.mit.edu 37 15 78917543 78917544 + Frame_Shift_Ins INS - C C IGROV1_OVARY NA IGROV1_OVARY NA g.chr15:78917543_78917544insC uc002bed.1 - 6 1540_1541 c.1428_1429insG c.(1426-1431)GGGCTCfs p.G476fs CHRNB4_uc002bee.1_Frame_Shift_Ins_p.G150fs|uc002bef.1_5'Flank NM_000750 NP_000741 P30926 ACHB4_HUMAN cholinergic receptor, nicotinic, beta 4 476_477 Helical; (Potential). regulation of neurotransmitter secretion|synaptic transmission involved in micturition|synaptic transmission, cholinergic cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity 0 GGTAGGAAGAGCCCCACAGTGC 0.624 0.48 13 12 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C IGROV1_OVARY NA IGROV1_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 26 211 PHF23 79142 broad.mit.edu 37 17 7139558 7139558 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr17:7139558delC uc002gfa.2 - 4 915 c.688delG c.(688-690)GATfs p.D230fs DVL2_uc002gez.1_5'Flank|DVL2_uc010vtr.1_5'Flank|DVL2_uc010clz.1_5'Flank|PHF23_uc010vtt.1_Frame_Shift_Del_p.D163fs|PHF23_uc010cma.2_Frame_Shift_Del_p.D100fs NM_024297 NP_077273 Q9BUL5 PHF23_HUMAN PHD finger protein 23 230 zinc ion binding 0 0.000 0.37 926 540 TP53 7157 broad.mit.edu 37 17 7579419 7579420 + Frame_Shift_Ins INS - G G IGROV1_OVARY NA IGROV1_OVARY NA g.chr17:7579419_7579420insG uc002gim.2 - 4 461_462 c.267_268insC c.(265-270)CCCTCCfs p.P89fs TP53_uc002gig.1_Frame_Shift_Ins_p.P89fs|TP53_uc002gih.2_Frame_Shift_Ins_p.P89fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Ins_p.P89fs|TP53_uc010cni.1_Frame_Shift_Ins_p.P89fs|TP53_uc002gij.2_Frame_Shift_Ins_p.P89fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Ins_p.P50fs|TP53_uc010cnk.1_Frame_Shift_Ins_p.P104fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 89_90 Interaction with WWOX. S -> F (in sporadic cancers; somatic mutation).|S -> Y (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.A76_S90del15(3)|p.P89S(3)|p.G59fs*23(3)|p.P89fs*60(1)|p.V73fs*9(1)|p.D48fs*55(1)|p.P85fs*58(1)|p.A88fs*52(1)|p.A86fs*33(1)|p.A86fs*32(1)|p.W91fs*13(1)|p.P87fs*54(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.P89L(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.21 697 187 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 IGROV1_OVARY NA IGROV1_OVARY NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.21 44 12 MAPK7 5598 broad.mit.edu 37 17 19286134 19286134 + Frame_Shift_Del DEL C - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr17:19286134delC uc002gvn.2 + 6 2558 c.2172delC c.(2170-2172)GACfs p.D724fs MAPK7_uc002gvo.2_Frame_Shift_Del_p.D585fs|MAPK7_uc002gvq.2_Frame_Shift_Del_p.D724fs|MAPK7_uc002gvp.2_Frame_Shift_Del_p.D724fs|uc010vyt.1_5'Flank NM_139033 NP_620602 Q13164 MK07_HUMAN mitogen-activated protein kinase 7 isoform 1 724 May not be required for kinase activity; required to stimulate MEF2C activity (By similarity). cell cycle|cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|MAP kinase activity|protein binding central_nervous_system(4)|lung(3)|stomach(1)|skin(1) 9 all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206) AGGTGGAGGACCCCCTGCCCC 0.567 0.15 47 8 FASN 2194 broad.mit.edu 37 17 80051614 80051615 + Frame_Shift_Del DEL GT - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr17:80051614_80051615delGT uc002kdu.2 - 4 430_431 c.313_314delAC c.(313-315)ACTfs p.T105fs NM_004104 NP_004095 P49327 FAS_HUMAN fatty acid synthase 105 Beta-ketoacyl synthase (By similarity). energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process cytosol|Golgi apparatus|melanosome|plasma membrane 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding central_nervous_system(1) 1 all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246) OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237) Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339) CCAGACGCCAGTGTGTGTTCCT 0.678 0.38 84 52 ROCK1 6093 broad.mit.edu 37 18 18533678 18533679 + Frame_Shift_Ins INS - T T IGROV1_OVARY NA IGROV1_OVARY NA g.chr18:18533678_18533679insT uc002kte.2 - 32 4862_4863 c.3921_3922insA c.(3919-3924)AAATGGfs p.K1307fs NM_005406 NP_005397 Q13464 ROCK1_HUMAN Rho-associated, coiled-coil containing protein 1307_1308 PH.|Auto-inhibitory. actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction centriole|cytosol|Golgi membrane ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity lung(2)|breast(2)|central_nervous_system(1) 5 Melanoma(1;0.165) TGAGTTACCCATTTTTTTTGTT 0.366 0.41 73 50 SMAD7 4092 broad.mit.edu 37 18 46474795 46474795 + Frame_Shift_Del DEL G - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr18:46474795delG uc002ldg.2 - 2 913 c.626delC c.(625-627)CCTfs p.P209fs SMAD7_uc010xde.1_5'UTR NM_005904 NP_005895 O15105 SMAD7_HUMAN SMAD family member 7 209 Poly-Pro.|PY-motif.|Important for interaction with SMURF2. Missing: Diminishes interaction with SMURF2. adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding 0 Colorectal(1;0.0518) GGAGTAAGGAGGGGGGGGAGA 0.388 0.25 138 47 SMAD4 4089 broad.mit.edu 37 18 48584514 48584514 + Frame_Shift_Del DEL G - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr18:48584514delG uc010xdp.1 + 6 1225 c.687delG c.(685-687)CTGfs p.L229fs SMAD4_uc010xdo.1_RNA|SMAD4_uc002lfb.3_Frame_Shift_Del_p.L74fs NM_005359 NP_005350 Q13485 SMAD4_HUMAN mothers against decapentaplegic homolog 4 229 BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway activin responsive factor complex|centrosome|cytosol I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity p.0?(35)|p.?(2) pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1) 369 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155) CCAGTATACTGGGGGGCAGCC 0.443 0.28 23 9 ALPK2 115701 broad.mit.edu 37 18 56246440 56246440 + Frame_Shift_Del DEL T - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr18:56246440delT uc002lhj.3 - 4 1782 c.1568delA c.(1567-1569)AAGfs p.K523fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 523 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 CCATAAGTCCTTTCCCCCCAC 0.522 0.34 367 191 NFATC1 4772 broad.mit.edu 37 18 77211010 77211011 + Frame_Shift_Del DEL GA - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr18:77211010_77211011delGA uc010xfg.1 + 5 2099_2100 c.1646_1647delGA c.(1645-1647)GGAfs p.G549fs NFATC1_uc002lnc.1_Frame_Shift_Del_p.G549fs|NFATC1_uc010xff.1_Frame_Shift_Del_p.G549fs|NFATC1_uc002lnd.2_Frame_Shift_Del_p.G549fs|NFATC1_uc002lne.2_Frame_Shift_Del_p.G77fs|NFATC1_uc010xfh.1_Frame_Shift_Del_p.G549fs|NFATC1_uc010xfi.1_Frame_Shift_Del_p.G536fs|NFATC1_uc010xfj.1_Frame_Shift_Del_p.G77fs|NFATC1_uc002lnf.2_Frame_Shift_Del_p.G536fs|NFATC1_uc002lng.2_Frame_Shift_Del_p.G536fs|NFATC1_uc010xfk.1_Frame_Shift_Del_p.G536fs NM_006162 NP_006153 O95644 NFAC1_HUMAN nuclear factor of activated T-cells, cytosolic 549 RHD. intracellular signal transduction|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter cytoplasm|nucleus FK506 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding large_intestine(1)|ovary(1) 2 Esophageal squamous(42;0.0157)|Melanoma(33;0.144) OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257) CTTCGGAAAGGAGAGACGGACA 0.569 0.31 22 10 SMARCA4 6597 broad.mit.edu 37 19 11144049 11144051 + In_Frame_Del DEL GGA - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr19:11144049_11144051delGGA uc002mqf.3 + 26 3914_3916 c.3630_3632delGGA c.(3628-3633)GTGGAG>GTG p.E1212del SMARCA4_uc010dxp.2_In_Frame_Del_p.E1212del|SMARCA4_uc010dxo.2_In_Frame_Del_p.E1212del|SMARCA4_uc010dxq.2_In_Frame_Del_p.E1212del|SMARCA4_uc010dxr.2_In_Frame_Del_p.E1212del|SMARCA4_uc002mqj.3_In_Frame_Del_p.E1212del|SMARCA4_uc010dxs.2_In_Frame_Del_p.E1212del|SMARCA4_uc010dxt.1_In_Frame_Del_p.E432del|SMARCA4_uc002mqh.3_In_Frame_Del_p.E335del|SMARCA4_uc002mqi.1_In_Frame_Del_p.E415del NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 1212 Helicase C-terminal. chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) TCAACAGCGTGGAGGAGAAGATC 0.635 0.50 88 88 PAK4 10298 broad.mit.edu 37 19 39663591 39663591 + Frame_Shift_Del DEL G - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr19:39663591delG uc002okj.1 + 5 699 c.238delG c.(238-240)GGGfs p.G80fs PAK4_uc002okl.1_Frame_Shift_Del_p.G80fs|PAK4_uc002okn.1_Frame_Shift_Del_p.G80fs|PAK4_uc002okm.1_Intron|PAK4_uc002oko.1_Intron|PAK4_uc002okp.1_Frame_Shift_Del_p.G80fs NM_001014831 NP_001014831 O96013 PAK4_HUMAN p21-activated kinase 4 isoform 1 80 Linker. cellular component movement|signal transduction Golgi apparatus ATP binding|protein binding|protein serine/threonine kinase activity lung(3)|ovary(1) 4 all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454) Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113) TGCCAAAGATGGGGCCCTCAC 0.677 0.39 25 16 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 IGROV1_OVARY NA IGROV1_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 110 82 LMTK3 114783 broad.mit.edu 37 19 49002845 49002846 + Frame_Shift_Ins INS - C C IGROV1_OVARY NA IGROV1_OVARY NA g.chr19:49002845_49002846insC uc002pjk.2 - 12 1567_1568 c.1567_1568insG c.(1567-1569)GCAfs p.A523fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.25 497 164 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 IGROV1_OVARY NA IGROV1_OVARY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 243 47 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 IGROV1_OVARY NA IGROV1_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 118 351 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 IGROV1_OVARY NA IGROV1_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 14 248 EP300 2033 broad.mit.edu 37 22 41525977 41525977 + Frame_Shift_Del DEL A - - IGROV1_OVARY NA IGROV1_OVARY NA g.chr22:41525977delA uc003azl.3 + 5 1647 c.1252delA c.(1252-1254)AAAfs p.K418fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 418 VCLPLK->NAAIRS: Inhibits interaction with HIF1A. Does not inhibit interaction with CITED2. apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 TCTCCCCCTCAAAAATGCTGG 0.373 0.11 233 30 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 IM95_STOMACH NA IM95_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.74 7 20 PLK3 1263 broad.mit.edu 37 1 45266761 45266761 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr1:45266761delT uc001cmn.2 + 3 472 c.372delT c.(370-372)CGTfs p.R124fs PLK3_uc001cmo.2_RNA NM_004073 NP_004064 Q9H4B4 PLK3_HUMAN polo-like kinase 3 124 Protein kinase. membrane ATP binding|protein binding|protein serine/threonine kinase activity 0 Acute lymphoblastic leukemia(166;0.155) ACATCGTGCGTTTTTCGCACC 0.542 0.46 170 145 ARHGAP29 9411 broad.mit.edu 37 1 94668131 94668131 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr1:94668131delT uc001dqj.3 - 11 1481 c.1112delA c.(1111-1113)AAGfs p.K371fs ARHGAP29_uc009wdq.1_RNA|ARHGAP29_uc001dql.2_Frame_Shift_Del_p.K371fs NM_004815 NP_004806 Q52LW3 RHG29_HUMAN PTPL1-associated RhoGAP 1 371 Potential. Rho protein signal transduction cytosol metal ion binding|Rho GTPase activator activity breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1) 11 all_lung(203;0.000732)|Lung NSC(277;0.00328) all cancers(265;0.0187)|Epithelial(280;0.159) CAACCTTCGCTTTTTTTCTAG 0.388 0.44 259 205 FMO4 2329 broad.mit.edu 37 1 171289040 171289041 + Frame_Shift_Ins INS - TGGA TGGA IM95_STOMACH NA IM95_STOMACH NA g.chr1:171289040_171289041insTGGA uc001gho.2 + 3 293_294 c.76_77insTGGA c.(76-78)CTGfs p.L26fs NM_002022 NP_002013 P31512 FMO4_HUMAN flavin containing monooxygenase 4 26 xenobiotic metabolic process integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding kidney(2)|skin(1) 3 all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181) GGATGAGGACCTGGAGCCCACC 0.480 0.29 95 38 RGL1 23179 broad.mit.edu 37 1 183881394 183881395 + Frame_Shift_Ins INS - A A IM95_STOMACH NA IM95_STOMACH NA g.chr1:183881394_183881395insA uc001gqo.2 + 15 1898_1899 c.1741_1742insA c.(1741-1743)CAAfs p.Q581fs RGL1_uc010pof.1_Frame_Shift_Ins_p.Q386fs|RGL1_uc001gqm.2_Frame_Shift_Ins_p.Q616fs|RGL1_uc010pog.1_Frame_Shift_Ins_p.Q579fs|RGL1_uc010poh.1_Frame_Shift_Ins_p.Q579fs|RGL1_uc010poi.1_Frame_Shift_Ins_p.Q552fs NM_015149 NP_055964 Q9NZL6 RGL1_HUMAN ral guanine nucleotide dissociation 581 Ser-rich. cellular lipid metabolic process|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction intracellular protein binding|Ral guanyl-nucleotide exchange factor activity breast(5)|ovary(4)|lung(2) 11 TGATGAGCCTCAAAAAAAGGTA 0.485 0.49 41 40 TPR 7175 broad.mit.edu 37 1 186291529 186291530 + Frame_Shift_Ins INS - A A IM95_STOMACH NA IM95_STOMACH NA g.chr1:186291529_186291530insA uc001grv.2 - 45 6678_6679 c.6381_6382insT c.(6379-6384)TTTGATfs p.F2127fs NM_003292 NP_003283 P12270 TPR_HUMAN nuclear pore complex-associated protein TPR 2127_2128 carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm ATP binding|protein binding|serine-tRNA ligase activity ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1) 7 Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157) Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553) TCTTCATCATCAAAAAAATGCT 0.342 0.37 164 98 TPR 7175 broad.mit.edu 37 1 186295329 186295330 + In_Frame_Ins INS - TCA TCA IM95_STOMACH NA IM95_STOMACH NA g.chr1:186295329_186295330insTCA uc001grv.2 - 41 6224_6225 c.5927_5928insTGA c.(5926-5928)GAA>GATGAA p.1975_1976insD NM_003292 NP_003283 P12270 TPR_HUMAN nuclear pore complex-associated protein TPR 1975_1976 Poly-Asp. carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm ATP binding|protein binding|serine-tRNA ligase activity ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1) 7 Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157) Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553) CTGTGtcatcttcatcatcatc 0.188 0.36 289 162 PIK3C2B 5287 broad.mit.edu 37 1 204426888 204426889 + Frame_Shift_Ins INS - T T IM95_STOMACH NA IM95_STOMACH NA g.chr1:204426888_204426889insT uc001haw.2 - 10 2159_2160 c.1680_1681insA c.(1678-1683)CCCTGCfs p.P560fs PIK3C2B_uc010pqv.1_Frame_Shift_Ins_p.P560fs|PIK3C2B_uc001hax.1_Frame_Shift_Ins_p.P560fs|PIK3C2B_uc009xbd.1_RNA NM_002646 NP_002637 O00750 P3C2B_HUMAN phosphoinositide-3-kinase, class 2 beta 560_561 cell communication|phosphatidylinositol-mediated signaling endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1) 7 all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227) GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193) CGGGAGGGGCAGGGGGGCAGCT 0.599 0.37 24 14 FMN2 56776 broad.mit.edu 37 1 240256023 240256024 + In_Frame_Ins INS - GCA GCA IM95_STOMACH NA IM95_STOMACH NA g.chr1:240256023_240256024insGCA uc010pyd.1 + 1 839_840 c.614_615insGCA c.(613-615)CTG>CTGCAG p.212_213insQ FMN2_uc010pye.1_In_Frame_Ins_p.212_213insQ NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 212_213 Potential.|Gln-rich. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) GCGATCCGCCTgcagcagcagc 0.436 0.26 51 18 FMN2 56776 broad.mit.edu 37 1 240256046 240256048 + In_Frame_Del DEL CTC - - IM95_STOMACH NA IM95_STOMACH NA g.chr1:240256046_240256048delCTC uc010pyd.1 + 1 862_864 c.637_639delCTC c.(637-639)CTCdel p.L213del FMN2_uc010pye.1_In_Frame_Del_p.L213del NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 213 Potential.|Gln-rich. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) 0.000 0.18 692 156 OR2L13 284521 broad.mit.edu 37 1 248263376 248263376 + Frame_Shift_Del DEL A - - IM95_STOMACH NA IM95_STOMACH NA g.chr1:248263376delA uc001ids.2 + 3 1036 c.699delA c.(697-699)AGAfs p.R233fs NM_175911 NP_787107 Q8N349 OR2LD_HUMAN olfactory receptor, family 2, subfamily L, 233 Cytoplasmic (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity|protein binding central_nervous_system(2)|ovary(1)|skin(1) 4 all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0132) AGGAGGGGAGAAAAAAGGCCT 0.443 0.44 267 213 PXDN 7837 broad.mit.edu 37 2 1652983 1652984 + Frame_Shift_Ins INS - G G IM95_STOMACH NA IM95_STOMACH NA g.chr2:1652983_1652984insG uc002qxa.2 - 17 2632_2633 c.2568_2569insC c.(2566-2571)CCCTGCfs p.P856fs NM_012293 NP_036425 Q92626 PXDN_HUMAN peroxidasin precursor 856_857 extracellular matrix organization|hydrogen peroxide catabolic process|immune response endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity pancreas(6)|ovary(2) 8 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716) all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228) ACAGAGAAGCAGGGGGGGTCGT 0.663 0.50 8 8 EPAS1 2034 broad.mit.edu 37 2 46609673 46609673 + Frame_Shift_Del DEL C - - IM95_STOMACH NA IM95_STOMACH NA g.chr2:46609673delC uc002ruv.2 + 15 2885 c.2397delC c.(2395-2397)TTCfs p.F799fs EPAS1_uc002ruw.2_Frame_Shift_Del_p.F265fs NM_001430 NP_001421 Q99814 EPAS1_HUMAN endothelial PAS domain protein 1 799 angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia transcription factor complex histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding ovary(1)|skin(1) 2 all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18) LUSC - Lung squamous cell carcinoma(58;0.151) 0.000 0.52 398 424 LRP1B 53353 broad.mit.edu 37 2 141245301 141245301 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr2:141245301delT uc002tvj.1 - 58 10100 c.9128delA c.(9127-9129)AACfs p.N3043fs NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 3043 Extracellular (Potential). protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) AATAACATTGTTTAATCCCTG 0.308 0.43 52 40 HOXD11 3237 broad.mit.edu 37 2 176973638 176973638 + Frame_Shift_Del DEL C - - IM95_STOMACH NA IM95_STOMACH NA g.chr2:176973638delC uc002uki.2 + 2 785 c.785delC c.(784-786)GCCfs p.A262fs HOXD11_uc010fqx.2_RNA NM_021192 NP_067015 P31277 HXD11_HUMAN homeobox D11 262 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678) CTTGCAGTTGCCCCCCAGCGG 0.617 0.51 44 45 TTN 7273 broad.mit.edu 37 2 179582703 179582703 + Frame_Shift_Del DEL C - - IM95_STOMACH NA IM95_STOMACH NA g.chr2:179582703delC uc010zfg.1 - 83 21522 c.21298delG c.(21298-21300)GCAfs p.A7100fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.A3761fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 8027 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GAAGCGACTGCCCCCACACTG 0.378 0.46 217 186 TTN 7273 broad.mit.edu 37 2 179584853 179584854 + Frame_Shift_Del DEL CT - - IM95_STOMACH NA IM95_STOMACH NA g.chr2:179584853_179584854delCT uc010zfg.1 - 78 20007_20008 c.19783_19784delAG c.(19783-19785)AGTfs p.S6595fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.S3256fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 7522 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GGTATTTTCACTCTCTCTGATG 0.431 0.44 160 124 HDLBP 3069 broad.mit.edu 37 2 242187454 242187454 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr2:242187454delT uc002waz.2 - 14 1923 c.1695delA c.(1693-1695)AAAfs p.K565fs HDLBP_uc002wba.2_Frame_Shift_Del_p.K565fs|HDLBP_uc002wbb.2_Frame_Shift_Del_p.K517fs NM_203346 NP_976221 Q00341 VIGLN_HUMAN high density lipoprotein binding protein 565 KH 6. cholesterol metabolic process|lipid transport cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane lipid binding|protein binding|RNA binding breast(3)|skin(1) 4 all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928) ATTTTGTGCATTTTTCCACCT 0.473 0.48 174 158 PDCD1 5133 broad.mit.edu 37 2 242795104 242795104 + Frame_Shift_Del DEL G - - rs41444844 byFrequency IM95_STOMACH NA IM95_STOMACH NA g.chr2:242795104delG uc002wcq.3 - 2 173 c.105delC c.(103-105)CCCfs p.P35fs PDCD1_uc010fzs.2_5'UTR|PDCD1_uc010fzt.2_RNA NM_005018 NP_005009 Q15116 PDCD1_HUMAN programmed cell death 1 precursor 35 Ig-like V-type.|Extracellular (Potential). apoptosis|humoral immune response|multicellular organismal development|T cell costimulation integral to membrane protein tyrosine phosphatase activity|signal transducer activity ovary(1) 1 all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0219) 0.000 0.39 472 301 SNRK 54861 broad.mit.edu 37 3 43389564 43389564 + Frame_Shift_Del DEL G - - IM95_STOMACH NA IM95_STOMACH NA g.chr3:43389564delG uc003cms.3 + 7 2145 c.1813delG c.(1813-1815)GGGfs p.G605fs SNRK_uc003cmt.3_Frame_Shift_Del_p.G605fs|SNRK_uc010hik.2_Frame_Shift_Del_p.G605fs|SNRK_uc011azr.1_Frame_Shift_Del_p.G399fs NM_017719 NP_060189 Q9NRH2 SNRK_HUMAN SNF related kinase 605 myeloid cell differentiation nucleus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity ovary(3)|stomach(1)|breast(1)|skin(1) 6 KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792) CAATGCTGGTGGGGGCAGTCC 0.682 0.40 28 19 TFDP2 7029 broad.mit.edu 37 3 141692947 141692947 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr3:141692947delT uc003eun.3 - 8 985 c.606delA c.(604-606)AAAfs p.K202fs TFDP2_uc003euk.3_Frame_Shift_Del_p.K115fs|TFDP2_uc010hur.2_Frame_Shift_Del_p.K142fs|TFDP2_uc003eul.3_Frame_Shift_Del_p.K142fs|TFDP2_uc011bnf.1_Frame_Shift_Del_p.K105fs|TFDP2_uc011bng.1_Frame_Shift_Del_p.K66fs|TFDP2_uc003eum.3_Frame_Shift_Del_p.K142fs NM_006286 NP_006277 Q14188 TFDP2_HUMAN transcription factor Dp-2 (E2F dimerization 202 DEF box.|Potential. cell cycle transcription factor complex DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding kidney(1) 1 ACTTGATTTCTTTTTTTTCCT 0.343 0.40 6 4 MAP3K13 9175 broad.mit.edu 37 3 185184699 185184699 + Frame_Shift_Del DEL A - - IM95_STOMACH NA IM95_STOMACH NA g.chr3:185184699delA uc010hyf.2 + 11 1857 c.1591delA c.(1591-1593)AAAfs p.K531fs MAP3K13_uc011brt.1_Frame_Shift_Del_p.K324fs|MAP3K13_uc011bru.1_Frame_Shift_Del_p.K387fs|MAP3K13_uc003fpi.2_Frame_Shift_Del_p.K531fs|MAP3K13_uc010hyg.2_Frame_Shift_Del_p.K221fs NM_004721 NP_004712 O43283 M3K13_HUMAN mitogen-activated protein kinase kinase kinase 531 activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation cytoplasm|membrane|membrane fraction ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding ovary(2)|skin(1) 3 all_cancers(143;7.21e-11)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;1.93e-20) TGCCATGGAGAAACTCATGAA 0.478 0.38 61 37 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 IM95_STOMACH NA IM95_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 81 143 ADAM29 11086 broad.mit.edu 37 4 175898771 175898771 + Frame_Shift_Del DEL A - - rs34732497 IM95_STOMACH NA IM95_STOMACH NA g.chr4:175898771delA uc003iuc.2 + 5 2765 c.2095delA c.(2095-2097)AAAfs p.K699fs ADAM29_uc003iud.2_Frame_Shift_Del_p.K699fs|ADAM29_uc010irr.2_Frame_Shift_Del_p.K699fs|ADAM29_uc011cki.1_Frame_Shift_Del_p.K699fs NM_014269 NP_055084 Q9UKF5 ADA29_HUMAN ADAM metallopeptidase domain 29 preproprotein 699 Cytoplasmic (Potential). proteolysis|spermatogenesis integral to plasma membrane metalloendopeptidase activity|zinc ion binding skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1) 16 Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164) all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286) TCGACTTTGTAAAAAAAGTAA 0.348 0.10 178 20 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 IM95_STOMACH NA IM95_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.35 108 58 RASA1 5921 broad.mit.edu 37 5 86675571 86675571 + Frame_Shift_Del DEL A - - IM95_STOMACH NA IM95_STOMACH NA g.chr5:86675571delA uc003kiw.2 + 19 2625 c.2507delA c.(2506-2508)GAAfs p.E836fs RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_Frame_Shift_Del_p.E659fs|RASA1_uc011ctv.1_Frame_Shift_Del_p.E669fs|RASA1_uc011ctw.1_Frame_Shift_Del_p.E670fs|RASA1_uc010jaw.2_Frame_Shift_Del_p.E658fs NM_002890 NP_002881 P20936 RASA1_HUMAN RAS p21 protein activator 1 isoform 1 836 Ras-GAP. cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis cytosol|intrinsic to internal side of plasma membrane glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding upper_aerodigestive_tract(3)|ovary(1)|lung(1) 5 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) TCAAAGTTAGAAAAAAATGAA 0.308 0.47 74 66 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 IM95_STOMACH NA IM95_STOMACH NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.27 24 9 SRPK1 6732 broad.mit.edu 37 6 35806115 35806115 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr6:35806115delT uc003olj.2 - 15 1905 c.1782delA c.(1780-1782)AAAfs p.K594fs SRPK1_uc011dtg.1_Frame_Shift_Del_p.K578fs|SRPK1_uc003olh.2_Frame_Shift_Del_p.K487fs|SRPK1_uc003oli.2_Frame_Shift_Del_p.K487fs NM_003137 NP_003128 Q96SB4 SRPK1_HUMAN SFRS protein kinase 1 594 Protein kinase. cell differentiation|chromosome segregation|interspecies interaction between organisms|intracellular protein kinase cascade|mRNA processing|negative regulation of viral genome replication|positive regulation of viral genome replication|regulation of mRNA processing|RNA splicing cytoplasm|nucleus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity ovary(1) 1 TTACTTTACCTTTTTTGGTGA 0.403 0.48 97 88 DGKB 1607 broad.mit.edu 37 7 14880871 14880871 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr7:14880871delT uc003ssz.2 - 1 205 c.18delA c.(16-18)AAAfs p.K6fs DGKB_uc011jxt.1_Frame_Shift_Del_p.K6fs|DGKB_uc003sta.2_Frame_Shift_Del_p.K6fs|DGKB_uc011jxu.1_Frame_Shift_Del_p.K6fs|DGKB_uc011jxv.1_Frame_Shift_Del_p.K6fs NM_004080 NP_004071 Q9Y6T7 DGKB_HUMAN diacylglycerol kinase, beta isoform 1 6 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation cytoplasm|plasma membrane ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding lung(5)|ovary(4)|breast(2)|skin(1) 12 Phosphatidylserine(DB00144) GGTGGGCCCATTTTTCCTGGT 0.403 0.57 97 129 HNRNPA2B1 3181 broad.mit.edu 37 7 26233271 26233272 + Frame_Shift_Ins INS - C C IM95_STOMACH NA IM95_STOMACH NA g.chr7:26233271_26233272insC uc003sxr.3 - 9 1016_1017 c.800_801insG c.(799-801)GGAfs p.G267fs HNRNPA2B1_uc003sxs.3_Frame_Shift_Ins_p.G255fs NM_031243 NP_112533 P22626 ROA2_HUMAN heterogeneous nuclear ribonucleoprotein A2/B1 267 Gly-rich. RNA transport catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm nucleotide binding|protein binding|protein binding|RNA binding|single-stranded telomeric DNA binding ovary(1)|central_nervous_system(1)|skin(1) 3 CACCATATCCTCCTCTTCCTCC 0.436 0.64 142 255 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes IM95_STOMACH NA IM95_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 2 17 MLL3 58508 broad.mit.edu 37 7 151845524 151845524 + Frame_Shift_Del DEL A - - IM95_STOMACH NA IM95_STOMACH NA g.chr7:151845524delA uc003wla.2 - 52 13707 c.13488delT c.(13486-13488)TTTfs p.F4496fs MLL3_uc003wkz.2_Frame_Shift_Del_p.F3614fs|MLL3_uc003wkx.2_Frame_Shift_Del_p.F654fs|MLL3_uc003wky.2_Frame_Shift_Del_p.F2060fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 4496 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTTTGTCCTTAAAAAACATGC 0.433 0.31 393 179 NBN 4683 broad.mit.edu 37 8 90967512 90967512 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr8:90967512delT uc003yej.1 - 10 1506 c.1396delA c.(1396-1398)AGGfs p.R466fs NBN_uc003yei.1_Frame_Shift_Del_p.R384fs|NBN_uc011lgb.1_Frame_Shift_Del_p.R466fs NM_002485 NP_002476 O60934 NBN_HUMAN nibrin 466 Nuclear localization signal. KR->AA: Blocks the association with KPNA2, and reduces nuclear foci formation in response to ionizing radiation. cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm protein N-terminus binding|transcription factor binding central_nervous_system(3)|kidney(3)|lung(1) 7 BRCA - Breast invasive adenocarcinoma(11;0.0344) AAAACAGACCTTTTTTTGGTA 0.338 0.30 353 148 RIMS2 9699 broad.mit.edu 37 8 104927779 104927779 + Frame_Shift_Del DEL A - - IM95_STOMACH NA IM95_STOMACH NA g.chr8:104927779delA uc003yls.2 + 5 1444 c.1203delA c.(1201-1203)GTAfs p.V401fs RIMS2_uc003ylp.2_Frame_Shift_Del_p.V623fs|RIMS2_uc003ylw.2_Frame_Shift_Del_p.V431fs|RIMS2_uc003ylq.2_Frame_Shift_Del_p.V431fs|RIMS2_uc003ylr.2_Frame_Shift_Del_p.V478fs|RIMS2_uc003ylt.2_Frame_Shift_Del_p.V24fs|RIMS2_uc003ylu.1_Frame_Shift_Del_p.V14fs|RIMS2_uc003ylv.1_Frame_Shift_Del_p.V14fs NM_014677 NP_055492 Q9UQ26 RIMS2_HUMAN regulating synaptic membrane exocytosis 2 701 PDZ. intracellular protein transport cell junction|presynaptic membrane metal ion binding|Rab GTPase binding ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1) 15 OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229) TTACTAAAGTAAAAAAAGGAA 0.323 0.26 314 108 TRPS1 7227 broad.mit.edu 37 8 116631383 116631384 + Frame_Shift_Ins INS - A A IM95_STOMACH NA IM95_STOMACH NA g.chr8:116631383_116631384insA uc003ynz.2 - 2 1361_1362 c.902_903insT c.(901-903)TTAfs p.L301fs TRPS1_uc011lhy.1_Frame_Shift_Ins_p.L305fs|TRPS1_uc003yny.2_Frame_Shift_Ins_p.L314fs|TRPS1_uc010mcy.2_Frame_Shift_Ins_p.L301fs NM_014112 NP_054831 Q9UHF7 TRPS1_HUMAN zinc finger transcription factor TRPS1 301 negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) TCCCATTTAGTAAAACAGGCCT 0.371 0.35 209 111 TRPS1 7227 broad.mit.edu 37 8 116631729 116631729 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr8:116631729delT uc003ynz.2 - 2 1016 c.557delA c.(556-558)AACfs p.N186fs TRPS1_uc011lhy.1_Frame_Shift_Del_p.N190fs|TRPS1_uc003yny.2_Frame_Shift_Del_p.N199fs|TRPS1_uc010mcy.2_Frame_Shift_Del_p.N186fs NM_014112 NP_054831 Q9UHF7 TRPS1_HUMAN zinc finger transcription factor TRPS1 186 negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) CACTTGTGGGTTTTTTGAGGC 0.488 0.30 113 48 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency IM95_STOMACH NA IM95_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.33 427 207 FOXE1 2304 broad.mit.edu 37 9 100616763 100616763 + Frame_Shift_Del DEL C - - IM95_STOMACH NA IM95_STOMACH NA g.chr9:100616763delC uc004axu.2 + 1 1227 c.567delC c.(565-567)CGCfs p.R189fs NM_004473 NP_004464 O00358 FOXE1_HUMAN forkhead box E1 189 Pro-rich.|Ala-rich. cell migration|embryonic organ morphogenesis|hair follicle morphogenesis|hard palate development|lens morphogenesis in camera-type eye|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|peripheral nervous system development|pharynx development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|soft palate development|thymus development|thyroid gland development|thyroid hormone generation transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding 0 Acute lymphoblastic leukemia(62;0.158) 0.000 0.38 61 38 CARD9 64170 broad.mit.edu 37 9 139266418 139266418 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr9:139266418delT uc004chg.3 - 2 279 c.113delA c.(112-114)AAGfs p.K38fs CARD9_uc011mdw.1_Frame_Shift_Del_p.K38fs|CARD9_uc011mdx.1_5'UTR|CARD9_uc010nbj.2_Frame_Shift_Del_p.K38fs NM_052813 NP_434700 Q9H257 CARD9_HUMAN caspase recruitment domain protein 9 isoform 1 38 CARD. positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JNK cascade|positive regulation of stress-activated MAPK cascade|regulation of apoptosis cytoplasm CARD domain binding|protein homodimerization activity pancreas(1)|lung(1)|skin(1) 3 Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06) GTTCAGGACCTTGCACTGCCG 0.642 0.31 36 16 EHMT1 79813 broad.mit.edu 37 9 140707945 140707945 + Frame_Shift_Del DEL C - - IM95_STOMACH NA IM95_STOMACH NA g.chr9:140707945delC uc011mfc.1 + 21 3180 c.3143delC c.(3142-3144)TCCfs p.S1048fs EHMT1_uc004coe.2_5'Flank NM_024757 NP_079033 Q9H9B1 EHMT1_HUMAN euchromatic histone-lysine N-methyltransferase 1 1048 DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation chromosome|nucleus histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding breast(2)|pancreas(1) 3 all_cancers(76;0.164) OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728) 0.000 0.28 937 369 SIRT1 23411 broad.mit.edu 37 10 69648795 69648795 + Frame_Shift_Del DEL A - - IM95_STOMACH NA IM95_STOMACH NA g.chr10:69648795delA uc001jnd.2 + 3 756 c.703delA c.(703-705)AAAfs p.K235fs SIRT1_uc010qis.1_Intron|SIRT1_uc009xpp.2_Frame_Shift_Del_p.K43fs|SIRT1_uc001jne.2_5'Flank NM_012238 NP_036370 Q96EB6 SIRT1_HUMAN sirtuin 1 isoform a 235 Interaction with HIST1H1E. apoptosis|cell aging|cellular response to hydrogen peroxide|cellular response to starvation|chromatin silencing at rDNA|DNA repair|DNA replication|establishment of chromatin silencing|histone H3 deacetylation|interspecies interaction between organisms|maintenance of chromatin silencing|muscle organ development|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of fat cell differentiation|negative regulation of helicase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine acetylation|peptidyl-lysine deacetylation|positive regulation of anti-apoptosis|positive regulation of chromatin silencing|positive regulation of DNA repair|regulation of apoptosis|regulation of cell proliferation|regulation of endodeoxyribonuclease activity|regulation of protein import into nucleus, translocation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|rRNA processing|transcription, DNA-dependent|triglyceride mobilization|white fat cell differentiation chromatin silencing complex|cytoplasm|nuclear euchromatin|nuclear heterochromatin|nuclear inner membrane|nucleolus|PML body|rDNA heterochromatin bHLH transcription factor binding|histone binding|HLH domain binding|identical protein binding|mitogen-activated protein kinase binding|NAD+ binding|NAD-dependent histone deacetylase activity (H3-K9 specific)|p53 binding|protein C-terminus binding|transcription corepressor activity|zinc ion binding 0 ACCAAAAAGGAAAAAAAGAAA 0.343 0.39 230 149 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 IM95_STOMACH NA IM95_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 287 121 MAML2 84441 broad.mit.edu 37 11 96075010 96075011 + Frame_Shift_Ins INS - C C IM95_STOMACH NA IM95_STOMACH NA g.chr11:96075010_96075011insC uc001pfw.1 - 1 1334_1335 c.49_50insG c.(49-51)GCCfs p.A17fs NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 17 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) CGCCCCAGAGGCCCCCCCTAGC 0.678 0.34 23 12 NPAT 4863 broad.mit.edu 37 11 108032183 108032183 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr11:108032183delT uc001pjz.3 - 17 3732 c.3630delA c.(3628-3630)AAAfs p.K1210fs NPAT_uc010rvv.1_Frame_Shift_Del_p.K266fs NM_002519 NP_002510 Q14207 NPAT_HUMAN nuclear protein, ataxia-telangiectasia locus 1210 positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle Cajal body protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity ovary(2) 2 all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116) ATGTGCCTTGTTTTTTGGTCA 0.363 0.17 403 81 SIK3 23387 broad.mit.edu 37 11 116734419 116734419 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr11:116734419delT uc001ppy.2 - 15 1786 c.1750delA c.(1750-1752)ATGfs p.M584fs SIK3_uc001ppz.2_Frame_Shift_Del_p.M483fs|SIK3_uc001pqa.2_Frame_Shift_Del_p.M584fs|SIK3_uc001ppw.2_Frame_Shift_Del_p.M1fs|SIK3_uc001ppx.2_Frame_Shift_Del_p.K58fs|SIK3_uc001pqb.2_5'Flank NM_025164 NP_079440 Q9Y2K2 SIK3_HUMAN serine/threonine-protein kinase QSK 584 cytoplasm ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1) 12 TTGTTGCCCATTTTTTCCAGG 0.582 0.49 147 139 ARHGEF12 23365 broad.mit.edu 37 11 120302576 120302577 + Frame_Shift_Del DEL TG - - IM95_STOMACH NA IM95_STOMACH NA g.chr11:120302576_120302577delTG uc001pxl.1 + 11 887_888 c.880_881delTG c.(880-882)TGTfs p.C294fs ARHGEF12_uc009zat.2_Frame_Shift_Del_p.C275fs|ARHGEF12_uc010rzn.1_Frame_Shift_Del_p.C191fs|ARHGEF12_uc009zau.1_Frame_Shift_Del_p.C191fs NM_015313 NP_056128 Q9NZN5 ARHGC_HUMAN Rho guanine nucleotide exchange factor (GEF) 12 294 apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|membrane G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity lung(2)|breast(2)|skin(2)|ovary(1) 7 Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231) CAGGACTGACTGTAGCAGTGGA 0.460 0.39 63 40 DCP1B 196513 broad.mit.edu 37 12 2062323 2062324 + In_Frame_Ins INS - TGCTGCTGC TGCTGCTGC rs149912567;rs112476192 by1000genomes IM95_STOMACH NA IM95_STOMACH NA g.chr12:2062323_2062324insTGCTGCTGC uc001qjx.1 - 7 862_863 c.782_783insGCAGCAGCA c.(781-783)CAA>CAGCAGCAGCAA p.261_261Q>QQQQ DCP1B_uc010sdy.1_In_Frame_Ins_p.159_159Q>QQQQ NM_152640 NP_689853 Q8IZD4 DCP1B_HUMAN decapping enzyme Dcp1b 261 Poly-Gln. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay cytosol|nucleus hydrolase activity|protein binding skin(1) 1 OV - Ovarian serous cystadenocarcinoma(31;0.00193) GAAGCTTCTCTtgctgctgctg 0.460 0.36 9 5 ATN1 1822 broad.mit.edu 37 12 7045892 7045903 + In_Frame_Del DEL CAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448 byFrequency;byFrequency;by1000genomes;byFrequency IM95_STOMACH NA IM95_STOMACH NA g.chr12:7045892_7045903delCAGCAGCAGCAG uc001qrw.1 + 5 1699_1710 c.1462_1473delCAGCAGCAGCAG c.(1462-1473)CAGCAGCAGCAGdel p.QQQQ496del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQ496del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 496_499 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagc 0.467 0.38 10 6 ACACB 32 broad.mit.edu 37 12 109671600 109671600 + Frame_Shift_Del DEL C - - IM95_STOMACH NA IM95_STOMACH NA g.chr12:109671600delC uc001tob.2 + 30 4306 c.4187delC c.(4186-4188)ACCfs p.T1396fs ACACB_uc001toc.2_Frame_Shift_Del_p.T1396fs|ACACB_uc010sxl.1_RNA|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Frame_Shift_Del_p.T62fs NM_001093 NP_001084 O00763 ACACB_HUMAN acetyl-Coenzyme A carboxylase beta 1396 acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation cytosol|endomembrane system|Golgi apparatus|membrane acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1) 8 Biotin(DB00121) CCCAAAGACACCCCCCTCTTC 0.612 0.39 111 72 NYNRIN 57523 broad.mit.edu 37 14 24884963 24884963 + Frame_Shift_Del DEL C - - IM95_STOMACH NA IM95_STOMACH NA g.chr14:24884963delC uc001wpf.3 + 9 4326 c.4008delC c.(4006-4008)AGCfs p.S1336fs NM_025081 NP_079357 Q9P2P1 NYNRI_HUMAN hypothetical protein LOC57523 1336 DNA integration integral to membrane DNA binding ovary(2)|central_nervous_system(1) 3 CGCCCACCAGCCCCCCTGTCT 0.612 0.45 159 131 AKAP6 9472 broad.mit.edu 37 14 33293481 33293482 + Frame_Shift_Ins INS - T T IM95_STOMACH NA IM95_STOMACH NA g.chr14:33293481_33293482insT uc001wrq.2 + 13 6632_6633 c.6462_6463insT c.(6460-6465)TGCTTTfs p.C2154fs NM_004274 NP_004265 Q13023 AKAP6_HUMAN A-kinase anchor protein 6 2154_2155 protein targeting calcium channel complex|nuclear membrane|sarcoplasmic reticulum protein kinase A binding|receptor binding breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1) 21 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) GBM - Glioblastoma multiforme(265;0.019) ATATTGAATGCTTTTTTGAGGC 0.480 0.45 278 228 TGFB3 7043 broad.mit.edu 37 14 76427407 76427409 + In_Frame_Del DEL CTC - - IM95_STOMACH NA IM95_STOMACH NA g.chr14:76427407_76427409delCTC uc001xsc.2 - 6 1793_1795 c.937_939delGAG c.(937-939)GAGdel p.E313del NM_003239 NP_003230 P10600 TGFB3_HUMAN transforming growth factor, beta 3 precursor 313 cell growth|cell-cell junction organization|detection of hypoxia|face morphogenesis|in utero embryonic development|induction of apoptosis|lung alveolus development|mammary gland development|menstrual cycle phase|negative regulation of cell proliferation|negative regulation of DNA replication|negative regulation of macrophage cytokine production|negative regulation of neuron apoptosis|odontogenesis|ossification involved in bone remodeling|palate development|platelet activation|platelet degranulation|positive regulation of bone mineralization|positive regulation of cell division|positive regulation of collagen biosynthetic process|positive regulation of DNA replication|positive regulation of epithelial to mesenchymal transition|positive regulation of filopodium assembly|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein secretion|positive regulation of SMAD protein import into nucleus|positive regulation of transcription from RNA polymerase II promoter|response to progesterone stimulus|salivary gland morphogenesis|transforming growth factor beta receptor signaling pathway extracellular matrix|platelet alpha granule lumen growth factor activity|identical protein binding|transforming growth factor beta binding|type I transforming growth factor beta receptor binding|type II transforming growth factor beta receptor binding breast(1)|skin(1) 2 BRCA - Breast invasive adenocarcinoma(234;0.0169) CACAGCAGTTCTCCTCCAAGTTG 0.448 0.37 49 29 TGFB3 7043 broad.mit.edu 37 14 76447066 76447067 + Frame_Shift_Ins INS - G G rs34019007 IM95_STOMACH NA IM95_STOMACH NA g.chr14:76447066_76447067insG uc001xsc.2 - 1 1026_1027 c.170_171insC c.(169-171)CCTfs p.P57fs TGFB3_uc001xsd.2_Frame_Shift_Ins_p.P55fs NM_003239 NP_003230 P10600 TGFB3_HUMAN transforming growth factor, beta 3 precursor 57 cell growth|cell-cell junction organization|detection of hypoxia|face morphogenesis|in utero embryonic development|induction of apoptosis|lung alveolus development|mammary gland development|menstrual cycle phase|negative regulation of cell proliferation|negative regulation of DNA replication|negative regulation of macrophage cytokine production|negative regulation of neuron apoptosis|odontogenesis|ossification involved in bone remodeling|palate development|platelet activation|platelet degranulation|positive regulation of bone mineralization|positive regulation of cell division|positive regulation of collagen biosynthetic process|positive regulation of DNA replication|positive regulation of epithelial to mesenchymal transition|positive regulation of filopodium assembly|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein secretion|positive regulation of SMAD protein import into nucleus|positive regulation of transcription from RNA polymerase II promoter|response to progesterone stimulus|salivary gland morphogenesis|transforming growth factor beta receptor signaling pathway extracellular matrix|platelet alpha granule lumen growth factor activity|identical protein binding|transforming growth factor beta binding|type I transforming growth factor beta receptor binding|type II transforming growth factor beta receptor binding breast(1)|skin(1) 2 BRCA - Breast invasive adenocarcinoma(234;0.0169) CCGTTGGCTCAGGGGGGCTGGT 0.594 0.36 163 93 TP53BP1 7158 broad.mit.edu 37 15 43712845 43712845 + Frame_Shift_Del DEL G - - rs67086944 IM95_STOMACH NA IM95_STOMACH NA g.chr15:43712845delG uc001zrs.2 - 21 4472 c.4324delC c.(4324-4326)CGAfs p.R1442fs TP53BP1_uc010udp.1_Frame_Shift_Del_p.R1442fs|TP53BP1_uc001zrq.3_Frame_Shift_Del_p.R1447fs|TP53BP1_uc001zrr.3_Frame_Shift_Del_p.R1447fs|TP53BP1_uc010udq.1_Frame_Shift_Del_p.R1447fs NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 1442 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) TCTGGCACTCGGGGCACGACA 0.532 0.52 41 44 UNC13C 440279 broad.mit.edu 37 15 54527276 54527276 + Frame_Shift_Del DEL A - - IM95_STOMACH NA IM95_STOMACH NA g.chr15:54527276delA uc002ack.2 + 4 3120 c.3120delA c.(3118-3120)AGAfs p.R1040fs NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 1040 exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) ATCTTCGCAGAAAAAAAACTT 0.368 0.46 148 128 CYLD 1540 broad.mit.edu 37 16 50825519 50825519 + Frame_Shift_Del DEL A - - IM95_STOMACH NA IM95_STOMACH NA g.chr16:50825519delA uc002egp.1 + 15 2574 c.2159delA c.(2158-2160)GAAfs p.E720fs CYLD_uc010cbs.1_Frame_Shift_Del_p.E717fs|CYLD_uc002egq.1_Frame_Shift_Del_p.E717fs|CYLD_uc002egr.1_Frame_Shift_Del_p.E717fs NM_015247 NP_056062 Q9NQC7 CYLD_HUMAN ubiquitin carboxyl-terminal hydrolase CYLD 720 cell cycle|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K63-linked deubiquitination|regulation of microtubule cytoskeleton organization|regulation of mitotic cell cycle|translation|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway cytosol|extrinsic to internal side of plasma membrane|microtubule|perinuclear region of cytoplasm|ribosome proline-rich region binding|protein kinase binding|structural constituent of ribosome|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding skin(19)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|central_nervous_system(3) 28 all_cancers(37;0.0156) ATTTTTATGGAAAAAAATGAG 0.338 0.41 103 72 CHD9 80205 broad.mit.edu 37 16 53337669 53337671 + In_Frame_Del DEL AGA - - IM95_STOMACH NA IM95_STOMACH NA g.chr16:53337669_53337671delAGA uc002ehb.2 + 30 5915_5917 c.5751_5753delAGA c.(5749-5754)ACAGAA>ACA p.E1919del CHD9_uc002egy.2_In_Frame_Del_p.E1919del|CHD9_uc002ehc.2_In_Frame_Del_p.E1919del|CHD9_uc002ehf.2_In_Frame_Del_p.E1033del|CHD9_uc010cbw.2_Intron|CHD9_uc002ehg.1_5'UTR NM_025134 NP_079410 Q3L8U1 CHD9_HUMAN chromodomain helicase DNA binding protein 9 1919 cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleoplasm ATP binding|DNA binding|helicase activity|protein binding lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1) 7 all_cancers(37;0.0212) AGCCCATCACAGAAGAACGTGCT 0.355 0.43 179 136 CDH1 999 broad.mit.edu 37 16 68835781 68835781 + Frame_Shift_Del DEL C - - IM95_STOMACH NA IM95_STOMACH NA g.chr16:68835781delC uc002ewg.1 + 3 496 c.372delC c.(370-372)CGCfs p.R124fs CDH1_uc010vlj.1_RNA|CDH1_uc010cfg.1_Frame_Shift_Del_p.R124fs NM_004360 NP_004351 P12830 CADH1_HUMAN cadherin 1, type 1 preproprotein 124 adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm cell adhesion molecule binding|gamma-catenin binding p.P126fs*89(1)|p.P127fs*41(1) breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1) 243 all_neural(199;0.0189)|Ovarian(137;0.0563) Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261) ACCACCACCGCCCCCCGCCCC 0.433 0.47 94 82 NLK 51701 broad.mit.edu 37 17 26369978 26369983 + In_Frame_Del DEL CACCAC - - IM95_STOMACH NA IM95_STOMACH NA g.chr17:26369978_26369983delCACCAC uc010crj.2 + 1 291_296 c.79_84delCACCAC c.(79-84)CACCACdel p.HH33del NLK_uc010cri.1_RNA NM_016231 NP_057315 Q9UBE8 NLK_HUMAN nemo like kinase 33_34 Poly-His. intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway cytoplasm|nucleus ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding ovary(1)|lung(1)|central_nervous_system(1) 3 all_lung(13;0.000343)|Lung NSC(42;0.00184) UCEC - Uterine corpus endometrioid carcinoma (53;0.168) AGCAGCAGGTcaccaccaccaccatc 0.476 0.26 53 19 STAC2 342667 broad.mit.edu 37 17 37371093 37371093 + Frame_Shift_Del DEL G - - IM95_STOMACH NA IM95_STOMACH NA g.chr17:37371093delG uc002hrs.2 - 7 1013 c.794delC c.(793-795)CCAfs p.P265fs STAC2_uc010cvt.2_Frame_Shift_Del_p.P123fs NM_198993 NP_945344 Q6ZMT1 STAC2_HUMAN SH3 and cysteine rich domain 2 265 intracellular signal transduction metal ion binding pancreas(1) 1 ACTCTCTGCTGGGGCTGTGAA 0.607 0.24 28 9 TRIM37 4591 broad.mit.edu 37 17 57126678 57126678 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr17:57126678delT uc002iwy.3 - 15 1835 c.1391delA c.(1390-1392)AATfs p.N464fs TRIM37_uc002iwz.3_Frame_Shift_Del_p.N464fs|TRIM37_uc002ixa.3_Frame_Shift_Del_p.N342fs|TRIM37_uc010woc.1_Frame_Shift_Del_p.N430fs NM_001005207 NP_001005207 O94972 TRI37_HUMAN tripartite motif-containing 37 protein 464 perinuclear region of cytoplasm|peroxisome ligase activity|protein binding|zinc ion binding lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1) 7 Medulloblastoma(34;0.0922)|all_neural(34;0.101) AGCATCATCATTTTGGGGGCT 0.438 0.51 171 180 USP32 84669 broad.mit.edu 37 17 58286062 58286062 + Frame_Shift_Del DEL A - - IM95_STOMACH NA IM95_STOMACH NA g.chr17:58286062delA uc002iyo.1 - 23 3012 c.2726delT c.(2725-2727)TTGfs p.L909fs USP32_uc002iyn.1_Frame_Shift_Del_p.L579fs NM_032582 NP_115971 Q8NFA0 UBP32_HUMAN ubiquitin specific protease 32 909 protein deubiquitination|ubiquitin-dependent protein catabolic process Golgi apparatus|membrane calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity lung(2)|breast(2)|large_intestine(1) 5 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198) TGGCAAAGACAAAAAATTGAA 0.348 0.44 48 37 FASN 2194 broad.mit.edu 37 17 80043423 80043423 + Frame_Shift_Del DEL G - - IM95_STOMACH NA IM95_STOMACH NA g.chr17:80043423delG uc002kdu.2 - 23 4174 c.4057delC c.(4057-4059)CTCfs p.L1353fs FASN_uc002kdw.1_Frame_Shift_Del_p.L569fs NM_004104 NP_004095 P49327 FAS_HUMAN fatty acid synthase 1353 LGDI -> SGH (in Ref. 2; AAA73576). energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process cytosol|Golgi apparatus|melanosome|plasma membrane 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding central_nervous_system(1) 1 all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246) OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237) Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339) ATGTCCCCGAGGGGGTGCCCC 0.706 0.82 2 9 ATP8B1 5205 broad.mit.edu 37 18 55351290 55351291 + Frame_Shift_Del DEL TG - - IM95_STOMACH NA IM95_STOMACH NA g.chr18:55351290_55351291delTG uc002lgw.2 - 14 1607_1608 c.1607_1608delCA c.(1606-1608)ACAfs p.T536fs uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 536 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) CCACCATGACTGTGTGGCAAAC 0.455 0.40 159 105 ATP8B1 5205 broad.mit.edu 37 18 55365040 55365040 + Frame_Shift_Del DEL T - - IM95_STOMACH NA IM95_STOMACH NA g.chr18:55365040delT uc002lgw.2 - 6 614 c.614delA c.(613-615)AATfs p.N205fs uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 205 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) AACAAAATCATTTTTTTTCAG 0.388 0.36 39 22 MAP2K7 5609 broad.mit.edu 37 19 7974714 7974714 + Frame_Shift_Del DEL C - - IM95_STOMACH NA IM95_STOMACH NA g.chr19:7974714delC uc002mit.2 + 2 264 c.199delC c.(199-201)CCCfs p.P67fs MAP2K7_uc002miv.2_Frame_Shift_Del_p.P67fs|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_Frame_Shift_Del_p.P67fs|MAP2K7_uc010dvv.2_5'UTR NM_145185 NP_660186 O14733 MP2K7_HUMAN mitogen-activated protein kinase kinase 7 67 activation of JUN kinase activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleus ATP binding|JUN kinase kinase activity|magnesium ion binding|protein binding|protein kinase binding|protein phosphatase binding|protein serine/threonine kinase activity|protein tyrosine kinase activity large_intestine(7)|central_nervous_system(2)|ovary(1)|lung(1) 11 Etoposide(DB00773) 0.000 0.27 936 347 MAP2K7 5609 broad.mit.edu 37 19 7976149 7976149 + Frame_Shift_Del DEL C - - IM95_STOMACH NA IM95_STOMACH NA g.chr19:7976149delC uc002mit.2 + 8 935 c.870delC c.(868-870)GACfs p.D290fs MAP2K7_uc002miv.2_Frame_Shift_Del_p.D290fs|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_Frame_Shift_Del_p.D290fs|MAP2K7_uc010dvv.2_Frame_Shift_Del_p.D165fs NM_145185 NP_660186 O14733 MP2K7_HUMAN mitogen-activated protein kinase kinase 7 290 Protein kinase. activation of JUN kinase activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleus ATP binding|JUN kinase kinase activity|magnesium ion binding|protein binding|protein kinase binding|protein phosphatase binding|protein serine/threonine kinase activity|protein tyrosine kinase activity p.D290D(1) large_intestine(7)|central_nervous_system(2)|ovary(1)|lung(1) 11 Etoposide(DB00773) AGCGCATTGACCCCCCAGACC 0.706 0.43 37 28 TPM4 7171 broad.mit.edu 37 19 16199871 16199873 + In_Frame_Del DEL GAA - - IM95_STOMACH NA IM95_STOMACH NA g.chr19:16199871_16199873delGAA uc002ndj.2 + 5 713_715 c.472_474delGAA c.(472-474)GAAdel p.E160del TPM4_uc002ndi.2_In_Frame_Del_p.E196del|TPM4_uc002ndk.1_In_Frame_Del_p.E70del NM_003290 NP_003281 P67936 TPM4_HUMAN tropomyosin 4 isoform 2 160 By similarity. cellular component movement|muscle filament sliding|response to oxidative stress cytosol|muscle thin filament tropomyosin|stress fiber actin binding|calcium ion binding|structural constituent of muscle TPM4/ALK(12) soft_tissue(10)|haematopoietic_and_lymphoid_tissue(2)|breast(1) 13 TGGTGACCTGGAAGAAGAACTCA 0.433 0.42 86 62 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT IM95_STOMACH NA IM95_STOMACH NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.13 634 92 CEBPA 1050 broad.mit.edu 37 19 33792755 33792760 + In_Frame_Del DEL GGCGGC - - IM95_STOMACH NA IM95_STOMACH NA g.chr19:33792755_33792760delGGCGGC uc002nun.2 - 1 671_676 c.561_566delGCCGCC c.(559-567)CCGCCGCCC>CCC p.187_189PPP>P LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 187_189 Poly-Pro. cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.P188del(4)|p.P185_P197del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.21 674 177 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 IM95_STOMACH NA IM95_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 35 22 LMTK3 114783 broad.mit.edu 37 19 49001891 49001892 + Frame_Shift_Ins INS - C C IM95_STOMACH NA IM95_STOMACH NA g.chr19:49001891_49001892insC uc002pjk.2 - 12 2521_2522 c.2521_2522insG c.(2521-2523)GCGfs p.A841fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.38 355 217 LMTK3 114783 broad.mit.edu 37 19 49002136 49002136 + Frame_Shift_Del DEL G - - IM95_STOMACH NA IM95_STOMACH NA g.chr19:49002136delG uc002pjk.2 - 12 2277 c.2277delC c.(2275-2277)CCCfs p.P759fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.36 537 298 RBL1 5933 broad.mit.edu 37 20 35696448 35696449 + Frame_Shift_Ins INS - A A IM95_STOMACH NA IM95_STOMACH NA g.chr20:35696448_35696449insA uc002xgi.2 - 3 510_511 c.431_432insT c.(430-432)TTAfs p.L144fs RBL1_uc010zvt.1_RNA|RBL1_uc002xgj.1_Frame_Shift_Ins_p.L144fs|RBL1_uc010gfv.1_RNA NM_002895 NP_002886 P28749 RBL1_HUMAN retinoblastoma-like protein 1 isoform a 144 cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent transcription factor binding lung(5)|skin(3)|ovary(2) 10 Myeloproliferative disorder(115;0.00878) GAAATATATCTAAAAAAATTGG 0.332 0.19 124 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 IM95_STOMACH NA IM95_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 43 327 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 IM95_STOMACH NA IM95_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 73 MYO18B 84700 broad.mit.edu 37 22 26164407 26164407 + Frame_Shift_Del DEL C - - IM95_STOMACH NA IM95_STOMACH NA g.chr22:26164407delC uc003abz.1 + 4 774 c.524delC c.(523-525)GCCfs p.A175fs MYO18B_uc003aca.1_Frame_Shift_Del_p.A56fs|MYO18B_uc010guy.1_Frame_Shift_Del_p.A56fs|MYO18B_uc010guz.1_Frame_Shift_Del_p.A56fs|MYO18B_uc011aka.1_5'UTR|MYO18B_uc011akb.1_5'Flank NM_032608 NP_115997 Q8IUG5 MY18B_HUMAN myosin XVIIIB 175 nucleus|sarcomere|unconventional myosin complex actin binding|ATP binding|motor activity ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2) 12 0.000 0.50 207 203 EP300 2033 broad.mit.edu 37 22 41545952 41545954 + In_Frame_Del DEL CAA - - rs145037345 byFrequency IM95_STOMACH NA IM95_STOMACH NA g.chr22:41545952_41545954delCAA uc003azl.3 + 14 2962_2964 c.2567_2569delCAA c.(2566-2571)GCAACA>GCA p.T858del NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 858 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 CAGCCACCAGCAACAACAATTCC 0.591 0.44 204 158 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 IPC298_SKIN NA IPC298_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 4 35 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - IPC298_SKIN NA IPC298_SKIN NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.26 332 116 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes IPC298_SKIN NA IPC298_SKIN NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.44 9 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 IPC298_SKIN NA IPC298_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.43 12 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 IPC298_SKIN NA IPC298_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 84 118 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 IPC298_SKIN NA IPC298_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 34 49 CHD1 1105 broad.mit.edu 37 5 98240622 98240623 + Frame_Shift_Ins INS - G G IPC298_SKIN NA IPC298_SKIN NA g.chr5:98240622_98240623insG uc003knf.2 - 2 381_382 c.233_234insC c.(232-234)CCAfs p.P78fs NM_001270 NP_001261 O14646 CHD1_HUMAN chromodomain helicase DNA binding protein 1 78 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117) COAD - Colon adenocarcinoma(37;0.0717) Epirubicin(DB00445) CAACTTTCGGTGGTTTTGCTTG 0.421 0.16 90 17 PHIP 55023 broad.mit.edu 37 6 79692608 79692609 + Frame_Shift_Ins INS - T T IPC298_SKIN NA IPC298_SKIN NA g.chr6:79692608_79692609insT uc003pir.2 - 23 2989_2990 c.2763_2764insA c.(2761-2766)AAACAAfs p.K921fs PHIP_uc003piq.2_5'UTR|PHIP_uc011dyp.1_Frame_Shift_Ins_p.K920fs NM_017934 NP_060404 Q8WWQ0 PHIP_HUMAN pleckstrin homology domain interacting protein 921_922 Lys-rich. insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis nucleus insulin receptor binding large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1) 6 all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219) BRCA - Breast invasive adenocarcinoma(397;0.231) CAAACCttttgttttctttctt 0.149 0.20 41 10 TBP 6908 broad.mit.edu 37 6 170871038 170871046 + In_Frame_Del DEL CAACAGCAA - - rs145348820;rs71010672;rs10592950;rs62430309 IPC298_SKIN NA IPC298_SKIN NA g.chr6:170871038_170871046delCAACAGCAA uc003qxt.2 + 3 446_454 c.214_222delCAACAGCAA c.(214-222)CAACAGCAAdel p.QQQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_95 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding p.Q72del(1) ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcagcagcagcaacagcaacagcagcagc 0.177 0.20 82 20 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes IPC298_SKIN NA IPC298_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.85 3 17 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G IPC298_SKIN NA IPC298_SKIN NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.12 238 31 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 IPC298_SKIN NA IPC298_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.48 15 14 PSKH2 85481 broad.mit.edu 37 8 87081752 87081753 + Frame_Shift_Ins INS - C C IPC298_SKIN NA IPC298_SKIN NA g.chr8:87081752_87081753insC uc011lfy.1 - 1 99_100 c.99_100insG c.(97-102)GGGCCTfs p.G33fs NM_033126 NP_149117 Q96QS6 KPSH2_HUMAN protein serine kinase H2 33_34 ATP binding|protein serine/threonine kinase activity stomach(2)|lung(2)|ovary(1) 5 STAD - Stomach adenocarcinoma(118;0.129) TCGGGCCCAGGCCCCGCGCCTC 0.713 0.34 31 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 IPC298_SKIN NA IPC298_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 491 248 SIK3 23387 broad.mit.edu 37 11 116729338 116729339 + Frame_Shift_Ins INS - G G IPC298_SKIN NA IPC298_SKIN NA g.chr11:116729338_116729339insG uc001ppy.2 - 20 2560_2561 c.2524_2525insC c.(2524-2526)CGGfs p.R842fs SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron|SIK3_uc001ppw.2_Intron|SIK3_uc001ppx.2_Intron|SIK3_uc001pqb.2_Frame_Shift_Ins_p.R145fs NM_025164 NP_079440 Q9Y2K2 SIK3_HUMAN serine/threonine-protein kinase QSK 842 Gln-rich. cytoplasm ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1) 12 GGGGGAACCCCGGGACTGGTCC 0.569 0.17 124 25 ARHGDIB 397 broad.mit.edu 37 12 15097753 15097753 + Frame_Shift_Del DEL T - - IPC298_SKIN NA IPC298_SKIN NA g.chr12:15097753delT uc001rcq.1 - 5 467 c.363delA c.(361-363)TCAfs p.S121fs ARHGDIB_uc001rcp.1_RNA NM_001175 NP_001166 P52566 GDIR2_HUMAN Rho GDP dissociation inhibitor (GDI) beta 121 actin cytoskeleton organization|cellular component movement|immune response|multicellular organismal development|negative regulation of cell adhesion|regulation of small GTPase mediated signal transduction|Rho protein signal transduction cytoplasmic membrane-bounded vesicle|cytoskeleton|cytosol GTPase activator activity|Rho GDP-dissociation inhibitor activity 0 ATTTCAGGCCTGACACAATAT 0.453 0.27 61 22 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency IPC298_SKIN NA IPC298_SKIN NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.14 103 17 CDK8 1024 broad.mit.edu 37 13 26959354 26959355 + Frame_Shift_Ins INS - G G IPC298_SKIN NA IPC298_SKIN NA g.chr13:26959354_26959355insG uc001uqr.1 + 6 547_548 c.521_522insG c.(520-522)ATGfs p.M174fs CDK8_uc001uqs.1_Frame_Shift_Ins_p.M174fs|CDK8_uc001uqt.1_Frame_Shift_Ins_p.M1fs NM_001260 NP_001251 P49336 CDK8_HUMAN cyclin-dependent kinase 8 174 Protein kinase. regulation of transcription, DNA-dependent|transcription, DNA-dependent mediator complex ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity lung(2)|large_intestine(1)|ovary(1)|skin(1) 5 Colorectal(5;0.000442) Lung SC(185;0.0156)|Breast(139;0.147) all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188) ACAGCTGACATGGGCTTTGCCC 0.342 0.10 63 7 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 IPC298_SKIN NA IPC298_SKIN NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.39 17 11 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes IPC298_SKIN NA IPC298_SKIN NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.11 93 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C IPC298_SKIN NA IPC298_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.83 3 15 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 IPC298_SKIN NA IPC298_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.47 69 60 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 IPC298_SKIN NA IPC298_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 43 341 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 IPC298_SKIN NA IPC298_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 9 131 SMARCB1 6598 broad.mit.edu 37 22 24134068 24134069 + Frame_Shift_Ins INS - C C IPC298_SKIN NA IPC298_SKIN NA g.chr22:24134068_24134069insC uc002zyb.2 + 2 426_427 c.219_220insC c.(217-222)AAACCTfs p.K73fs SMARCB1_uc002zyg.2_Frame_Shift_Ins_p.K73fs|SMARCB1_uc011ajb.1_Intron|SMARCB1_uc002zya.2_Frame_Shift_Ins_p.K73fs|SMARCB1_uc002zyc.2_Intron|SMARCB1_uc002zyd.2_Intron|SMARCB1_uc002zye.1_Frame_Shift_Ins_p.K36fs|SMARCB1_uc002zyf.1_Intron|SMARCB1_uc010gue.1_Intron NM_003073 NP_003064 Q12824 SNF5_HUMAN SWI/SNF related, matrix associated, actin 73_74 cell cycle|chromatin remodeling|DNA integration|interspecies interaction between organisms|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|retroviral genome replication|transcription, DNA-dependent nBAF complex|npBAF complex|nucleolus|nucleoplasm|SWI/SNF complex p53 binding p.?(2) soft_tissue(193)|central_nervous_system(172)|haematopoietic_and_lymphoid_tissue(23)|meninges(5)|skin(5)|bone(4)|ovary(2)|endometrium(1)|lung(1)|pancreas(1) 407 Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05) AAAAAACAAAACCTAACACTAA 0.436 0.16 62 12 KIAA2022 340533 broad.mit.edu 37 X 73960933 73960934 + Frame_Shift_Ins INS - T T ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chrX:73960933_73960934insT uc004eby.2 - 3 4075_4076 c.3458_3459insA c.(3457-3459)AACfs p.N1153fs NM_001008537 NP_001008537 Q5QGS0 K2022_HUMAN hypothetical protein LOC340533 1153 base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle delta DNA polymerase complex 3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 ACAGGCAAGGGTTTTTTTGGAG 0.401 0.45 127 106 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.82 11 51 PIK3CD 5293 broad.mit.edu 37 1 9780216 9780216 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr1:9780216delC uc001aqb.3 + 11 1594 c.1386delC c.(1384-1386)AACfs p.N462fs PIK3CD_uc010oaf.1_Frame_Shift_Del_p.N462fs|PIK3CD_uc001aqe.3_Frame_Shift_Del_p.N427fs NM_005026 NP_005017 O00329 PK3CD_HUMAN catalytic phosphatidylinositol 3-kinase delta 462 phosphatidylinositol-mediated signaling|protein phosphorylation phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding lung(4)|skin(2)|central_nervous_system(1) 7 all_lung(157;0.222) all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419) TGCGCAGTAACCCCAACACGG 0.657 0.45 41 34 ARID1A 8289 broad.mit.edu 37 1 27106804 27106804 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr1:27106804delC uc001bmv.1 + 20 6788 c.6415delC c.(6415-6417)CCCfs p.P2139fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.P1922fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.P985fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.P467fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.P381fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 2139 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.F2141fs*59(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) TCTGGCCACACCCCCCTTCAG 0.587 0.32 89 42 SOX11 6664 broad.mit.edu 37 2 5833526 5833528 + In_Frame_Del DEL GAC - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr2:5833526_5833528delGAC uc002qyj.2 + 1 728_730 c.673_675delGAC c.(673-675)GACdel p.D233del NM_003108 NP_003099 P35716 SOX11_HUMAN SRY-box 11 233 Poly-Asp. cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis cytoplasm|nucleolus enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding central_nervous_system(3) 3 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) OV - Ovarian serous cystadenocarcinoma(76;0.132) 0.000 0.39 224 146 LRP1B 53353 broad.mit.edu 37 2 141113924 141113925 + Frame_Shift_Ins INS - T T ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr2:141113924_141113925insT uc002tvj.1 - 75 12488_12489 c.11516_11517insA c.(11515-11517)AACfs p.N3839fs NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 3839 Extracellular (Potential).|EGF-like 8. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) CACATTGTCTGTTTTTCATGTT 0.356 0.52 30 32 MYO3B 140469 broad.mit.edu 37 2 171376043 171376043 + Frame_Shift_Del DEL A - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr2:171376043delA uc002ufy.2 + 30 3711 c.3568delA c.(3568-3570)AAAfs p.K1190fs MYO3B_uc002ufv.2_Frame_Shift_Del_p.K1177fs|MYO3B_uc010fqb.1_Frame_Shift_Del_p.K1177fs|MYO3B_uc002ufz.2_Frame_Shift_Del_p.K1163fs|MYO3B_uc002ufw.2_RNA|MYO3B_uc002ufx.2_RNA|MYO3B_uc002ugb.2_RNA NM_138995 NP_620482 Q8WXR4 MYO3B_HUMAN myosin IIIB isoform 2 1190 response to stimulus|visual perception cytoplasm|myosin complex actin binding|ATP binding|motor activity|protein serine/threonine kinase activity lung(8)|ovary(6)|skin(4)|central_nervous_system(1) 19 TGTCACAGAGAAAAATGGGTG 0.433 0.31 24 11 IDH1 3417 broad.mit.edu 37 2 209116262 209116263 + Frame_Shift_Ins INS - T T ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr2:209116262_209116263insT uc002vcs.2 - 3 259_260 c.13_14insA c.(13-15)ATCfs p.I5fs IDH1_uc002vct.2_Frame_Shift_Ins_p.I5fs|IDH1_uc002vcu.2_Frame_Shift_Ins_p.I5fs NM_005896 NP_005887 O75874 IDHC_HUMAN isocitrate dehydrogenase 1 (NADP+), soluble 5 2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle cytosol|peroxisomal matrix isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1) 2868 Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136) ACCGCCACTGATTTTTTTGGAC 0.317 0.47 82 73 ROBO1 6091 broad.mit.edu 37 3 78649281 78649282 + In_Frame_Ins INS - TCT TCT ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr3:78649281_78649282insTCT uc003dqe.2 - 30 5130_5131 c.4922_4923insAGA c.(4921-4923)GAT>GAAGAT p.1640_1641insE ROBO1_uc003dqb.2_In_Frame_Ins_p.1601_1602insE|ROBO1_uc003dqc.2_In_Frame_Ins_p.1540_1541insE|ROBO1_uc003dqd.2_In_Frame_Ins_p.1595_1596insE|ROBO1_uc010hoh.2_In_Frame_Ins_p.832_833insE NM_002941 NP_002932 Q9Y6N7 ROBO1_HUMAN roundabout 1 isoform a 1640_1641 Cytoplasmic (Potential). activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway cell surface|cytoplasm|integral to plasma membrane axon guidance receptor activity|identical protein binding|LRR domain binding large_intestine(2) 2 Lung SC(41;0.0257)|Lung NSC(201;0.0439) LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274) CTTCATTATTATCTTCTCCTCT 0.361 0.42 93 66 PIK3R4 30849 broad.mit.edu 37 3 130454761 130454762 + Frame_Shift_Ins INS - A A rs55951445 ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr3:130454761_130454762insA uc003enj.2 - 3 1399_1400 c.818_819insT c.(817-819)TTCfs p.F273fs NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 273 Protein kinase. fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGTTCAGGGAAAAAATGTCC 0.342 0.55 30 37 CXCL9 4283 broad.mit.edu 37 4 76924816 76924817 + Frame_Shift_Ins INS - T T ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr4:76924816_76924817insT uc003hjh.1 - 4 351_352 c.312_313insA c.(310-315)AAACATfs p.K104fs NM_002416 NP_002407 Q07325 CXCL9_HUMAN small inducible cytokine B9 precursor 104_105 cell-cell signaling|cellular defense response|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response extracellular space chemokine activity p.K104N(1) ovary(1) 1 Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934) TTTTTTTGATGTTTTTTCCCAT 0.337 0.39 101 65 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 52 69 TRIO 7204 broad.mit.edu 37 5 14482694 14482694 + Frame_Shift_Del DEL A - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr5:14482694delA uc003jff.2 + 46 6475 c.6469delA c.(6469-6471)AAAfs p.K2157fs TRIO_uc003jfg.2_RNA|TRIO_uc003jfh.1_Frame_Shift_Del_p.K1806fs NM_007118 NP_009049 O75962 TRIO_HUMAN triple functional domain (PTPRF interacting) 2157 PH 2. apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway cytosol ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1) 18 Lung NSC(4;0.000742) GTTTTAGGGGAAAATCGTTGC 0.453 0.49 21 20 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.29 42 17 RASA1 5921 broad.mit.edu 37 5 86665639 86665639 + Frame_Shift_Del DEL T - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr5:86665639delT uc003kiw.2 + 12 1738 c.1620delT c.(1618-1620)TGTfs p.C540fs RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_Frame_Shift_Del_p.C363fs|RASA1_uc011ctv.1_Frame_Shift_Del_p.C373fs|RASA1_uc011ctw.1_Frame_Shift_Del_p.C374fs|RASA1_uc010jaw.2_Frame_Shift_Del_p.C362fs NM_002890 NP_002881 P20936 RASA1_HUMAN RAS p21 protein activator 1 isoform 1 540 PH. C -> Y (in CMAVM). cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis cytosol|intrinsic to internal side of plasma membrane glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding upper_aerodigestive_tract(3)|ovary(1)|lung(1) 5 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) GGCCAAACTGTTTTCAGATAG 0.299 0.59 30 44 BAT3 7917 broad.mit.edu 37 6 31617055 31617055 + Frame_Shift_Del DEL G - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr6:31617055delG uc003nvg.3 - 4 658 c.344delC c.(343-345)CCTfs p.P115fs BAT3_uc003nvf.3_Frame_Shift_Del_p.P115fs|BAT3_uc003nvh.3_Frame_Shift_Del_p.P115fs|BAT3_uc003nvi.3_Frame_Shift_Del_p.P115fs|BAT3_uc011dnw.1_Frame_Shift_Del_p.P115fs|BAT3_uc011dnx.1_Frame_Shift_Del_p.P115fs|BAT3_uc003nvj.1_Frame_Shift_Del_p.P115fs NM_004639 NP_004630 P46379 BAG6_HUMAN HLA-B associated transcript-3 isoform a 115 apoptosis in response to endoplasmic reticulum stress|brain development|cell differentiation|chromatin modification|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|embryo development|internal peptidyl-lysine acetylation|kidney development|lung development|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|protein stabilization|spermatogenesis|synaptonemal complex assembly|tail-anchored membrane protein insertion into ER membrane|transport|ubiquitin-dependent protein catabolic process BAT3 complex|nucleus polyubiquitin binding|proteasome binding|ribosome binding 0 CCGAGTACCAGGGGGGGATCC 0.592 0.35 93 51 DST 667 broad.mit.edu 37 6 56382364 56382365 + Frame_Shift_Ins INS - T T ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr6:56382364_56382365insT uc003pdf.2 - 64 11854_11855 c.11826_11827insA c.(11824-11829)AAATTGfs p.K3942fs DST_uc003pcz.3_Frame_Shift_Ins_p.K3764fs|DST_uc011dxj.1_Frame_Shift_Ins_p.K3793fs|DST_uc011dxk.1_Frame_Shift_Ins_p.K3804fs|DST_uc003pcy.3_Frame_Shift_Ins_p.K3438fs NM_001144769 NP_001138241 Q03001 DYST_HUMAN dystonin isoform 2 5850_5851 Spectrin 10. cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1) 14 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) AGAGACATCAATTTTTTTTCTG 0.391 0.44 76 59 ROS1 6098 broad.mit.edu 37 6 117642513 117642513 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr6:117642513delC uc003pxp.1 - 35 5885 c.5686delG c.(5686-5688)GTGfs p.V1896fs ROS1_uc011ebi.1_RNA|GOPC_uc003pxq.1_Frame_Shift_Del_p.V208fs NM_002944 NP_002935 P08922 ROS_HUMAN proto-oncogene c-ros-1 protein precursor 1896 Cytoplasmic (Potential). transmembrane receptor protein tyrosine kinase signaling pathway membrane fraction|sodium:potassium-exchanging ATPase complex ATP binding|transmembrane receptor protein tyrosine kinase activity lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1) 25 all_cancers(87;0.00846)|all_epithelial(87;0.0242) GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137) AGCACTGTCACCCCTTCCTTG 0.398 0.36 178 99 PRKAR1B 5575 broad.mit.edu 37 7 720281 720281 + Frame_Shift_Del DEL G - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr7:720281delG uc003siu.1 - 4 366 c.260delC c.(259-261)CCGfs p.P87fs PRKAR1B_uc003siv.2_Frame_Shift_Del_p.P87fs|PRKAR1B_uc003siw.1_Frame_Shift_Del_p.P87fs NM_002735 NP_002726 P31321 KAP1_HUMAN protein kinase, cAMP-dependent, regulatory, type 87 Dimerization and phosphorylation. activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport cAMP-dependent protein kinase complex|cytosol cAMP binding|cAMP-dependent protein kinase regulator activity 0 Ovarian(82;0.0779) UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152) CACAGGGTTCGGGGGGGTGGG 0.617 0.36 96 53 GPR141 353345 broad.mit.edu 37 7 37780680 37780680 + Frame_Shift_Del DEL T - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr7:37780680delT uc003tfm.1 + 1 685 c.685delT c.(685-687)TTTfs p.F229fs uc003tfl.2_Intron NM_181791 NP_861456 Q7Z602 GP141_HUMAN G protein-coupled receptor 141 229 Helical; Name=6; (Potential). integral to membrane|plasma membrane G-protein coupled receptor activity ovary(3) 3 GAAAAACCTATTTTTTATAGG 0.433 0.10 263 29 AKAP9 10142 broad.mit.edu 37 7 91643633 91643633 + Frame_Shift_Del DEL T - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr7:91643633delT uc003ulg.2 + 10 3828 c.3603delT c.(3601-3603)TATfs p.Y1201fs AKAP9_uc003ule.2_Frame_Shift_Del_p.Y1213fs|AKAP9_uc003ulf.2_Frame_Shift_Del_p.Y1201fs|AKAP9_uc003uli.2_Frame_Shift_Del_p.Y826fs NM_005751 NP_005742 Q99996 AKAP9_HUMAN A-kinase anchor protein 9 isoform 2 1213 G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport centrosome|cytosol|Golgi apparatus receptor binding breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1) 26 all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) AATGTTCTTATTTTTTACAGG 0.199 0.43 53 40 SMURF1 57154 broad.mit.edu 37 7 98659462 98659463 + Splice_Site INS - A A ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr7:98659462_98659463insA uc003upu.1 - 2 376 c.56_splice c.e2-1 p.V19_splice SMURF1_uc003upv.1_Splice_Site_p.V19_splice|SMURF1_uc003upt.2_Splice_Site_p.V19_splice NM_020429 NP_065162 Q9HCE7 SMUF1_HUMAN Smad ubiquitination regulatory factor 1 isoform BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process cytosol|plasma membrane activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity p.?(1) skin(2)|ovary(1)|lung(1) 4 all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274) STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224) CACATAACACTAAAAACAAAGA 0.287 0.39 22 14 BRAF 673 broad.mit.edu 37 7 140482927 140482927 + Frame_Shift_Del DEL G - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr7:140482927delG uc003vwc.3 - 10 1269 c.1208delC c.(1207-1209)CCTfs p.P403fs NM_004333 NP_004324 P15056 BRAF_HUMAN B-Raf 403 activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission cytosol|nucleus|plasma membrane ATP binding|metal ion binding KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2) thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1) 18290 Melanoma(164;0.00956) Sorafenib(DB00398) TAATGAGGCAGGGGGGGTAGC 0.428 0.32 82 38 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.93 1 13 NBN 4683 broad.mit.edu 37 8 90967512 90967512 + Frame_Shift_Del DEL T - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr8:90967512delT uc003yej.1 - 10 1506 c.1396delA c.(1396-1398)AGGfs p.R466fs NBN_uc003yei.1_Frame_Shift_Del_p.R384fs|NBN_uc011lgb.1_Frame_Shift_Del_p.R466fs NM_002485 NP_002476 O60934 NBN_HUMAN nibrin 466 Nuclear localization signal. KR->AA: Blocks the association with KPNA2, and reduces nuclear foci formation in response to ionizing radiation. cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm protein N-terminus binding|transcription factor binding central_nervous_system(3)|kidney(3)|lung(1) 7 BRCA - Breast invasive adenocarcinoma(11;0.0344) AAAACAGACCTTTTTTTGGTA 0.338 0.50 99 98 FBXO43 286151 broad.mit.edu 37 8 101154029 101154029 + Frame_Shift_Del DEL T - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr8:101154029delT uc003yjd.2 - 2 1166 c.453delA c.(451-453)AAAfs p.K151fs FBXO43_uc003yje.2_Frame_Shift_Del_p.K117fs|FBXO43_uc010mbp.1_Frame_Shift_Del_p.K151fs NM_001029860 NP_001025031 Q4G163 FBX43_HUMAN F-box protein 43 isoform b 151 meiosis zinc ion binding kidney(1)|skin(1) 2 all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798) Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957) GAGGTAAACATTTTTTCCCAC 0.348 0.45 136 110 POU5F1B 5462 broad.mit.edu 37 8 128428292 128428292 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr8:128428292delC uc003ysf.2 + 1 436 c.181delC c.(181-183)CCCfs p.P61fs uc003ysc.1_Intron|uc003ysd.1_Intron|LOC727677_uc003yse.1_Intron|uc011liu.1_RNA NM_001159542 NP_001153014 Q06416 P5F1B_HUMAN POU class 5 homeobox 1B 61 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 GTGGGGGATTCCCCCTTGCCC 0.657 0.49 37 36 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 22 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.50 305 305 SMARCA2 6595 broad.mit.edu 37 9 2047308 2047309 + Frame_Shift_Ins INS - C C ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr9:2047308_2047309insC uc003zhc.2 + 5 969_970 c.870_871insC c.(868-873)GCGCCCfs p.A290fs SMARCA2_uc003zhd.2_Frame_Shift_Ins_p.A290fs|SMARCA2_uc010mha.2_Frame_Shift_Ins_p.A281fs NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 290_291 chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.36 9 5 PTCH1 5727 broad.mit.edu 37 9 98209617 98209617 + Frame_Shift_Del DEL G - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr9:98209617delG uc004avk.3 - 23 4109 c.3921delC c.(3919-3921)CCCfs p.P1307fs PTCH1_uc010mrn.2_Frame_Shift_Del_p.P99fs|PTCH1_uc010mro.2_Frame_Shift_Del_p.P1156fs|PTCH1_uc010mrp.2_Frame_Shift_Del_p.P1156fs|PTCH1_uc010mrq.2_Frame_Shift_Del_p.P1156fs|PTCH1_uc004avl.3_Frame_Shift_Del_p.P1156fs|PTCH1_uc010mrr.2_Frame_Shift_Del_p.P1241fs|PTCH1_uc004avm.3_Frame_Shift_Del_p.P1306fs NM_000264 NP_000255 Q13635 PTC1_HUMAN patched isoform L 1307 Cytoplasmic (Potential). embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway integral to plasma membrane hedgehog receptor activity skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1) 379 Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136) 0.000 0.48 251 232 FNBP1 23048 broad.mit.edu 37 9 132687242 132687243 + Frame_Shift_Ins INS - T T ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr9:132687242_132687243insT uc004byw.1 - 9 1202_1203 c.983_984insA c.(982-984)AATfs p.N328fs FNBP1_uc011mbv.1_Frame_Shift_Ins_p.N328fs|FNBP1_uc011mbw.1_Frame_Shift_Ins_p.N328fs|FNBP1_uc004bza.2_Frame_Shift_Ins_p.N328fs|FNBP1_uc004byz.1_Frame_Shift_Ins_p.N328fs|FNBP1_uc004byx.1_Frame_Shift_Ins_p.N249fs|FNBP1_uc004byy.1_Frame_Shift_Ins_p.N249fs NM_015033 NP_055848 Q96RU3 FNBP1_HUMAN formin binding protein 1 328 Interaction with microtubules (By similarity).|Required for self-association and induction of membrane tubulation. endocytosis cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane identical protein binding|lipid binding 0 Ovarian(14;0.000536) GBM - Glioblastoma multiforme(294;0.0378) TCAGTACCTTATTTTTTTTGAT 0.381 0.40 79 53 MYO3A 53904 broad.mit.edu 37 10 26462760 26462760 + Frame_Shift_Del DEL A - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr10:26462760delA uc001isn.2 + 30 3927 c.3567delA c.(3565-3567)CCAfs p.P1189fs MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron NM_017433 NP_059129 Q8NEV4 MYO3A_HUMAN myosin IIIA 1189 protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception cytoplasm|filamentous actin|filopodium|myosin complex actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 18 ATCAGACTCCAAAAAAAATGA 0.403 0.44 36 28 PTEN 5728 broad.mit.edu 37 10 89720712 89720712 + Frame_Shift_Del DEL A - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr10:89720712delA uc001kfb.2 + 9 1894 c.863delA c.(862-864)GAAfs p.E288fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 288 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.E288fs*3(6)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.E288*(2)|p.G165_*404del(1)|p.S287fs*1(1)|p.G165_K342del(1)|p.E288fs*8(1)|p.S287fs*8(1)|p.W274_F341del(1)|p.E288K(1)|p.E288fs*9(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GAAACCTCAGAAAAAGTAGAA 0.299 0.44 33 26 PTEN 5728 broad.mit.edu 37 10 89720799 89720802 + Frame_Shift_Del DEL TACT - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr10:89720799_89720802delTACT uc001kfb.2 + 9 1981_1984 c.950_953delTACT c.(949-954)GTACTTfs p.V317fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 317_318 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.L318fs*2(17)|p.V317fs*3(16)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.V317fs*6(2)|p.G165_*404del(1)|p.G165_K342del(1)|p.L316fs*1(1)|p.W274_F341del(1)|p.V317_K322del(1)|p.L318F(1)|p.T318fs*2(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GAATATCTAGTACTTACTTTAACA 0.333 0.41 51 35 FGFR2 2263 broad.mit.edu 37 10 123239376 123239376 + Frame_Shift_Del DEL T - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr10:123239376delT uc010qtk.1 - 19 3108 c.2461delA c.(2461-2463)ACAfs p.T821fs FGFR2_uc010qtg.1_Frame_Shift_Del_p.T709fs|FGFR2_uc010qth.1_Frame_Shift_Del_p.T706fs|FGFR2_uc010qti.1_Intron|FGFR2_uc010qtj.1_Frame_Shift_Del_p.T822fs|FGFR2_uc010qtl.1_Frame_Shift_Del_p.T705fs|FGFR2_uc010qtm.1_Frame_Shift_Del_p.T704fs|FGFR2_uc001lfg.3_Frame_Shift_Del_p.T429fs|FGFR2_uc001lfk.1_RNA NM_000141 NP_000132 P21802 FGFR2_HUMAN fibroblast growth factor receptor 2 isoform 1 821 Cytoplasmic (Potential). angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1) 96 Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107) STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722) all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845) Palifermin(DB00039) GTCATTCATGTTTTAACACTG 0.488 0.49 64 62 HIPK3 10114 broad.mit.edu 37 11 33358692 33358693 + Frame_Shift_Ins INS - T T ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr11:33358692_33358693insT uc001mul.1 + 4 1563_1564 c.1293_1294insT c.(1291-1296)AGATTTfs p.R431fs HIPK3_uc001mum.1_Frame_Shift_Ins_p.R431fs|HIPK3_uc009yjv.1_Frame_Shift_Ins_p.R431fs|HIPK3_uc009yjw.1_RNA NM_005734 NP_005725 Q9H422 HIPK3_HUMAN homeodomain interacting protein kinase 3 isoform 431_432 Protein kinase. anti-apoptosis|apoptosis|negative regulation of JUN kinase activity|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm ATP binding|protein serine/threonine kinase activity large_intestine(1)|skin(1)|stomach(1)|ovary(1)|pancreas(1) 5 AATCCACAAGATTTTTTTGCAA 0.312 0.34 51 26 CTSW 1521 broad.mit.edu 37 11 65648935 65648937 + In_Frame_Del DEL AGG - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr11:65648935_65648937delAGG uc001ogc.1 + 3 272_274 c.230_232delAGG c.(229-234)CAGGAG>CAG p.E79del CTSW_uc001ogb.1_In_Frame_Del_p.E79del NM_001335 NP_001326 P56202 CATW_HUMAN cathepsin W preproprotein 79 immune response|proteolysis cysteine-type endopeptidase activity central_nervous_system(1) 1 READ - Rectum adenocarcinoma(159;0.168) CAGAGGCTGCAGGAGGAGGACTT 0.576 0.42 264 190 NUMA1 4926 broad.mit.edu 37 11 71746965 71746965 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr11:71746965delC uc001orl.1 - 3 197 c.25delG c.(25-27)GCTfs p.A9fs NUMA1_uc001ork.1_Frame_Shift_Del_p.A9fs|NUMA1_uc001orm.1_Frame_Shift_Del_p.A9fs|NUMA1_uc009ysx.1_Frame_Shift_Del_p.A9fs|NUMA1_uc001oro.1_Frame_Shift_Del_p.A9fs|NUMA1_uc009ysy.1_Frame_Shift_Del_p.A9fs|NUMA1_uc001orp.2_Frame_Shift_Del_p.A9fs|NUMA1_uc001orq.2_Frame_Shift_Del_p.A9fs NM_006185 NP_006176 Q14980 NUMA1_HUMAN nuclear mitotic apparatus protein 1 9 G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole protein binding|structural molecule activity ovary(3)|lung(2)|skin(2)|central_nervous_system(1) 8 AGGAGTGCAGCCCCCCGGGTG 0.502 0.31 83 37 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 236 109 ATM 472 broad.mit.edu 37 11 108155141 108155142 + Frame_Shift_Del DEL AG - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr11:108155141_108155142delAG uc001pkb.1 + 26 4319_4320 c.3934_3935delAG c.(3934-3936)AGAfs p.R1312fs ATM_uc009yxr.1_Frame_Shift_Del_p.R1312fs|ATM_uc001pkd.3_5'Flank|ATM_uc001pke.1_5'Flank NM_000051 NP_000042 Q13315 ATM_HUMAN ataxia telangiectasia mutated isoform 1 1312 cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence cytoplasmic membrane-bounded vesicle|nucleoplasm 1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding p.V1292_Q1331del(1) haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1) 240 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147) GGCACAGCAAAGAGAGACTGCT 0.376 0.37 121 71 MLL 4297 broad.mit.edu 37 11 118344186 118344186 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr11:118344186delC uc001pta.2 + 3 2335 c.2312delC c.(2311-2313)ACCfs p.T771fs MLL_uc001ptb.2_Frame_Shift_Del_p.T771fs|MLL_uc001psz.1_Frame_Shift_Del_p.T804fs|MLL_uc001ptd.1_Intron NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 771 apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) TCACCTCTCACCCCCCCGTCT 0.453 0.44 110 85 NCAPD3 23310 broad.mit.edu 37 11 134078847 134078848 + Splice_Site INS - A A ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr11:134078847_134078848insA uc001qhd.1 - 7 1401 c.795_splice c.e7-1 p.R265_splice NCAPD3_uc010scm.1_Splice_Site|NCAPD3_uc009zda.1_Splice_Site NM_015261 NP_056076 P42695 CNDD3_HUMAN non-SMC condensin II complex, subunit D3 cell division|mitotic chromosome condensation nuclear centromeric heterochromatin|nuclear condensin complex methylated histone residue binding ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1) 5 all_hematologic(175;0.127) all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227) TTAAGAGCTCTAAAAAAAAAAG 0.337 0.24 29 9 DYRK4 8798 broad.mit.edu 37 12 4719362 4719362 + Frame_Shift_Del DEL A - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr12:4719362delA uc001qmx.2 + 11 1217 c.1057delA c.(1057-1059)AAAfs p.K353fs DYRK4_uc009zeh.1_Frame_Shift_Del_p.K468fs|DYRK4_uc001qmy.1_Frame_Shift_Del_p.K353fs|DYRK4_uc001qmz.1_Frame_Shift_Del_p.K67fs|DYRK4_uc001qna.1_5'UTR|DYRK4_uc010ser.1_5'UTR NM_003845 NP_003836 Q9NR20 DYRK4_HUMAN dual-specificity tyrosine-(Y)-phosphorylation 353 Protein kinase. Golgi apparatus ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(2)|skin(1) 3 Colorectal(7;0.103) CAACAGGGGGAAAAAAAGATA 0.398 0.30 31 13 CDKN1B 1027 broad.mit.edu 37 12 12870972 12870973 + Frame_Shift_Del DEL CA - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr12:12870972_12870973delCA uc001rat.2 + 1 671_672 c.199_200delCA c.(199-201)CACfs p.H67fs NM_004064 NP_004055 P46527 CDN1B_HUMAN cyclin-dependent kinase inhibitor 1B 67 autophagic cell death|cell cycle arrest|cellular response to lithium ion|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of transcription, DNA-dependent|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process|S phase of mitotic cell cycle cytosol|endosome|nucleoplasm cyclin-dependent protein kinase inhibitor activity|protein phosphatase binding|transforming growth factor beta receptor, cytoplasmic mediator activity ovary(1)|lung(1) 2 Prostate(47;0.0322)|all_epithelial(100;0.159) BRCA - Breast invasive adenocarcinoma(232;0.0336) TTTTCAGAATCACAAACCCCTA 0.584 0.32 224 104 ITGA7 3679 broad.mit.edu 37 12 56092301 56092301 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr12:56092301delC uc001shh.2 - 7 1290 c.1070delG c.(1069-1071)GGTfs p.G357fs ITGA7_uc001shg.2_Frame_Shift_Del_p.G353fs|ITGA7_uc010sps.1_Frame_Shift_Del_p.G260fs|ITGA7_uc009znw.2_5'Flank|ITGA7_uc009znx.2_Frame_Shift_Del_p.G240fs NM_001144996 NP_001138468 Q13683 ITA7_HUMAN integrin alpha 7 isoform 1 precursor 397 FG-GAP 5.|Extracellular (Potential). cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development|regulation of cell shape integrin complex receptor activity ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1) 5 ATACACAGCACCCCCCAGCTC 0.607 0.28 26 10 GLI1 2735 broad.mit.edu 37 12 57860075 57860075 + Frame_Shift_Del DEL G - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr12:57860075delG uc001snx.2 + 8 893 c.815delG c.(814-816)TGGfs p.W272fs GLI1_uc009zpq.2_Frame_Shift_Del_p.W144fs NM_005269 NP_005260 P08151 GLI1_HUMAN GLI family zinc finger 1 isoform 1 272 C2H2-type 2. epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter cytosol|nucleus transcription regulatory region DNA binding|zinc ion binding skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1) 15 GBM - Glioblastoma multiforme(3;3.99e-32) GTGTGCCACTGGGGGGGCTGC 0.597 0.29 344 140 TBK1 29110 broad.mit.edu 37 12 64891001 64891003 + In_Frame_Del DEL GAA - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr12:64891001_64891003delGAA uc001ssc.1 + 18 1983_1985 c.1921_1923delGAA c.(1921-1923)GAAdel p.E643del NM_013254 NP_037386 Q9UHD2 TBK1_HUMAN TANK-binding kinase 1 643 Potential. I-kappaB kinase/NF-kappaB cascade|innate immune response|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription from RNA polymerase II promoter|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|endosome membrane|plasma membrane ATP binding|phosphoprotein binding|protein serine/threonine kinase activity central_nervous_system(2)|ovary(1)|large_intestine(1)|breast(1) 5 GBM - Glioblastoma multiforme(28;0.0386) TTTTGATATTGAAGAAGAAGTAT 0.305 0.26 102 36 POLE 5426 broad.mit.edu 37 12 133244156 133244156 + Frame_Shift_Del DEL T - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr12:133244156delT uc001uks.1 - 20 2296 c.2252delA c.(2251-2253)AACfs p.N751fs POLE_uc010tbq.1_RNA|POLE_uc009zyu.1_Frame_Shift_Del_p.N724fs NM_006231 NP_006222 Q07864 DPOE1_HUMAN DNA-directed DNA polymerase epsilon 751 base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair nucleoplasm chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding ovary(3)|skin(3)|lung(1)|central_nervous_system(1) 8 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.0416) OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05) 0.000 0.22 743 209 RB1 5925 broad.mit.edu 37 13 48939048 48939048 + Frame_Shift_Del DEL A - - rs66519118 ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr13:48939048delA uc001vcb.2 + 9 1046 c.880delA c.(880-882)AAAfs p.K294fs RB1_uc010act.1_5'UTR NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 294 androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.?(6) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) TGTTTATTTCAAAAATTTTAT 0.214 0.42 23 17 ATP11A 23250 broad.mit.edu 37 13 113487269 113487270 + Frame_Shift_Ins INS - G G ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr13:113487269_113487270insG uc001vsi.3 + 14 1579_1580 c.1491_1492insG c.(1489-1494)GACGGGfs p.D497fs ATP11A_uc001vsj.3_Frame_Shift_Ins_p.D497fs|ATP11A_uc001vsm.1_Frame_Shift_Ins_p.D373fs NM_015205 NP_056020 P98196 AT11A_HUMAN ATPase, class VI, type 11A isoform a 497_498 Cytoplasmic (Potential). ATP biosynthetic process integral to membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity large_intestine(2)|ovary(2) 4 all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163) all_lung(25;0.134)|all_epithelial(44;0.141) AATCGCCGGACGGGGGGAAATC 0.619 0.44 65 51 ATP10A 57194 broad.mit.edu 37 15 25972376 25972377 + Frame_Shift_Ins INS - T T ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr15:25972376_25972377insT uc010ayu.2 - 4 883_884 c.777_778insA c.(775-780)AAAGAAfs p.K259fs NM_024490 NP_077816 O60312 AT10A_HUMAN ATPase, class V, type 10A 259_260 Cytoplasmic (Potential). ATP biosynthetic process|regulation of cell shape integral to membrane|plasma membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity pancreas(2)|ovary(1)|breast(1)|liver(1) 5 all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125) all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244) AGCAGGTTTTCTTTATACAGCC 0.589 0.39 70 45 FBN1 2200 broad.mit.edu 37 15 48796128 48796129 + Frame_Shift_Del DEL TG - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr15:48796128_48796129delTG uc001zwx.1 - 17 2296_2297 c.1968_1969delCA c.(1966-1971)CACATGfs p.H656fs NM_000138 NP_000129 P35555 FBN1_HUMAN fibrillin 1 precursor 656_657 heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development basement membrane|extracellular space|microfibril calcium ion binding|extracellular matrix structural constituent|protein binding ovary(2)|large_intestine(1) 3 all_lung(180;0.00279) all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05) GTGCTCCGCATGTGTGTGTCTA 0.450 0.46 25 21 BLM 641 broad.mit.edu 37 15 91347484 91347484 + Frame_Shift_Del DEL A - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr15:91347484delA uc002bpr.2 + 19 3743 c.3646delA c.(3646-3648)AAAfs p.K1216fs BLM_uc010uqh.1_Frame_Shift_Del_p.K1216fs|BLM_uc010uqi.1_Frame_Shift_Del_p.K841fs|BLM_uc010bnx.2_Intron|BLM_uc002bpt.2_Frame_Shift_Del_p.K191fs NM_000057 NP_000048 P54132 BLM_HUMAN Bloom syndrome protein 1216 HRDC. double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray cytoplasm|lateral element|nuclear matrix|nucleolus|PML body ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding ovary(3)|skin(2)|breast(1) 6 Lung NSC(78;0.0875)|all_lung(78;0.109) Lung(145;0.189) AGAGATGGTTAAAAAATGTCT 0.368 0.41 64 44 CREBBP 1387 broad.mit.edu 37 16 3779604 3779604 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr16:3779604delC uc002cvv.2 - 31 5648 c.5444delG c.(5443-5445)GGCfs p.G1815fs CREBBP_uc002cvw.2_Frame_Shift_Del_p.G1777fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1815 TAZ-type 2.|Interaction with TRERF1. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) CACCGGGCAGCCCCCGTTGGT 0.612 0.53 17 19 CREBBP 1387 broad.mit.edu 37 16 3781324 3781326 + In_Frame_Del DEL AGG - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr16:3781324_3781326delAGG uc002cvv.2 - 30 5243_5245 c.5039_5041delCCT c.(5038-5043)TCCTTG>TTG p.S1680del CREBBP_uc002cvw.2_In_Frame_Del_p.S1642del NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1680 Interaction with TRERF1. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) 0.000 0.45 543 442 MAPK3 5595 broad.mit.edu 37 16 30134505 30134505 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr16:30134505delC uc002dws.2 - 1 126 c.26delG c.(25-27)GGCfs p.G9fs uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MAPK3_uc002dwr.2_5'Flank|MAPK3_uc002dwv.3_Frame_Shift_Del_p.G9fs|MAPK3_uc002dwt.2_Frame_Shift_Del_p.G9fs|MAPK3_uc002dwu.2_RNA|MAPK3_uc010bzp.2_RNA NM_002746 NP_002737 P27361 MK03_HUMAN mitogen-activated protein kinase 3 isoform 1 9 activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle|cellular response to mechanical stimulus|epidermal growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway|interleukin-1-mediated signaling pathway|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of transcription from RNA polymerase II promoter|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription initiation from RNA polymerase I promoter cytosol|nucleoplasm ATP binding|MAP kinase activity|phosphatase binding 0 Arsenic trioxide(DB01169)|Isoproterenol(DB01064)|Simvastatin(DB00641)|Sulindac(DB00605) cccgcccccgcccccctgagc 0.328 0.50 8 8 BCKDK 10295 broad.mit.edu 37 16 31120696 31120698 + In_Frame_Del DEL CCT - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr16:31120696_31120698delCCT uc002eaw.3 + 2 468_470 c.152_154delCCT c.(151-156)ACCTCC>ACC p.S52del BCKDK_uc002eav.3_In_Frame_Del_p.S52del|BCKDK_uc010cah.2_RNA|BCKDK_uc010cai.2_In_Frame_Del_p.S52del NM_005881 NP_005872 O14874 BCKD_HUMAN branched chain ketoacid dehydrogenase kinase 52 branched chain family amino acid catabolic process|peptidyl-histidine phosphorylation mitochondrial alpha-ketoglutarate dehydrogenase complex [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity|ATP binding|protein binding|protein serine/threonine kinase activity|two-component sensor activity stomach(1)|breast(1) 2 AAGACCGTCACCTCCTTTTACAA 0.700 0.44 14 11 ZNF423 23090 broad.mit.edu 37 16 49670510 49670510 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr16:49670510delC uc002efs.2 - 5 2851 c.2553delG c.(2551-2553)AAGfs p.K851fs ZNF423_uc010vgn.1_Frame_Shift_Del_p.K734fs NM_015069 NP_055884 Q2M1K9 ZN423_HUMAN zinc finger protein 423 851 cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus zinc ion binding ovary(1)|lung(1)|kidney(1)|pancreas(1) 4 all_cancers(37;0.0155) GCTCAGCTTTCTTGGTGGCCA 0.607 0.53 50 56 NLRP1 22861 broad.mit.edu 37 17 5461960 5461961 + Frame_Shift_Del DEL TC - - rs61753138 byFrequency ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr17:5461960_5461961delTC uc002gci.2 - 4 2610_2611 c.2055_2056delGA c.(2053-2058)GAGATGfs p.E685fs NLRP1_uc002gcg.1_Frame_Shift_Del_p.E685fs|NLRP1_uc002gck.2_Frame_Shift_Del_p.E685fs|NLRP1_uc002gcj.2_Frame_Shift_Del_p.E685fs|NLRP1_uc002gcl.2_Frame_Shift_Del_p.E685fs|NLRP1_uc002gch.3_Frame_Shift_Del_p.E685fs|NLRP1_uc010clh.2_Frame_Shift_Del_p.E685fs NM_033004 NP_127497 Q9C000 NALP1_HUMAN NLR family, pyrin domain containing 1 isoform 1 685_686 defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide cytoplasm|NALP1 inflammasome complex|nucleus ATP binding|caspase activator activity|enzyme binding|protein domain specific binding lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1) 9 Colorectal(1115;3.48e-05) ATGTTCTCCATCTCTCTCTCCC 0.540 0.46 104 87 MAP2K4 6416 broad.mit.edu 37 17 11958296 11958296 + Frame_Shift_Del DEL A - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr17:11958296delA uc002gnj.2 + 2 275 c.206delA c.(205-207)CAAfs p.Q69fs MAP2K4_uc002gnk.2_Frame_Shift_Del_p.Q80fs NM_003010 NP_003001 P45985 MP2K4_HUMAN mitogen-activated protein kinase kinase 4 69 cellular response to mechanical stimulus|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|JUN kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity large_intestine(14)|breast(12)|lung(8)|ovary(8)|pancreas(8)|stomach(2)|central_nervous_system(1)|biliary_tract(1)|testis(1)|endometrium(1)|urinary_tract(1)|skin(1) 58 all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163) Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681) ACAGGAGTTCAAAACCCACAC 0.348 0.52 42 45 STAT5B 6777 broad.mit.edu 37 17 40362447 40362447 + Frame_Shift_Del DEL T - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr17:40362447delT uc002hzh.2 - 14 1918 c.1749delA c.(1747-1749)AAAfs p.K583fs NM_012448 NP_036580 P51692 STA5B_HUMAN signal transducer and activator of transcription 583 2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|JAK-STAT cascade involved in growth hormone signaling pathway|oxaloacetate metabolic process|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process cytosol|nucleoplasm calcium ion binding|glucocorticoid receptor binding|sequence-specific DNA binding transcription factor activity ovary(3)|lung(2)|skin(1) 6 all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.135) Dasatinib(DB01254) GCTTGAGATGTTTTTTTAACA 0.433 0.51 54 57 RNF43 54894 broad.mit.edu 37 17 56435161 56435161 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr17:56435161delC uc002iwf.2 - 8 3932 c.1976delG c.(1975-1977)GGTfs p.G659fs RNF43_uc010wnv.1_Frame_Shift_Del_p.G618fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.G659fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.G659fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.G532fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 659 Pro-rich.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.13 204 31 ASPSCR1 79058 broad.mit.edu 37 17 79967378 79967379 + Frame_Shift_Ins INS - C C ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr17:79967378_79967379insC uc002kcx.2 + 9 1202_1203 c.1105_1106insC c.(1105-1107)GCCfs p.A369fs ASPSCR1_uc002kcw.1_Frame_Shift_Ins_p.A369fs|ASPSCR1_uc002kcy.2_Frame_Shift_Ins_p.A369fs|ASPSCR1_uc002kcz.2_Frame_Shift_Ins_p.A263fs|ASPSCR1_uc002kda.2_Frame_Shift_Ins_p.A292fs|ASPSCR1_uc002kdb.1_Frame_Shift_Ins_p.A292fs NM_024083 NP_076988 Q9BZE9 ASPC1_HUMAN alveolar soft part sarcoma chromosome region, 369 Interaction with GLUT4 (By similarity). protein binding ASPSCR1/TFE3(161) soft_tissue(118)|kidney(43)|breast(1) 162 all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246) BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191) CCTGGAAGAAGCCCCCTTGGTG 0.634 0.33 32 16 SMAD4 4089 broad.mit.edu 37 18 48584514 48584514 + Frame_Shift_Del DEL G - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr18:48584514delG uc010xdp.1 + 6 1225 c.687delG c.(685-687)CTGfs p.L229fs SMAD4_uc010xdo.1_RNA|SMAD4_uc002lfb.3_Frame_Shift_Del_p.L74fs NM_005359 NP_005350 Q13485 SMAD4_HUMAN mothers against decapentaplegic homolog 4 229 BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway activin responsive factor complex|centrosome|cytosol I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity p.0?(35)|p.?(2) pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1) 369 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155) 0.000 0.15 493 87 BRD4 23476 broad.mit.edu 37 19 15376248 15376248 + Frame_Shift_Del DEL G - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr19:15376248delG uc002nar.2 - 5 988 c.766delC c.(766-768)CAGfs p.Q256fs BRD4_uc002nas.2_Frame_Shift_Del_p.Q256fs|BRD4_uc002nat.3_Frame_Shift_Del_p.Q256fs|BRD4_uc002nau.3_Frame_Shift_Del_p.Q256fs NM_058243 NP_490597 O60885 BRD4_HUMAN bromodomain-containing protein 4 isoform long 256 interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle condensed nuclear chromosome|cytoplasm protein binding ovary(2) 2 OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18) 0.000 0.14 292 47 JAK3 3718 broad.mit.edu 37 19 17955111 17955112 + Frame_Shift_Ins INS - G G rs67296869 ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr19:17955111_17955112insG uc002nhn.3 - 2 215_216 c.115_116insC c.(115-117)CAGfs p.Q39fs JAK3_uc010ebh.2_RNA|JAK3_uc002nho.2_Frame_Shift_Ins_p.Q39fs|JAK3_uc010xpx.1_Frame_Shift_Ins_p.Q39fs|JAK3_uc010xpy.1_Frame_Shift_Ins_p.Q39fs NM_000215 NP_000206 P52333 JAK3_HUMAN Janus kinase 3 39 FERM.|Interaction with cytokine/interferon/growth hormone receptors (By similarity). B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis cytoskeleton|cytosol|endomembrane system|membrane ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1) 56 0.000 0.42 227 166 LMTK3 114783 broad.mit.edu 37 19 49000740 49000740 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr19:49000740delC uc002pjk.2 - 12 3673 c.3673delG c.(3673-3675)GACfs p.D1225fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.27 317 116 LMTK3 114783 broad.mit.edu 37 19 49002059 49002060 + Frame_Shift_Del DEL GG - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr19:49002059_49002060delGG uc002pjk.2 - 12 2353_2354 c.2353_2354delCC c.(2353-2355)CCGfs p.P785fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.34 180 92 TRIB3 57761 broad.mit.edu 37 20 372045 372045 + Frame_Shift_Del DEL T - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr20:372045delT uc002wdm.2 + 3 912 c.406delT c.(406-408)TTTfs p.F136fs TRIB3_uc002wdn.2_Frame_Shift_Del_p.F163fs NM_021158 NP_066981 Q96RU7 TRIB3_HUMAN tribbles 3 136 Protein kinase. apoptosis|cellular lipid metabolic process|insulin receptor signaling pathway|negative regulation of fat cell differentiation|negative regulation of fatty acid biosynthetic process|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein binding|positive regulation of ubiquitin-protein ligase activity|regulation of glucose transport|regulation of MAP kinase activity|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent cytosol|nucleus|plasma membrane ATP binding|protein kinase activity|protein kinase binding|protein kinase inhibitor activity|transcription corepressor activity|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity central_nervous_system(2) 2 all_epithelial(17;0.165)|Lung NSC(37;0.191)|Breast(17;0.231) Colorectal(46;0.101)|COAD - Colon adenocarcinoma(99;0.112) CCTCTACGCCTTTTTCACTCG 0.672 0.15 81 14 TP53RK 112858 broad.mit.edu 37 20 45315440 45315440 + Frame_Shift_Del DEL T - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr20:45315440delT uc002xsk.2 - 2 937 c.714delA c.(712-714)AAAfs p.K238fs SLC13A3_uc002xsg.1_5'Flank|SLC13A3_uc010gho.1_5'Flank|TP53RK_uc002xsj.2_3'UTR NM_033550 NP_291028 Q96S44 PRPK_HUMAN p53-related protein kinase 238 Protein kinase. lipopolysaccharide biosynthetic process membrane|nucleus ATP binding|p53 binding|protein serine/threonine kinase activity|protein tyrosine kinase activity 0 Myeloproliferative disorder(115;0.0122) CTTCATCTAATTTTTTTAGCA 0.448 0.34 121 62 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.15 61 11 COL18A1 80781 broad.mit.edu 37 21 46897723 46897723 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr21:46897723delC uc011afs.1 + 7 2331 c.2310delC c.(2308-2310)GGCfs p.G770fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.G355fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.G535fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 770 Triple-helical region 1 (COL1). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.51 414 435 COL18A1 80781 broad.mit.edu 37 21 46900748 46900749 + Frame_Shift_Ins INS - C C ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr21:46900748_46900749insC uc011afs.1 + 12 2853_2854 c.2832_2833insC c.(2830-2835)GGTCCCfs p.G944fs COL18A1_uc002zhg.2_Frame_Shift_Ins_p.G529fs|COL18A1_uc002zhi.2_Frame_Shift_Ins_p.G709fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 944_945 Triple-helical region 3 (COL3). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.40 1080 707 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 242 531 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 6 49 DDX17 10521 broad.mit.edu 37 22 38897211 38897211 + Frame_Shift_Del DEL T - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr22:38897211delT uc003avy.3 - 2 465 c.362delA c.(361-363)AAGfs p.K121fs DDX17_uc003avx.3_Frame_Shift_Del_p.K121fs|DDX17_uc011anu.1_Frame_Shift_Del_p.K34fs NM_001098504 NP_001091974 Q92841 DDX17_HUMAN DEAD box polypeptide 17 isoform 3 42 RNA processing nucleus ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity skin(3)|upper_aerodigestive_tract(1) 4 Melanoma(58;0.0286) 0.000 0.45 192 158 EP300 2033 broad.mit.edu 37 22 41574679 41574679 + Frame_Shift_Del DEL C - - ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA ISHIKAWAHERAKLIO02ER_ENDOMETRIUM NA g.chr22:41574679delC uc003azl.3 + 31 7359 c.6964delC c.(6964-6966)CCCfs p.P2322fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 2322 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 ACAGTCCCAGCCCCCCCACTC 0.612 0.55 34 41 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 8 77 ODZ1 10178 broad.mit.edu 37 X 123526173 123526183 + Frame_Shift_Del DEL ATGGAGAGTAG - - ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chrX:123526173_123526183delATGGAGAGTAG uc004euj.2 - 27 5450_5460 c.5386_5396delCTACTCTCCAT c.(5386-5397)CTACTCTCCATAfs p.L1796fs ODZ1_uc011muj.1_Frame_Shift_Del_p.L1802fs|ODZ1_uc010nqy.2_Frame_Shift_Del_p.L1803fs NM_014253 NP_055068 Q9UKZ4 TEN1_HUMAN odz, odd Oz/ten-m homolog 1 isoform 3 1796_1799 Extracellular (Potential). immune response|negative regulation of cell proliferation|nervous system development|signal transduction extracellular region heparin binding ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1) 23 ATCAAAATCTATGGAGAGTAGGTTTCTGTTG 0.417 0.45 18 15 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 260 84 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.43 16 12 BAP1 8314 broad.mit.edu 37 3 52436788 52436794 + Splice_Site DEL CACCCAC - - ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr3:52436788_52436794delCACCCAC uc003ddx.2 - 15 2098 c.1983_splice c.e15+1 p.K661_splice BAP1_uc003ddw.2_Splice_Site|BAP1_uc010hmg.2_Splice_Site|BAP1_uc010hmh.2_Splice_Site NM_004656 NP_004647 Q92560 BAP1_HUMAN BRCA1 associated protein-1 monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process cytoplasm|nucleolus|PR-DUB complex chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1) 65 BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277) CTGGAGAAATCACCCACCTTGAACTTC 0.541 0.93 8 112 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.39 34 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 95 146 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.17 72 15 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.32 47 22 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.83 4 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 747 390 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.63 23 40 SMARCA4 6597 broad.mit.edu 37 19 11101916 11101934 + Frame_Shift_Del DEL TCCCTGCGCGAGGCCCGCA - - rs147558972;rs140328531 by1000genomes;by1000genomes ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr19:11101916_11101934delTCCCTGCGCGAGGCCCGCA uc002mqf.3 + 8 1620_1638 c.1336_1354delTCCCTGCGCGAGGCCCGCA c.(1336-1356)TCCCTGCGCGAGGCCCGCATCfs p.S446fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.S446fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.S446fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.S446fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.S446fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.S446fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.S446fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.S446fs|SMARCA4_uc002mqe.2_Frame_Shift_Del_p.S446fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 446_452 chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) 0.000 0.20 986 252 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 126 94 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 136 533 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.99 1 67 MED15 51586 broad.mit.edu 37 22 20920814 20920822 + In_Frame_Del DEL CAGCAGCAG - - rs11281025 ISTMES1_PLEURA NA ISTMES1_PLEURA NA g.chr22:20920814_20920822delCAGCAGCAG uc002zsp.2 + 7 831_839 c.751_759delCAGCAGCAG c.(751-759)CAGCAGCAGdel p.QQQ260del MED15_uc002zso.2_In_Frame_Del_p.QQQ189del|MED15_uc002zsq.2_In_Frame_Del_p.QQQ260del|MED15_uc010gso.2_In_Frame_Del_p.QQQ260del|MED15_uc002zsr.2_In_Frame_Del_p.QQQ234del|MED15_uc011ahs.1_In_Frame_Del_p.QQQ234del|MED15_uc002zss.2_In_Frame_Del_p.QQQ179del|MED15_uc011ahu.1_5'UTR NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 260_262 Poly-Gln. Missing. Missing (in Ref. 3; BAB85034). regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) acaacagcaacagcagcagcagcagcagc 0.325 0.31 20 9 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 72 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.46 274 230 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.58 19 26 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.38 25 15 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.15 99 17 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.31 174 77 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 129 232 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.17 52 11 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 2 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 5 116 PRKG1 5592 broad.mit.edu 37 10 54042008 54042032 + Frame_Shift_Del DEL CAAAGGCCATGACATTTCAGCCGAC - - ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr10:54042008_54042032delCAAAGGCCATGACATTTCAGCCGAC uc001jjm.2 + 14 1790_1814 c.1596_1620delCAAAGGCCATGACATTTCAGCCGAC c.(1594-1620)AACAAAGGCCATGACATTTCAGCCGACfs p.N532fs PRKG1_uc001jjo.2_Frame_Shift_Del_p.N547fs|PRKG1_uc009xow.1_Frame_Shift_Del_p.N250fs|uc001jjq.1_Intron NM_001098512 NP_001091982 Q13976 KGP1_HUMAN protein kinase, cGMP-dependent, type I isoform 532_540 Protein kinase. actin cytoskeleton organization|platelet activation|signal transduction cytosol ATP binding|cGMP binding|cGMP-dependent protein kinase activity lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1) 6 all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173) all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606) TCATCCTGAACAAAGGCCATGACATTTCAGCCGACTACTGGTCAC 0.431 0.22 114 33 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.65 7 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 1108 528 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.30 55 24 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.78 61 215 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 37 278 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ISTMES2_PLEURA NA ISTMES2_PLEURA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 7 141 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 4 62 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 263 101 PHOX2B 8929 broad.mit.edu 37 4 41748014 41748028 + In_Frame_Del DEL GCCGCCGCTGCCGCG - - rs17882335 J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chr4:41748014_41748028delGCCGCCGCTGCCGCG uc003gwf.3 - 3 1101_1115 c.741_755delCGCGGCAGCGGCGGC c.(739-756)GCCGCGGCAGCGGCGGCG>GCG p.247_252AAAAAA>A NM_003924 NP_003915 Q99453 PHX2B_HUMAN paired-like homeobox 2b 247_252 Poly-Ala. positive regulation of transcription from RNA polymerase II promoter nuclear chromatin RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity p.A241fs*64(1) autonomic_ganglia(7)|lung(2)|ovary(2)|central_nervous_system(1) 12 0.000 0.29 64 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.40 99 65 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.49 41 40 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.37 270 160 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 2 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 64 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.56 16 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 379 88 ADAMTS20 80070 broad.mit.edu 37 12 43925919 43925919 + Frame_Shift_Del DEL C - - J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chr12:43925919delC uc010skx.1 - 3 533 c.533delG c.(532-534)GGTfs p.G178fs NM_025003 NP_079279 P59510 ATS20_HUMAN a disintegrin-like and metalloprotease with 178 proteinaceous extracellular matrix zinc ion binding p.G178fs*13(1) central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1) 19 all_cancers(12;2.6e-05)|Lung SC(27;0.184) Lung NSC(34;0.0569)|all_lung(34;0.129) GBM - Glioblastoma multiforme(48;0.0473) CTTGTTGTGACCATCTTCATA 0.353 0.63 52 90 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.70 39 91 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 49 414 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 J82_URINARY_TRACT NA J82_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 92 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 4 40 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.49 98 95 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 11 8 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 34 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.69 43 94 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 8 18 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.30 160 70 ZNF608 57507 broad.mit.edu 37 5 124080264 124080291 + Frame_Shift_Del DEL TGGACTTCCTGCCTCTTGCCAGTGCTGC - - JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:124080264_124080291delTGGACTTCCTGCCTCTTGCCAGTGCTGC uc003ktq.1 - 1 515_542 c.392_419delGCAGCACTGGCAAGAGGCAGGAAGTCCA c.(391-420)AGCAGCACTGGCAAGAGGCAGGAAGTCCAAfs p.S131fs ZNF608_uc003ktr.1_RNA|ZNF608_uc003kts.1_Frame_Shift_Del_p.S131fs|ZNF608_uc003ktt.1_Frame_Shift_Del_p.S131fs NM_020747 NP_065798 Q9ULD9 ZN608_HUMAN zinc finger protein 608 131_140 intracellular zinc ion binding skin(3)|ovary(2)|lung(1) 6 all_cancers(142;0.186)|Prostate(80;0.081) KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221) OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783) AGGGCGCCCTTGGACTTCCTGCCTCTTGCCAGTGCTGCTGATCTCGGG 0.522 0.27 24 9 MAP3K4 4216 broad.mit.edu 37 6 161470722 161470722 + Frame_Shift_Del DEL A - - JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:161470722delA uc003qtn.2 + 3 1560 c.1418delA c.(1417-1419)GAAfs p.E473fs MAP3K4_uc010kkc.1_Frame_Shift_Del_p.E473fs|MAP3K4_uc003qto.2_Frame_Shift_Del_p.E473fs|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_5'UTR NM_005922 NP_005913 Q9Y6R4 M3K4_HUMAN mitogen-activated protein kinase kinase kinase 4 473 activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity perinuclear region of cytoplasm ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding ovary(3)|lung(3)|skin(2)|stomach(1) 9 Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771) OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05) AGGGTACCGGAAATCAGACAG 0.478 0.47 16 14 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 2 12 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.78 4 14 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.58 5 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 347 190 TP53 7157 broad.mit.edu 37 17 7579514 7579514 + Frame_Shift_Del DEL G - - rs144386518 JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:7579514delG uc002gim.2 - 4 367 c.173delC c.(172-174)CCAfs p.P58fs TP53_uc002gig.1_Frame_Shift_Del_p.P58fs|TP53_uc002gih.2_Frame_Shift_Del_p.P58fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.P58fs|TP53_uc010cni.1_Frame_Shift_Del_p.P58fs|TP53_uc002gij.2_Frame_Shift_Del_p.P58fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.P19fs|TP53_uc010cnk.1_Frame_Shift_Del_p.P73fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 58 Interaction with HRMT1L2. P -> T (in a sporadic cancer; somatic mutation).|P -> Q (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.P58L(1)|p.P58fs*65(1)|p.E51fs*59(1)|p.D48fs*55(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.D57_A76del20(1)|p.D57fs*86(1)|p.P58Q(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.96 35 955 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 23 62 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.28 38 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 107 391 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.86 7 44 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JHH1_LIVER NA JHH1_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 18 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JHH1_LIVER NA JHH1_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.42 124 90 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes JHH1_LIVER NA JHH1_LIVER NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.36 9 5 MAGI1 9223 broad.mit.edu 37 3 65425561 65425572 + In_Frame_Del DEL CTGCTGCTGCTG - - JHH1_LIVER NA JHH1_LIVER NA g.chr3:65425561_65425572delCTGCTGCTGCTG uc003dmn.2 - 9 1778_1789 c.1252_1263delCAGCAGCAGCAG c.(1252-1263)CAGCAGCAGCAGdel p.QQQQ418del MAGI1_uc003dmm.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc003dmo.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc003dmp.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc010hny.2_In_Frame_Del_p.QQQQ303del NM_001033057 NP_001028229 Q96QZ7 MAGI1_HUMAN membrane associated guanylate kinase, WW and PDZ 418_421 Poly-Gln. cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly tight junction ATP binding|protein C-terminus binding lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1) 6 Lung NSC(201;0.0016) BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133) AACCTTCTGTctgctgctgctgctgctgctgc 0.368 0.39 35 22 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A JHH1_LIVER NA JHH1_LIVER NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.23 51 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHH1_LIVER NA JHH1_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.35 70 38 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JHH1_LIVER NA JHH1_LIVER NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 18 36 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 JHH1_LIVER NA JHH1_LIVER NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.11 168 21 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 JHH1_LIVER NA JHH1_LIVER NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.54 29 34 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JHH1_LIVER NA JHH1_LIVER NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 1 18 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency JHH1_LIVER NA JHH1_LIVER NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) agcagcagcaacagcagcagca 0.267 0.14 63 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JHH1_LIVER NA JHH1_LIVER NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 302 113 SIK2 23235 broad.mit.edu 37 11 111571666 111571667 + Frame_Shift_Ins INS - G G JHH1_LIVER NA JHH1_LIVER NA g.chr11:111571666_111571667insG uc001plt.2 + 5 653_654 c.535_536insG c.(535-537)AGCfs p.S179fs NM_015191 NP_056006 Q9H0K1 SIK2_HUMAN SNF1-like kinase 2 179 Protein kinase. intracellular protein kinase cascade|regulation of insulin receptor signaling pathway Golgi apparatus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|skin(1) 3 ATGGTGTGGCAGCCCCCCTTAT 0.431 0.21 161 43 PIK3C2G 5288 broad.mit.edu 37 12 18466932 18466933 + Frame_Shift_Del DEL AG - - JHH1_LIVER NA JHH1_LIVER NA g.chr12:18466932_18466933delAG uc001rdt.2 + 6 1187_1188 c.1071_1072delAG c.(1069-1074)AAAGATfs p.K357fs PIK3C2G_uc010sia.1_RNA|PIK3C2G_uc010sib.1_Frame_Shift_Del_p.K357fs|PIK3C2G_uc010sic.1_Frame_Shift_Del_p.K135fs NM_004570 NP_004561 O75747 P3C2G_HUMAN phosphoinositide-3-kinase, class 2 gamma 357_358 cell communication|phosphatidylinositol-mediated signaling membrane|phosphatidylinositol 3-kinase complex 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2) 21 Hepatocellular(102;0.194) TGTTTCAAAAAGATAAATCTGT 0.391 0.34 19 10 ULK3 25989 broad.mit.edu 37 15 75131066 75131070 + Frame_Shift_Del DEL CCGGG - - JHH1_LIVER NA JHH1_LIVER NA g.chr15:75131066_75131070delCCGGG uc010bkf.1 - 10 1122_1126 c.1016_1020delCCCGG c.(1015-1020)TCCCGGfs p.S339fs ULK3_uc010ulp.1_Frame_Shift_Del_p.S249fs|ULK3_uc010ulq.1_Frame_Shift_Del_p.S350fs|ULK3_uc010ulr.1_Frame_Shift_Del_p.S222fs|ULK3_uc002ayv.2_Frame_Shift_Del_p.S339fs|ULK3_uc010uls.1_Frame_Shift_Del_p.S222fs NM_001099436 NP_001092906 Q6PHR2 ULK3_HUMAN unc-51-like kinase 3 339_340 MIT 1. cytoplasm ATP binding|protein serine/threonine kinase activity breast(2) 2 GCTCCTCAGCCCGGGACACGTACTG 0.615 0.31 25 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JHH1_LIVER NA JHH1_LIVER NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.41 79 54 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHH1_LIVER NA JHH1_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 96 299 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHH1_LIVER NA JHH1_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 86 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JHH4_LIVER NA JHH4_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.87 7 47 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JHH4_LIVER NA JHH4_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.39 213 139 TTN 7273 broad.mit.edu 37 2 179422685 179422687 + In_Frame_Del DEL AAT - - JHH4_LIVER NA JHH4_LIVER NA g.chr2:179422685_179422687delAAT uc010zfg.1 - 277 79914_79916 c.79690_79692delATT c.(79690-79692)ATTdel p.I26564del uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.I20259del|TTN_uc010zfi.1_In_Frame_Del_p.I20192del|TTN_uc010zfj.1_In_Frame_Del_p.I20067del NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 27491 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CTAGCACAACAATGTTAATGAAA 0.448 0.46 68 58 MAGI1 9223 broad.mit.edu 37 3 65425561 65425572 + In_Frame_Del DEL CTGCTGCTGCTG - - JHH4_LIVER NA JHH4_LIVER NA g.chr3:65425561_65425572delCTGCTGCTGCTG uc003dmn.2 - 9 1778_1789 c.1252_1263delCAGCAGCAGCAG c.(1252-1263)CAGCAGCAGCAGdel p.QQQQ418del MAGI1_uc003dmm.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc003dmo.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc003dmp.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc010hny.2_In_Frame_Del_p.QQQQ303del NM_001033057 NP_001028229 Q96QZ7 MAGI1_HUMAN membrane associated guanylate kinase, WW and PDZ 418_421 Poly-Gln. cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly tight junction ATP binding|protein C-terminus binding lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1) 6 Lung NSC(201;0.0016) BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133) AACCTTCTGTctgctgctgctgctgctgctgc 0.368 0.46 32 27 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHH4_LIVER NA JHH4_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 115 100 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes JHH4_LIVER NA JHH4_LIVER NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.50 6 6 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes JHH4_LIVER NA JHH4_LIVER NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 4 24 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JHH4_LIVER NA JHH4_LIVER NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 23 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 JHH4_LIVER NA JHH4_LIVER NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.50 11 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JHH4_LIVER NA JHH4_LIVER NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 763 172 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 JHH4_LIVER NA JHH4_LIVER NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.50 18 18 SALL1 6299 broad.mit.edu 37 16 51175655 51175656 + In_Frame_Ins INS - GCT GCT rs113614842 JHH4_LIVER NA JHH4_LIVER NA g.chr16:51175655_51175656insGCT uc010vgs.1 - 2 508_509 c.477_478insAGC c.(475-480)insAGC p.159_160insS SALL1_uc010vgr.1_In_Frame_Ins_p.62_63insS|SALL1_uc010cbv.2_Intron NM_002968 NP_002959 Q9NSC2 SALL1_HUMAN sal-like 1 isoform a 159_160 Poly-Gly. adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development chromocenter|cytoplasm|heterochromatin|nucleus beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding skin(5)|ovary(3) 8 all_cancers(37;0.0322) COAD - Colon adenocarcinoma(2;0.24) ccgccgccgccgctgctgctgc 0.460 0.31 9 4 CDH11 1009 broad.mit.edu 37 16 65026849 65026849 + Frame_Shift_Del DEL T - - JHH4_LIVER NA JHH4_LIVER NA g.chr16:65026849delT uc002eoi.2 - 5 1046 c.612delA c.(610-612)GGAfs p.G204fs CDH11_uc010cdn.2_RNA|CDH11_uc002eoj.2_Frame_Shift_Del_p.G204fs|CDH11_uc010vin.1_Frame_Shift_Del_p.G78fs NM_001797 NP_001788 P55287 CAD11_HUMAN cadherin 11, type 2 preproprotein 204 Cadherin 2.|Extracellular (Potential). adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development integral to membrane|plasma membrane calcium ion binding|protein binding lung(10)|ovary(3)|skin(1) 14 Ovarian(137;0.0973) OV - Ovarian serous cystadenocarcinoma(108;0.205) AATAGGGTTGTCCTTCGAGGA 0.448 0.12 127 17 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C JHH4_LIVER NA JHH4_LIVER NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.84 12 65 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JHH4_LIVER NA JHH4_LIVER NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.53 105 119 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHH4_LIVER NA JHH4_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 47 323 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHH4_LIVER NA JHH4_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 10 97 MED15 51586 broad.mit.edu 37 22 20918817 20918819 + In_Frame_Del DEL CAG - - JHH4_LIVER NA JHH4_LIVER NA g.chr22:20918817_20918819delCAG uc002zsp.2 + 6 612_614 c.532_534delCAG c.(532-534)CAGdel p.Q188del MED15_uc002zsn.1_In_Frame_Del_p.Q107del|MED15_uc002zso.2_In_Frame_Del_p.Q117del|MED15_uc002zsq.2_In_Frame_Del_p.Q188del|MED15_uc010gso.2_In_Frame_Del_p.Q188del|MED15_uc002zsr.2_In_Frame_Del_p.Q162del|MED15_uc011ahs.1_In_Frame_Del_p.Q162del|MED15_uc011aht.1_In_Frame_Del_p.Q162del|MED15_uc002zss.2_In_Frame_Del_p.Q107del|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 188 Poly-Gln. regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) ggcggcgctacagcagcagcagc 0.148 0.30 81 35 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JHH5_LIVER NA JHH5_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 46 DFFB 1677 broad.mit.edu 37 1 3782497 3782499 + In_Frame_Del DEL CCT - - JHH5_LIVER NA JHH5_LIVER NA g.chr1:3782497_3782499delCCT uc001alc.2 + 3 686_688 c.363_365delCCT c.(361-366)GACCTC>GAC p.L123del DFFB_uc001ale.2_RNA|DFFB_uc009vlp.2_RNA|DFFB_uc001alb.2_RNA|DFFB_uc010nzn.1_In_Frame_Del_p.L147del|DFFB_uc009vlq.2_RNA|DFFB_uc009vlr.2_In_Frame_Del_p.L74del|DFFB_uc001ald.2_In_Frame_Del_p.L59del|DFFB_uc009vln.1_3'UTR|DFFB_uc001ala.1_Intron|DFFB_uc009vlo.1_In_Frame_Del_p.L123del NM_004402 NP_004393 O76075 DFFB_HUMAN DNA fragmentation factor, 40 kD, beta 123 apoptotic chromosome condensation|DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction cytosol|nucleoplasm deoxyribonuclease activity|enzyme binding 0 all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227) all_cancers(23;2.05e-30)|all_epithelial(116;6.22e-21)|all_lung(118;2.65e-08)|Lung NSC(185;6.25e-06)|Breast(487;0.000659)|Renal(390;0.00121)|all_neural(13;0.0019)|Hepatocellular(190;0.00705)|Colorectal(325;0.0113)|all_hematologic(16;0.0194)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0548)|Medulloblastoma(700;0.211) Epithelial(90;1.18e-39)|OV - Ovarian serous cystadenocarcinoma(86;7.28e-23)|GBM - Glioblastoma multiforme(42;2.95e-17)|Colorectal(212;1.23e-05)|COAD - Colon adenocarcinoma(227;5.94e-05)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00038)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124) TGCTGGCTGACCTCCTGCACAAC 0.660 0.98 1 50 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JHH5_LIVER NA JHH5_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.51 377 393 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes JHH5_LIVER NA JHH5_LIVER NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.31 9 4 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 JHH5_LIVER NA JHH5_LIVER NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.54 6 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 JHH5_LIVER NA JHH5_LIVER NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.55 15 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHH5_LIVER NA JHH5_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 71 103 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JHH5_LIVER NA JHH5_LIVER NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.39 94 60 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 JHH5_LIVER NA JHH5_LIVER NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.81 49 209 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes JHH5_LIVER NA JHH5_LIVER NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 18 MLL3 58508 broad.mit.edu 37 7 151878347 151878347 + Frame_Shift_Del DEL A - - JHH5_LIVER NA JHH5_LIVER NA g.chr7:151878347delA uc003wla.2 - 36 6817 c.6598delT c.(6598-6600)TCTfs p.S2200fs MLL3_uc003wkz.2_Frame_Shift_Del_p.S1261fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 2200 Pro-rich. intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TATGGATCAGAATGCCTCTGA 0.483 0.23 256 78 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JHH5_LIVER NA JHH5_LIVER NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 23 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency JHH5_LIVER NA JHH5_LIVER NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.30 16 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JHH5_LIVER NA JHH5_LIVER NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 271 130 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency JHH5_LIVER NA JHH5_LIVER NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.16 47 9 AXIN1 8312 broad.mit.edu 37 16 397008 397009 + Frame_Shift_Del DEL CT - - JHH5_LIVER NA JHH5_LIVER NA g.chr16:397008_397009delCT uc002cgp.1 - 2 194_195 c.17_18delAG c.(16-18)CAGfs p.Q6fs AXIN1_uc002cgq.1_Frame_Shift_Del_p.Q6fs NM_003502 NP_003493 O15169 AXIN1_HUMAN axin 1 isoform a 6 activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding breast(1)|liver(1) 2 all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187) AGGGGAAACCCTGCTCTTGGAT 0.545 1.00 0 39 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C JHH5_LIVER NA JHH5_LIVER NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 1 18 TP53 7157 broad.mit.edu 37 17 7578269 7578280 + In_Frame_Del DEL GATGCTGAGGAG - - JHH5_LIVER NA JHH5_LIVER NA g.chr17:7578269_7578280delGATGCTGAGGAG uc002gim.2 - 6 763_774 c.569_580delCTCCTCAGCATC c.(568-582)CCTCCTCAGCATCTT>CTT p.PPQH190del TP53_uc002gig.1_In_Frame_Del_p.PPQH190del|TP53_uc002gih.2_In_Frame_Del_p.PPQH190del|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_In_Frame_Del_p.PPQH58del|TP53_uc010cng.1_In_Frame_Del_p.PPQH58del|TP53_uc002gii.1_In_Frame_Del_p.PPQH58del|TP53_uc010cnh.1_In_Frame_Del_p.PPQH190del|TP53_uc010cni.1_In_Frame_Del_p.PPQH190del|TP53_uc002gij.2_In_Frame_Del_p.PPQH190del|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_In_Frame_Del_p.PPQH97del|TP53_uc002gio.2_In_Frame_Del_p.PPQH58del|TP53_uc010vug.1_In_Frame_Del_p.PPQH151del NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 190_193 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). H -> D (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> Y (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> R (in LFS; germline mutation and in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.H193R(67)|p.Q192*(64)|p.H193L(31)|p.H193Y(26)|p.P190L(21)|p.L194F(16)|p.H193P(12)|p.P190fs*57(8)|p.H193D(7)|p.0?(7)|p.P190del(6)|p.P190S(6)|p.Q192R(5)|p.P191del(5)|p.P190T(4)|p.H193N(4)|p.A189_V197delAPPQHLIRV(4)|p.H193fs*16(3)|p.Q192H(3)|p.P191fs*56(3)|p.P191L(2)|p.P191fs*53(2)|p.L194fs*15(2)|p.P191R(2)|p.P191S(2)|p.G187fs*16(2)|p.H193H(2)|p.Q192Q(2)|p.P190A(2)|p.P190R(2)|p.K164_P219del(1)|p.L194V(1)|p.Q192del(1)|p.L194I(1)|p.A189_Q192>E(1)|p.H193_I195delHLI(1)|p.P97fs*57(1)|p.P191fs*15(1)|p.?(1)|p.P191H(1)|p.P191fs*57(1)|p.P191fs*18(1)|p.P191P(1)|p.A189_P190>X(1)|p.P191T(1)|p.L194fs*52(1)|p.D186_P191delDGLAPP(1)|p.L188_P191del(1)|p.Q192>XXXXXXXXX(1)|p.P58fs*>33(1)|p.P190fs*19(1)|p.Q192K(1)|p.A189fs*53(1)|p.Q192fs*56(1)|p.P190H(1)|p.P191fs*6(1)|p.P190P(1)|p.Q192fs*16(1)|p.H100L(1)|p.I195fs*52(1)|p.Q192fs*30(1)|p.H61L(1)|p.P191_Q192delPQ(1)|p.H193_I195>AP(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) ACTCGGATAAGATGCTGAGGAGGGGCCAGACC 0.552 0.72 41 107 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT JHH5_LIVER NA JHH5_LIVER NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.10 696 78 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 JHH5_LIVER NA JHH5_LIVER NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.19 133 31 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHH5_LIVER NA JHH5_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 49 406 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHH5_LIVER NA JHH5_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 7 92 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JHH6_LIVER NA JHH6_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.63 14 24 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JHH6_LIVER NA JHH6_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.13 489 71 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHH6_LIVER NA JHH6_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.49 56 54 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JHH6_LIVER NA JHH6_LIVER NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.83 16 79 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes JHH6_LIVER NA JHH6_LIVER NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.80 2 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JHH6_LIVER NA JHH6_LIVER NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 25 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JHH6_LIVER NA JHH6_LIVER NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 270 101 TP53 7157 broad.mit.edu 37 17 7574009 7574019 + Frame_Shift_Del DEL TCTCGAAGCGC - - rs17882252;rs150293825;rs121912664 JHH6_LIVER NA JHH6_LIVER NA g.chr17:7574009_7574019delTCTCGAAGCGC uc002gim.2 - 10 1202_1212 c.1008_1018delGCGCTTCGAGA c.(1006-1020)GAGCGCTTCGAGATGfs p.E336fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Intron|TP53_uc010cne.1_Intron|TP53_uc010cnf.1_3'UTR|TP53_uc010cng.1_3'UTR|TP53_uc002gii.1_Frame_Shift_Del_p.E204fs|TP53_uc010cnh.1_3'UTR|TP53_uc010cni.1_3'UTR|TP53_uc002gij.2_Frame_Shift_Del_p.E336fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 336_340 Oligomerization.|Interaction with HIPK1 (By similarity).|Interaction with CARM1.|Nuclear export signal.|Interaction with HIPK2. activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.R337C(12)|p.E339*(10)|p.0?(7)|p.R337L(5)|p.E336*(5)|p.F338fs*9(2)|p.E339fs*8(2)|p.R337H(2)|p.E339Q(1)|p.F338I(1)|p.?(1)|p.M340V(1)|p.F338fs*6(1)|p.F338_E339>L(1)|p.E339fs*13(1)|p.E336fs*12(1)|p.I332fs*5(1)|p.E339K(1)|p.F338F(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.96 2 54 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 JHH6_LIVER NA JHH6_LIVER NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.27 89 33 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHH6_LIVER NA JHH6_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 56 195 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHH6_LIVER NA JHH6_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 7 68 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JHH7_LIVER NA JHH7_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 4 71 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JHH7_LIVER NA JHH7_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.53 191 219 FMN2 56776 broad.mit.edu 37 1 240370858 240370890 + In_Frame_Del DEL CCCGGAGCGGGCATACCTCCTCCGCCGCCTCTA - - rs149443295;rs148496994;rs146568244 byFrequency JHH7_LIVER NA JHH7_LIVER NA g.chr1:240370858_240370890delCCCGGAGCGGGCATACCTCCTCCGCCGCCTCTA uc010pyd.1 + 5 2971_3003 c.2746_2778delCCCGGAGCGGGCATACCTCCTCCGCCGCCTCTA c.(2746-2778)CCCGGAGCGGGCATACCTCCTCCGCCGCCTCTAdel p.PGAGIPPPPPL916del FMN2_uc010pye.1_In_Frame_Del_p.PGAGIPPPPPL920del NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 916_926 Pro-rich.|FH1. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding p.P1064P(1) ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) CCCTCCTCTTCCCGGAGCGGGCATACCTCCTCCGCCGCCTCTACCCGGAGCAG 0.661 0.46 84 71 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes JHH7_LIVER NA JHH7_LIVER NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.39 20 13 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 JHH7_LIVER NA JHH7_LIVER NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.50 27 27 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHH7_LIVER NA JHH7_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 96 159 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 JHH7_LIVER NA JHH7_LIVER NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.24 391 126 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes JHH7_LIVER NA JHH7_LIVER NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.77 3 10 GRM3 2913 broad.mit.edu 37 7 86394504 86394516 + Frame_Shift_Del DEL TTTTCAAAGGGAT - - rs138292549 JHH7_LIVER NA JHH7_LIVER NA g.chr7:86394504_86394516delTTTTCAAAGGGAT uc003uid.2 + 2 1142_1154 c.43_55delTTTTCAAAGGGAT c.(43-57)TTTTCAAAGGGATTTfs p.F15fs GRM3_uc010lef.2_Frame_Shift_Del_p.F13fs|GRM3_uc010leg.2_Intron|GRM3_uc010leh.2_Intron NM_000840 NP_000831 Q14832 GRM3_HUMAN glutamate receptor, metabotropic 3 precursor 15_19 synaptic transmission integral to plasma membrane lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1) 13 Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142) Acamprosate(DB00659)|Nicotine(DB00184) 0.000 0.25 311 102 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes JHH7_LIVER NA JHH7_LIVER NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 19 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency JHH7_LIVER NA JHH7_LIVER NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.28 83 33 MASTL 84930 broad.mit.edu 37 10 27458899 27458913 + In_Frame_Del DEL AATGATGAGTTGGAA - - rs144503451 byFrequency JHH7_LIVER NA JHH7_LIVER NA g.chr10:27458899_27458913delAATGATGAGTTGGAA uc001itm.2 + 8 1650_1664 c.1011_1025delAATGATGAGTTGGAA c.(1009-1026)ACAATGATGAGTTGGAAT>ACT p.MMSWN338del MASTL_uc001itl.2_In_Frame_Del_p.MMSWN338del|MASTL_uc009xkw.1_In_Frame_Del_p.MMSWN338del|MASTL_uc009xkx.1_RNA NM_032844 NP_116233 Q96GX5 GWL_HUMAN microtubule associated serine/threonine 338_342 Protein kinase. cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus centrosome|cleavage furrow|nucleus ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity stomach(1)|ovary(1)|lung(1) 3 TGGGCCCAACAATGATGAGTTGGAATGCAGTTGAA 0.363 0.32 26 12 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 JHH7_LIVER NA JHH7_LIVER NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.25 21 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JHH7_LIVER NA JHH7_LIVER NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 1039 496 ITPR2 3709 broad.mit.edu 37 12 26709269 26709289 + In_Frame_Del DEL TCATTGGGCTGAACTGGTGCT - - JHH7_LIVER NA JHH7_LIVER NA g.chr12:26709269_26709289delTCATTGGGCTGAACTGGTGCT uc001rhg.2 - 36 5258_5278 c.4841_4861delAGCACCAGTTCAGCCCAATGA c.(4840-4863)GAGCACCAGTTCAGCCCAATGATG>GTG p.1614_1621EHQFSPMM>V NM_002223 NP_002214 Q14571 ITPR2_HUMAN inositol 1,4,5-triphosphate receptor, type 2 1614_1621 Cytoplasmic (Potential). activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 14 Colorectal(261;0.0847) TCAGCCTGCATCATTGGGCTGAACTGGTGCTCCAAGGAGGC 0.457 0.24 173 55 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency JHH7_LIVER NA JHH7_LIVER NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.54 98 113 SRP14 6727 broad.mit.edu 37 15 40328591 40328596 + In_Frame_Del DEL GGCAGG - - JHH7_LIVER NA JHH7_LIVER NA g.chr15:40328591_40328596delGGCAGG uc001zkq.2 - 5 421_426 c.349_354delCCTGCC c.(349-354)CCTGCCdel p.PA117del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 117_118 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ttgctgctgcggcaggtgctgctgct 0.233 0.16 142 27 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C JHH7_LIVER NA JHH7_LIVER NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.79 6 23 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT JHH7_LIVER NA JHH7_LIVER NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.15 912 156 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JHH7_LIVER NA JHH7_LIVER NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.56 116 150 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 JHH7_LIVER NA JHH7_LIVER NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 89 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHH7_LIVER NA JHH7_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 120 446 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHH7_LIVER NA JHH7_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.87 20 139 ARID1A 8289 broad.mit.edu 37 1 27023258 27023258 + Frame_Shift_Del DEL G - - JHOC5_OVARY NA JHOC5_OVARY NA g.chr1:27023258delG uc001bmv.1 + 1 737 c.364delG c.(364-366)GGCfs p.G122fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.G122fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.G122fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 122 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.46 372 312 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JHOC5_OVARY NA JHOC5_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.58 145 203 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHOC5_OVARY NA JHOC5_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 41 23 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes JHOC5_OVARY NA JHOC5_OVARY NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.67 121 251 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JHOC5_OVARY NA JHOC5_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.55 32 39 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes JHOC5_OVARY NA JHOC5_OVARY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.67 5 10 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency JHOC5_OVARY NA JHOC5_OVARY NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.31 251 113 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JHOC5_OVARY NA JHOC5_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 111 19 TOX3 27324 broad.mit.edu 37 16 52473764 52473765 + In_Frame_Ins INS - ACT ACT JHOC5_OVARY NA JHOC5_OVARY NA g.chr16:52473764_52473765insACT uc002egw.2 - 7 1274_1275 c.1103_1104insAGT c.(1102-1104)GTG>GTAGTG p.368_368V>VV TOX3_uc010vgt.1_In_Frame_Ins_p.363_363V>VV|TOX3_uc010vgu.1_In_Frame_Ins_p.368_368V>VV NM_001080430 NP_001073899 O15405 TOX3_HUMAN TOX high mobility group box family member 3 368 apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity 0 GTGATGCTGACACTGTTCCATG 0.520 0.19 79 18 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT JHOC5_OVARY NA JHOC5_OVARY NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.14 694 110 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JHOC5_OVARY NA JHOC5_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.62 14 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHOC5_OVARY NA JHOC5_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 34 264 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHOC5_OVARY NA JHOC5_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 77 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JHOM1_OVARY NA JHOM1_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 35 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JHOM1_OVARY NA JHOM1_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 217 48 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A JHOM1_OVARY NA JHOM1_OVARY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.24 90 28 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHOM1_OVARY NA JHOM1_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.22 49 14 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JHOM1_OVARY NA JHOM1_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 16 29 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 JHOM1_OVARY NA JHOM1_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.76 40 125 ARID1B 57492 broad.mit.edu 37 6 157099403 157099417 + In_Frame_Del DEL CAGCAGCAGCAGCAG - - JHOM1_OVARY NA JHOM1_OVARY NA g.chr6:157099403_157099417delCAGCAGCAGCAGCAG uc003qqn.2 + 1 318_332 c.166_180delCAGCAGCAGCAGCAG c.(166-180)CAGCAGCAGCAGCAGdel p.QQQQQ66del ARID1B_uc003qqo.2_In_Frame_Del_p.QQQQQ66del|ARID1B_uc003qqp.2_In_Frame_Del_p.QQQQQ66del NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 124_128 Gln-rich. chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) AAACCAGTTCcagcagcagcagcagcagcagcaac 0.153 0.33 16 8 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 JHOM1_OVARY NA JHOM1_OVARY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.53 38 43 PTEN 5728 broad.mit.edu 37 10 89720801 89720802 + Frame_Shift_Ins INS - T T JHOM1_OVARY NA JHOM1_OVARY NA g.chr10:89720801_89720802insT uc001kfb.2 + 9 1983_1984 c.952_953insT c.(952-954)CTTfs p.L318fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 318 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.L318fs*2(24)|p.V317fs*3(16)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.V317fs*6(2)|p.G165_*404del(1)|p.L318fs*3(1)|p.G165_K342del(1)|p.L316fs*1(1)|p.W274_F341del(1)|p.V317_K322del(1)|p.L318F(1)|p.T318fs*2(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) ATATCTAGTACTTACTTTAACA 0.332 0.96 7 171 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 JHOM1_OVARY NA JHOM1_OVARY NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.61 9 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JHOM1_OVARY NA JHOM1_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 189 34 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 JHOM1_OVARY NA JHOM1_OVARY NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.36 14 8 SGK269 79834 broad.mit.edu 37 15 77472863 77472864 + Frame_Shift_Ins INS - G G JHOM1_OVARY NA JHOM1_OVARY NA g.chr15:77472863_77472864insG uc002bcm.2 - 3 1713_1714 c.1405_1406insC c.(1405-1407)CAGfs p.Q469fs SGK269_uc002bcn.2_Frame_Shift_Ins_p.Q469fs NM_024776 NP_079052 Q9H792 PEAK1_HUMAN NKF3 kinase family member 469 cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading actin cytoskeleton|cytoplasm|focal adhesion ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding 0 STAD - Stomach adenocarcinoma(199;0.124) GCACAATGGCTGTTCCAGGTTC 0.505 0.16 58 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C JHOM1_OVARY NA JHOM1_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.76 4 13 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT JHOM1_OVARY NA JHOM1_OVARY NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.18 543 118 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHOM1_OVARY NA JHOM1_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 28 220 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHOM1_OVARY NA JHOM1_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 52 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JHOM2B_OVARY NA JHOM2B_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 46 CDKL4 344387 broad.mit.edu 37 2 39414801 39414802 + Frame_Shift_Ins INS - AA AA JHOM2B_OVARY NA JHOM2B_OVARY NA g.chr2:39414801_39414802insAA uc002rrm.2 - 6 701_702 c.701_702insTT c.(700-702)TTCfs p.F234fs CDKL4_uc010fal.1_Frame_Shift_Ins_p.F234fs NM_001009565 NP_001009565 Q5MAI5 CDKL4_HUMAN cyclin-dependent kinase-like 4 234 Protein kinase. cytoplasm ATP binding|cyclin-dependent protein kinase activity ovary(1) 1 all_hematologic(82;0.248) TGATGCCATGGAAAAACCCGTT 0.327 0.37 43 25 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 JHOM2B_OVARY NA JHOM2B_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.14 42 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHOM2B_OVARY NA JHOM2B_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.25 55 18 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JHOM2B_OVARY NA JHOM2B_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 20 39 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - JHOM2B_OVARY NA JHOM2B_OVARY NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.75 3 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JHOM2B_OVARY NA JHOM2B_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JHOM2B_OVARY NA JHOM2B_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 128 15 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C JHOM2B_OVARY NA JHOM2B_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 34 216 SMAD4 4089 broad.mit.edu 37 18 48573605 48573605 + Frame_Shift_Del DEL A - - JHOM2B_OVARY NA JHOM2B_OVARY NA g.chr18:48573605delA uc010xdp.1 + 2 727 c.189delA c.(187-189)ACAfs p.T63fs SMAD4_uc010xdo.1_RNA NM_005359 NP_005350 Q13485 SMAD4_HUMAN mothers against decapentaplegic homolog 4 63 MH1. BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway activin responsive factor complex|centrosome|cytosol I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity p.0?(35)|p.?(5) pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1) 369 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155) CTATAACTACAAATGGAGCTC 0.363 0.98 1 44 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JHOM2B_OVARY NA JHOM2B_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.56 16 20 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 JHOM2B_OVARY NA JHOM2B_OVARY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 86 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHOM2B_OVARY NA JHOM2B_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 91 424 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHOM2B_OVARY NA JHOM2B_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 3 21 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JHOS2_OVARY NA JHOS2_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 16 363 NRD1 4898 broad.mit.edu 37 1 52306064 52306066 + In_Frame_Del DEL TCT - - rs145326984;rs72496486 JHOS2_OVARY NA JHOS2_OVARY NA g.chr1:52306064_52306066delTCT uc001ctc.3 - 2 784_786 c.462_464delAGA c.(460-465)GAAGAT>GAT p.E154del NRD1_uc009vzb.2_Translation_Start_Site|NRD1_uc001ctd.3_In_Frame_Del_p.E154del|NRD1_uc001cte.2_In_Frame_Del_p.E22del|NRD1_uc001ctf.2_In_Frame_Del_p.E154del|NRD1_uc010ong.1_RNA|NRD1_uc009vzc.1_In_Frame_Del_p.E22del|NRD1_uc001ctg.1_5'Flank NM_002525 NP_002516 O43847 NRDC_HUMAN nardilysin isoform a Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity cell surface|cytosol epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding 0 ttcatcatcatcttcttcttctt 0.158 0.70 3 7 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JHOS2_OVARY NA JHOS2_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 1976 513 VRK2 7444 broad.mit.edu 37 2 58386688 58386689 + Frame_Shift_Ins INS - ACTT ACTT rs149451697 byFrequency JHOS2_OVARY NA JHOS2_OVARY NA g.chr2:58386688_58386689insACTT uc002rzo.2 + 16 2132_2133 c.1387_1388insACTT c.(1387-1389)GACfs p.D463fs VRK2_uc010fcb.2_3'UTR|VRK2_uc002rzs.2_3'UTR|VRK2_uc002rzr.2_3'UTR|VRK2_uc010fcc.2_Frame_Shift_Ins_p.D345fs|VRK2_uc002rzv.2_Frame_Shift_Ins_p.D463fs|VRK2_uc010fcd.2_Frame_Shift_Ins_p.D440fs|VRK2_uc002rzp.2_Frame_Shift_Ins_p.D463fs|VRK2_uc010ypg.1_Frame_Shift_Ins_p.D463fs|VRK2_uc002rzq.2_3'UTR|VRK2_uc002rzu.2_3'UTR|VRK2_uc002rzt.2_Frame_Shift_Ins_p.D345fs|FANCL_uc002rzw.3_3'UTR|FANCL_uc002rzx.3_3'UTR|FANCL_uc010fce.2_3'UTR NM_001130482 NP_001123954 Q86Y07 VRK2_HUMAN vaccinia related kinase 2 isoform 2 463 integral to membrane ATP binding|protein binding|protein serine/threonine kinase activity ovary(1) 1 GGGGATCACAGACTTAGAAAGT 0.391 0.39 867 556 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes JHOS2_OVARY NA JHOS2_OVARY NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.59 7 10 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 JHOS2_OVARY NA JHOS2_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.20 81 20 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A JHOS2_OVARY NA JHOS2_OVARY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 395 75 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 JHOS2_OVARY NA JHOS2_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.49 28 27 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHOS2_OVARY NA JHOS2_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.35 183 99 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 JHOS2_OVARY NA JHOS2_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.43 183 139 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes JHOS2_OVARY NA JHOS2_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 2 16 PAXIP1 22976 broad.mit.edu 37 7 154760608 154760609 + In_Frame_Ins INS - CTG CTG rs151102688 by1000genomes JHOS2_OVARY NA JHOS2_OVARY NA g.chr7:154760608_154760609insCTG uc003wlp.2 - 7 1345_1346 c.1302_1303insCAG c.(1300-1305)insCAG p.434_435insQ PAXIP1_uc003wlq.1_In_Frame_Ins_p.400_401insQ|PAXIP1_uc011kvs.1_In_Frame_Ins_p.398_399insQ|PAXIP1_uc003wlr.1_In_Frame_Ins_p.343_344insQ NM_007349 NP_031375 Q6ZW49 PAXI1_HUMAN PAX interacting protein 1 434_435 Gln-rich. DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent histone methyltransferase complex|nuclear matrix lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_neural(206;0.119) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.0296) UCEC - Uterine corpus endometrioid carcinoma (81;0.178) TGCTGAGAGATctgctgctgct 0.287 0.41 47 33 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 JHOS2_OVARY NA JHOS2_OVARY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.37 254 149 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency JHOS2_OVARY NA JHOS2_OVARY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.66 159 309 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 JHOS2_OVARY NA JHOS2_OVARY NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.58 8 11 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes JHOS2_OVARY NA JHOS2_OVARY NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.14 43 7 ADAMTS20 80070 broad.mit.edu 37 12 43833806 43833807 + Frame_Shift_Del DEL TC - - JHOS2_OVARY NA JHOS2_OVARY NA g.chr12:43833806_43833807delTC uc010skx.1 - 17 2356_2357 c.2356_2357delGA c.(2356-2358)GAAfs p.E786fs ADAMTS20_uc001rno.1_5'Flank|ADAMTS20_uc001rnp.1_5'Flank NM_025003 NP_079279 P59510 ATS20_HUMAN a disintegrin-like and metalloprotease with 786 Spacer. proteinaceous extracellular matrix zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1) 19 all_cancers(12;2.6e-05)|Lung SC(27;0.184) Lung NSC(34;0.0569)|all_lung(34;0.129) GBM - Glioblastoma multiforme(48;0.0473) CACATTGATTTCTTTTTTTGAC 0.302 0.54 676 805 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C JHOS2_OVARY NA JHOS2_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 25 409 TP53 7157 broad.mit.edu 37 17 7577495 7577514 + Splice_Site DEL TGACCTGGAGTCTTCCAGTG - - rs121912652;rs28934577 JHOS2_OVARY NA JHOS2_OVARY NA g.chr17:7577495_7577514delTGACCTGGAGTCTTCCAGTG uc002gim.2 - 7 976 c.782_splice c.e7+1 p.S261_splice TP53_uc002gig.1_Splice_Site_p.R261_splice|TP53_uc002gih.2_Splice_Site_p.S261_splice|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Splice_Site_p.S129_splice|TP53_uc010cng.1_Splice_Site_p.S129_splice|TP53_uc002gii.1_Splice_Site_p.S129_splice|TP53_uc010cnh.1_Splice_Site_p.S261_splice|TP53_uc010cni.1_Splice_Site_p.S261_splice|TP53_uc002gij.2_Splice_Site_p.S261_splice|TP53_uc010cnj.1_3'UTR|TP53_uc002gin.2_3'UTR|TP53_uc002gio.2_3'UTR NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.E258K(37)|p.?(27)|p.D259Y(17)|p.D259V(13)|p.E258*(12)|p.E258Q(8)|p.E258D(8)|p.L257P(8)|p.E258G(7)|p.L257Q(7)|p.0?(7)|p.D259N(6)|p.E258V(5)|p.E258A(5)|p.T256T(5)|p.D259fs*86(4)|p.S260S(4)|p.D259G(4)|p.L257V(4)|p.S261fs*84(3)|p.S260C(3)|p.S260fs*85(3)|p.S260F(3)|p.S260_S261insX(3)|p.D259E(3)|p.D259fs*5(3)|p.S261T(3)|p.S260A(2)|p.S260fs*3(2)|p.D259D(2)|p.S260Y(2)|p.L257fs*6(2)|p.L257L(2)|p.S261G(2)|p.T256I(2)|p.T256K(2)|p.T256del(1)|p.E258>XX(1)|p.E258fs*71(1)|p.S260del(1)|p.E258L(1)|p.S261fs*151(1)|p.T256fs*8(1)|p.S260P(1)|p.D259S(1)|p.S260fs*4(1)|p.E258fs*2(1)|p.L257R(1)|p.D259H(1)|p.I254_T256del(1)|p.T256fs*90(1)|p.E258del(1)|p.E258_S260delEDS(1)|p.I254fs*7(1)|p.T256fs*87(1)|p.L257fs*7(1)|p.E258fs*87(1)|p.S261C(1)|p.E258fs*85(1)|p.S261N(1)|p.S260_S261delSS(1)|p.L257fs*88(1)|p.S261R(1)|p.R249_T256delRPILTIIT(1)|p.S261fs*4(1)|p.S261fs*3(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) AAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGATGATGGT 0.568 0.48 51 47 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT JHOS2_OVARY NA JHOS2_OVARY NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.19 699 166 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JHOS2_OVARY NA JHOS2_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.65 22 40 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHOS2_OVARY NA JHOS2_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 86 396 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHOS2_OVARY NA JHOS2_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 29 204 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JHOS4_OVARY NA JHOS4_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 3 37 SLC6A8 6535 broad.mit.edu 37 X 152957541 152957541 + Frame_Shift_Del DEL G - - JHOS4_OVARY NA JHOS4_OVARY NA g.chrX:152957541delG uc004fib.3 + 4 1034 c.756delG c.(754-756)AAGfs p.K252fs SLC6A8_uc004fic.3_Frame_Shift_Del_p.K252fs|SLC6A8_uc011myx.1_Frame_Shift_Del_p.K137fs|SLC6A8_uc010nuj.2_5'Flank|SLC6A8_uc010nui.1_Frame_Shift_Del_p.K137fs NM_005629 NP_005620 P48029 SC6A8_HUMAN solute carrier family 6 member 8 isoform 1 252 Cytoplasmic (Potential). creatine metabolic process|muscle contraction integral to plasma membrane creatine:sodium symporter activity|neurotransmitter:sodium symporter activity pancreas(1) 1 all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) Creatine(DB00148) GTGTCTGGAAGGGGGTCAAAT 0.632 0.25 154 50 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JHOS4_OVARY NA JHOS4_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.46 188 163 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHOS4_OVARY NA JHOS4_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 62 35 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 JHOS4_OVARY NA JHOS4_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.68 60 130 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - JHOS4_OVARY NA JHOS4_OVARY NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.88 2 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JHOS4_OVARY NA JHOS4_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 39 TET1 80312 broad.mit.edu 37 10 70404997 70404999 + In_Frame_Del DEL TTC - - JHOS4_OVARY NA JHOS4_OVARY NA g.chr10:70404997_70404999delTTC uc001jok.3 + 4 3016_3018 c.2511_2513delTTC c.(2509-2514)CATTCT>CAT p.S839del NM_030625 NP_085128 Q8NFU7 TET1_HUMAN CXXC finger 6 839 DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding ovary(5)|lung(2)|prostate(1)|breast(1) 9 CCATTCCACATTCTTCACACTCC 0.394 0.23 115 34 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JHOS4_OVARY NA JHOS4_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 534 138 TMEM123 114908 broad.mit.edu 37 11 102272737 102272739 + In_Frame_Del DEL TTG - - JHOS4_OVARY NA JHOS4_OVARY NA g.chr11:102272737_102272739delTTG uc001pha.2 - 3 777_779 c.356_358delCAA c.(355-360)ACAAGT>AGT p.T119del TMEM123_uc009yxc.2_In_Frame_Del_p.T100del NM_052932 NP_443164 Q8N131 PORIM_HUMAN transmembrane protein 123 precursor 119 Thr-rich.|Extracellular (Potential). oncosis external side of plasma membrane|integral to membrane receptor activity breast(2) 2 all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227) Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033) Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151) BRCA - Breast invasive adenocarcinoma(274;0.0149) TGTGAAACACTTGTTGTTTTGGG 0.409 0.24 563 179 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C JHOS4_OVARY NA JHOS4_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 36 460 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JHOS4_OVARY NA JHOS4_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.65 22 40 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHOS4_OVARY NA JHOS4_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 209 802 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHOS4_OVARY NA JHOS4_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 82 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.65 11 20 F8 2157 broad.mit.edu 37 X 154158764 154158765 + Frame_Shift_Ins INS - T T JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chrX:154158764_154158765insT uc004fmt.2 - 14 3471_3472 c.3300_3301insA c.(3298-3303)AAAGAGfs p.K1100fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1100_1101 B. "acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation" extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) ATGGGGCCCTCTTTTTTCTGTT 0.381 0.14 235 38 F8 2157 broad.mit.edu 37 X 154159120 154159120 + Frame_Shift_Del DEL T - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chrX:154159120delT uc004fmt.2 - 14 3116 c.2945delA c.(2944-2946)AATfs p.N982fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 982 B. "acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation" extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) TGACGATACATTTTTTCCCCA 0.373 0.23 85 26 EPHA2 1969 broad.mit.edu 37 1 16462199 16462199 + Frame_Shift_Del DEL G - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr1:16462199delG uc001aya.1 - 6 1516 c.1379delC c.(1378-1380)CCGfs p.P460fs EPHA2_uc010oca.1_Frame_Shift_Del_p.P460fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 460 Extracellular (Potential).|Fibronectin type-III 2. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) 0.000 0.23 365 109 ARID1A 8289 broad.mit.edu 37 1 27023486 27023486 + Frame_Shift_Del DEL C - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr1:27023486delC uc001bmv.1 + 1 965 c.592delC c.(592-594)CCCfs p.P198fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.P198fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.P198fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 198 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.25 833 278 ARID1A 8289 broad.mit.edu 37 1 27106709 27106710 + Frame_Shift_Ins INS - C C JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr1:27106709_27106710insC uc001bmv.1 + 20 6693_6694 c.6320_6321insC c.(6319-6321)GGCfs p.G2107fs ARID1A_uc001bmu.1_Frame_Shift_Ins_p.G1890fs|ARID1A_uc001bmx.1_Frame_Shift_Ins_p.G953fs|ARID1A_uc009vsm.1_Frame_Shift_Ins_p.G435fs|ARID1A_uc009vsn.1_Frame_Shift_Ins_p.G349fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 2107 "androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent" nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) TCCACCCTGGGCCCCAATGCCG 0.589 0.54 37 44 JAK1 3716 broad.mit.edu 37 1 65330610 65330611 + Frame_Shift_Ins INS - T T JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr1:65330610_65330611insT uc001dbu.1 - 8 1284_1285 c.1035_1036insA c.(1033-1038)AAACTGfs p.K345fs JAK1_uc009wam.1_Frame_Shift_Ins_p.K333fs NM_002227 NP_002218 P23458 JAK1_HUMAN janus kinase 1 345_346 FERM. interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway cytoskeleton|cytosol|endomembrane system|membrane|nucleus ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1) 61 BRCA - Breast invasive adenocarcinoma(111;0.0485) TTATTTTCCAGTTTTTTCCGCT 0.342 0.45 31 25 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.48 119 111 CDC42BPA 8476 broad.mit.edu 37 1 227182042 227182042 + Frame_Shift_Del DEL G - - rs67581567 JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr1:227182042delG uc001hqr.2 - 36 6030 c.5087delC c.(5086-5088)CCAfs p.P1696fs CDC42BPA_uc001hqq.2_Frame_Shift_Del_p.P995fs|CDC42BPA_uc001hqs.2_Frame_Shift_Del_p.P1615fs|CDC42BPA_uc009xes.2_Frame_Shift_Del_p.P1668fs|CDC42BPA_uc010pvs.1_Frame_Shift_Del_p.P1676fs|CDC42BPA_uc001hqp.2_Frame_Shift_Del_p.P914fs NM_003607 NP_003598 Q5VT25 MRCKA_HUMAN CDC42-binding protein kinase alpha isoform B 1709 actin cytoskeleton reorganization|intracellular signal transduction cell leading edge|cell-cell junction|cytoplasm ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1) 11 all_cancers(173;0.156)|Prostate(94;0.0792) AGCTGGGCTTGGGGGGCTGCT 0.552 0.57 22 29 MSH2 4436 broad.mit.edu 37 2 47643465 47643466 + Frame_Shift_Del DEL TC - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr2:47643465_47643466delTC uc002rvy.1 + 6 1041_1042 c.973_974delTC c.(973-975)TCTfs p.S325fs MSH2_uc010yoh.1_Frame_Shift_Del_p.S259fs|MSH2_uc002rvz.2_Frame_Shift_Del_p.S325fs|MSH2_uc010fbg.2_Frame_Shift_Del_p.S135fs NM_000251 NP_000242 P43246 MSH2_HUMAN mutS homolog 2 325 "B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes" MutSalpha complex|MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1) 55 all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) TGGCTCTCAGTCTCTGGCTGCC 0.401 0.32 45 21 ITGAV 3685 broad.mit.edu 37 2 187541638 187541639 + Frame_Shift_Ins INS - G G rs145060863 by1000genomes JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr2:187541638_187541639insG uc002upq.2 + 29 3303_3304 c.3027_3028insG c.(3025-3030)GCTGTTfs p.A1009fs ITGAV_uc010frs.2_Frame_Shift_Ins_p.A973fs|ITGAV_uc010zfv.1_Frame_Shift_Ins_p.A963fs NM_002210 NP_002201 P06756 ITAV_HUMAN integrin alpha-V isoform 1 precursor 1009_1010 Helical; (Potential). angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance integrin complex receptor activity|transforming growth factor beta binding ovary(2)|kidney(1)|skin(1) 4 OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189) STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108) TGCTACTGGCTGTTTTGGTATT 0.337 0.1 61 7 IRS1 3667 broad.mit.edu 37 2 227661395 227661396 + In_Frame_Ins INS - TGC TGC rs138975702 by1000genomes JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr2:227661395_227661396insTGC uc002voh.3 - 1 2111_2112 c.2059_2060insGCA c.(2059-2061)AAC>AGCAAC p.686_687insS NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 686_687 fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) AGGGACGGCGTtgctgctgctg 0.55 0.14 42 7 SMARCC1 6599 broad.mit.edu 37 3 47779602 47779603 + Splice_Site INS - A A JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr3:47779602_47779603insA uc003crq.2 - 4 520 c.402_splice c.e4-1 p.W134_splice SMARCC1_uc011bbd.1_Splice_Site_p.W25_splice NM_003074 NP_003065 Q92922 SMRC1_HUMAN SWI/SNF-related matrix-associated chromatin remodeling|nervous system development|transcription, DNA-dependent nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex DNA binding|protein N-terminus binding|transcription coactivator activity skin(2)|lung(1) 3 BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01) 0.000 0.40 56 37 EPHA3 2042 broad.mit.edu 37 3 89521627 89521628 + Frame_Shift_Ins INS - T T JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr3:89521627_89521628insT uc003dqy.2 + 16 2929_2930 c.2704_2705insT c.(2704-2706)CTTfs p.L902fs EPHA3_uc010hon.1_RNA NM_005233 NP_005224 P29320 EPHA3_HUMAN ephrin receptor EphA3 isoform a precursor 902 Cytoplasmic (Potential). extracellular region|integral to plasma membrane ATP binding lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1) 33 all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612) Lung NSC(201;0.0782) LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942) ATCAAACCTTCTTCTGGACCAA 0.47 0.16 36 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs "SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA;" GAAGAAGTCGATTAGGAGTTCA 0.545 0.32 15 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.81 13 54 NIPBL 25836 broad.mit.edu 37 5 37064899 37064899 + Frame_Shift_Del DEL A - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr5:37064899delA uc003jkl.3 + 47 8819 c.8320delA c.(8320-8322)AAAfs p.K2774fs NIPBL_uc003jkk.3_3'UTR|NIPBL_uc003jkn.2_3'UTR NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 2774 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) CATTATTTACAAAAAAATTGC 0.463 0.39 43 28 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 1 0 31 STK32A 202374 broad.mit.edu 37 5 146754743 146754745 + In_Frame_Del DEL AAG - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr5:146754743_146754745delAAG uc010jgn.1 + 11 1274_1276 c.994_996delAAG c.(994-996)AAGdel p.K333del STK32A_uc003lom.2_In_Frame_Del_p.K333del|STK32A_uc011dbw.1_In_Frame_Del_p.K333del NM_001112724 NP_001106195 Q8WU08 ST32A_HUMAN serine/threonine kinase 32A isoform 1 333 ATP binding|metal ion binding|protein serine/threonine kinase activity lung(2)|skin(1) 3 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GCGTCTGGCAAAGAAGGAGAAGG 0.448 0.5 12 12 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.32 15 7 HMMR 3161 broad.mit.edu 37 5 162905742 162905742 + Frame_Shift_Del DEL C - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr5:162905742delC uc003lzf.2 + 12 1500 c.1318delC c.(1318-1320)CTTfs p.L440fs HMMR_uc003lzh.2_Frame_Shift_Del_p.L441fs|HMMR_uc003lzg.2_Frame_Shift_Del_p.L425fs|HMMR_uc011dem.1_Frame_Shift_Del_p.L354fs NM_012484 NP_036616 O75330 HMMR_HUMAN hyaluronan-mediated motility receptor isoform b 440 cell surface|cytoplasm hyaluronic acid binding 0 Renal(175;0.000281) Medulloblastoma(196;0.00853)|all_neural(177;0.0408) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848) GGCCACCCTGCTTTTGCAGGA 0.393 0.56 38 48 NSD1 64324 broad.mit.edu 37 5 176673750 176673750 + Frame_Shift_Del DEL A - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr5:176673750delA uc003mfr.3 + 10 4588 c.4450delA c.(4450-4452)AAAfs p.K1484fs NSD1_uc003mft.3_Frame_Shift_Del_p.K1215fs|NSD1_uc003mfs.1_Frame_Shift_Del_p.K1381fs|NSD1_uc011dfx.1_Frame_Shift_Del_p.K1132fs NM_022455 NP_071900 Q96L73 NSD1_HUMAN nuclear receptor binding SET domain protein 1 1484 "negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent" chromosome|nucleus androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding ovary(2)|kidney(1) 3 all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002) all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198) Kidney(146;0.235) GATGCAGTGTAAAAAAGTGAA 0.418 0.45 23 19 ATXN1 6310 broad.mit.edu 37 6 16327910 16327921 + In_Frame_Del DEL TGCTGATGCTGC - - rs11969612;rs28555263;rs142039862 by1000genomes;by1000genomes JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr6:16327910_16327921delTGCTGATGCTGC uc003nbt.2 - 8 1592_1603 c.621_632delGCAGCATCAGCA c.(619-633)CAGCAGCATCAGCAT>CAT p.QQHQ207del ATXN1_uc010jpi.2_In_Frame_Del_p.QQHQ207del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 207_210 Poly-Gln. "cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing" cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgatgctgatgctgctgctgctgct 0.392 0.64 4 7 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 "cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent" cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.22 28 8 RUNX2 860 broad.mit.edu 37 6 45514856 45514856 + Frame_Shift_Del DEL G - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr6:45514856delG uc011dvx.1 + 9 1590 c.1380delG c.(1378-1380)CCGfs p.P460fs RUNX2_uc011dvy.1_Frame_Shift_Del_p.P438fs|RUNX2_uc003oxt.2_Frame_Shift_Del_p.P446fs NM_001024630 NP_001019801 Q13950 RUNX2_HUMAN runt-related transcription factor 2 isoform a 460 Pro/Ser/Thr-rich.|Interaction with MYST4. "negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent" nucleus ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity ovary(2)|skin(1) 3 CCATGGTGCCGGGGGGAGACC 0.542 0.28 87 34 FLNC 2318 broad.mit.edu 37 7 128481273 128481273 + Frame_Shift_Del DEL G - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr7:128481273delG uc003vnz.3 + 12 2072 c.1863delG c.(1861-1863)AAGfs p.K621fs FLNC_uc003voa.3_Frame_Shift_Del_p.K621fs NM_001458 NP_001449 Q14315 FLNC_HUMAN gamma filamin isoform a 621 Filamin 4. cell junction assembly cytoskeleton|cytosol|plasma membrane|sarcomere actin binding breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1) 12 GTGACGACAAGGGGGATGGCT 0.617 0.54 11 13 KIAA1549 57670 broad.mit.edu 37 7 138602139 138602140 + Frame_Shift_Ins INS - A A JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr7:138602139_138602140insA uc011kql.1 - 2 2281_2282 c.2232_2233insT c.(2230-2235)TTTACCfs p.F744fs KIAA1549_uc003vuk.3_Frame_Shift_Ins_p.F694fs|KIAA1549_uc011kqj.1_Frame_Shift_Ins_p.F744fs NM_020910 NP_065961 Q9HCM3 K1549_HUMAN hypothetical protein LOC57670 isoform 1 744_745 Ser-rich. integral to membrane KIAA1549/BRAF(229) central_nervous_system(229)|pancreas(1) 230 AAAGCTGAGGTAAAATGAGCTT 0.485 0.75 3 9 WEE2 494551 broad.mit.edu 37 7 141420783 141420783 + Frame_Shift_Del DEL C - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr7:141420783delC uc003vwn.2 + 5 1213 c.807delC c.(805-807)CACfs p.H269fs FLJ40852_uc011krh.1_Intron|FLJ40852_uc010lnm.2_Intron|FLJ40852_uc010lnn.2_Intron|FLJ40852_uc003vwm.3_Intron|FLJ40852_uc010lno.2_Intron NM_001105558 NP_001099028 P0C1S8 WEE2_HUMAN WEE1 homolog 2 269 Protein kinase. egg activation|female meiosis|female pronucleus assembly|meiotic metaphase II|meiotic prophase I|mitosis|negative regulation of oocyte development|regulation of meiosis I centrosome|nucleus ATP binding|magnesium ion binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Melanoma(164;0.0171) TTGGGCATCACCCCCATGTGG 0.398 0.42 56 40 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 1 10 MLL3 58508 broad.mit.edu 37 7 151874147 151874148 + Frame_Shift_Ins INS - T T JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr7:151874147_151874148insT uc003wla.2 - 38 8609_8610 c.8390_8391insA c.(8389-8391)AAGfs p.K2797fs MLL3_uc003wkz.2_Frame_Shift_Ins_p.K1858fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.K306fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 2797 K -> R (in Ref. 1; AAK00583). "intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent" DNA binding|protein binding|zinc ion binding p.K2797fs*26(18) large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTTCTTGTTCCTTTTTTTTTGG 0.347 0.34 152 78 WRN 7486 broad.mit.edu 37 8 30922431 30922431 + Frame_Shift_Del DEL T - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr8:30922431delT uc003xio.3 + 5 1144 c.356delT c.(355-357)GTTfs p.V119fs NM_000553 NP_000544 Q14191 WRN_HUMAN Werner syndrome protein 119 Interaction with WRNIP1 (By similarity).|3'-5' exonuclease. base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance centrosome|nucleolus|nucleoplasm 3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1) 7 Breast(100;0.195) KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192) AATGTTACAGTTTTTCCCCAG 0.318 0.5 18 18 WHSC1L1 54904 broad.mit.edu 37 8 38187222 38187222 + Frame_Shift_Del DEL T - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr8:38187222delT uc003xli.2 - 6 1773 c.1255delA c.(1255-1257)ACCfs p.T419fs WHSC1L1_uc011lbm.1_Frame_Shift_Del_p.T419fs|WHSC1L1_uc010lwe.2_Frame_Shift_Del_p.T419fs|WHSC1L1_uc003xlj.2_Frame_Shift_Del_p.T419fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 419 "cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent" chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) GGTCGTCGGGTTTTTTTAACT 0.428 0.42 138 99 MCM4 4173 broad.mit.edu 37 8 48883979 48883979 + Frame_Shift_Del DEL A - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr8:48883979delA uc003xqk.1 + 13 1974 c.1879delA c.(1879-1881)AAAfs p.K627fs MCM4_uc003xql.1_Frame_Shift_Del_p.K627fs|MCM4_uc011ldi.1_Frame_Shift_Del_p.K614fs NM_182746 NP_877423 P33991 MCM4_HUMAN minichromosome maintenance complex component 4 627 MCM. cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle MCM complex ATP binding|DNA binding|helicase activity|protein binding ovary(2)|skin(2) 4 all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354) GTGGAATCCTAAAAAAACAAC 0.408 0.54 28 33 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1 0 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.35 17 9 MYST4 23522 broad.mit.edu 37 10 76788689 76788690 + In_Frame_Ins INS - GAA GAA JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr10:76788689_76788690insGAA uc001jwn.1 + 18 4600_4601 c.4107_4108insGAA c.(4105-4110)insGAA p.1373_1374insE MYST4_uc001jwo.1_In_Frame_Ins_p.1081_1082insE|MYST4_uc001jwp.1_In_Frame_Ins_p.1190_1191insE NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1373_1374 "histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent" MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding p.E1373G(1) central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) aagaggaaggggaagaagaaga 0.233 0.46 44 38 MARK2 2011 broad.mit.edu 37 11 63671582 63671582 + Frame_Shift_Del DEL C - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr11:63671582delC uc001nxw.2 + 15 2218 c.1639delC c.(1639-1641)CCCfs p.P547fs MARK2_uc001nxx.2_Intron|MARK2_uc001nxy.2_Intron|MARK2_uc001nxv.3_Intron|MARK2_uc001nxz.3_Frame_Shift_Del_p.P513fs|MARK2_uc009yoy.2_Frame_Shift_Del_p.P467fs NM_001039469 NP_001034558 Q7KZI7 MARK2_HUMAN MAP/microtubule affinity-regulating kinase 2 547 cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress plasma membrane ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity stomach(1)|ovary(1)|lung(1) 3 0.000 0.36 368 206 ANO1 55107 broad.mit.edu 37 11 69950138 69950138 + Frame_Shift_Del DEL A - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr11:69950138delA uc001opj.2 + 4 879 c.574delA c.(574-576)AAAfs p.K192fs ANO1_uc001opk.1_Frame_Shift_Del_p.K164fs|ANO1_uc001opl.1_RNA NM_018043 NP_060513 Q5XXA6 ANO1_HUMAN anoctamin 1, calcium activated chloride channel 192 Cytoplasmic (Potential). multicellular organismal development chloride channel complex|cytoplasm|plasma membrane intracellular calcium activated chloride channel activity ovary(1)|pancreas(1) 2 0.000 0.51 748 793 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 142 63 PGR 5241 broad.mit.edu 37 11 100996755 100996757 + In_Frame_Del DEL AAG - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr11:100996755_100996757delAAG uc001pgh.2 - 2 2513_2515 c.1770_1772delCTT c.(1768-1773)TTCTTT>TTT p.590_591FF>F PGR_uc001pgi.2_In_Frame_Del_p.590_591FF>F|PGR_uc009yww.1_RNA|PGR_uc001pgj.2_RNA|PGR_uc009ywx.1_RNA NM_000926 NP_000917 P06401 PRGR_HUMAN progesterone receptor 590_591 Nuclear receptor. cell-cell signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor cytoplasm|nucleoplasm enzyme binding|receptor binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding lung(1)|liver(1)|central_nervous_system(1)|pancreas(1) 4 Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014) LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164) Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Mifepristone(DB00834)|Norethindrone(DB00717)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396) TGCCCTCTTAAAGAAGACCTTAC 0.399 0.56 16 20 NCAPD3 23310 broad.mit.edu 37 11 134072785 134072786 + Frame_Shift_Ins INS - T T JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr11:134072785_134072786insT uc001qhd.1 - 13 2146_2147 c.1540_1541insA c.(1540-1542)AGGfs p.R514fs NCAPD3_uc010scm.1_RNA|NCAPD3_uc009zda.1_RNA NM_015261 NP_056076 P42695 CNDD3_HUMAN "non-SMC condensin II complex, subunit D3" 514 cell division|mitotic chromosome condensation nuclear centromeric heterochromatin|nuclear condensin complex methylated histone residue binding ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1) 5 all_hematologic(175;0.127) all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227) AGATGTCTGCCTTTGGTAGGAA 0.366 0.45 46 38 ADAMTS20 80070 broad.mit.edu 37 12 43833808 43833808 + Frame_Shift_Del DEL T - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr12:43833808delT uc010skx.1 - 17 2355 c.2355delA c.(2353-2355)AAAfs p.K785fs ADAMTS20_uc001rno.1_5'Flank|ADAMTS20_uc001rnp.1_5'Flank NM_025003 NP_079279 P59510 ATS20_HUMAN a disintegrin-like and metalloprotease with 785 Spacer. proteinaceous extracellular matrix zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1) 19 all_cancers(12;2.6e-05)|Lung SC(27;0.184) Lung NSC(34;0.0569)|all_lung(34;0.129) GBM - Glioblastoma multiforme(48;0.0473) CATTGATTTCTTTTTTTGACG 0.303 0.26 111 40 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). "histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent" NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.69 17 38 FLT1 2321 broad.mit.edu 37 13 29041262 29041262 + Frame_Shift_Del DEL C - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr13:29041262delC uc001usb.3 - 3 451 c.166delG c.(166-168)GAAfs p.E56fs FLT1_uc010aar.1_Frame_Shift_Del_p.E56fs|FLT1_uc001usc.3_Frame_Shift_Del_p.E56fs|FLT1_uc010tdp.1_Frame_Shift_Del_p.E56fs|FLT1_uc001usd.2_Frame_Shift_Del_p.E56fs NM_002019 NP_002010 P17948 VGFR1_HUMAN fms-related tyrosine kinase 1 isoform 1 56 Ig-like C2-type 1.|Extracellular (Potential). cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway extracellular space|Golgi apparatus|integral to plasma membrane|nucleus ATP binding|growth factor binding|vascular endothelial growth factor receptor activity lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1) 24 Acute lymphoblastic leukemia(6;0.04) Lung SC(185;0.0262)|Breast(139;0.188) Colorectal(13;0.000674) all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207) Sunitinib(DB01268) TGGGCTGCTTCCCCCCTGCAA 0.453 0.25 67 22 FOXO1 2308 broad.mit.edu 37 13 41133898 41133898 + Frame_Shift_Del DEL C - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr13:41133898delC uc001uxl.3 - 2 2115 c.1730delG c.(1729-1731)GGCfs p.G577fs FOXO1_uc010acc.1_Frame_Shift_Del_p.G392fs NM_002015 NP_002006 Q12778 FOXO1_HUMAN forkhead box O1 577 anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding PAX3/FOXO1(749)|PAX7/FOXO1(197) soft_tissue(946)|lung(1)|central_nervous_system(1) 948 Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194) all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815) GGAGGAGTAGCCCCCCAGGGC 0.582 0.1 105 12 ABCC4 10257 broad.mit.edu 37 13 95735432 95735432 + Frame_Shift_Del DEL A - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr13:95735432delA uc001vmd.3 - 21 2767 c.2648delT c.(2647-2649)TTGfs p.L883fs ABCC4_uc010afk.2_Frame_Shift_Del_p.L836fs NM_005845 NP_005836 O15439 MRP4_HUMAN "ATP-binding cassette, sub-family C, member 4" 883 ABC transmembrane type-1 2. platelet activation|platelet degranulation integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane "15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity" central_nervous_system(3)|skin(1) 4 all_neural(89;0.0878)|Medulloblastoma(90;0.163) Cefazolin(DB01327) TGACGTTTCCAAAAAATATCG 0.443 0.54 21 25 NOVA1 4857 broad.mit.edu 37 14 27066542 27066542 + Frame_Shift_Del DEL G - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr14:27066542delG uc001wpy.2 - 1 419 c.101delC c.(100-102)CCTfs p.P34fs NOVA1_uc001wpz.2_Frame_Shift_Del_p.P34fs|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_Frame_Shift_Del_p.P34fs NM_002515 NP_002506 P51513 NOVA1_HUMAN neuro-oncological ventral antigen 1 isoform 1 34 Bipartite nuclear localization signal (Potential). locomotory behavior|RNA splicing|synaptic transmission nucleus RNA binding skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1) 5 GBM - Glioblastoma multiforme(265;0.0135) 0.000 0.39 1032 658 TCL6 27004 broad.mit.edu 37 14 96136870 96136872 + In_Frame_Del DEL CTC - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr14:96136870_96136872delCTC uc001yeq.2 + 6 1819_1821 c.350_352delCTC c.(349-354)TCTCCT>TCT p.P118del TCL6_uc001yep.1_RNA|TCL6_uc001yes.2_3'UTR|TCL6_uc001yet.1_In_Frame_Del_p.P60del|TCL6_uc001yeu.2_3'UTR|TCL6_uc001yev.2_Intron|TCL1B_uc001yew.2_RNA|TCL1B_uc001yex.2_RNA|TCL1B_uc010avj.2_RNA|TCL6_uc010avk.1_RNA NM_020554 NP_065579 SubName: Full=T-cell leukemia/lymphoma 6 ORF163; 0 all_cancers(154;0.103) Epithelial(152;0.0655)|all cancers(159;0.149)|BRCA - Breast invasive adenocarcinoma(234;0.206)|COAD - Colon adenocarcinoma(157;0.207) TTCCTTCCTTCTCCTTCTTGGAG 0.507 0.28 21 8 MAPKBP1 23005 broad.mit.edu 37 15 42106826 42106826 + Frame_Shift_Del DEL G - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr15:42106826delG uc001zok.3 + 11 1363 c.1077delG c.(1075-1077)CTGfs p.L359fs MAPKBP1_uc001zoj.3_Frame_Shift_Del_p.L353fs|MAPKBP1_uc010bcj.2_Intron|MAPKBP1_uc010bci.2_Frame_Shift_Del_p.L353fs|MAPKBP1_uc010udb.1_Frame_Shift_Del_p.L241fs|MAPKBP1_uc010bck.2_5'UTR|MAPKBP1_uc010bcl.2_Intron NM_001128608 NP_001122080 O60336 MABP1_HUMAN mitogen-activated protein kinase binding protein 359 WD 5. central_nervous_system(5)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1) 10 all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262) OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225) ATCAGTGGCTGTCTTGTGTGT 0.507 0.15 130 23 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 41 564 ALPK2 115701 broad.mit.edu 37 18 56246440 56246440 + Frame_Shift_Del DEL T - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr18:56246440delT uc002lhj.3 - 4 1782 c.1568delA c.(1567-1569)AAGfs p.K523fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 523 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 CCATAAGTCCTTTCCCCCCAC 0.522 0.42 75 54 INSR 3643 broad.mit.edu 37 19 7168023 7168023 + Frame_Shift_Del DEL G - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr19:7168023delG uc002mgd.1 - 7 1675 c.1566delC c.(1564-1566)CCCfs p.P522fs INSR_uc002mge.1_Frame_Shift_Del_p.P522fs|INSR_uc002mgf.2_Frame_Shift_Del_p.P522fs NM_000208 NP_000199 P06213 INSR_HUMAN insulin receptor isoform Long precursor 522 "activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus" caveola|endosome membrane|insulin receptor complex|microsome ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1) 12 "Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)" CTCGGAAGTCGGGGGGCCAGT 0.478 0.42 7 5 MAP2K7 5609 broad.mit.edu 37 19 7974714 7974714 + Frame_Shift_Del DEL C - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr19:7974714delC uc002mit.2 + 2 264 c.199delC c.(199-201)CCCfs p.P67fs MAP2K7_uc002miv.2_Frame_Shift_Del_p.P67fs|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_Frame_Shift_Del_p.P67fs|MAP2K7_uc010dvv.2_5'UTR NM_145185 NP_660186 O14733 MP2K7_HUMAN mitogen-activated protein kinase kinase 7 67 activation of JUN kinase activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleus ATP binding|JUN kinase kinase activity|magnesium ion binding|protein binding|protein kinase binding|protein phosphatase binding|protein serine/threonine kinase activity|protein tyrosine kinase activity large_intestine(7)|central_nervous_system(2)|ovary(1)|lung(1) 11 Etoposide(DB00773) 0.000 0.21 819 222 CPAMD8 27151 broad.mit.edu 37 19 17039884 17039884 + Frame_Shift_Del DEL C - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr19:17039884delC uc002nfb.2 - 24 3185 c.3153delG c.(3151-3153)GGGfs p.G1051fs NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN "C3 and PZP-like, alpha-2-macroglobulin domain" 1004 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 TGTTCTGATGCCCCCCCAGGA 0.587 0.1 64 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.65 26 49 LMTK3 114783 broad.mit.edu 37 19 49002159 49002159 + Frame_Shift_Del DEL C - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr19:49002159delC uc002pjk.2 - 12 2254 c.2254delG c.(2254-2256)GCCfs p.A752fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.38 271 167 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 32 179 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.89 2 17 MN1 4330 broad.mit.edu 37 22 28194535 28194535 + Frame_Shift_Del DEL G - - JHUEM1_ENDOMETRIUM NA JHUEM1_ENDOMETRIUM NA g.chr22:28194535delG uc003adj.2 - 1 2952 c.1997delC c.(1996-1998)CCTfs p.P666fs NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 666 binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 0.000 0.52 308 340 HDAC6 10013 broad.mit.edu 37 X 48681901 48681901 + Frame_Shift_Del DEL C - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chrX:48681901delC uc011mmi.1 + 25 3187 c.3092delC c.(3091-3093)ACCfs p.T1031fs HDAC6_uc004dks.1_Frame_Shift_Del_p.T1031fs|HDAC6_uc010nig.1_Frame_Shift_Del_p.T879fs|HDAC6_uc004dkt.1_Frame_Shift_Del_p.T1031fs|HDAC6_uc011mmk.1_Frame_Shift_Del_p.T1012fs|HDAC6_uc004dkv.1_Frame_Shift_Del_p.T679fs|HDAC6_uc004dkw.1_Frame_Shift_Del_p.T679fs|HDAC6_uc004dkx.1_Frame_Shift_Del_p.T394fs NM_006044 NP_006035 Q9UBN7 HDAC6_HUMAN histone deacetylase 6 1031 "aggresome assembly|cellular response to hydrogen peroxide|Hsp90 deacetylation|lysosome localization|macroautophagy|misfolded or incompletely synthesized protein catabolic process|negative regulation of proteolysis|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|polyubiquitinated misfolded protein transport|positive regulation of apoptosis|positive regulation of cellular chaperone-mediated protein complex assembly|positive regulation of epithelial cell migration|positive regulation of receptor biosynthetic process|positive regulation of signal transduction|regulation of androgen receptor signaling pathway|regulation of receptor activity|response to growth factor stimulus|response to toxin|transcription, DNA-dependent|tubulin deacetylation" aggresome|caveola|cell leading edge|cytosol|histone deacetylase complex|microtubule associated complex|perinuclear region of cytoplasm actin binding|alpha-tubulin binding|beta-catenin binding|dynein complex binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|Hsp90 protein binding|microtubule binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|polyubiquitin binding|tau protein binding|tubulin deacetylase activity|zinc ion binding ovary(3)|upper_aerodigestive_tract(1) 4 Vorinostat(DB02546) GACCACCAGACCCCCCCAACC 0.592 0.45 83 67 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.96 3 67 F8 2157 broad.mit.edu 37 X 154156923 154156924 + Frame_Shift_Ins INS - G G JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chrX:154156923_154156924insG uc004fmt.2 - 14 5312_5313 c.5141_5142insC c.(5140-5142)ACAfs p.T1714fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1714 F5/8 type A 3.|Plastocyanin-like 5. T -> S (in HEMA; moderate). "acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation" extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AATAGTGTCGTGTTTTCTTTTG 0.396 0.13 110 16 ARID1A 8289 broad.mit.edu 37 1 27097708 27097709 + Frame_Shift_Del DEL TC - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr1:27097708_27097709delTC uc001bmv.1 + 12 3670_3671 c.3297_3298delTC c.(3295-3300)TGTCTCfs p.C1099fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.C1099fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.C1099fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.C716fs|ARID1A_uc001bmx.1_5'UTR|ARID1A_uc009vsm.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1099_1100 ARID. "androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent" nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) ATATCCAGTGTCTCTATGCCTT 0.5 0.41 96 68 CELF3 11189 broad.mit.edu 37 1 151678722 151678723 + In_Frame_Ins INS - TGC TGC JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr1:151678722_151678723insTGC uc001eys.1 - 10 1897_1898 c.1103_1104insGCA c.(1102-1104)CAA>CAGCAA p.368_368Q>QQ CELF3_uc010pdh.1_In_Frame_Ins_p.154_154Q>QQ|CELF3_uc001eyr.2_In_Frame_Ins_p.367_367Q>QQ|CELF3_uc009wmy.2_In_Frame_Ins_p.318_318Q>QQ|CELF3_uc009wmx.1_In_Frame_Ins_p.367_367Q>QQ NM_007185 NP_009116 Q5SZQ8 CELF3_HUMAN trinucleotide repeat containing 4 368 Gln-rich. "nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome" cytoplasm|nucleus mRNA binding|nucleotide binding ovary(1)|central_nervous_system(1) 2 gctgctgctgttgctgctgctg 0.505 0.22 62 17 GLI2 2736 broad.mit.edu 37 2 121708914 121708914 + Frame_Shift_Del DEL C - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr2:121708914delC uc010flp.2 + 3 380 c.350delC c.(349-351)GCCfs p.A117fs GLI2_uc010yyu.1_Frame_Shift_Del_p.A117fs|GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Intron|GLI2_uc002tmu.3_Intron|GLI2_uc002tmv.1_Intron|GLI2_uc010flo.1_5'UTR|GLI2_uc002tmw.1_Frame_Shift_Del_p.A117fs NM_005270 NP_005261 P10070 GLI2_HUMAN GLI-Kruppel family member GLI2 117 axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis nucleus|nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1) 13 Renal(3;0.0496) Prostate(154;0.0623) CCCTTCAACGCCCCCCACCCG 0.672 0.32 50 23 FGF2 2247 broad.mit.edu 37 4 123748258 123748259 + Frame_Shift_Ins INS - G G JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr4:123748258_123748259insG uc003iev.1 + 1 396_397 c.328_329insG c.(328-330)CGGfs p.R110fs NM_002006 NP_001997 P09038 FGF2_HUMAN fibroblast growth factor 2 110 activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing extracellular space fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity ovary(1)|lung(1)|central_nervous_system(1) 3 Pentosan Polysulfate(DB00686) 0.000 0.10 225 24 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 136 164 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 81 49 PIK3R1 5295 broad.mit.edu 37 5 67593371 67593373 + In_Frame_Del DEL ACA - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr5:67593371_67593373delACA uc003jva.2 + 16 2677_2679 c.2117_2119delACA c.(2116-2121)CACAAC>CAC p.N707del PIK3R1_uc003jvb.2_In_Frame_Del_p.N707del|PIK3R1_uc003jvc.2_In_Frame_Del_p.N407del|PIK3R1_uc003jvd.2_In_Frame_Del_p.N437del|PIK3R1_uc003jve.2_In_Frame_Del_p.N386del NM_181523 NP_852664 P27986 P85A_HUMAN "phosphoinositide-3-kinase, regulatory subunit 1" 707 SH2 2. epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway "1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex" 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.?(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) CTTGTGCAGCACAACGACTCCCT 0.493 0.43 96 73 CDC25C 995 broad.mit.edu 37 5 137627690 137627690 + Frame_Shift_Del DEL T - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr5:137627690delT uc003lcp.1 - 8 1002 c.731delA c.(730-732)AAGfs p.K244fs CDC25C_uc003lcq.1_Frame_Shift_Del_p.K171fs|CDC25C_uc003lcr.1_Frame_Shift_Del_p.K244fs|CDC25C_uc011cyp.1_Frame_Shift_Del_p.K261fs|CDC25C_uc003lcs.1_Frame_Shift_Del_p.K322fs NM_001790 NP_001781 P30307 MPIP3_HUMAN cell division cycle 25C isoform a 244 cell cycle checkpoint|cell division|cell proliferation|DNA replication|G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis|traversing start control point of mitotic cell cycle cytosol|nucleoplasm protein tyrosine phosphatase activity|WW domain binding lung(3) 3 KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592) AGAAAAATACTTTTTTTTAAC 0.388 0.49 78 74 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.6 4 6 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 "cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent" cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.24 29 9 EPHB6 2051 broad.mit.edu 37 7 142562052 142562054 + In_Frame_Del DEL CCT - - rs67146761;rs8177142 JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr7:142562052_142562054delCCT uc011kst.1 + 7 1281_1283 c.494_496delCCT c.(493-498)CCCTCC>CCC p.S176del EPHB6_uc011ksu.1_In_Frame_Del_p.S176del|EPHB6_uc003wbs.2_5'UTR|EPHB6_uc003wbt.2_Intron|EPHB6_uc003wbu.2_5'UTR|EPHB6_uc003wbv.2_5'Flank NM_004445 NP_004436 O15197 EPHB6_HUMAN ephrin receptor EphB6 precursor 176 Extracellular (Potential).|Poly-Ser. extracellular region|integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1) 19 Melanoma(164;0.059) GAGAGCTTTCcctcctcctcctc 0.522 0.29 202 83 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1 0 28 CSMD3 114788 broad.mit.edu 37 8 113259328 113259328 + Frame_Shift_Del DEL T - - rs142018478 JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr8:113259328delT uc003ynu.2 - 64 10302 c.10143delA c.(10141-10143)AAAfs p.K3381fs CSMD3_uc003yns.2_Frame_Shift_Del_p.K2583fs|CSMD3_uc003ynt.2_Frame_Shift_Del_p.K3341fs|CSMD3_uc011lhx.1_Frame_Shift_Del_p.K3212fs NM_198123 NP_937756 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 isoform 1 3381 Extracellular (Potential).|Sushi 27. integral to membrane|plasma membrane ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1) 63 GAAGGTGTCCTTTTTTGCAAT 0.408 0.44 40 32 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 71 SMARCA2 6595 broad.mit.edu 37 9 2181665 2181665 + Frame_Shift_Del DEL A - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr9:2181665delA uc003zhc.2 + 30 4447 c.4348delA c.(4348-4350)AAAfs p.K1450fs SMARCA2_uc003zhd.2_Frame_Shift_Del_p.K1432fs|SMARCA2_uc010mha.2_Frame_Shift_Del_p.K1365fs|SMARCA2_uc011llw.1_Frame_Shift_Del_p.K136fs|SMARCA2_uc003zhf.2_Frame_Shift_Del_p.K114fs|SMARCA2_uc011llx.1_Frame_Shift_Del_p.K96fs|SMARCA2_uc003zhe.2_Frame_Shift_Del_p.K138fs|SMARCA2_uc003zhg.2_Frame_Shift_Del_p.K96fs|SMARCA2_uc010mhb.2_Frame_Shift_Del_p.K120fs NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 1450 Bromo. chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.31 146 67 DAPK1 1612 broad.mit.edu 37 9 90321802 90321802 + Frame_Shift_Del DEL G - - rs56169226 JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr9:90321802delG uc004apc.2 + 26 3954 c.3816delG c.(3814-3816)ATGfs p.M1272fs DAPK1_uc004apd.2_Frame_Shift_Del_p.M1272fs|DAPK1_uc011ltg.1_Frame_Shift_Del_p.M1206fs|DAPK1_uc011lth.1_Frame_Shift_Del_p.M1009fs|DAPK1_uc004apg.2_Frame_Shift_Del_p.M249fs NM_004938 NP_004929 P53355 DAPK1_HUMAN death-associated protein kinase 1 1272 apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade actin cytoskeleton|cytoplasm ATP binding|calmodulin binding|protein serine/threonine kinase activity ovary(1)|breast(1) 2 CCAACACCATGGGGGGGTACA 0.582 0.38 58 36 ROR2 4920 broad.mit.edu 37 9 94519745 94519745 + Frame_Shift_Del DEL G - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr9:94519745delG uc004arj.1 - 3 471 c.272delC c.(271-273)CCTfs p.P91fs ROR2_uc004ari.1_5'UTR|ROR2_uc004ark.2_Frame_Shift_Del_p.P91fs NM_004560 NP_004551 Q01974 ROR2_HUMAN receptor tyrosine kinase-like orphan receptor 2 91 Extracellular (Potential).|Ig-like C2-type. negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1) 20 CCGCACGTTAGGGGGTGGGTT 0.537 0.41 335 237 TRAF2 7186 broad.mit.edu 37 9 139793212 139793212 + Frame_Shift_Del DEL C - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr9:139793212delC uc010nbu.2 + 3 193 c.20delC c.(19-21)ACCfs p.T7fs TRAF2_uc010nbv.1_Frame_Shift_Del_p.T7fs|TRAF2_uc004cjv.2_Frame_Shift_Del_p.T7fs|TRAF2_uc011mek.1_Frame_Shift_Del_p.T7fs|TRAF2_uc010nbw.2_Frame_Shift_Del_p.T7fs NM_021138 NP_066961 Q12933 TRAF2_HUMAN TNF receptor-associated factor 2 7 activation of caspase activity|activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cellular protein complex assembly|induction of apoptosis by extracellular signals|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|protein autoubiquitination|protein homotrimerization|protein K63-linked ubiquitination|tumor necrosis factor-mediated signaling pathway CD40 receptor complex|cytosol|internal side of plasma membrane CD40 receptor binding|enzyme binding|protein binding|signal transducer activity|sphingolipid binding|ubiquitin-protein ligase activity|zinc ion binding ovary(1)|lung(1)|breast(1)|skin(1) 4 all_cancers(76;0.11) Myeloproliferative disorder(178;0.0511) STAD - Stomach adenocarcinoma(284;0.229) OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06) GCTAGCGTGACCCCCCCTGGC 0.592 0.37 80 47 CACNB2 783 broad.mit.edu 37 10 18828598 18828599 + Frame_Shift_Ins INS - A A JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr10:18828598_18828599insA uc001ipr.2 + 14 1988_1989 c.1928_1929insA c.(1927-1929)TCAfs p.S643fs CACNB2_uc009xjz.1_Frame_Shift_Ins_p.S393fs|CACNB2_uc001ips.2_Frame_Shift_Ins_p.S619fs|CACNB2_uc001ipt.2_Frame_Shift_Ins_p.S605fs|CACNB2_uc001ipu.2_Frame_Shift_Ins_p.S615fs|CACNB2_uc001ipv.2_Frame_Shift_Ins_p.S591fs|CACNB2_uc009xka.1_Frame_Shift_Ins_p.S577fs|CACNB2_uc001ipw.2_Frame_Shift_Ins_p.S550fs|CACNB2_uc001ipx.2_Frame_Shift_Ins_p.S588fs|CACNB2_uc001ipz.2_Frame_Shift_Ins_p.S565fs|CACNB2_uc001ipy.2_Frame_Shift_Ins_p.S589fs|CACNB2_uc010qco.1_Frame_Shift_Ins_p.S557fs|CACNB2_uc001iqa.2_Frame_Shift_Ins_p.S595fs|NSUN6_uc001iqb.2_Intron NM_201596 NP_963890 Q08289 CACB2_HUMAN "calcium channel, voltage-dependent, beta 2" 643 axon guidance|neuromuscular junction development integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity large_intestine(1)|central_nervous_system(1)|skin(1) 3 Magnesium Sulfate(DB00653)|Verapamil(DB00661) GAAGTGATATCAAAAAAACGGA 0.45 0.56 157 203 FADD 8772 broad.mit.edu 37 11 70049816 70049817 + Frame_Shift_Ins INS - G G JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr11:70049816_70049817insG uc001opm.2 + 1 548_549 c.251_252insG c.(250-252)GCGfs p.A84fs NM_003824 NP_003815 Q13158 FADD_HUMAN Fas-associated via death domain 84 activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction cytosol death receptor binding|identical protein binding ovary(1)|lung(1)|pancreas(1) 3 Esophageal squamous(2;1.19e-45) LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) 0.000 0.10 599 68 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 910 365 NCAM1 4684 broad.mit.edu 37 11 113076861 113076861 + Frame_Shift_Del DEL G - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr11:113076861delG uc009yyq.1 + 5 927 c.233delG c.(232-234)CGGfs p.R78fs NCAM1_uc001pno.2_Frame_Shift_Del_p.R78fs NM_001076682 NP_001070150 P13591 NCAM1_HUMAN neural cell adhesion molecule 1 isoform 3 196 Ig-like C2-type 2.|Extracellular (Potential). axon guidance|interferon-gamma-mediated signaling pathway anchored to membrane|extracellular region|Golgi membrane|integral to membrane ovary(1) 1 all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207) BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212) ATCCTGGCACGGGGGGAGATC 0.498 0.4 107 72 IKZF4 64375 broad.mit.edu 37 12 56429093 56429093 + Frame_Shift_Del DEL G - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr12:56429093delG uc001sjb.1 + 9 1895 c.1736delG c.(1735-1737)CGGfs p.R579fs IKZF4_uc010sqa.1_Frame_Shift_Del_p.R532fs|IKZF4_uc001sjc.1_Frame_Shift_Del_p.R579fs|IKZF4_uc001sjd.1_Frame_Shift_Del_p.R477fs|IKZF4_uc009zoi.1_Frame_Shift_Del_p.R534fs|IKZF4_uc001sje.1_Frame_Shift_Del_p.R538fs NM_022465 NP_071910 Q9H2S9 IKZF4_HUMAN "zinc finger protein, subfamily 1A, 4" 579 C2H2-type 6. "negative regulation of transcription, DNA-dependent" nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1) 1 UCEC - Uterine corpus endometrioid carcinoma (6;0.025)|OV - Ovarian serous cystadenocarcinoma(18;0.123) CACATTGTCCGGGGGGAGCAT 0.552 0.49 23 22 GLI1 2735 broad.mit.edu 37 12 57864217 57864218 + Frame_Shift_Ins INS - C C JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr12:57864217_57864218insC uc001snx.2 + 12 1772_1773 c.1694_1695insC c.(1693-1695)TTCfs p.F565fs GLI1_uc009zpq.2_Frame_Shift_Ins_p.F437fs NM_005269 NP_005260 P08151 GLI1_HUMAN GLI family zinc finger 1 isoform 1 565 epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter cytosol|nucleus transcription regulatory region DNA binding|zinc ion binding skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1) 15 GBM - Glioblastoma multiforme(3;3.99e-32) GCCTCTCCTTTCCCCCCTGGCT 0.644 0.37 57 33 KSR2 283455 broad.mit.edu 37 12 117977605 117977605 + Frame_Shift_Del DEL G - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr12:117977605delG uc001two.2 - 10 1574 c.1519delC c.(1519-1521)CTCfs p.L507fs NM_173598 NP_775869 Q6VAB6 KSR2_HUMAN kinase suppressor of ras 2 536 Pro-rich. intracellular signal transduction cytoplasm|membrane ATP binding|metal ion binding|protein serine/threonine kinase activity lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1) 15 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) CTAGGAGGGAGGGGGGGTGCT 0.632 0.55 20 24 ABCC4 10257 broad.mit.edu 37 13 95696015 95696016 + Frame_Shift_Ins INS - T T JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr13:95696015_95696016insT uc001vmd.3 - 29 3774_3775 c.3655_3656insA c.(3655-3657)ATCfs p.I1219fs ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_Frame_Shift_Ins_p.I1172fs NM_005845 NP_005836 O15439 MRP4_HUMAN "ATP-binding cassette, sub-family C, member 4" 1219 ABC transporter 2. platelet activation|platelet degranulation integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane "15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity" central_nervous_system(3)|skin(1) 4 all_neural(89;0.0878)|Medulloblastoma(90;0.163) Cefazolin(DB01327) TTTCTCCCGGATTTTTTTTTGT 0.376 0.3 42 18 KTN1 3895 broad.mit.edu 37 14 56078834 56078836 + In_Frame_Del DEL TCT - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr14:56078834_56078836delTCT uc001xcb.2 + 3 370_372 c.68_70delTCT c.(67-72)CTCTTC>CTC p.F25del KTN1_uc001xce.2_In_Frame_Del_p.F25del|KTN1_uc001xcc.2_In_Frame_Del_p.F25del|KTN1_uc001xcd.2_In_Frame_Del_p.F25del|KTN1_uc010trb.1_In_Frame_Del_p.F25del|KTN1_uc001xcf.1_In_Frame_Del_p.F25del NM_182926 NP_891556 Q86UP2 KTN1_HUMAN kinectin 1 isoform a 25 Helical; Signal-anchor for type II membrane protein; (Potential). microtubule-based movement endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction breast(3)|ovary(2)|lung(1)|central_nervous_system(1) 7 GTAATTTTCCTCTTCTTCTGGCT 0.276 0.2 28 7 HERC2 8924 broad.mit.edu 37 15 28463819 28463820 + Splice_Site INS - A A JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr15:28463819_28463820insA uc001zbj.2 - 38 5952 c.5846_splice c.e38-1 p.E1949_splice NM_004667 NP_004658 O95714 HERC2_HUMAN hect domain and RLD 2 DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process nucleus guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1) 13 all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227) all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199) GTTCGGCTTCTAAAAAAAATAA 0.332 0.39 45 29 CLTC 1213 broad.mit.edu 37 17 57752129 57752130 + Frame_Shift_Ins INS - A A JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr17:57752129_57752130insA uc002ixq.1 + 16 2929_2930 c.2486_2487insA c.(2485-2487)ATAfs p.I829fs CLTC_uc002ixp.2_Frame_Shift_Ins_p.I829fs|CLTC_uc002ixr.1_Frame_Shift_Ins_p.I833fs NM_004859 NP_004850 Q00610 CLH1_HUMAN clathrin heavy chain 1 829 Heavy chain arm.|Proximal segment. axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle protein binding|structural molecule activity CLTC/ALK(44)|CLTC/TFE3(2) haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1) 48 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) GAAGATGTCATAAAAAACTTGA 0.351 0.4 42 28 CPAMD8 27151 broad.mit.edu 37 19 17081703 17081703 + Frame_Shift_Del DEL G - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr19:17081703delG uc002nfb.2 - 18 2384 c.2352delC c.(2350-2352)CCCfs p.P784fs NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 737 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 0.000 0.19 206 48 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 118 77 LMTK3 114783 broad.mit.edu 37 19 49002814 49002815 + Frame_Shift_Ins INS - G G JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr19:49002814_49002815insG uc002pjk.2 - 12 1598_1599 c.1598_1599insC c.(1597-1599)CCGfs p.P533fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.20 249 63 PTPRT 11122 broad.mit.edu 37 20 40709520 40709521 + Frame_Shift_Ins INS - A A JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr20:40709520_40709521insA uc002xkg.2 - 31 4508_4509 c.4324_4325insT c.(4324-4326)TAGfs p.*1442fs PTPRT_uc010ggj.2_Frame_Shift_Ins_p.*1461fs|PTPRT_uc010ggi.2_Frame_Shift_Ins_p.*645fs NM_007050 NP_008981 O14522 PTPRT_HUMAN protein tyrosine phosphatase, receptor type, T 1442 homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway cell surface|integral to membrane|plasma membrane alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity skin(8)|ovary(7)|lung(5) 20 Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783) 0.000 0.44 617 477 COL18A1 80781 broad.mit.edu 37 21 46900749 46900749 + Frame_Shift_Del DEL C - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr21:46900749delC uc011afs.1 + 12 2854 c.2833delC c.(2833-2835)CCCfs p.P945fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.P530fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.P710fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 945 Triple-helical region 3 (COL3). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.48 714 654 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 53 316 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.94 7 116 EWSR1 2130 broad.mit.edu 37 22 29695765 29695765 + Frame_Shift_Del DEL G - - JHUEM2_ENDOMETRIUM NA JHUEM2_ENDOMETRIUM NA g.chr22:29695765delG uc003aet.2 + 16 2183 c.1855delG c.(1855-1857)GGGfs p.G619fs EWSR1_uc003aev.2_Frame_Shift_Del_p.G624fs|EWSR1_uc003aew.2_Frame_Shift_Del_p.G563fs|EWSR1_uc003aex.2_Frame_Shift_Del_p.G618fs|EWSR1_uc003aey.2_Frame_Shift_Del_p.G414fs|EWSR1_uc003aez.2_Frame_Shift_Del_p.G280fs NM_005243 NP_005234 Q01844 EWS_HUMAN Ewing sarcoma breakpoint region 1 isoform 2 619 Arg/Gly/Pro-rich. "regulation of transcription, DNA-dependent|transcription, DNA-dependent" cytoplasm|nucleus|plasma membrane calmodulin binding|nucleotide binding|RNA binding|zinc ion binding EWSR1/FLI1(2266)|EWSR1/ATF1(323)|EWSR1/WT1(231)|EWSR1/ERG(162)|EWSR1/NR4A3(140)|EWSR1/DDIT3(43)|EWSR1/CREB1(42)|EWSR1/FEV(10)|EWSR1/POU5F1(10)|EWSR1/ETV1(7)|EWSR1/ETV4(6)|EWSR1/ZNF384(4)|EWSR1/PBX1(3)|EWSR1/SP3(3)|EWSR1/PATZ1(2) bone(2526)|soft_tissue(702)|skin(8)|autonomic_ganglia(4)|haematopoietic_and_lymphoid_tissue(4)|salivary_gland(2)|central_nervous_system(2)|NS(2)|pancreas(2)|lung(1)|ovary(1) 3254 AGGTGGCCCTGGGGGGCCCCC 0.592 0.36 7 4 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.93 7 95 ARID1A 8289 broad.mit.edu 37 1 27094361 27094362 + Frame_Shift_Ins INS - GT GT JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr1:27094361_27094362insGT uc001bmv.1 + 11 3442_3443 c.3069_3070insGT c.(3067-3072)TGGGTGfs p.W1023fs ARID1A_uc001bmt.1_Frame_Shift_Ins_p.W1023fs|ARID1A_uc001bmu.1_Frame_Shift_Ins_p.W1023fs|ARID1A_uc001bmw.1_Frame_Shift_Ins_p.W640fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1023_1024 ARID. "androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent" nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GGAAGATGTGGGTGGACCGTTA 0.5 0.36 300 168 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 442 175 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0 0.35 15 8 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. "regulation of transcription, DNA-dependent" membrane|nucleus "calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity" skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.36 0.58 27 37 FAM157A 728262 broad.mit.edu 37 3 197880130 197880131 + In_Frame_Ins INS - GCA GCA JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr3:197880130_197880131insGCA uc011bup.1 + 2 209_210 c.209_210insGCA c.(208-210)TGG>TGGCAG p.84_85insQ NM_001145248 NP_001138720 C9JC47 F157A_HUMAN "family with sequence similarity 157, member A" 84_85 Gln-rich. 0 TACAAGAACTGgcagcagcagc 0.396 0.23 61 18 HTT 3064 broad.mit.edu 37 4 3076665 3076666 + In_Frame_Ins INS - GCCGCCACC GCCGCCACC rs61792466 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr4:3076665_3076666insGCCGCCACC uc011bvq.1 + 2 264_265 c.119_120insGCCGCCACC c.(118-120)CAG>CAGCCGCCACCG p.49_50insPPP NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 47_48 Poly-Pro. "establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule" autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) cagcagcaacagccgccaccgc 0.099 0.11 91 11 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs "SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA;" GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 31 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.69 116 258 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 34 97 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.69 4 9 MICA 4276 broad.mit.edu 37 6 31380161 31380162 + Splice_Site INS - CTGCTGCTGCT CTGCTGCTGCT rs72548004;rs9279200 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr6:31380161_31380162insCTGCTGCTGCT uc003ntk.1 + 6 988 c.949_splice c.e6-1 p.A317_splice MICA_uc003rxz.1_Frame_Shift_Ins_p.G180fs RecName: Full=MHC class I polypeptide-related sequence A; Short=MIC-A; Flags: Precursor; 0 Ovarian(999;0.0253) TGTTGCTGCTGGCTGCTGCTAT 0.45 1 0 10 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 "cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent" cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.3 52 22 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.17 0.1 261 28 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 2 27 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 35 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.51 482 495 MEF2A 4205 broad.mit.edu 37 15 100252709 100252710 + In_Frame_Ins INS - CAGCAGCAG CAGCAGCAG JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr15:100252709_100252710insCAGCAGCAG uc010urw.1 + 11 1616_1617 c.1257_1258insCAGCAGCAG c.(1255-1260)insCAGCAGCAG p.428_429insQQQ MEF2A_uc010urv.1_In_Frame_Ins_p.358_359insQQQ|MEF2A_uc010bos.2_In_Frame_Ins_p.418_419insQQQ|MEF2A_uc002bvf.2_In_Frame_Ins_p.420_421insQQQ|MEF2A_uc002bve.2_In_Frame_Ins_p.426_427insQQQ|MEF2A_uc002bvg.2_In_Frame_Ins_p.418_419insQQQ|MEF2A_uc002bvi.2_In_Frame_Ins_p.418_419insQQQ|MEF2A_uc010bot.2_In_Frame_Ins_p.350_351insQQQ NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 428_429 Gln/Pro-rich. apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) CATCGGGCTTCcagcagcagca 0.485 0.22 58 16 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.44 117 92 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 95 254 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHUEM3_ENDOMETRIUM NA JHUEM3_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.88 13 97 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.01 -1 89 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.44 166 133 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.58 5 7 KALRN 8997 broad.mit.edu 37 3 124044906 124044906 + Frame_Shift_Del DEL T - - JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr3:124044906delT uc003ehg.2 + 7 1293 c.1166delT c.(1165-1167)ATCfs p.I389fs KALRN_uc010hrv.1_Frame_Shift_Del_p.I389fs|KALRN_uc003ehf.1_Frame_Shift_Del_p.I389fs|KALRN_uc011bjy.1_Frame_Shift_Del_p.I389fs NM_001024660 NP_001019831 O60229 KALRN_HUMAN kalirin, RhoGEF kinase isoform 1 389 Spectrin 2. apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport actin cytoskeleton|cytosol ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1) 6 TCACAACAAATCAAGCAGATC 0.552 0.19 194 45 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 75 86 AKAP9 10142 broad.mit.edu 37 7 91631047 91631047 + Frame_Shift_Del DEL G - - JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr7:91631047delG uc003ulg.2 + 8 2041 c.1816delG c.(1816-1818)GAAfs p.E606fs AKAP9_uc003ule.2_Frame_Shift_Del_p.E618fs|AKAP9_uc003ulf.2_Frame_Shift_Del_p.E606fs|AKAP9_uc003uli.2_Frame_Shift_Del_p.E231fs NM_005751 NP_005742 Q99996 AKAP9_HUMAN A-kinase anchor protein 9 isoform 2 618 Glu-rich.|Potential. G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport centrosome|cytosol|Golgi apparatus receptor binding breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1) 26 all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) 0.000 0.16 348 65 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.36 28 16 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 14 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.34 540 282 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 177 49 BRCA2 675 broad.mit.edu 37 13 32913079 32913080 + Frame_Shift_Ins INS - A A rs80358692 JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr13:32913079_32913080insA uc001uub.1 + 11 4814_4815 c.4587_4588insA c.(4585-4590)GGGAAAfs p.G1529fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 1529_1530 BRCA2 4. cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) CAGCTAGCGGGAAAAAAGTTAA 0.386 0.40 62 42 HIRIP3 8479 broad.mit.edu 37 16 30006480 30006480 + Frame_Shift_Del DEL G - - JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr16:30006480delG uc002dve.2 - 3 706 c.245delC c.(244-246)CCTfs p.P82fs uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|INO80E_uc002dvg.1_5'Flank|INO80E_uc002dvh.1_5'Flank|INO80E_uc002dvi.1_5'Flank|INO80E_uc002dvj.1_5'Flank|INO80E_uc002dvk.1_5'Flank|HIRIP3_uc002dvf.2_Frame_Shift_Del_p.P82fs NM_003609 NP_003600 Q9BW71 HIRP3_HUMAN HIRA interacting protein 3 82 chromatin assembly or disassembly nucleus protein binding central_nervous_system(1) 1 0.000 0.91 1 10 RBL2 5934 broad.mit.edu 37 16 53513829 53513830 + Frame_Shift_Ins INS - A A JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr16:53513829_53513830insA uc002ehi.3 + 19 2925_2926 c.2807_2808insA c.(2806-2808)AGAfs p.R936fs RBL2_uc002ehj.2_Frame_Shift_Ins_p.R646fs|RBL2_uc010vgw.1_Intron NM_005611 NP_005602 Q08999 RBL2_HUMAN retinoblastoma-like 2 (p130) 936 Domain B.|Pocket; binds E1A. cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleolus DNA binding|protein binding ovary(2)|lung(2)|upper_aerodigestive_tract(1) 5 AAAGGGAAAAGAAAAAGAAGAA 0.376 0.39 23 15 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 4 29 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.70 10 23 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.14 127 21 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 27 345 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 51 EP300 2033 broad.mit.edu 37 22 41573305 41573306 + Frame_Shift_Ins INS - CCACC CCACC JHUEM7_ENDOMETRIUM NA JHUEM7_ENDOMETRIUM NA g.chr22:41573305_41573306insCCACC uc003azl.3 + 31 5985_5986 c.5590_5591insCCACC c.(5590-5592)ACCfs p.T1864fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1864 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 0.000 0.43 648 485 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JIMT1_BREAST NA JIMT1_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 5 50 ARID1A 8289 broad.mit.edu 37 1 27058045 27058047 + In_Frame_Del DEL CAG - - JIMT1_BREAST NA JIMT1_BREAST NA g.chr1:27058045_27058047delCAG uc001bmv.1 + 3 2126_2128 c.1753_1755delCAG c.(1753-1755)CAGdel p.Q586del ARID1A_uc001bmt.1_In_Frame_Del_p.Q586del|ARID1A_uc001bmu.1_In_Frame_Del_p.Q586del|ARID1A_uc001bmw.1_In_Frame_Del_p.Q203del NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 586 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GCCCCAGTCTCAGCAGTCCCAGC 0.606 0.94 4 66 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 JIMT1_BREAST NA JIMT1_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.26 29 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JIMT1_BREAST NA JIMT1_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 58 95 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JIMT1_BREAST NA JIMT1_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 18 36 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes JIMT1_BREAST NA JIMT1_BREAST NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.73 3 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes JIMT1_BREAST NA JIMT1_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.82 2 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JIMT1_BREAST NA JIMT1_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 3 64 EIF3A 8661 broad.mit.edu 37 10 120795657 120795674 + In_Frame_Del DEL TCTCTTTCTCGGTCTCGG - - JIMT1_BREAST NA JIMT1_BREAST NA g.chr10:120795657_120795674delTCTCTTTCTCGGTCTCGG uc001ldu.2 - 22 4172_4189 c.4026_4043delCCGAGACCGAGAAAGAGA c.(4024-4044)GACCGAGACCGAGAAAGAGAA>GAA p.DRDRER1342del EIF3A_uc010qsu.1_In_Frame_Del_p.DRDRER1308del NM_003750 NP_003741 Q14152 EIF3A_HUMAN eukaryotic translation initiation factor 3, 1342_1347 formation of translation initiation complex cytosol|eukaryotic translation initiation factor 3 complex protein binding|structural molecule activity|translation initiation factor activity 0 Lung NSC(174;0.094)|all_lung(145;0.123) all cancers(201;0.0236) TTTTTCACCTTCTCTTTCTCGGTCTCGGTCTCTTTCTC 0.514 0.13 162 24 TPH1 7166 broad.mit.edu 37 11 18057540 18057541 + Frame_Shift_Del DEL CA - - JIMT1_BREAST NA JIMT1_BREAST NA g.chr11:18057540_18057541delCA uc001mnp.2 - 2 292_293 c.266_267delTG c.(265-267)GTGfs p.V89fs TPH1_uc009yhe.2_RNA NM_004179 NP_004170 P17752 TPH1_HUMAN tryptophan hydroxylase 1 89 ACT. aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process cytosol amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity 0 L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360) CTGGTAGATTCACAGAGAGAAC 0.327 0.10 179 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JIMT1_BREAST NA JIMT1_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 813 341 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes JIMT1_BREAST NA JIMT1_BREAST NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.47 10 9 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency JIMT1_BREAST NA JIMT1_BREAST NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.57 66 86 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JIMT1_BREAST NA JIMT1_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.59 103 149 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JIMT1_BREAST NA JIMT1_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 148 409 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JIMT1_BREAST NA JIMT1_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.87 10 68 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.50 17 17 TPRXL 348825 broad.mit.edu 37 3 14105871 14105885 + In_Frame_Del DEL CAGCAGCAGCCCCAG - - rs4684179;rs113575909 by1000genomes JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105871_14105885delCAGCAGCAGCCCCAG uc011avd.1 + 3 650_664 c.195_209delCAGCAGCAGCCCCAG c.(193-210)CCCAGCAGCAGCCCCAGC>CCC p.SSSPS71del TPRXL_uc003byh.1_In_Frame_Del_p.SSSPS71del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSPS71del NR_002223 RecName: Full=Putative protein TPRXL; 0 gcagcagccccagcagcagccccagcagcagcagc 0.033 0.38 8 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 123 188 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.81 23 100 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.81 4 17 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 12 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.17 106 22 ZNF384 171017 broad.mit.edu 37 12 6777070 6777075 + In_Frame_Del DEL TGCTGC - - rs151322806;rs111332695;rs78573212;rs1052680 JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:6777070_6777075delTGCTGC uc010sfh.1 - 11 1747_1752 c.1539_1544delGCAGCA c.(1537-1545)CAGCAGCAA>CAA p.513_515QQQ>Q ZNF384_uc001qpz.2_In_Frame_Del_p.452_454QQQ>Q|ZNF384_uc001qqa.2_In_Frame_Del_p.452_454QQQ>Q|ZNF384_uc001qqb.2_In_Frame_Del_p.436_438QQQ>Q|ZNF384_uc001qqc.2_In_Frame_Del_p.452_454QQQ>Q|ZNF384_uc001qqd.2_In_Frame_Del_p.397_399QQQ>Q|ZNF384_uc001qqe.2_In_Frame_Del_p.436_438QQQ>Q NM_001135734 NP_001129206 Q8TF68 ZN384_HUMAN nuclear matrix transcription factor 4 isoform d 513_515 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding EWSR1/ZNF384(4) haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1) 8 TGGTGgctgttgctgctgctgctgct 0.335 0.17 185 39 PLEKHA5 54477 broad.mit.edu 37 12 19427887 19427888 + Frame_Shift_Ins INS - G G JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:19427887_19427888insG uc001reb.2 + 10 1351_1352 c.1265_1266insG c.(1264-1266)AAGfs p.K422fs PLEKHA5_uc010sie.1_Frame_Shift_Ins_p.K428fs|PLEKHA5_uc001rea.2_Frame_Shift_Ins_p.K422fs|PLEKHA5_uc009zin.2_Frame_Shift_Ins_p.K180fs|PLEKHA5_uc010sif.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc010sig.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc010sih.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc001rec.1_Frame_Shift_Ins_p.K110fs NM_019012 NP_061885 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A 422 1-phosphatidylinositol binding|protein binding ovary(1)|kidney(1)|skin(1) 3 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) AAAATCCAGAAGGGGAGGGGTC 0.470 0.11 75 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.60 88 130 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 92 280 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 8 58 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 41 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 297 62 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 70 81 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.23 209 63 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 20 TSC1 7248 broad.mit.edu 37 9 135771987 135771988 + In_Frame_Ins INS - GCT GCT rs118203743 JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:135771987_135771988insGCT uc004cca.2 - 23 3363_3364 c.3129_3130insAGC c.(3127-3132)insAGC p.1043_1044insS TSC1_uc004ccb.3_In_Frame_Ins_p.1042_1043insS|TSC1_uc011mcq.1_In_Frame_Ins_p.992_993insS|TSC1_uc011mcr.1_In_Frame_Ins_p.236_236A>AA NM_000368 NP_000359 Q92574 TSC1_HUMAN tuberous sclerosis 1 protein isoform 1 1043_1044 activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus cell cortex|lamellipodium|membrane|TSC1-TSC2 complex chaperone binding|protein N-terminus binding p.S1043N(1)|p.?(1) lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1) 14 OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06) GTAGAAAGCTCgctgctgctgc 0.574 0.48 48 45 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.35 15 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 186 67 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 48 437 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 3 94 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 70 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.38 31 19 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.14 57 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 120 173 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 21 43 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.73 4 11 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 3 36 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 64 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.50 9 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 751 297 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.42 37 27 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.63 164 278 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 53 471 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 8 92 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.67 8 16 ARID1A 8289 broad.mit.edu 37 1 27089776 27089777 + Splice_Site INS - GT GT JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr1:27089776_27089777insGT uc001bmv.1 + 8 3105 c.2732_splice c.e8+1 p.R911_splice ARID1A_uc001bmt.1_Splice_Site_p.R911_splice|ARID1A_uc001bmu.1_Splice_Site_p.R911_splice|ARID1A_uc001bmw.1_Splice_Site_p.R528_splice NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) ATCCAAAACAGGTAAGGCCTGG 0.510 0.94 6 96 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.32 268 125 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.40 12 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.66 47 90 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.69 4 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.89 4 33 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.93 1 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 267 129 NCOR2 9612 broad.mit.edu 37 12 124887059 124887067 + In_Frame_Del DEL GCTGCTGCT - - rs67031864 JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr12:124887059_124887067delGCTGCTGCT uc010tba.1 - 14 1640_1648 c.1523_1531delAGCAGCAGC c.(1522-1533)CAGCAGCAGCCC>CCC p.QQQ508del NCOR2_uc010tay.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010taz.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010tbb.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010tbc.1_In_Frame_Del_p.QQQ507del|NCOR2_uc001ugj.1_In_Frame_Del_p.QQQ508del NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 508_510 Poly-Gln. cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) CGGGGCATGGgctgctgctgctgctgctg 0.316 0.37 12 7 RB1 5925 broad.mit.edu 37 13 48878077 48878108 + Frame_Shift_Del DEL CCGCCACCGCCGCCGCTGCCGCCGCGGAACCC - - rs148980395 JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr13:48878077_48878108delCCGCCACCGCCGCCGCTGCCGCCGCGGAACCC uc001vcb.2 + 1 195_226 c.29_60delCCGCCACCGCCGCCGCTGCCGCCGCGGAACCC c.(28-60)GCCGCCACCGCCGCCGCTGCCGCCGCGGAACCCfs p.A10fs RB1_uc010acs.1_RNA|uc001vca.2_5'Flank NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 10_20 Poly-Pro. androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.0?(13)|p.A14A(1)|p.?(1)|p.A16fs*3(1) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) 0.000 0.81 8 34 ZFHX3 463 broad.mit.edu 37 16 72822034 72822039 + In_Frame_Del DEL GCTGCT - - rs149197237 JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr16:72822034_72822039delGCTGCT uc002fck.2 - 10 10809_10814 c.10136_10141delAGCAGC c.(10135-10143)CAGCAGCGG>CGG p.QQ3379del ZFHX3_uc002fcl.2_In_Frame_Del_p.QQ2465del NM_006885 NP_008816 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 isoform A 3379_3380 Poly-Gln. Missing. muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation transcription factor complex enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding ovary(2)|skin(2) 4 Ovarian(137;0.13) tgtagttgccgctgctgctgctgctg 0.442 0.24 25 8 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.80 13 51 KIAA0802 23255 broad.mit.edu 37 18 8821464 8821464 + Splice_Site DEL G - - JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr18:8821464delG uc002knr.2 + 14 3299 c.3157_splice c.e14-1 p.E1053_splice KIAA0802_uc002knq.2_Splice_Site_p.E1012_splice|KIAA0802_uc002kns.2_Splice_Site_p.E393_splice NM_015210 NP_056025 Q9Y4B5 CC165_HUMAN hypothetical protein LOC23255 0 CTTCTTTATAGGAAGAAGAAA 0.328 0.20 36 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 22 54 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.22 56 16 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 106 513 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JMSU1_URINARY_TRACT NA JMSU1_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 52 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 46 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 478 126 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 25 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.46 25 21 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.71 167 415 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 44 87 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.35 42 23 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 3 74 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.48 504 469 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 10 192 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.32 130 62 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 220 560 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 7 199 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 5 91 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.40 200 134 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.46 7 6 PLD1 5337 broad.mit.edu 37 3 171455436 171455436 + Frame_Shift_Del DEL G - - JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:171455436delG uc003fhs.2 - 3 290 c.174delC c.(172-174)TTCfs p.F58fs PLD1_uc003fht.2_Frame_Shift_Del_p.F58fs NM_002662 NP_002653 Q13393 PLD1_HUMAN phospholipase D1 isoform a 58 cell communication|chemotaxis|Ras protein signal transduction endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity ovary(2)|lung(1) 3 all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186) LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14) Choline(DB00122) AAATAGCAGAGAAAGGGATAT 0.333 0.40 62 41 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 67 85 RAPGEF2 9693 broad.mit.edu 37 4 160262725 160262726 + Frame_Shift_Ins INS - A A JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:160262725_160262726insA uc003iqg.3 + 14 2371_2372 c.2061_2062insA c.(2059-2064)CTGAAAfs p.L687fs NM_014247 NP_055062 Q9Y4G8 RPGF2_HUMAN Rap guanine nucleotide exchange factor 2 687_688 Ras-associating. cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction integral to plasma membrane|intracellular calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity lung(2)|upper_aerodigestive_tract(1)|skin(1) 4 all_hematologic(180;0.24) COAD - Colon adenocarcinoma(41;0.0817) GGTATTATCTGAAAAACAACAT 0.366 0.37 19 11 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.60 25 37 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 190 59 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 3 27 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.50 17 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 82 620 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 6 56 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 31 STIL 6491 broad.mit.edu 37 1 47745984 47745985 + Frame_Shift_Del DEL TC - - JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:47745984_47745985delTC uc001crc.1 - 12 2300_2301 c.2145_2146delGA c.(2143-2148)ATGATGfs p.M715fs TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Frame_Shift_Del_p.M668fs|STIL_uc010omo.1_Frame_Shift_Del_p.M715fs|STIL_uc001crd.1_Frame_Shift_Del_p.M715fs|STIL_uc001cre.1_Frame_Shift_Del_p.M715fs|STIL_uc001crf.1_Frame_Shift_Del_p.M328fs|STIL_uc001crg.1_Frame_Shift_Del_p.M668fs NM_003035 NP_003026 Q15468 STIL_HUMAN SCL/TAL1 interrupting locus isoform 2 715_716 PIN1-binding (By similarity). cell proliferation|multicellular organismal development centrosome|cytosol lung(2)|skin(1) 3 Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444) GATAGTCCCATCATTCCATTAT 0.475 0.15 71 13 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 243 63 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.27 83 31 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.57 34 46 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.82 2 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 123 13 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.45 6 5 UNC13C 440279 broad.mit.edu 37 15 54556507 54556509 + In_Frame_Del DEL AAG - - JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:54556507_54556509delAAG uc002ack.2 + 7 3590_3592 c.3590_3592delAAG c.(3589-3594)AAAGAA>AAA p.E1198del UNC13C_uc002acl.2_In_Frame_Del_p.E28del NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 1198 exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) CAGATTTCTAAAGAAGATTTTGT 0.374 0.42 79 58 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 17 175 SERPINB4 6318 broad.mit.edu 37 18 61306960 61306960 + Frame_Shift_Del DEL G - - JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr18:61306960delG uc002ljf.2 - 6 606 c.520delC c.(520-522)CTGfs p.L174fs SERPINB4_uc002lje.2_Frame_Shift_Del_p.L174fs|SERPINB4_uc002ljg.2_Intron NM_002974 NP_002965 P48594 SPB4_HUMAN serine (or cysteine) proteinase inhibitor, clade 174 immune response|regulation of proteolysis cytoplasm|extracellular region protein binding|serine-type endopeptidase inhibitor activity ovary(2)|lung(1) 3 ACAAGAACCAGTGTCGTATCA 0.348 0.50 61 60 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.21 27 7 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 99 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 61 356 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 K029AX_SKIN NA K029AX_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 4 67 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - K029AX_SKIN NA K029AX_SKIN NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.19 606 138 TPO 7173 broad.mit.edu 37 2 1507747 1507748 + Frame_Shift_Ins INS - C C K029AX_SKIN NA K029AX_SKIN NA g.chr2:1507747_1507748insC uc002qww.2 + 14 2505_2506 c.2414_2415insC c.(2413-2415)CACfs p.H805fs TPO_uc010ewj.2_RNA|TPO_uc002qwu.2_Frame_Shift_Ins_p.H748fs|TPO_uc002qwr.2_Frame_Shift_Ins_p.H805fs|TPO_uc002qwx.2_Frame_Shift_Ins_p.H748fs|TPO_uc010yio.1_Frame_Shift_Ins_p.H632fs|TPO_uc010yip.1_Intron|TPO_uc002qwy.1_Intron|TPO_uc002qwz.2_Intron NM_000547 NP_000538 P07202 PERT_HUMAN thyroid peroxidase isoform a 805 Extracellular (Potential).|EGF-like; calcium-binding (Potential). cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process cell surface|cytoplasm|integral to plasma membrane calcium ion binding|heme binding|iodide peroxidase activity p.H805L(1) ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1) 20 all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627) all_cancers(51;0.0338) all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12) Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550) 0.000 0.42 999 711 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 K029AX_SKIN NA K029AX_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 25 18 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A K029AX_SKIN NA K029AX_SKIN NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.13 103 16 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 K029AX_SKIN NA K029AX_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.44 15 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 K029AX_SKIN NA K029AX_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 80 93 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 K029AX_SKIN NA K029AX_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.51 44 46 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes K029AX_SKIN NA K029AX_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 37 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 K029AX_SKIN NA K029AX_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.31 29 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency K029AX_SKIN NA K029AX_SKIN NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.11 272 32 CDKN2A 1029 broad.mit.edu 37 9 21971133 21971133 + Frame_Shift_Del DEL G - - K029AX_SKIN NA K029AX_SKIN NA g.chr9:21971133delG uc003zpk.2 - 2 437 c.225delC c.(223-225)CCCfs p.P75fs MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Frame_Shift_Del_p.R131fs NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 75 cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.?(13)|p.P75L(2)|p.A76fs*70(2)|p.P75H(1)|p.E61_L94del(1)|p.A76fs*64(1)|p.L65fs*38(1)|p.A68fs*3(1)|p.P75fs*71(1)|p.P75S(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) 0.000 0.26 612 215 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 K029AX_SKIN NA K029AX_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 681 258 IRS2 8660 broad.mit.edu 37 13 110436296 110436297 + In_Frame_Ins INS - CGG CGG rs34412495 K029AX_SKIN NA K029AX_SKIN NA g.chr13:110436296_110436297insCGG uc001vqv.2 - 1 2618_2619 c.2104_2105insCCG c.(2104-2106)GTG>GCCGTG p.701_702insA NM_003749 NP_003740 Q9Y4H2 IRS2_HUMAN insulin receptor substrate 2 701_702 fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus cytosol|plasma membrane insulin receptor binding|signal transducer activity large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|skin(1)|ovary(1)|kidney(1) 8 all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155) Breast(118;0.159) all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147) 0.000 0.43 791 596 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C K029AX_SKIN NA K029AX_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 6 78 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 K029AX_SKIN NA K029AX_SKIN NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.12 58 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 K029AX_SKIN NA K029AX_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.82 41 183 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 K029AX_SKIN NA K029AX_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 82 718 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 K029AX_SKIN NA K029AX_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 10 169 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 3 51 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 270 92 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 91 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 44 30 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 23 41 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 11 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.46 30 26 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.46 745 636 TCERG1L 256536 broad.mit.edu 37 10 133107556 133107557 + Frame_Shift_Ins INS - C C rs145740488 by1000genomes KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr10:133107556_133107557insC uc001lkp.2 - 2 434_435 c.348_349insG c.(346-351)CTGTTTfs p.L116fs NM_174937 NP_777597 Q5VWI1 TCRGL_HUMAN transcription elongation regulator 1-like 116_117 large_intestine(2)|ovary(2) 4 all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09) all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276) TGGCCACCAAACAGCCACTGCA 0.530 0.15 46 8 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.35 15 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 85 34 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 9 67 NF1 4763 broad.mit.edu 37 17 29684320 29684320 + Frame_Shift_Del DEL G - - KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr17:29684320delG uc002hgg.2 + 54 8236 c.7903delG c.(7903-7905)GATfs p.D2635fs NF1_uc002hgh.2_Frame_Shift_Del_p.D2614fs|NF1_uc010cso.2_Frame_Shift_Del_p.D823fs|NF1_uc010wbt.1_Frame_Shift_Del_p.D113fs|NF1_uc010wbu.1_RNA NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 2635 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.D2635fs*9(1) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) AGATGAGTTTGATCAACGAAT 0.363 0.98 2 103 STK11 6794 broad.mit.edu 37 19 1207113 1207114 + Frame_Shift_Del DEL GG - - KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr19:1207113_1207114delGG uc002lrl.1 + 1 1316_1317 c.201_202delGG c.(199-204)CTGGACfs p.L67fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 67_68 Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.?(3)|p.G52_P179del(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.32 1091 518 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 15 41 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 71 840 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KALS1_CENTRAL_NERVOUS_SYSTEM NA KALS1_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.87 12 77 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 1 0 66 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.1 566 64 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. "regulation of transcription, DNA-dependent" membrane|nucleus "calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity" skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.5 6 6 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs "SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA;" GAAGAAGTCGATTAGGAGTTCA 0.545 0.23 40 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.49 122 117 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.7 19 44 ARID1B 57492 broad.mit.edu 37 6 157099402 157099403 + In_Frame_Ins INS - CAG CAG KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:157099402_157099403insCAG uc003qqn.2 + 1 317_318 c.165_166insCAG c.(163-168)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 "chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent" SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) TAAACCAGTTCcagcagcagca 0.124 0.21 58 15 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 2 21 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 62 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). "histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent" NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.51 45 46 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.49 18 17 RAI1 10743 broad.mit.edu 37 17 17697093 17697094 + In_Frame_Ins INS - CAG CAG KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:17697093_17697094insCAG uc002grm.2 + 3 1300_1301 c.831_832insCAG c.(829-834)insCAG p.291_292insQ RAI1_uc002grn.1_In_Frame_Ins_p.291_292insQ NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291_292 Gln-rich. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) TCAGCTATGACcagcagcagca 0.51 0.27 19 7 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 "B melanoma antigen family, member 2 precursor" 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.33 50 25 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 33 305 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.96 2 48 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.82 8 36 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.31 9 4 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.35 24 13 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.47 9 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 60 107 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 16 36 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.17 143 30 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.11 80 10 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 21 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.82 3 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 3 45 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 863 356 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.32 49 23 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 153 95 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 102 326 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 6 81 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 24 F8 2157 broad.mit.edu 37 X 154194939 154194940 + Frame_Shift_Ins INS - T T rs137852371 KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:154194939_154194940insT uc004fmt.2 - 8 1203_1204 c.1032_1033insA c.(1030-1035)AAAGTAfs p.K344fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 344_345 Plastocyanin-like 2.|F5/8 type A 1. V -> A (in HEMA).|V -> L (in HEMA; severe). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) CAGCTGTCTACTTTGACATAAG 0.322 0.93 8 102 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.46 146 124 OBSCN 84033 broad.mit.edu 37 1 228461641 228461642 + Frame_Shift_Ins INS - A A KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:228461641_228461642insA uc009xez.1 + 18 5352_5353 c.5308_5309insA c.(5308-5310)CAGfs p.Q1770fs OBSCN_uc001hsn.2_Frame_Shift_Ins_p.Q1770fs NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 1770 Fibronectin type-III 2. apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) GACAGCCAGCCAGGGGGACACC 0.663 0.31 9 4 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 1.00 0 10 GRK7 131890 broad.mit.edu 37 3 141497729 141497729 + Frame_Shift_Del DEL T - - KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:141497729delT uc011bnd.1 + 1 687 c.603delT c.(601-603)GGTfs p.G201fs NM_139209 NP_631948 Q8WTQ7 GRK7_HUMAN G-protein-coupled receptor kinase 7 precursor 201 ATP (By similarity).|Protein kinase. visual perception membrane ATP binding|G-protein coupled receptor kinase activity|signal transducer activity lung(2)|stomach(1)|ovary(1)|skin(1) 5 GGAAAGGTGGTTTTGGGGAGG 0.468 0.47 67 60 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.20 40 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.33 71 35 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.31 34 15 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.47 193 169 RIOK1 83732 broad.mit.edu 37 6 7404202 7404203 + Frame_Shift_Ins INS - A A KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:7404202_7404203insA uc003mxn.2 + 9 970_971 c.796_797insA c.(796-798)GAAfs p.E266fs RIOK1_uc003mxo.2_Frame_Shift_Ins_p.E25fs NM_031480 NP_113668 Q9BRS2 RIOK1_HUMAN RIO kinase 1 isoform 1 266 Protein kinase. ATP binding|protein serine/threonine kinase activity ovary(2)|stomach(1)|skin(1) 4 Ovarian(93;0.0418) ACCATGTCCAGAACCAATAATG 0.351 0.49 75 71 ARID1B 57492 broad.mit.edu 37 6 157099426 157099427 + In_Frame_Ins INS - CAG CAG rs78253128 KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:157099426_157099427insCAG uc003qqn.2 + 1 341_342 c.189_190insCAG c.(187-192)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) agcagcagcaacagcagcagca 0.193 0.22 28 8 PDGFA 5154 broad.mit.edu 37 7 557111 557112 + Frame_Shift_Ins INS - G G KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:557111_557112insG uc003sir.2 - 2 922_923 c.79_80insC c.(79-81)CGCfs p.R27fs PDGFA_uc003sis.2_Frame_Shift_Ins_p.R27fs NM_002607 NP_002598 P04085 PDGFA_HUMAN platelet-derived growth factor alpha isoform 1 27 actin cytoskeleton organization|angiogenesis|cell projection assembly|embryo development|hair follicle development|lung alveolus development|negative chemotaxis|negative regulation of phosphatidylinositol biosynthetic process|negative regulation of platelet activation|organ morphogenesis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of DNA replication|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|positive regulation of MAP kinase activity|positive regulation of mesenchymal cell proliferation|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein autophosphorylation|positive regulation of protein kinase B signaling cascade|regulation of actin cytoskeleton organization|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling|regulation of peptidyl-tyrosine phosphorylation|regulation of smooth muscle cell migration|skin development cell surface|endoplasmic reticulum lumen|extracellular space|Golgi membrane|microvillus|platelet alpha granule lumen collagen binding|eukaryotic cell surface binding|growth factor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein heterodimerization activity|protein homodimerization activity 0 Ovarian(82;0.0112) UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15) 0.000 0.56 130 165 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.90 1 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 167 34 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 30 225 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.21 53 14 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.51 22 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 271 1211 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 64 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.84 7 37 EPHA10 284656 broad.mit.edu 37 1 38200950 38200950 + Frame_Shift_Del DEL G - - KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:38200950delG uc009vvi.2 - 6 1556 c.1470delC c.(1468-1470)TACfs p.Y490fs EPHA10_uc001cbu.2_RNA|EPHA10_uc001cbv.1_RNA NM_001099439 NP_001092909 Q5JZY3 EPHAA_HUMAN EPH receptor A10 isofom 3 490 Fibronectin type-III 2.|Extracellular (Potential). extracellular region|integral to membrane|integral to plasma membrane ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity breast(4)|stomach(3)|lung(1) 8 Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197) Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) ATCGGATCTCGTACTCCGTGT 0.652 0.36 7 4 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.47 21 19 ULK4 54986 broad.mit.edu 37 3 41860984 41860985 + Frame_Shift_Ins INS - T T KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:41860984_41860985insT uc003ckv.3 - 19 1979_1980 c.1778_1779insA c.(1777-1779)AAGfs p.K593fs ULK4_uc003ckw.2_Frame_Shift_Ins_p.K593fs NM_017886 NP_060356 Q96C45 ULK4_HUMAN unc-51-like kinase 4 593 ATP binding|protein serine/threonine kinase activity 0 KIRC - Kidney renal clear cell carcinoma(284;0.214) CTCTAGGGTTCTTTTTTTTTTC 0.450 0.10 60 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.33 20 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 101 183 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.42 43 31 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.41 137 95 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.15 203 35 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.36 9 5 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 2 39 WT1 7490 broad.mit.edu 37 11 32417849 32417850 + Frame_Shift_Del DEL TC - - KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:32417849_32417850delTC uc001mtn.1 - 7 1398_1399 c.1202_1203delGA c.(1201-1203)AGAfs p.R401fs WT1_uc001mtl.1_Frame_Shift_Del_p.R189fs|WT1_uc001mtm.1_Frame_Shift_Del_p.R172fs|WT1_uc001mto.1_Frame_Shift_Del_p.R401fs|WT1_uc001mtp.1_Frame_Shift_Del_p.R384fs|WT1_uc001mtq.1_Frame_Shift_Del_p.R384fs|WT1_uc009yjs.1_RNA NM_024426 NP_077744 P19544 WT1_HUMAN Wilms tumor 1 isoform D 333 C2H2-type 1. adrenal cortex formation|branching involved in ureteric bud morphogenesis|camera-type eye development|cardiac muscle cell fate commitment|cellular response to cAMP|cellular response to gonadotropin stimulus|germ cell development|glomerular basement membrane development|glomerular visceral epithelial cell differentiation|induction of apoptosis|male genitalia development|male gonad development|mesenchymal to epithelial transition|metanephric epithelium development|metanephric S-shaped body morphogenesis|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of female gonad development|negative regulation of metanephric glomerular mesangial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of translation|positive regulation of male gonad development|positive regulation of transcription, DNA-dependent|posterior mesonephric tubule development|regulation of organ formation|RNA splicing|sex determination|vasculogenesis|visceral serous pericardium development cytoplasm|nuclear speck|nucleoplasm C2H2 zinc finger domain binding|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding p.V380_S410del(1)|p.R333K(1) EWSR1/WT1(231) haematopoietic_and_lymphoid_tissue(318)|soft_tissue(231)|kidney(132)|pleura(2)|lung(2)|upper_aerodigestive_tract(1)|peritoneum(1) 687 Breast(20;0.247) OV - Ovarian serous cystadenocarcinoma(30;0.128) GCTTAAAATATCTCTTATTGCA 0.530 0.46 166 139 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 862 459 Unknown 0 broad.mit.edu 37 14 22090720 22090721 + Frame_Shift_Del DEL AC - - KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:22090720_22090721delAC uc001wbi.2 + 2 372_373 c.359_360delAC c.(358-360)GACfs p.D120fs SubName: Full=Putative uncharacterized protein ENSP00000374929; GCTGTGAGAGACACAGTGACTA 0.446 0.50 24 24 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 15 104 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 140 104 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 59 450 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 10 135 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.16 416 80 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KATOIII_STOMACH NA KATOIII_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 2 131 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.48 764 695 LRP2 4036 broad.mit.edu 37 2 170137030 170137031 + Splice_Site INS - TAAATG TAAATG KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr2:170137030_170137031insTAAATG uc002ues.2 - 11 1385 c.1172_splice c.e11-1 p.F391_splice LRP2_uc010zdf.1_Splice_Site_p.F391_splice NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) GCCTCGCCAACTAAATGCGAAG 0.416 0.28 274 107 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.14 68 11 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.23 234 69 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.43 211 161 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.20 129 32 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 26 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 26 PTCH1 5727 broad.mit.edu 37 9 98220562 98220562 + Frame_Shift_Del DEL C - - KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr9:98220562delC uc004avk.3 - 18 3089 c.2901delG c.(2899-2901)GAGfs p.E967fs PTCH1_uc010mro.2_Frame_Shift_Del_p.E816fs|PTCH1_uc010mrp.2_Frame_Shift_Del_p.E816fs|PTCH1_uc010mrq.2_Frame_Shift_Del_p.E816fs|PTCH1_uc004avl.3_Frame_Shift_Del_p.E816fs|PTCH1_uc010mrr.2_Frame_Shift_Del_p.E901fs|PTCH1_uc004avm.3_Frame_Shift_Del_p.E966fs NM_000264 NP_000255 Q13635 PTC1_HUMAN patched isoform L 967 Extracellular (Potential). embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway integral to plasma membrane hedgehog receptor activity p.I963fs*2(1) skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1) 379 Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136) 0.000 0.10 356 39 PCDH15 65217 broad.mit.edu 37 10 55582178 55582204 + In_Frame_Del DEL CAGGAGGAGGAGCAAGAGGAGCAGGAG - - rs58461416 byFrequency;by1000genomes KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr10:55582178_55582204delCAGGAGGAGGAGCAAGAGGAGCAGGAG uc001jju.1 - 33 5677_5703 c.5282_5308delCTCCTGCTCCTCTTGCTCCTCCTCCTG c.(5281-5310)GCTCCTGCTCCTCTTGCTCCTCCTCCTGAC>GAC p.APAPLAPPP1761del PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_In_Frame_Del_p.APAPLAPPP1758del|PCDH15_uc010qhw.1_In_Frame_Del_p.APAPLAPPP1721del|PCDH15_uc010qhx.1_In_Frame_Del_p.APAPLAPPP1692del|PCDH15_uc010qhy.1_In_Frame_Del_p.APAPLAPPP1768del|PCDH15_uc010qhz.1_In_Frame_Del_p.APAPLAPPP1763del|PCDH15_uc010qia.1_In_Frame_Del_p.APAPLAPPP1741del|PCDH15_uc010qib.1_In_Frame_Del_p.APAPLAPPP1738del NM_033056 NP_149045 Q96QU1 PCD15_HUMAN protocadherin 15 isoform CD1-4 precursor 1761_1769 Cytoplasmic (Potential). equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse calcium ion binding pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2) 13 Melanoma(3;0.117)|Lung SC(717;0.238) ggagaaatgtcaggaggaggagcaagaggagcaggagcaggaggagg 0.137 0.50 213 216 ZFHX3 463 broad.mit.edu 37 16 72831358 72831363 + In_Frame_Del DEL TTGTTG - - KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr16:72831358_72831363delTTGTTG uc002fck.2 - 9 5891_5896 c.5218_5223delCAACAA c.(5218-5223)CAACAAdel p.QQ1740del ZFHX3_uc002fcl.2_In_Frame_Del_p.QQ826del NM_006885 NP_008816 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 isoform A 1740_1741 Poly-Gln. muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation transcription factor complex enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding ovary(2)|skin(2) 4 Ovarian(137;0.13) GCGTTTGTGCttgttgttgttgttgt 0.413 0.54 11 13 MLLT6 4302 broad.mit.edu 37 17 36865780 36865780 + Frame_Shift_Del DEL G - - KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr17:36865780delG uc002hqi.3 + 6 517 c.504delG c.(502-504)GTGfs p.V168fs MLLT6_uc010wdr.1_Frame_Shift_Del_p.V168fs|MLLT6_uc010cvm.1_Frame_Shift_Del_p.V168fs NM_005937 NP_005928 P55198 AF17_HUMAN myeloid/lymphoid or mixed-lineage leukemia 168 PHD-type 2. regulation of transcription, DNA-dependent nucleus protein binding|zinc ion binding breast(3)|prostate(1)|lung(1)|skin(1) 6 Breast(7;4.43e-21) TGCTGGAGGTGGACAACGTCA 0.562 0.73 300 807 STAT5A 6776 broad.mit.edu 37 17 40462605 40462606 + Frame_Shift_Ins INS - A A KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr17:40462605_40462606insA uc002hzj.1 + 20 2945_2946 c.2303_2304insA c.(2302-2304)TTAfs p.L768fs STAT5A_uc010cya.1_Frame_Shift_Ins_p.L768fs|STAT5A_uc010cyb.1_Frame_Shift_Ins_p.L737fs|STAT5A_uc010cyc.1_Frame_Shift_Ins_p.L738fs NM_003152 NP_003143 P42229 STA5A_HUMAN signal transducer and activator of transcription 768 2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|oxaloacetate metabolic process|succinate metabolic process|taurine metabolic process|valine metabolic process cytosol|nucleoplasm calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity lung(1) 1 all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.128) GAGGAACTCTTACGCCGACCAA 0.564 0.69 247 554 NOTCH3 4854 broad.mit.edu 37 19 15311677 15311688 + In_Frame_Del DEL GGCGACGGCGGC - - KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr19:15311677_15311688delGGCGACGGCGGC uc002nan.2 - 1 105_116 c.29_40delGCCGCCGTCGCC c.(28-42)CGCCGCCGTCGCCCG>CCG p.RRRR10del NOTCH3_uc002nao.1_In_Frame_Del_p.RRRR10del NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 10_13 Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.11 72 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.51 61 63 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.64 201 362 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KATOIII_STOMACH NA KATOIII_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 34 493 NUDT10 170685 broad.mit.edu 37 X 51075965 51075965 + Frame_Shift_Del DEL G - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:51075965delG uc004dph.2 + 2 368 c.148delG c.(148-150)GGGfs p.G50fs NUDT10_uc004dpi.3_Frame_Shift_Del_p.G50fs NM_153183 NP_694853 Q8NFP7 NUD10_HUMAN nudix-type motif 10 50 Nudix box.|Nudix hydrolase. cytoplasm diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding 0 Ovarian(276;0.236) CGTGCCGGGCGGGGGCATGGA 0.697 0.46 42 36 SSX7 280658 broad.mit.edu 37 X 52679424 52679424 + Frame_Shift_Del DEL C - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:52679424delC uc004dqx.1 - 5 468 c.309delG c.(307-309)AGGfs p.R103fs NM_173358 NP_775494 Q7RTT5 SSX7_HUMAN synovial sarcoma, X breakpoint 7 103 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus nucleic acid binding skin(1) 1 Ovarian(276;0.236) TTCTCTGGAGCCTGCAAAAAG 0.418 0.32 30 14 HEPH 9843 broad.mit.edu 37 X 65393489 65393489 + Frame_Shift_Del DEL G - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:65393489delG uc011moz.1 + 4 540 c.480delG c.(478-480)CCGfs p.P160fs HEPH_uc004dwn.2_Frame_Shift_Del_p.P160fs|HEPH_uc004dwo.2_5'UTR|HEPH_uc010nkr.2_Frame_Shift_Del_p.P160fs|HEPH_uc011mpa.1_Frame_Shift_Del_p.P160fs NM_138737 NP_620074 Q9BQS7 HEPH_HUMAN hephaestin isoform a 157 Extracellular (Potential).|Plastocyanin-like 1. cellular iron ion homeostasis|copper ion transport|transmembrane transport integral to membrane|plasma membrane copper ion binding|oxidoreductase activity lung(5)|ovary(4) 9 CTGTTCCCCCGGGGGGCAGCC 0.532 0.46 64 55 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 4 53 IRAK1 3654 broad.mit.edu 37 X 153279549 153279554 + In_Frame_Del DEL GGCCCA - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:153279549_153279554delGGCCCA uc004fjs.1 - 11 1557_1562 c.1478_1483delTGGGCC c.(1477-1485)CTGGGCCAG>CAG p.LG493del IRAK1_uc004fjr.1_In_Frame_Del_p.LG493del|IRAK1_uc004fjt.1_Intron|IRAK1_uc010nur.2_Intron|IRAK1_uc004fju.2_In_Frame_Del_p.LG519del NM_001569 NP_001560 P51617 IRAK1_HUMAN interleukin-1 receptor-associated kinase 1 493_494 Protein kinase. activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|anti-apoptosis|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|lipopolysaccharide-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|protein autophosphorylation|protein oligomerization|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transmembrane receptor protein serine/threonine kinase signaling pathway cytosol|endosome membrane|interleukin-1 receptor complex ATP binding|NF-kappaB-inducing kinase activity|protein binding|protein heterodimerization activity|protein homodimerization activity|ubiquitin-protein ligase activity lung(5)|ovary(2)|breast(1)|central_nervous_system(1) 9 all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) CAGGCCAGCTGGCCCAGGCCCAGGCC 0.684 0.31 31 14 SPEN 23013 broad.mit.edu 37 1 16259043 16259043 + Frame_Shift_Del DEL G - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:16259043delG uc001axk.1 + 11 6512 c.6308delG c.(6307-6309)AGGfs p.R2103fs SPEN_uc010obp.1_Frame_Shift_Del_p.R2062fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2103 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) GTCAGTCCCAGGGGGGCTGCA 0.512 0.37 74 44 ARHGAP29 9411 broad.mit.edu 37 1 94668155 94668155 + Frame_Shift_Del DEL T - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:94668155delT uc001dqj.3 - 11 1457 c.1088delA c.(1087-1089)AATfs p.N363fs ARHGAP29_uc009wdq.1_RNA|ARHGAP29_uc001dql.2_Frame_Shift_Del_p.N363fs NM_004815 NP_004806 Q52LW3 RHG29_HUMAN PTPL1-associated RhoGAP 1 363 Potential. Rho protein signal transduction cytosol metal ion binding|Rho GTPase activator activity breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1) 11 all_lung(203;0.000732)|Lung NSC(277;0.00328) all cancers(265;0.0187)|Epithelial(280;0.159) CTTGTTGAGATTTTTTGCTAA 0.378 0.32 69 33 EGLN1 54583 broad.mit.edu 37 1 231557367 231557367 + Frame_Shift_Del DEL C - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:231557367delC uc001huv.2 - 1 3424 c.268delG c.(268-270)GCCfs p.A90fs EGLN1_uc001huu.3_5'Flank NM_022051 NP_071334 Q9GZT9 EGLN1_HUMAN egl nine homolog 1 90 negative regulation of sequence-specific DNA binding transcription factor activity|oxygen homeostasis|response to hypoxia cytosol iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptidyl-proline dioxygenase activity|protein binding|zinc ion binding 0 Prostate(94;0.194)|Acute lymphoblastic leukemia(190;0.244) Vitamin C(DB00126) 0.000 0.30 124 52 OR2L13 284521 broad.mit.edu 37 1 248263376 248263376 + Frame_Shift_Del DEL A - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:248263376delA uc001ids.2 + 3 1036 c.699delA c.(697-699)AGAfs p.R233fs NM_175911 NP_787107 Q8N349 OR2LD_HUMAN olfactory receptor, family 2, subfamily L, 233 Cytoplasmic (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity|protein binding central_nervous_system(2)|ovary(1)|skin(1) 4 all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0132) AGGAGGGGAGAAAAAAGGCCT 0.443 0.10 201 22 SOX11 6664 broad.mit.edu 37 2 5833526 5833528 + In_Frame_Del DEL GAC - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:5833526_5833528delGAC uc002qyj.2 + 1 728_730 c.673_675delGAC c.(673-675)GACdel p.D233del NM_003108 NP_003099 P35716 SOX11_HUMAN SRY-box 11 233 Poly-Asp. cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis cytoplasm|nucleolus enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding central_nervous_system(3) 3 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) OV - Ovarian serous cystadenocarcinoma(76;0.132) 0.000 0.39 76 49 MAP3K2 10746 broad.mit.edu 37 2 128079791 128079791 + Frame_Shift_Del DEL C - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:128079791delC uc002toj.1 - 11 941 c.876delG c.(874-876)GGGfs p.G292fs NM_006609 NP_006600 Q9Y2U5 M3K2_HUMAN mitogen-activated protein kinase kinase kinase 292 activation of JUN kinase activity|cellular response to mechanical stimulus nucleus ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein kinase binding lung(3)|ovary(2)|large_intestine(1)|central_nervous_system(1) 7 Colorectal(110;0.1) BRCA - Breast invasive adenocarcinoma(221;0.0706) GTAAGCTGGTCCCCTGGGTCC 0.373 0.45 47 39 TTN 7273 broad.mit.edu 37 2 179535860 179535860 + Frame_Shift_Del DEL T - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179535860delT uc010zfg.1 - 151 31586 c.31362delA c.(31360-31362)AAAfs p.K10454fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.K7115fs|TTN_uc010fre.1_Intron|TTN_uc010zfk.1_5'UTR NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 11381 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TAGTGGGCGGTTTTTTTGGAG 0.368 0.45 36 29 TTN 7273 broad.mit.edu 37 2 179611375 179611375 + Frame_Shift_Del DEL C - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179611375delC uc002unb.2 - 46 15976 c.15752delG c.(15751-15753)GGAfs p.G5251fs TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron NM_133379 NP_596870 Q8WZ42 TITIN_HUMAN titin isoform novex-3 8770 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGTACTCTCCCCCTTCTCC 0.408 0.40 122 83 CREB1 1385 broad.mit.edu 37 2 208425864 208425865 + Frame_Shift_Del DEL AG - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:208425864_208425865delAG uc002vcc.2 + 4 534_535 c.283_284delAG c.(283-285)AGAfs p.R95fs CREB1_uc010ziz.1_Intron|CREB1_uc002vcd.2_Intron|CREB1_uc010zja.1_RNA NM_134442 NP_604391 P16220 CREB1_HUMAN cAMP responsive element binding protein 1 95 activation of phospholipase C activity|axon guidance|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway protein dimerization activity|transcription cofactor activity EWSR1/CREB1(42) soft_tissue(42)|breast(1)|central_nervous_system(1) 44 LUSC - Lung squamous cell carcinoma(261;0.0768)|Epithelial(149;0.127)|Lung(261;0.145) Adenosine monophosphate(DB00131)|Bromocriptine(DB01200)|Naloxone(DB01183) GGACTTAAAAAGACTTTTCTCC 0.366 0.51 22 23 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.17 33 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.51 117 123 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.41 27 19 FBN2 2201 broad.mit.edu 37 5 127627259 127627259 + Frame_Shift_Del DEL G - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:127627259delG uc003kuu.2 - 49 6693 c.6254delC c.(6253-6255)CCTfs p.P2085fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 2085 EGF-like 35; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) TACAAAGCCAGGGGGGCAGAG 0.433 0.36 79 44 FBN2 2201 broad.mit.edu 37 5 127636541 127636541 + Frame_Shift_Del DEL G - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:127636541delG uc003kuu.2 - 48 6573 c.6134delC c.(6133-6135)CCAfs p.P2045fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 2045 EGF-like 34; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) TTCATACCCTGGGGGACAGAT 0.448 0.39 57 36 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.70 3 7 MAP3K4 4216 broad.mit.edu 37 6 161469829 161469829 + Frame_Shift_Del DEL A - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:161469829delA uc003qtn.2 + 3 667 c.525delA c.(523-525)CCAfs p.P175fs MAP3K4_uc010kkc.1_Frame_Shift_Del_p.P175fs|MAP3K4_uc003qto.2_Frame_Shift_Del_p.P175fs|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_5'UTR NM_005922 NP_005913 Q9Y6R4 M3K4_HUMAN mitogen-activated protein kinase kinase kinase 4 175 activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity perinuclear region of cytoplasm ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding ovary(3)|lung(3)|skin(2)|stomach(1) 9 Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771) OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05) GATCTTTGCCAAAAAAATCAA 0.438 0.29 152 61 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.83 2 10 STAR 6770 broad.mit.edu 37 8 38003815 38003815 + Frame_Shift_Del DEL C - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:38003815delC uc003xkv.1 - 4 721 c.457delG c.(457-459)GAGfs p.E153fs STAR_uc010lwc.1_Frame_Shift_Del_p.E115fs NM_001007243 NP_001007244 P49675 STAR_HUMAN steroidogenic acute regulatory protein isoform 153 START. C21-steroid hormone biosynthetic process mitochondrial intermembrane space cholesterol transporter activity ovary(1) 1 Colorectal(12;0.000442) all_lung(54;0.0151)|Lung NSC(58;0.0295) READ - Rectum adenocarcinoma(644;0.188) ACCTTGATCTCCTTGACATTG 0.597 0.19 450 108 PLAG1 5324 broad.mit.edu 37 8 57079754 57079754 + Frame_Shift_Del DEL T - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:57079754delT uc003xsq.3 - 3 1002 c.551delA c.(550-552)AAGfs p.K184fs PLAG1_uc003xsr.3_Frame_Shift_Del_p.K184fs|PLAG1_uc010lyi.2_Frame_Shift_Del_p.K184fs|PLAG1_uc010lyj.2_Frame_Shift_Del_p.K102fs NM_001114635 NP_001108107 Q6DJT9 PLAG1_HUMAN pleiomorphic adenoma gene 1 isoform b 184 Decreased nuclear import with localization in the nucleus but also in the cytoplasm. nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding CTNNB1/PLAG1(60)|FGFR1_ENST00000447712/PLAG1(28)|CHCHD7/PLAG1(12)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|COL1A2/PLAG1(3)|TCEA1_ENST00000521604/PLAG1(3) salivary_gland(113)|soft_tissue(13)|lung(1)|central_nervous_system(1)|breast(1) 129 all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125) Epithelial(17;0.00179)|all cancers(17;0.0125) GCACTGGTGCTTTTTTTCTTT 0.483 0.27 266 96 CSMD3 114788 broad.mit.edu 37 8 113303789 113303789 + Frame_Shift_Del DEL A - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:113303789delA uc003ynu.2 - 56 9083 c.8924delT c.(8923-8925)TTGfs p.L2975fs CSMD3_uc003yns.2_Frame_Shift_Del_p.L2177fs|CSMD3_uc003ynt.2_Frame_Shift_Del_p.L2935fs|CSMD3_uc011lhx.1_Frame_Shift_Del_p.L2806fs NM_198123 NP_937756 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 isoform 1 2975 Extracellular (Potential).|Sushi 20. integral to membrane|plasma membrane ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1) 63 TTGACATATCAAAACTGAAGA 0.328 0.21 45 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 69 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 480 51 TEK 7010 broad.mit.edu 37 9 27158026 27158026 + Frame_Shift_Del DEL A - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:27158026delA uc003zqi.3 + 2 692 c.250delA c.(250-252)AAAfs p.K84fs TEK_uc010mjc.1_Intron|TEK_uc011lnn.1_Frame_Shift_Del_p.K84fs|TEK_uc011lno.1_Frame_Shift_Del_p.K84fs|TEK_uc011lnp.1_Intron|TEK_uc003zqj.1_Frame_Shift_Del_p.K61fs NM_000459 NP_000450 Q02763 TIE2_HUMAN TEK tyrosine kinase, endothelial precursor 84 Extracellular (Potential).|Ig-like C2-type 1. angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1) 12 all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255) Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027) AGAATGGGCTAAAAAAGTTGT 0.468 0.45 54 44 ROR2 4920 broad.mit.edu 37 9 94493250 94493250 + Frame_Shift_Del DEL G - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:94493250delG uc004arj.1 - 7 1324 c.1125delC c.(1123-1125)CCCfs p.P375fs ROR2_uc004ari.1_Frame_Shift_Del_p.P235fs|ROR2_uc004ark.2_Frame_Shift_Del_p.P375fs NM_004560 NP_004551 Q01974 ROR2_HUMAN receptor tyrosine kinase-like orphan receptor 2 375 Extracellular (Potential).|Kringle. negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1) 20 TAAAGCACCAGGGGCCCTCCA 0.542 0.37 38 22 NR4A3 8013 broad.mit.edu 37 9 102590616 102590618 + In_Frame_Del DEL CAC - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:102590616_102590618delCAC uc004baf.1 + 3 1021_1023 c.292_294delCAC c.(292-294)CACdel p.H108del NR4A3_uc004bae.2_In_Frame_Del_p.H108del|NR4A3_uc004bag.1_In_Frame_Del_p.H108del|NR4A3_uc004bai.2_In_Frame_Del_p.H119del NM_006981 NP_008912 Q92570 NR4A3_HUMAN nuclear receptor subfamily 4, group A, member 3 108 Poly-His. regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor steroid hormone receptor activity|thyroid hormone receptor activity|zinc ion binding EWSR1/NR4A3(140)|TAF15/NR4A3(33) bone(173) 173 Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189) ccatcaccatcaccaccaccacc 0.483 0.32 43 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 792 306 NCAPD3 23310 broad.mit.edu 37 11 134048586 134048586 + Frame_Shift_Del DEL G - - rs138442478 KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:134048586delG uc001qhd.1 - 22 3331 c.2725delC c.(2725-2727)CAGfs p.Q909fs NCAPD3_uc010scm.1_RNA|NCAPD3_uc009zda.1_RNA NM_015261 NP_056076 P42695 CNDD3_HUMAN non-SMC condensin II complex, subunit D3 909 cell division|mitotic chromosome condensation nuclear centromeric heterochromatin|nuclear condensin complex methylated histone residue binding ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1) 5 all_hematologic(175;0.127) all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227) CCTCTGACCTGGGGGGGTGGC 0.522 0.26 20 7 ZNF384 171017 broad.mit.edu 37 12 6777070 6777075 + In_Frame_Del DEL TGCTGC - - rs151322806;rs111332695;rs78573212;rs1052680 KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:6777070_6777075delTGCTGC uc010sfh.1 - 11 1747_1752 c.1539_1544delGCAGCA c.(1537-1545)CAGCAGCAA>CAA p.513_515QQQ>Q ZNF384_uc001qpz.2_In_Frame_Del_p.452_454QQQ>Q|ZNF384_uc001qqa.2_In_Frame_Del_p.452_454QQQ>Q|ZNF384_uc001qqb.2_In_Frame_Del_p.436_438QQQ>Q|ZNF384_uc001qqc.2_In_Frame_Del_p.452_454QQQ>Q|ZNF384_uc001qqd.2_In_Frame_Del_p.397_399QQQ>Q|ZNF384_uc001qqe.2_In_Frame_Del_p.436_438QQQ>Q NM_001135734 NP_001129206 Q8TF68 ZN384_HUMAN nuclear matrix transcription factor 4 isoform d 513_515 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding EWSR1/ZNF384(4) haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1) 8 TGGTGgctgttgctgctgctgctgct 0.335 0.19 210 49 ACVR1B 91 broad.mit.edu 37 12 52345607 52345607 + Frame_Shift_Del DEL G - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:52345607delG uc001rzn.2 + 1 122 c.80delG c.(79-81)CGGfs p.R27fs ACVR1B_uc001rzl.2_Frame_Shift_Del_p.R27fs|ACVR1B_uc001rzm.2_Frame_Shift_Del_p.R27fs|ACVR1B_uc010snn.1_Frame_Shift_Del_p.R27fs NM_004302 NP_004293 P36896 ACV1B_HUMAN activin A receptor, type IB isoform a precursor 27 Extracellular (Potential). G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|peptidyl-threonine phosphorylation|positive regulation of activin receptor signaling pathway|positive regulation of erythrocyte differentiation|protein autophosphorylation|transmembrane receptor protein serine/threonine kinase signaling pathway cell surface activin receptor activity, type I|ATP binding|metal ion binding|SMAD binding|transforming growth factor beta receptor activity|ubiquitin protein ligase binding pancreas(4)|breast(2)|ovary(1)|lung(1)|kidney(1) 9 BRCA - Breast invasive adenocarcinoma(357;0.104) Adenosine triphosphate(DB00171) 0.000 0.27 64 24 BRCA2 675 broad.mit.edu 37 13 32912345 32912346 + Frame_Shift_Ins INS - A A rs120074207;rs80359406 KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:32912345_32912346insA uc001uub.1 + 11 4080_4081 c.3853_3854insA c.(3853-3855)GAAfs p.E1285fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 1285 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) AACTGTAAGTGAAAAAAATAAT 0.262 0.43 12 9 RAB15 376267 broad.mit.edu 37 14 65417741 65417741 + Frame_Shift_Del DEL C - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:65417741delC uc001xhz.2 - 4 456 c.375delG c.(373-375)GGGfs p.G125fs FNTB_uc010tsl.1_Intron|FNTB_uc010tsm.1_Intron|RAB15_uc010aqk.2_RNA NM_198686 NP_941959 P59190 RAB15_HUMAN RAB15, member RAS onocogene family Error:Variant_position_missing_in_P59190_after_alignment protein transport|small GTPase mediated signal transduction plasma membrane GTP binding ovary(1) 1 all cancers(60;0.00136)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.0102) GCCTTGCCTTCCCCGGTGAGG 0.592 0.41 230 163 TP53 7157 broad.mit.edu 37 17 7577036 7577036 + Frame_Shift_Del DEL G - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:7577036delG uc002gim.2 - 8 1096 c.902delC c.(901-903)CCAfs p.P301fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Frame_Shift_Del_p.P301fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.P169fs|TP53_uc010cng.1_Frame_Shift_Del_p.P169fs|TP53_uc002gii.1_Frame_Shift_Del_p.P169fs|TP53_uc010cnh.1_Frame_Shift_Del_p.P301fs|TP53_uc010cni.1_Frame_Shift_Del_p.P301fs|TP53_uc002gij.2_Frame_Shift_Del_p.P301fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 301 Interaction with HIPK1 (By similarity).|Interaction with CARM1. P -> T (in a sporadic cancer; somatic mutation).|P -> A (in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.P301fs*44(9)|p.0?(7)|p.G302fs*4(4)|p.?(3)|p.P301fs*5(3)|p.P301S(3)|p.P301_S303delPGS(1)|p.L299fs*2(1)|p.P301P(1)|p.L265_K305del41(1)|p.P301Q(1)|p.P301fs*45(1)|p.P301T(1)|p.G293fs*1(1)|p.P301L(1)|p.P301A(1)|p.E298_P301delELPP(1)|p.H296_S303delHHELPPGS(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) AGTGCTCCCTGGGGGCAGCTC 0.557 0.95 1 21 FASN 2194 broad.mit.edu 37 17 80041282 80041283 + Frame_Shift_Ins INS - T T KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:80041282_80041283insT uc002kdu.2 - 32 5477_5478 c.5360_5361insA c.(5359-5361)AAGfs p.K1787fs FASN_uc002kdv.1_5'Flank NM_004104 NP_004095 P49327 FAS_HUMAN fatty acid synthase 1787 Enoyl reductase (By similarity). energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process cytosol|Golgi apparatus|melanosome|plasma membrane 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding central_nervous_system(1) 1 all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246) OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237) Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339) ATGTCACGTTCTTCAGGAAGAT 0.658 0.54 48 56 SS18 6760 broad.mit.edu 37 18 23615012 23615014 + In_Frame_Del DEL CTG - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr18:23615012_23615014delCTG uc002kvm.2 - 9 1129_1131 c.1051_1053delCAG c.(1051-1053)CAGdel p.Q351del SS18_uc002kvn.2_In_Frame_Del_p.Q320del|SS18_uc010xbf.1_In_Frame_Del_p.Q269del|SS18_uc010xbg.1_In_Frame_Del_p.Q268del|SS18_uc010xbh.1_In_Frame_Del_p.Q268del|SS18_uc010xbi.1_In_Frame_Del_p.Q328del|SS18_uc010dlz.1_In_Frame_Del_p.Q299del NM_001007559 NP_001007560 Q15532 SSXT_HUMAN synovial sarcoma translocation, chromosome 18 351 Gln-rich.|2 X 13 AA imperfect tandem repeats.|1. positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleus ligand-dependent nuclear receptor transcription coactivator activity|protein binding SS18/SSX1(1169)|SS18/SSX2(702)|SS18/SSX4(12) soft_tissue(1883)|ovary(1) 1884 all_cancers(21;0.000194)|Lung NSC(5;0.000413)|all_lung(6;0.00118)|Ovarian(20;0.124) GCCCTGGGTACTGCTGCTGCTGG 0.468 0.36 199 114 RGL3 57139 broad.mit.edu 37 19 11526761 11526762 + Frame_Shift_Ins INS - G G KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:11526761_11526762insG uc002mrp.2 - 5 552_553 c.488_489insC c.(487-489)CCTfs p.P163fs RGL3_uc002mrn.2_5'UTR|RGL3_uc002mrm.2_5'UTR|RGL3_uc002mro.2_Frame_Shift_Ins_p.P163fs NM_001035223 NP_001030300 Q3MIN7 RGL3_HUMAN ral guanine nucleotide dissociation 163 N-terminal Ras-GEF. regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction intracellular ovary(1) 1 CCGAATGGGCAGGGGGGTCTCG 0.619 0.41 52 36 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 50 207 ADCK4 79934 broad.mit.edu 37 19 41197963 41197963 + Frame_Shift_Del DEL C - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41197963delC uc002oor.2 - 15 1914 c.1612delG c.(1612-1614)GACfs p.D538fs NUMBL_uc010xvq.1_5'Flank|NUMBL_uc002oon.2_5'Flank|NUMBL_uc002ooo.2_5'Flank|NUMBL_uc010xvr.1_5'Flank|ADCK4_uc002oop.1_Frame_Shift_Del_p.D215fs|ADCK4_uc002ooq.1_Frame_Shift_Del_p.D497fs NM_024876 NP_079152 Q96D53 ADCK4_HUMAN aarF domain containing kinase 4 isoform a 538 integral to membrane protein serine/threonine kinase activity 0 Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219) ACCCAGGAGTCCCCTTTGGTG 0.652 0.18 50 11 CD79A 973 broad.mit.edu 37 19 42383610 42383610 + Frame_Shift_Del DEL C - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:42383610delC uc002orv.2 + 3 570 c.385delC c.(385-387)CCCfs p.P129fs CD79A_uc002oru.2_Frame_Shift_Del_p.P91fs NM_001783 NP_001774 P11912 CD79A_HUMAN CD79A antigen isoform 1 precursor 129 Extracellular (Potential). B cell differentiation|B cell proliferation|B cell receptor signaling pathway B cell receptor complex|external side of plasma membrane|integral to membrane|membrane raft|multivesicular body transmembrane receptor activity ovary(2)|pancreas(1) 3 0.000 0.31 472 217 GSK3A 2931 broad.mit.edu 37 19 42736238 42736238 + Frame_Shift_Del DEL C - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:42736238delC uc002otb.1 - 10 1468 c.1349delG c.(1348-1350)GGCfs p.G450fs GSK3A_uc002ota.1_Frame_Shift_Del_p.G368fs|GSK3A_uc002otc.2_RNA NM_019884 NP_063937 P49840 GSK3A_HUMAN glycogen synthase kinase 3 alpha 450 insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of insulin receptor signaling pathway|negative regulation of transferase activity|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process beta-catenin destruction complex|cytosol ATP binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|tau-protein kinase activity ovary(2)|lung(2) 4 Prostate(69;0.00682) 0.000 0.19 745 177 STRN4 29888 broad.mit.edu 37 19 47231884 47231884 + Frame_Shift_Del DEL G - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:47231884delG uc002pfl.2 - 7 1063 c.1030delC c.(1030-1032)CATfs p.H344fs STRN4_uc002pfm.2_Frame_Shift_Del_p.H344fs|STRN4_uc010xyf.1_RNA|STRN4_uc010xyg.1_RNA NM_013403 NP_037535 Q9NRL3 STRN4_HUMAN zinedin isoform 1 344 cytoplasm|membrane armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding 0 Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212) OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035) CCCAGCTCATGGGGGCTCCCA 0.632 0.32 285 137 LMTK3 114783 broad.mit.edu 37 19 49002150 49002151 + Frame_Shift_Ins INS - G G KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:49002150_49002151insG uc002pjk.2 - 12 2262_2263 c.2262_2263insC c.(2260-2265)CCCGCCfs p.P754fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.10 281 31 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 167 428 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 10 130 MED15 51586 broad.mit.edu 37 22 20918916 20918918 + In_Frame_Del DEL CAG - - KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:20918916_20918918delCAG uc002zsp.2 + 6 711_713 c.631_633delCAG c.(631-633)CAGdel p.Q218del MED15_uc002zsn.1_In_Frame_Del_p.Q137del|MED15_uc002zso.2_In_Frame_Del_p.Q147del|MED15_uc002zsq.2_In_Frame_Del_p.Q218del|MED15_uc010gso.2_In_Frame_Del_p.Q218del|MED15_uc002zsr.2_In_Frame_Del_p.Q192del|MED15_uc011ahs.1_In_Frame_Del_p.Q192del|MED15_uc011aht.1_In_Frame_Del_p.Q192del|MED15_uc002zss.2_In_Frame_Del_p.Q137del|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 218 Poly-Gln. Missing (in Ref. 4; CAG30423). regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) gcagcagctccagcagcagcagc 0.187 0.11 117 15 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 31 CDK11A 728642 broad.mit.edu 37 1 1635536 1635537 + Frame_Shift_Ins INS - A A KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:1635536_1635537insA uc009vks.2 - 16 1843_1844 c.1735_1736insT c.(1735-1737)TACfs p.Y579fs CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agv.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc001ahh.3_Intron|SLC35E2_uc009vkm.1_Intron|CDK11A_uc001ahj.3_Frame_Shift_Ins_p.Y86fs|CDK11A_uc009vkp.2_Frame_Shift_Ins_p.Y196fs|CDK11A_uc009vkq.2_Intron|CDK11A_uc009vkr.2_Frame_Shift_Ins_p.Y569fs NM_024011 NP_076916 Q9UQ88 CD11A_HUMAN cell division cycle 2-like 2 isoform 1 582 Protein kinase. apoptosis|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent cytoplasm|nucleus ATP binding|cyclin-dependent protein kinase activity|protein binding stomach(1) 1 GACCGGGGTGTAGGCCTTCAGA 0.673 0.30 16 7 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 221 50 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 84 58 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 13 26 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 105 27 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.83 5 25 TP53 7157 broad.mit.edu 37 17 7578474 7578475 + Frame_Shift_Ins INS - G G KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:7578474_7578475insG uc002gim.2 - 5 649_650 c.455_456insC c.(454-456)CCGfs p.P152fs TP53_uc002gig.1_Frame_Shift_Ins_p.P152fs|TP53_uc002gih.2_Frame_Shift_Ins_p.P152fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Ins_p.P20fs|TP53_uc010cng.1_Frame_Shift_Ins_p.P20fs|TP53_uc002gii.1_Frame_Shift_Ins_p.P20fs|TP53_uc010cnh.1_Frame_Shift_Ins_p.P152fs|TP53_uc010cni.1_Frame_Shift_Ins_p.P152fs|TP53_uc002gij.2_Frame_Shift_Ins_p.P152fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Ins_p.P59fs|TP53_uc002gio.2_Frame_Shift_Ins_p.P20fs|TP53_uc010vug.1_Frame_Shift_Ins_p.P113fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 152 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). P -> R (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|P -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> A (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.P152L(57)|p.P152S(21)|p.P152fs*18(17)|p.P153fs*28(8)|p.P152T(7)|p.0?(7)|p.P152fs*29(5)|p.P152P(5)|p.P152Q(4)|p.P152fs*14(4)|p.P152fs*28(3)|p.P152R(3)|p.T150fs*16(3)|p.P152A(2)|p.P153fs*16(1)|p.P151_V173del23(1)|p.P152_P153del(1)|p.G154fs*16(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.P153fs*20(1)|p.D148fs*23(1)|p.P152del(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.Q144_G154del11(1)|p.G154fs*27(1)|p.P152_P153insXXX(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGGTGCCGGGCGGGGGTGTGGA 0.614 0.27 30 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.35 17 9 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 68 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KE39_STOMACH NA KE39_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.85 8 47 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KE39_STOMACH NA KE39_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.45 249 207 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KE39_STOMACH NA KE39_STOMACH NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.26 96 34 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KE39_STOMACH NA KE39_STOMACH NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.12 51 7 ALPK1 80216 broad.mit.edu 37 4 113360940 113360941 + Frame_Shift_Del DEL AG - - KE39_STOMACH NA KE39_STOMACH NA g.chr4:113360940_113360941delAG uc003iap.3 + 14 3729_3730 c.3450_3451delAG c.(3448-3453)ACAGAAfs p.T1150fs ALPK1_uc003ian.3_Frame_Shift_Del_p.T1150fs|ALPK1_uc011cfx.1_Frame_Shift_Del_p.T1072fs|ALPK1_uc003iao.3_RNA|ALPK1_uc010imo.2_Frame_Shift_Del_p.T978fs NM_025144 NP_079420 Q96QP1 ALPK1_HUMAN alpha-kinase 1 1150_1151 Alpha-type protein kinase. ATP binding|protein serine/threonine kinase activity ovary(5) 5 Ovarian(17;0.0446)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.00325) TGGTGAAAACAGAATACAAAGC 0.366 0.59 9 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KE39_STOMACH NA KE39_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 53 69 NIPBL 25836 broad.mit.edu 37 5 37045620 37045623 + Frame_Shift_Del DEL TTCT - - KE39_STOMACH NA KE39_STOMACH NA g.chr5:37045620_37045623delTTCT uc003jkl.3 + 37 6918_6921 c.6419_6422delTTCT c.(6418-6423)CTTCTTfs p.L2140fs NIPBL_uc003jkk.3_Frame_Shift_Del_p.L2140fs NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 2140_2141 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) AAACCAGCACTTCTTAGATCCCTT 0.343 0.11 232 28 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KE39_STOMACH NA KE39_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 20 39 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KE39_STOMACH NA KE39_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KE39_STOMACH NA KE39_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KE39_STOMACH NA KE39_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.41 431 304 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KE39_STOMACH NA KE39_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 442 91 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KE39_STOMACH NA KE39_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 80 328 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KE39_STOMACH NA KE39_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 3 89 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 15 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.45 17 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 46 51 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 13 28 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.12 276 39 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.32 506 235 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.55 5 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 172 49 NEK3 4752 broad.mit.edu 37 13 52725278 52725279 + Splice_Site INS - A A KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:52725278_52725279insA uc001vgi.2 - 7 783 c.548_splice c.e7+1 p.S183_splice NEK3_uc001vgg.2_Splice_Site_p.S177_splice|NEK3_uc001vgh.2_Splice_Site_p.S204_splice|NEK3_uc010tgx.1_Splice_Site|NEK3_uc010tgy.1_Splice_Site_p.S183_splice NM_152720 NP_689933 P51956 NEK3_HUMAN NIMA-related kinase 3 isoform a cell division|mitosis nucleus ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173) GBM - Glioblastoma multiforme(99;2.81e-08) ATGCAGCACTCACCTTTTATTG 0.421 0.50 59 58 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.47 26 23 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.14 107 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 135 405 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 58 CACNA1F 778 broad.mit.edu 37 X 49076194 49076195 + In_Frame_Ins INS - TCTTCCTCT TCTTCCTCT KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chrX:49076194_49076195insTCTTCCTCT uc004dnb.2 - 20 2536_2537 c.2474_2475insAGAGGAAGA c.(2473-2475)GAG>GAAGAGGAAGAG p.825_825E>EEEE CACNA1F_uc010nip.2_In_Frame_Ins_p.814_814E>EEEE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 825 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) CCCCTGCACcctcttcctcttc 0.347 0.24 62 20 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 2 26 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.31 11 5 BMP2K 55589 broad.mit.edu 37 4 79831985 79831987 + In_Frame_Del DEL GAA - - KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr4:79831985_79831987delGAA uc003hlk.2 + 16 2450_2452 c.2284_2286delGAA c.(2284-2286)GAAdel p.E763del PAQR3_uc003hlm.2_Intron|PAQR3_uc003hln.2_Intron|uc010ijm.1_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 763 nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 GCAAGATGATGAAGAAGTTCTTC 0.429 0.46 7 6 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.26 26 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 79 80 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.78 8 29 TMEM229A 730130 broad.mit.edu 37 7 123672457 123672459 + In_Frame_Del DEL GCT - - KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr7:123672457_123672459delGCT uc011kob.1 - 1 1065_1067 c.599_601delAGC c.(598-603)CAGCGG>CGG p.Q200del uc011koc.1_Intron NM_001136002 NP_001129474 B2RXF0 T229A_HUMAN transmembrane protein 229A 200 host cell nucleus|integral to membrane sequence-specific DNA binding transcription factor activity 0 GCGCCCCTCCgctgctgctgctg 0.601 0.38 8 5 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 2 14 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.45 16 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 37 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 418 146 SDHD 6392 broad.mit.edu 37 11 111959735 111959738 + Splice_Site DEL GGCA - - KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr11:111959735_111959738delGGCA uc001pmz.2 + 3 375 c.314_splice c.e3+1 p.W105_splice TIMM8B_uc001pmx.2_5'Flank|TIMM8B_uc001pmy.2_5'Flank NM_003002 NP_002993 O14521 DHSD_HUMAN succinate dehydrogenase complex, subunit D respiratory electron transport chain|transport|tricarboxylic acid cycle integral to membrane|mitochondrial respiratory chain complex II electron carrier activity|heme binding|succinate dehydrogenase activity|ubiquinone binding 0 all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425) Epithelial(105;6.13e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;1.05e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0515) Succinic acid(DB00139) CATGGTCACTGGCAAGTATAGCAA 0.441 0.44 62 49 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.62 15 25 SRP14 6727 broad.mit.edu 37 15 40328597 40328599 + In_Frame_Del DEL TGC - - KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr15:40328597_40328599delTGC uc001zkq.2 - 5 418_420 c.346_348delGCA c.(346-348)GCAdel p.A116del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgcggcaggtgctgctgctgct 0.227 0.11 55 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.48 50 47 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 163 790 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KELLY_AUTONOMIC_GANGLIA NA KELLY_AUTONOMIC_GANGLIA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 7 150 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 60 RPL14 9045 broad.mit.edu 37 3 40503519 40503521 + In_Frame_Del DEL TAC - - rs111899316;rs147295890 by1000genomes KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:40503519_40503521delTAC uc003ckg.2 + 6 495_497 c.444_446delTAC c.(442-447)GGTACT>GGT p.T149del RPL14_uc003ckh.2_In_Frame_Del_p.T149del|RPL14_uc003cki.2_In_Frame_Del_p.T100del NM_003973 NP_003964 P50914 RL14_HUMAN ribosomal protein L14 149 endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription cytosolic large ribosomal subunit protein binding|RNA binding|structural constituent of ribosome 0 KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065) GTACTAAGGGTActgctgctgct 0.365 0.50 5 5 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.36 21 12 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 66 16 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.11 56 7 CASP6 839 broad.mit.edu 37 4 110618922 110618923 + Frame_Shift_Del DEL TC - - KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:110618922_110618923delTC uc003hzn.1 - 3 163_164 c.85_86delGA c.(85-87)GAAfs p.E29fs CASP6_uc003hzo.1_Intron NM_001226 NP_001217 P55212 CASP6_HUMAN caspase 6 isoform alpha preproprotein 29 cellular component disassembly involved in apoptosis|induction of apoptosis|proteolysis cytosol|nucleoplasm cysteine-type endopeptidase activity|protein binding ovary(1)|breast(1) 2 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.000171) ATCAAACATTTCTCTGTTAATG 0.381 0.41 79 56 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 133 201 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.44 53 42 ATXN1 6310 broad.mit.edu 37 6 16327915 16327916 + In_Frame_Ins INS - TGC TGC rs11969612 by1000genomes KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:16327915_16327916insTGC uc003nbt.2 - 8 1597_1598 c.626_627insGCA c.(625-627)CAT>CAGCAT p.208_209insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.208_209insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 208_209 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) gctgatgctgatgctgctgctg 0.381 0.13 104 15 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.23 56 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 4 119 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.96 1 23 PCSK7 9159 broad.mit.edu 37 11 117077805 117077806 + Frame_Shift_Ins INS - T T KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:117077805_117077806insT uc001pqr.2 - 15 2058_2059 c.1857_1858insA c.(1855-1860)GCAGTAfs p.A619fs uc001pqq.1_RNA|PCSK7_uc001pqs.1_Intron NM_004716 NP_004707 Q16549 PCSK7_HUMAN proprotein convertase subtilisin/kexin type 7 619_620 Extracellular (Potential). peptide hormone processing integral to Golgi membrane serine-type endopeptidase activity 0 all_hematologic(175;0.0487) Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234) BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537) CTGATGTCTACTGCACTCCACA 0.604 0.43 90 67 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.82 16 73 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.26 46 16 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.79 38 139 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.23 140 42 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 174 717 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 135 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.12 -2 19 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 483 103 IL17RD 54756 broad.mit.edu 37 3 57132383 57132384 + Frame_Shift_Del DEL AG - - KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:57132383_57132384delAG uc003dil.2 - 12 1436_1437 c.1347_1348delCT c.(1345-1350)CTCTTCfs p.L449fs IL17RD_uc003dik.2_Frame_Shift_Del_p.L425fs|IL17RD_uc010hna.2_Frame_Shift_Del_p.L305fs|IL17RD_uc011bex.1_Frame_Shift_Del_p.L305fs NM_017563 NP_060033 Q8NFM7 I17RD_HUMAN interleukin 17 receptor D precursor 449_450 SEFIR.|Cytoplasmic (Potential). Golgi membrane|integral to membrane|plasma membrane receptor activity 0 KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204) GCCACCAGGAAGAGCTCTCCTT 0.515 0.48 11 10 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 59 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.23 55 16 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 21 43 PMS2 5395 broad.mit.edu 37 7 6022510 6022526 + Frame_Shift_Del DEL ACTTCTCGTCCGTGGCA - - KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:6022510_6022526delACTTCTCGTCCGTGGCA uc003spl.2 - 12 2190_2206 c.2103_2119delTGCCACGGACGAGAAGT c.(2101-2121)CATGCCACGGACGAGAAGTATfs p.H701fs PMS2_uc003spj.2_Frame_Shift_Del_p.H595fs|PMS2_uc003spk.2_Frame_Shift_Del_p.H566fs|PMS2_uc011jwl.1_Frame_Shift_Del_p.H566fs|PMS2_uc010ktg.2_Frame_Shift_Del_p.H390fs|PMS2_uc010kte.2_Frame_Shift_Del_p.H300fs|PMS2_uc010ktf.1_Intron NM_000535 NP_000526 P54278 PMS2_HUMAN PMS2 postmeiotic segregation increased 2 isoform 701_707 mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes MutLalpha complex ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding lung(1)|central_nervous_system(1) 2 Ovarian(82;0.0694) UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15) TCGAAGTTATACTTCTCGTCCGTGGCATGCTGGTCCA 0.456 0.19 29 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 211 49 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 12 146 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.15 141 25 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 140 355 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 2 32 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 4 52 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.20 530 132 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 19 14 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.14 143 23 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 111 143 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.25 149 49 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 2 31 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.32 537 248 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 466 184 SCYL2 55681 broad.mit.edu 37 12 100711599 100711600 + Frame_Shift_Ins INS - A A KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:100711599_100711600insA uc001thn.2 + 10 1341_1342 c.1291_1292insA c.(1291-1293)CAAfs p.Q431fs SCYL2_uc009ztw.1_Frame_Shift_Ins_p.Q258fs|SCYL2_uc001thm.1_Frame_Shift_Ins_p.Q431fs NM_017988 NP_060458 Q6P3W7 SCYL2_HUMAN SCY1-like 2 protein 431 endosome to lysosome transport|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of clathrin-mediated endocytosis|positive regulation of receptor internalization clathrin-coated vesicle|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm ATP binding|protein kinase activity|receptor binding lung(3)|ovary(2)|skin(1) 6 AATTTTCCTACAAAAAATGGAT 0.337 0.33 73 36 C14orf43 91748 broad.mit.edu 37 14 74205941 74205942 + In_Frame_Ins INS - TGCTGT TGCTGT KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:74205941_74205942insTGCTGT uc001xot.2 - 2 1553_1554 c.770_771insACAGCA c.(769-771)CAG>CAACAGCAG p.257_257Q>QQQ C14orf43_uc001xou.2_In_Frame_Ins_p.257_257Q>QQQ|C14orf43_uc010tud.1_In_Frame_Ins_p.257_257Q>QQQ|C14orf43_uc010arw.2_RNA NM_194278 NP_919254 Q6PJG2 CN043_HUMAN hypothetical protein LOC91748 257 Pro-rich.|Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding ovary(4)|central_nervous_system(1) 5 BRCA - Breast invasive adenocarcinoma(234;0.00358)|KIRC - Kidney renal clear cell carcinoma(182;0.0878)|OV - Ovarian serous cystadenocarcinoma(108;0.115) gctgctgctgctgctgctgtgg 0.465 0.26 48 17 THAP11 57215 broad.mit.edu 37 16 67876824 67876832 + In_Frame_Del DEL CAGCAGCAG - - rs34213159;rs3982383;rs63117363;rs141903290 byFrequency;byFrequency KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:67876824_67876832delCAGCAGCAG uc002euo.2 + 1 612_620 c.367_375delCAGCAGCAG c.(367-375)CAGCAGCAGdel p.QQQ129del CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 129_131 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) gcagcagcaacagcagcagcagcagcagc 0.311 0.59 39 57 RBBP8 5932 broad.mit.edu 37 18 20596833 20596834 + Frame_Shift_Ins INS - A A KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr18:20596833_20596834insA uc002ktw.2 + 17 2731_2732 c.2400_2401insA c.(2398-2403)CGGAAAfs p.R800fs RBBP8_uc002kty.2_Frame_Shift_Ins_p.R800fs|RBBP8_uc002ktz.2_Intron|RBBP8_uc002kua.2_Frame_Shift_Ins_p.R805fs|RBBP8_uc010xap.1_Frame_Shift_Ins_p.R138fs NM_002894 NP_002885 Q99708 COM1_HUMAN retinoblastoma binding protein 8 isoform a 800_801 cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter nucleus damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity ovary(1)|lung(1)|skin(1) 3 all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19) OV - Ovarian serous cystadenocarcinoma(1;0.00196) AGGTGGTTCGGAAAAAAGAGGA 0.351 0.61 42 65 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 78 59 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 180 468 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 11 107 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KLE_ENDOMETRIUM NA KLE_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 4 79 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KLE_ENDOMETRIUM NA KLE_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.41 137 94 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KLE_ENDOMETRIUM NA KLE_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 57 79 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KLE_ENDOMETRIUM NA KLE_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 19 42 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KLE_ENDOMETRIUM NA KLE_ENDOMETRIUM NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.93 1 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KLE_ENDOMETRIUM NA KLE_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 2 23 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KLE_ENDOMETRIUM NA KLE_ENDOMETRIUM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.60 4 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KLE_ENDOMETRIUM NA KLE_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 199 70 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KLE_ENDOMETRIUM NA KLE_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.88 2 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KLE_ENDOMETRIUM NA KLE_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 184 565 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KLE_ENDOMETRIUM NA KLE_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 43 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes KLE_ENDOMETRIUM NA KLE_ENDOMETRIUM NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.19 183 44 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 45 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.45 278 230 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.47 9 8 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.60 4 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 108 118 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.19 68 16 CDKN1A 1026 broad.mit.edu 37 6 36651978 36651979 + Frame_Shift_Del DEL TG - - KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr6:36651978_36651979delTG uc003omm.3 + 2 222_223 c.100_101delTG c.(100-102)TGTfs p.C34fs CDKN1A_uc011dtq.1_Frame_Shift_Del_p.C68fs|CDKN1A_uc003oml.2_Frame_Shift_Del_p.C34fs|CDKN1A_uc003omn.2_Frame_Shift_Del_p.C34fs NM_000389 NP_000380 P38936 CDN1A_HUMAN cyclin-dependent kinase inhibitor 1A 34 C4-type (Potential). cell cycle arrest|cellular response to extracellular stimulus|cellular response to ionizing radiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|induction of apoptosis by intracellular signals|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of fibroblast proliferation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|S phase of mitotic cell cycle|stress-induced premature senescence cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleoplasm|PCNA-p21 complex cyclin-dependent protein kinase activating kinase activity|cyclin-dependent protein kinase inhibitor activity|metal ion binding ovary(1)|breast(1) 2 GAGCCGCGACTGTGATGCGCTA 0.644 0.47 31 28 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.42 32 23 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.40 603 406 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 310 79 NCOR2 9612 broad.mit.edu 37 12 124887059 124887067 + In_Frame_Del DEL GCTGCTGCT - - rs67031864 KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr12:124887059_124887067delGCTGCTGCT uc010tba.1 - 14 1640_1648 c.1523_1531delAGCAGCAGC c.(1522-1533)CAGCAGCAGCCC>CCC p.QQQ508del NCOR2_uc010tay.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010taz.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010tbb.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010tbc.1_In_Frame_Del_p.QQQ507del|NCOR2_uc001ugj.1_In_Frame_Del_p.QQQ508del NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 508_510 Poly-Gln. cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) CGGGGCATGGgctgctgctgctgctgctg 0.316 0.36 7 4 USP32 84669 broad.mit.edu 37 17 58282850 58282850 + Frame_Shift_Del DEL G - - KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr17:58282850delG uc002iyo.1 - 26 3493 c.3207delC c.(3205-3207)GACfs p.D1069fs USP32_uc002iyn.1_Frame_Shift_Del_p.D739fs NM_032582 NP_115971 Q8NFA0 UBP32_HUMAN ubiquitin specific protease 32 1069 protein deubiquitination|ubiquitin-dependent protein catabolic process Golgi apparatus|membrane calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity lung(2)|breast(2)|large_intestine(1) 5 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198) TAAAGGGGCTGTCAGGAAGAG 0.423 0.10 85 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.53 18 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 91 361 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KMBC2_URINARY_TRACT NA KMBC2_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 4 29 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 5 68 RPL22 6146 broad.mit.edu 37 1 6253023 6253025 + In_Frame_Del DEL ATC - - KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:6253023_6253025delATC uc001amd.2 - 3 253_255 c.207_209delGAT c.(205-210)AAGATC>AAC p.69_70KI>N RPL22_uc001ame.2_In_Frame_Del_p.69_70KI>N NM_000983 NP_000974 P35268 RL22_HUMAN ribosomal protein L22 proprotein 69_70 endocrine pancreas development|translational elongation|translational termination|viral transcription cytosolic large ribosomal subunit heparin binding|RNA binding|structural constituent of ribosome 0 Ovarian(185;0.0634) all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211) Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182) TGTCACGGTGATCTTGCTCTTGC 0.542 0.74 71 199 ITGB6 3694 broad.mit.edu 37 2 160994161 160994161 + Frame_Shift_Del DEL G - - KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:160994161delG uc002ubh.2 - 10 1460 c.1444delC c.(1444-1446)CACfs p.H482fs ITGB6_uc010fou.2_Frame_Shift_Del_p.H482fs|ITGB6_uc010zcq.1_Frame_Shift_Del_p.H440fs|ITGB6_uc010fov.1_Frame_Shift_Del_p.H482fs NM_000888 NP_000879 P18564 ITB6_HUMAN integrin, beta 6 precursor 482 Extracellular (Potential).|Cysteine-rich tandem repeats.|I. cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|multicellular organismal development integrin complex receptor activity ovary(1)|lung(1)|skin(1) 3 TGGCCAGGGTGGCAGGCACAC 0.597 0.18 246 53 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 108 110 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.98 15 752 RICTOR 253260 broad.mit.edu 37 5 38960526 38960527 + Frame_Shift_Ins INS - A A KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:38960526_38960527insA uc003jlp.2 - 20 1848_1849 c.1824_1825insT c.(1822-1827)TTTACAfs p.F608fs RICTOR_uc003jlo.2_Frame_Shift_Ins_p.F608fs|RICTOR_uc010ivf.2_Frame_Shift_Ins_p.F323fs NM_152756 NP_689969 Q6R327 RICTR_HUMAN rapamycin-insensitive companion of mTOR 608_609 actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation cytosol|TORC2 complex protein binding ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1) 10 all_lung(31;0.000396) AGAAATTCTGTAAACTGGCAAC 0.401 0.23 155 47 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 24 56 CARD11 84433 broad.mit.edu 37 7 2978436 2978441 + In_Frame_Del DEL GTCTGA - - KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:2978436_2978441delGTCTGA uc003smv.2 - 7 1293_1298 c.889_894delTCAGAC c.(889-894)TCAGACdel p.SD297del NM_032415 NP_115791 Q9BXL7 CAR11_HUMAN caspase recruitment domain family, member 11 297_298 Potential. positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway cytosol|membrane raft|plasma membrane CARD domain binding|guanylate kinase activity haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1) 50 Ovarian(82;0.0115) OV - Ovarian serous cystadenocarcinoma(56;8.44e-14) GGATGGCCTTGTCTGAGTCTGGCAGG 0.660 0.36 144 81 CDK13 8621 broad.mit.edu 37 7 40039017 40039017 + Frame_Shift_Del DEL C - - KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:40039017delC uc003thh.3 + 4 2382 c.2100delC c.(2098-2100)CGCfs p.R700fs CDK13_uc003thi.3_Frame_Shift_Del_p.R700fs|CDK13_uc011kbf.1_Frame_Shift_Del_p.R86fs NM_003718 NP_003709 Q14004 CDK13_HUMAN cell division cycle 2-like 5 isoform 1 700 alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity lung(2)|skin(2)|ovary(1) 5 GGGGAAAACGCTGCGTGGATA 0.363 0.45 48 39 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.85 3 17 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.60 8 12 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.19 1134 268 FANCF 2188 broad.mit.edu 37 11 22647190 22647190 + Frame_Shift_Del DEL G - - KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:22647190delG uc001mql.1 - 1 198 c.167delC c.(166-168)ACGfs p.T56fs NM_022725 NP_073562 Q9NPI8 FANCF_HUMAN Fanconi anemia, complementation group F 56 DNA repair nucleoplasm protein binding skin(1) 1 CTCCAGAGCCGTGCGAATGGG 0.687 0.31 24 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 240 74 PIK3C2G 5288 broad.mit.edu 37 12 18658316 18658316 + Frame_Shift_Del DEL C - - KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:18658316delC uc001rdt.2 + 23 3237 c.3121delC c.(3121-3123)CTGfs p.L1041fs PIK3C2G_uc010sia.1_RNA|PIK3C2G_uc010sib.1_Frame_Shift_Del_p.L1082fs|PIK3C2G_uc010sic.1_Frame_Shift_Del_p.L860fs NM_004570 NP_004561 O75747 P3C2G_HUMAN phosphoinositide-3-kinase, class 2 gamma 1041 PI3K/PI4K. cell communication|phosphatidylinositol-mediated signaling membrane|phosphatidylinositol 3-kinase complex 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2) 21 Hepatocellular(102;0.194) TAATATCATGCTGACAAAGTC 0.403 0.24 123 39 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.76 8 25 CHRNA5 1138 broad.mit.edu 37 15 78882853 78882853 + Frame_Shift_Del DEL T - - KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:78882853delT uc002bdy.2 + 5 1282 c.1120delT c.(1120-1122)TTCfs p.F374fs CHRNA5_uc002bdz.2_Intron NM_000745 NP_000736 P30532 ACHA5_HUMAN cholinergic receptor, nicotinic, alpha 5 374 Cytoplasmic (Potential). behavioral response to nicotine cell junction|postsynaptic membrane acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity ovary(1)|central_nervous_system(1)|skin(1) 3 AGACAGGTACTTCACTCAGAA 0.438 0.52 51 56 GRB2 2885 broad.mit.edu 37 17 73322036 73322037 + Frame_Shift_Ins INS - CATCGTG CATCGTG KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:73322036_73322037insCATCGTG uc002jnx.3 - 4 598_599 c.241_242insCACGATG c.(241-243)GGGfs p.G81fs GRB2_uc002jny.3_Intron NM_002086 NP_002077 P62993 GRB2_HUMAN growth factor receptor-bound protein 2 isoform 81 SH2. axon guidance|blood coagulation|cell junction assembly|cell-cell signaling|cellular response to ionizing radiation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|receptor internalization|signal transduction in response to DNA damage|T cell costimulation cytosol|Golgi apparatus epidermal growth factor receptor binding|insulin receptor substrate binding|SH3/SH2 adaptor activity ovary(3) 3 all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222) all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185) Pegademase bovine(DB00061) AAGAAAGGCCCCATCGTGCCGC 0.515 0.35 117 64 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.31 61 28 GNAS 2778 broad.mit.edu 37 20 57429555 57429555 + Frame_Shift_Del DEL A - - KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:57429555delA uc002xzw.2 + 1 1520 c.1235delA c.(1234-1236)GACfs p.D412fs GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_RNA NM_080425 NP_536350 P63092 GNAS2_HUMAN GNAS complex locus XLas Error:Variant_position_missing_in_P63092_after_alignment activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1) 292 all_lung(29;0.0104) BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109) 0.000 0.15 530 95 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 129 610 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 96 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 1 20 EPHA2 1969 broad.mit.edu 37 1 16474972 16474972 + Frame_Shift_Del DEL C - - KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:16474972delC uc001aya.1 - 3 861 c.724delG c.(724-726)GAGfs p.E242fs EPHA2_uc010oca.1_Frame_Shift_Del_p.E242fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 242 Extracellular (Potential).|Cys-rich. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) ATACGGGGCTCTTCACCCCCC 0.667 0.56 24 30 PINK1 65018 broad.mit.edu 37 1 20960210 20960211 + In_Frame_Ins INS - GCAGGG GCAGGG rs45630564 KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:20960210_20960211insGCAGGG uc001bdm.2 + 1 263_264 c.169_170insGCAGGG c.(169-171)CGC>CGCAGGGGC p.57_58insRG NM_032409 NP_115785 Q9BXM7 PINK1_HUMAN PTEN induced putative kinase 1 precursor 57_58 cell death|intracellular protein kinase cascade|mitochondrion degradation|peptidyl-serine phosphorylation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of release of cytochrome c from mitochondria|regulation of protein complex assembly|regulation of protein ubiquitination|response to stress cytosol|integral to membrane|mitochondrial outer membrane ATP binding|C3HC4-type RING finger domain binding|calcium-dependent protein kinase activity|magnesium ion binding|protein serine/threonine kinase activity|ubiquitin protein ligase binding ovary(2)|central_nervous_system(1) 3 all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199) 0.000 0.39 161 102 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 208 45 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 67 104 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.26 25 9 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.20 171 44 STK19 8859 broad.mit.edu 37 6 31939829 31939830 + Frame_Shift_Ins INS - A A KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:31939829_31939830insA uc003nyv.2 + 1 184_185 c.56_57insA c.(55-57)GCAfs p.A19fs DOM3Z_uc003nyo.1_5'UTR|DOM3Z_uc003nyp.1_5'UTR|DOM3Z_uc003nyq.1_5'UTR|DOM3Z_uc003nyr.1_5'UTR|DOM3Z_uc003nys.1_5'Flank|DOM3Z_uc010jtl.1_5'UTR|STK19_uc003nyt.2_5'UTR|DOM3Z_uc003nyu.1_5'UTR|STK19_uc011dow.1_Frame_Shift_Ins_p.A19fs|STK19_uc011dox.1_5'UTR|STK19_uc003nyw.2_Frame_Shift_Ins_p.A19fs|STK19_uc010jtn.1_5'Flank NM_032454 NP_115830 P49842 STK19_HUMAN serine/threonine kinase 19 isoform 2 19 nucleus ATP binding|protein binding|protein serine/threonine kinase activity skin(4) 4 CAGTGGCGGGCAAACCCCTCCC 0.634 0.16 43 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.75 3 9 MLLT3 4300 broad.mit.edu 37 9 20414311 20414313 + In_Frame_Del DEL CTG - - KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:20414311_20414313delCTG uc003zoe.2 - 5 790_792 c.531_533delCAG c.(529-534)AGCAGT>AGT p.177_178SS>S MLLT3_uc011lne.1_In_Frame_Del_p.145_146SS>S|MLLT3_uc011lnf.1_In_Frame_Del_p.174_175SS>S|MLLT3_uc003zof.2_5'UTR NM_004529 NP_004520 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia 177_178 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding lung(2)|ovary(1) 3 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) gctgctgctactgctgctgctgc 0.143 0.17 155 32 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 473 183 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.58 16 22 ADAM6 8755 broad.mit.edu 37 14 106110827 106110838 + Splice_Site DEL TCTCACCAACTG - - rs111294937 KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:106110827_106110838delTCTCACCAACTG uc010tyt.1 - 3640 c.60928_splice c.e3640+1 uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Splice_Site Parts of antibodies, mostly variable regions. 0 TGAGCTGGCCTCTCACCAACTGTCTTGTCCAC 0.646 0.42 7 5 POLG 5428 broad.mit.edu 37 15 89876821 89876822 + In_Frame_Ins INS - TGCTGT TGCTGT KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:89876821_89876822insTGCTGT uc002bns.3 - 2 446_447 c.164_165insACAGCA c.(163-165)CAG>CAACAGCAG p.55_55Q>QQQ POLG_uc002bnr.3_In_Frame_Ins_p.55_55Q>QQQ NM_002693 NP_002684 P54098 DPOG1_HUMAN DNA-directed DNA polymerase gamma 55 Poly-Gln. Q -> QQ.|Q -> QQQ. base-excision repair, gap-filling|cell death|DNA-dependent DNA replication mitochondrial nucleoid DNA binding|DNA-directed DNA polymerase activity|protease binding ovary(1)|lung(1) 2 Lung NSC(78;0.0472)|all_lung(78;0.089) STAD - Stomach adenocarcinoma(125;0.165) gctgctgaggctgctgttgctg 0.455 0.48 15 14 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 53 178 ZNF217 7764 broad.mit.edu 37 20 52193034 52193035 + Frame_Shift_Ins INS - GCATCCA GCATCCA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:52193034_52193035insGCATCCA uc002xwq.3 - 3 2539_2540 c.2268_2269insTGGATGC c.(2266-2271)TGCCCGfs p.C756fs ZNF217_uc010gij.1_Frame_Shift_Ins_p.C748fs NM_006526 NP_006517 O75362 ZN217_HUMAN zinc finger protein 217 756_757 negative regulation of transcription, DNA-dependent histone deacetylase complex protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding skin(2)|ovary(1)|large_intestine(1)|lung(1)|breast(1) 6 all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398) BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198) AACGCTGGCGGGCATCCGGTAC 0.495 0.23 89 27 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 117 329 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 81 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 1 0 72 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.2 453 110 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0 0.7 7 16 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. "regulation of transcription, DNA-dependent" membrane|nucleus "calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity" skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.36 0.45 18 15 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs "SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA;" GAAGAAGTCGATTAGGAGTTCA 0.545 0.16 41 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 102 139 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.29 55 23 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.73 82 219 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.6 4 6 STK38 11329 broad.mit.edu 37 6 36483214 36483214 + Frame_Shift_Del DEL C - - KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr6:36483214delC uc003omg.2 - 6 1158 c.570delG c.(568-570)CAGfs p.Q190fs STK38_uc003omh.2_Frame_Shift_Del_p.Q190fs|STK38_uc003omi.2_Frame_Shift_Del_p.Q190fs NM_007271 NP_009202 Q15208 STK38_HUMAN serine/threonine kinase 38 190 Protein kinase. intracellular protein kinase cascade|negative regulation of MAP kinase activity cytoplasm|MLL5-L complex ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1) 6 CTATATAAAACTGAGTCTCCT 0.373 0.45 167 136 GRM8 2918 broad.mit.edu 37 7 126173171 126173171 + Frame_Shift_Del DEL G - - KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr7:126173171delG uc003vlr.2 - 8 2576 c.2265delC c.(2263-2265)TACfs p.Y755fs GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Frame_Shift_Del_p.Y755fs|GRM8_uc010lkz.1_RNA NM_000845 NP_000836 O00222 GRM8_HUMAN glutamate receptor, metabotropic 8 isoform a 755 Helical; Name=5; (Potential). negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception integral to plasma membrane lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1) 23 Prostate(267;0.186) L-Glutamic Acid(DB00142) 0.000 0.43 1047 792 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 4 63 RHEB 6009 broad.mit.edu 37 7 151188048 151188050 + In_Frame_Del DEL GTA - - KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr7:151188048_151188050delGTA uc003wkh.1 - 2 516_518 c.103_105delTAC c.(103-105)TACdel p.Y35del NM_005614 NP_005605 Q15382 RHEB_HUMAN Ras homolog enriched in brain precursor 35 Effector region (By similarity).|GTP. cell cycle arrest|insulin receptor signaling pathway|positive regulation of TOR signaling cascade|small GTPase mediated signal transduction cytosol|plasma membrane GTP binding|GTPase activity|metal ion binding|protein binding large_intestine(1)|lung(1) 2 OV - Ovarian serous cystadenocarcinoma(82;0.00306) UCEC - Uterine corpus endometrioid carcinoma (81;0.174) TGGTTGGATCGTAGGAGTCCACA 0.36 0.44 96 75 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane "calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle" ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.42 25 18 MYST4 23522 broad.mit.edu 37 10 76788480 76788481 + Frame_Shift_Ins INS - C C KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr10:76788480_76788481insC uc001jwn.1 + 18 4391_4392 c.3898_3899insC c.(3898-3900)ACCfs p.T1300fs MYST4_uc001jwo.1_Frame_Shift_Ins_p.T1008fs|MYST4_uc001jwp.1_Frame_Shift_Ins_p.T1117fs NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1300 "histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent" MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) AGAAGGAAAAACCAGCCCCAGT 0.51 0.1 141 15 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.26 23 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.38 647 393 HIF1A 3091 broad.mit.edu 37 14 62193464 62193465 + Frame_Shift_Ins INS - T T KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr14:62193464_62193465insT uc001xfq.2 + 5 902_903 c.498_499insT c.(496-501)AGCTTTfs p.S166fs HIF1A_uc010tsc.1_Frame_Shift_Ins_p.S83fs|HIF1A_uc001xfr.2_Frame_Shift_Ins_p.S166fs|HIF1A_uc001xfs.2_Frame_Shift_Ins_p.S167fs NM_001530 NP_001521 Q16665 HIF1A_HUMAN "hypoxia-inducible factor 1, alpha subunit" 166_167 Interaction with TSGA10 (By similarity). cellular response to hypoxia|collagen metabolic process|connective tissue replacement involved in inflammatory response wound healing|elastin metabolic process|epithelial to mesenchymal transition|oxygen homeostasis|positive regulation of chemokine production|positive regulation of epithelial cell migration|positive regulation of hormone biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|regulation of transforming growth factor-beta2 production cytoplasm|nucleolus|transcription factor complex histone acetyltransferase binding|Hsp90 protein binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding kidney(3)|lung(1) 4 OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189) CACAGCGAAGCTTTTTTCTCAG 0.317 0.78 9 31 EEF2K 29904 broad.mit.edu 37 16 22284966 22284966 + Frame_Shift_Del DEL C - - KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr16:22284966delC uc002dki.2 + 16 2269 c.1784delC c.(1783-1785)ACCfs p.T595fs EEF2K_uc002dkh.2_RNA NM_013302 NP_037434 O00418 EF2K_HUMAN elongation factor-2 kinase 595 Calmodulin-binding (Potential). insulin receptor signaling pathway|translational elongation cytosol "ATP binding|calcium ion binding|calmodulin binding|elongation factor-2 kinase activity|translation factor activity, nucleic acid binding" large_intestine(1) 1 GBM - Glioblastoma multiforme(48;0.0223) GAGAACAAAACCAAAGGATTT 0.493 0.58 5 7 IL21R 50615 broad.mit.edu 37 16 27460536 27460546 + Frame_Shift_Del DEL CGGAGCTACCT - - rs142141390 by1000genomes KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr16:27460536_27460546delCGGAGCTACCT uc002doq.1 + 9 1782_1792 c.1549_1559delCGGAGCTACCT c.(1549-1560)CGGAGCTACCTCfs p.R517fs IL21R_uc002dor.1_Frame_Shift_Del_p.R517fs|IL21R_uc002dos.1_Frame_Shift_Del_p.R517fs|uc002dot.2_RNA NM_181078 NP_851564 Q9HBE5 IL21R_HUMAN interleukin 21 receptor precursor 517_520 Cytoplasmic (Potential). natural killer cell activation integral to membrane interleukin-21 receptor activity ovary(2)|lung(1)|breast(1) 4 AGGACCCCCCCGGAGCTACCTCCGCCAGTGG 0.645 0.12 123 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 10 91 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.69 69 154 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 59 380 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KMRC20_KIDNEY NA KMRC20_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.93 9 116 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.92 4 45 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. "regulation of transcription, DNA-dependent" membrane|nucleus "calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity" skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.36 0.43 21 16 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN "phosphoinositide-3-kinase, regulatory subunit 4" fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.1 80 9 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs "SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA;" GAAGAAGTCGATTAGGAGTTCA 0.545 0.12 65 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 132 174 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.22 69 19 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.73 3 8 HMGA1 3159 broad.mit.edu 37 6 34208666 34208666 + Frame_Shift_Del DEL C - - KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr6:34208666delC uc003oit.2 + 3 431 c.109delC c.(109-111)CCCfs p.P37fs HMGA1_uc011dso.1_Frame_Shift_Del_p.P37fs|HMGA1_uc003oiv.2_Intron|HMGA1_uc003oiw.2_Intron|HMGA1_uc003oiu.2_Frame_Shift_Del_p.P37fs|HMGA1_uc003oiy.2_Intron|HMGA1_uc003oiz.2_Frame_Shift_Del_p.P37fs|HMGA1_uc003oja.2_Intron|HMGA1_uc003oix.2_Intron|HMGA1_uc010jvl.2_RNA|HMGA1_uc003ojc.2_Intron|HMGA1_uc011dsp.1_RNA|HMGA1_uc003ojd.2_Intron NM_145899 NP_665906 P17096 HMGA1_HUMAN high mobility group AT-hook 1 isoform a 37 DNA unwinding involved in replication|initiation of viral infection|interspecies interaction between organisms|loss of chromatin silencing|nucleosome disassembly|protein complex assembly|provirus integration chromatin|cytosol|transcription factor complex AT DNA binding|enzyme binding|ligand-dependent nuclear receptor transcription coactivator activity|peroxisome proliferator activated receptor binding|protein binding|retinoid X receptor binding|sequence-specific DNA binding transcription factor activity 0 0.000 0.57 48 63 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 27 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane "calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle" ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.36 25 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 44 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 705 280 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). "histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent" NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.22 90 25 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.42 129 92 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 "B melanoma antigen family, member 2 precursor" 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.3 67 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 6 29 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KMRC2_KIDNEY NA KMRC2_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.94 8 126 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 2 21 XIAP 331 broad.mit.edu 37 X 123025155 123025157 + In_Frame_Del DEL GAG - - KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chrX:123025155_123025157delGAG uc010nqu.2 + 4 1171_1173 c.1045_1047delGAG c.(1045-1047)GAGdel p.E350del XIAP_uc004etx.2_In_Frame_Del_p.E350del|XIAP_uc010nqv.2_5'UTR NM_001167 NP_001158 P98170 XIAP_HUMAN baculoviral IAP repeat-containing protein 4 350 anti-apoptosis|apoptosis|induction of apoptosis by intracellular signals|response to DNA damage stimulus cytosol caspase inhibitor activity|ligase activity|protein binding|zinc ion binding ovary(1)|lung(1) 2 TCATTCACTTGAGGAGTGTCTGG 0.197 0.88 4 30 HOXD13 3239 broad.mit.edu 37 2 176957786 176957797 + In_Frame_Del DEL GGCGGCGGCGGC - - rs3832095 KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr2:176957786_176957797delGGCGGCGGCGGC uc002ukf.1 + 1 255_266 c.168_179delGGCGGCGGCGGC c.(166-180)CGGGCGGCGGCGGCG>CGG p.AAAA65del NM_000523 NP_000514 P35453 HXD13_HUMAN homeobox D13 65_68 Poly-Ala. skeletal system development|transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding lung(1) 1 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0526)|READ - Rectum adenocarcinoma(9;0.0678) 0.000 0.40 287 193 PBRM1 55193 broad.mit.edu 37 3 52610609 52610609 + Frame_Shift_Del DEL T - - KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr3:52610609delT uc003des.2 - 22 3651 c.3639delA c.(3637-3639)AAAfs p.K1213fs PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.K1213fs|PBRM1_uc003der.2_Frame_Shift_Del_p.K1181fs|PBRM1_uc003det.2_Frame_Shift_Del_p.K1228fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.K1228fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.K1213fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.K1188fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.K1188fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.K1212fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 1213 BAH 2. Missing (found in a case of clear cell renal carcinoma; somatic mutation). chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding p.M1209_E1214delMFYKKE(1) kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.99 1 110 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 63 16 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.19 35 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 74 41 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 30 47 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.25 332 108 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.62 5 8 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.35 36 19 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.35 526 280 CUBN 8029 broad.mit.edu 37 10 16981066 16981067 + Frame_Shift_Ins INS - G G KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr10:16981066_16981067insG uc001ioo.2 - 38 5680_5681 c.5628_5629insC c.(5626-5631)TCCAATfs p.S1876fs NM_001081 NP_001072 O60494 CUBN_HUMAN cubilin precursor 1876_1877 CUB 13. cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1) 19 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) CATTGGTAATTGGAGTTATGTG 0.401 0.45 91 75 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 149 30 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.46 7 6 ATP10A 57194 broad.mit.edu 37 15 25969139 25969149 + Frame_Shift_Del DEL CTTGATACCGC - - rs77355852;rs144743073 KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr15:25969139_25969149delCTTGATACCGC uc010ayu.2 - 6 1105_1115 c.999_1009delGCGGTATCAAG c.(997-1011)TGGCGGTATCAAGAGfs p.W333fs NM_024490 NP_077816 O60312 AT10A_HUMAN ATPase, class V, type 10A 333_337 Extracellular (Potential). ATP biosynthetic process|regulation of cell shape integral to membrane|plasma membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity pancreas(2)|ovary(1)|breast(1)|liver(1) 5 all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125) all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244) GACTTCTTCTCTTGATACCGCCATATCCACA 0.360 0.39 14 9 MGA 23269 broad.mit.edu 37 15 41961346 41961346 + Frame_Shift_Del DEL G - - KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr15:41961346delG uc001zog.1 + 2 345 c.254delG c.(253-255)TGGfs p.W85fs MGA_uc010ucy.1_Frame_Shift_Del_p.W85fs|MGA_uc010ucz.1_Frame_Shift_Del_p.W85fs NM_001080541 NP_001074010 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 2 85 T-box. MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) AATAGTATGTGGAATGAGTTC 0.403 0.47 111 99 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 32 315 TUBG2 27175 broad.mit.edu 37 17 40818665 40818666 + Frame_Shift_Ins INS - T T KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr17:40818665_40818666insT uc010wgr.1 + 11 1459_1460 c.1203_1204insT c.(1201-1206)CGGGATfs p.R401fs TUBG2_uc002iaq.2_3'UTR|TUBG2_uc002iar.2_Frame_Shift_Ins_p.R248fs|TUBG2_uc002ias.2_Frame_Shift_Ins_p.R243fs|TUBG2_uc002iap.2_Frame_Shift_Ins_p.R248fs NM_016437 NP_057521 Q9NRH3 TBG2_HUMAN tubulin, gamma 2 401_402 G2/M transition of mitotic cell cycle|microtubule-based process|protein polymerization cytosol GTP binding|GTPase activity|structural molecule activity ovary(1) 1 Breast(137;0.00116) BRCA - Breast invasive adenocarcinoma(366;0.141) 0.000 0.93 1 14 UBE2O 63893 broad.mit.edu 37 17 74397224 74397226 + In_Frame_Del DEL GAA - - KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr17:74397224_74397226delGAA uc002jrm.3 - 6 825_827 c.760_762delTTC c.(760-762)TTCdel p.F254del UBE2O_uc002jrn.3_In_Frame_Del_p.F254del|UBE2O_uc002jrl.3_5'Flank NM_022066 NP_071349 Q9C0C9 UBE2O_HUMAN ubiquitin-conjugating enzyme E2O 254 ATP binding|ubiquitin-protein ligase activity breast(2)|skin(2)|lung(1) 5 AGGAATCATCGAAGAAGAGACCC 0.616 0.34 65 34 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.29 42 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 150 479 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KMRC3_KIDNEY NA KMRC3_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 56 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 56 EPHA2 1969 broad.mit.edu 37 1 16456051 16456052 + Frame_Shift_Ins INS - G G KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:16456051_16456052insG uc001aya.1 - 16 2839_2840 c.2702_2703insC c.(2701-2703)TCGfs p.S901fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 901 Mediates interaction with ARHGEF16 and ELMO2.|Cytoplasmic (Potential).|Negatively regulates interaction with ARHGEF16. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) GCACCCCCTCCGAGCCGCTCGT 0.431 0.11 72 9 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.16 43 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.34 143 74 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.26 81 28 ZNF608 57507 broad.mit.edu 37 5 123982406 123982406 + Frame_Shift_Del DEL T - - KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:123982406delT uc003ktq.1 - 4 3794 c.3671delA c.(3670-3672)CAGfs p.Q1224fs ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Frame_Shift_Del_p.Q1224fs|ZNF608_uc003ktt.1_Frame_Shift_Del_p.Q1224fs|ZNF608_uc003ktp.1_5'Flank NM_020747 NP_065798 Q9ULD9 ZN608_HUMAN zinc finger protein 608 1224 intracellular zinc ion binding skin(3)|ovary(2)|lung(1) 6 all_cancers(142;0.186)|Prostate(80;0.081) KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221) OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783) TACACCTGTCTGCTTCATAGA 0.473 0.27 163 59 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.47 370 322 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.71 7 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 61 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 5 36 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.68 12 26 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 56 435 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.83 10 49 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0 0.32 15 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. "regulation of transcription, DNA-dependent" membrane|nucleus "calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity" skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.36 0.73 12 32 HTT 3064 broad.mit.edu 37 4 3076604 3076609 + In_Frame_Del DEL CAGCAG - - rs10618869 KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:3076604_3076609delCAGCAG uc011bvq.1 + 2 203_208 c.58_63delCAGCAG c.(58-63)CAGCAGdel p.QQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment "establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule" autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagc 0.33 0.23 71 21 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs "SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA;" GAAGAAGTCGATTAGGAGTTCA 0.545 0.12 81 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.66 126 242 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 37 98 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.82 2 9 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.84 4 21 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.38 10 6 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 55 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.24 99 31 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.37 568 332 NEK3 4752 broad.mit.edu 37 13 52725278 52725279 + Splice_Site INS - A A KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:52725278_52725279insA uc001vgi.2 - 7 783 c.548_splice c.e7+1 p.S183_splice NEK3_uc001vgg.2_Splice_Site_p.S177_splice|NEK3_uc001vgh.2_Splice_Site_p.S204_splice|NEK3_uc010tgx.1_Splice_Site|NEK3_uc010tgy.1_Splice_Site_p.S183_splice NM_152720 NP_689933 P51956 NEK3_HUMAN NIMA-related kinase 3 isoform a cell division|mitosis nucleus ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173) GBM - Glioblastoma multiforme(99;2.81e-08) ATGCAGCACTCACCTTTTATTG 0.421 0.39 172 111 Unknown 0 broad.mit.edu 37 14 23574096 23574098 + In_Frame_Del DEL GCA - - KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:23574096_23574098delGCA uc010aki.1 - 1 80_82 c.32_34delTGC c.(31-36)CTGCCG>CCG p.L11del Homo sapiens cDNA clone IMAGE:40134016. ACTAGTGgcggcagcagcagcag 0.448 0.33 12 6 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 26 404 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 130 84 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 46 305 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.94 7 115 HEPH 9843 broad.mit.edu 37 X 65393494 65393495 + Frame_Shift_Ins INS - C C KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:65393494_65393495insC uc011moz.1 + 4 545_546 c.485_486insC c.(484-486)GGCfs p.G162fs HEPH_uc004dwn.2_Frame_Shift_Ins_p.G162fs|HEPH_uc004dwo.2_5'UTR|HEPH_uc010nkr.2_Frame_Shift_Ins_p.G162fs|HEPH_uc011mpa.1_Frame_Shift_Ins_p.G162fs NM_138737 NP_620074 Q9BQS7 HEPH_HUMAN hephaestin isoform a 159 Extracellular (Potential).|Plastocyanin-like 1. cellular iron ion homeostasis|copper ion transport|transmembrane transport integral to membrane|plasma membrane copper ion binding|oxidoreductase activity lung(5)|ovary(4) 9 CCCCCGGGGGGCAGCCATATCT 0.535 0.2 35 9 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 1 0 20 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 502 133 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN "phosphoinositide-3-kinase, regulatory subunit 4" fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.12 98 14 PRKCI 5584 broad.mit.edu 37 3 169993017 169993025 + In_Frame_Del DEL TAATTCCAT - - KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:169993017_169993025delTAATTCCAT uc003fgs.2 + 8 885_893 c.647_655delTAATTCCAT c.(646-657)GTAATTCCATAT>GAT p.216_219VIPY>D NM_002740 NP_002731 P41743 KPCI_HUMAN "protein kinase C, iota" 216_219 Regulatory domain. anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport cytosol|endosome|nucleus|polarisome ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding lung(2)|ovary(1)|breast(1)|skin(1) 5 all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169) Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197) GGGTTTTTAGTAATTCCATATAATCCTTC 0.278 0.49 34 33 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.31 72 33 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.39 34 22 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.37 103 61 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane "calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle" ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.33 43 21 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 134 31 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.47 10 9 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). "histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent" NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.21 33 9 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 17 139 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 "B melanoma antigen family, member 2 precursor" 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.18 128 28 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 105 395 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 1 0 27 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.62 15 25 F8 2157 broad.mit.edu 37 X 154130434 154130435 + Frame_Shift_Ins INS - A A KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:154130434_154130435insA uc004fmt.2 - 19 6177_6178 c.6006_6007insT c.(6004-6009)TTTGAGfs p.F2002fs F8_uc010nvi.1_Intron NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 2002_2003 F5/8 type A 3.|Plastocyanin-like 6. acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) TCCACTGTCTCAAAAACACCTT 0.386 0.96 1 27 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.33 296 149 YSK4 80122 broad.mit.edu 37 2 135744280 135744281 + Frame_Shift_Ins INS - T T KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:135744280_135744281insT uc002tue.1 - 7 2192_2193 c.2161_2162insA c.(2161-2163)ACAfs p.T721fs YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Frame_Shift_Ins_p.T608fs|YSK4_uc010zbg.1_Intron|YSK4_uc002tuh.3_Frame_Shift_Ins_p.T449fs|YSK4_uc002tui.3_Frame_Shift_Ins_p.T738fs NM_025052 NP_079328 Q56UN5 YSK4_HUMAN Yeast Sps1/Ste20-related kinase 4 isoform 1 721 ATP binding|protein serine/threonine kinase activity stomach(2)|urinary_tract(1)|ovary(1)|breast(1) 5 BRCA - Breast invasive adenocarcinoma(221;0.112) TTTCATATGTGTTTTTTTCTGA 0.381 0.32 64 30 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.23 24 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.46 22 19 GMPS 8833 broad.mit.edu 37 3 155652835 155652835 + Frame_Shift_Del DEL G - - KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:155652835delG uc003faq.2 + 14 2142 c.1807delG c.(1807-1809)GGGfs p.G603fs GMPS_uc011bom.1_Frame_Shift_Del_p.G504fs NM_003875 NP_003866 P49915 GUAA_HUMAN guanine monophosphate synthetase 603 glutamine metabolic process|purine base biosynthetic process cytosol ATP binding|GMP synthase (glutamine-hydrolyzing) activity|GMP synthase activity ovary(2)|lung(1) 3 Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114) L-Glutamic Acid(DB00142)|L-Glutamine(DB00130) CAGGGAGTCTGGTAAGTTGCT 0.413 0.17 40 8 GAK 2580 broad.mit.edu 37 4 887199 887200 + Frame_Shift_Ins INS - T T KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:887199_887200insT uc003gbm.3 - 9 1154_1155 c.955_956insA c.(955-957)GCCfs p.A319fs GAK_uc003gbn.3_Frame_Shift_Ins_p.A240fs|GAK_uc010ibk.1_Frame_Shift_Ins_p.A213fs|GAK_uc003gbl.3_Frame_Shift_Ins_p.A183fs NM_005255 NP_005246 O14976 GAK_HUMAN cyclin G associated kinase 319 cell cycle focal adhesion|Golgi apparatus|perinuclear region of cytoplasm ATP binding|heat shock protein binding|protein serine/threonine kinase activity lung(2)|central_nervous_system(1)|skin(1) 4 Colorectal(103;0.219) 0.000 0.41 633 446 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.66 133 253 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.55 141 175 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.34 62 32 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.27 112 41 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.60 4 6 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 12 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.88 2 15 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.31 9 4 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.22 395 114 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.39 783 504 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.34 110 56 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 137 86 NCOA6 23054 broad.mit.edu 37 20 33345712 33345732 + In_Frame_Del DEL TGCTGTTGTTGCTGCTGCTGC - - rs141107883;rs112688909 KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:33345712_33345732delTGCTGTTGTTGCTGCTGCTGC uc002xav.2 - 8 3390_3410 c.819_839delGCAGCAGCAGCAACAACAGCA c.(817-840)CAGCAGCAGCAGCAACAACAGCAA>CAA p.273_280QQQQQQQQ>Q NCOA6_uc002xaw.2_In_Frame_Del_p.273_280QQQQQQQQ>Q|NCOA6_uc010gew.1_In_Frame_Del_p.230_237QQQQQQQQ>Q NM_014071 NP_054790 Q14686 NCOA6_HUMAN nuclear receptor coactivator 6 273_280 TBP/GTF2A-binding region.|NCOA1-binding region.|Gln-rich.|CREBBP-binding region. brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter transcription factor complex chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding p.Q275Q(1) ovary(3)|breast(3)|central_nervous_system(1) 7 ttgctgctgttgctgttgttgctgctgctgctgctgctgct 0.335 0.34 56 29 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.32 26 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 56 271 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 2 34 MAGEB16 139604 broad.mit.edu 37 X 35820679 35820679 + Frame_Shift_Del DEL T - - KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:35820679delT uc010ngt.1 + 2 645 c.366delT c.(364-366)AATfs p.N122fs NM_001099921 NP_001093391 A2A368 MAGBG_HUMAN melanoma antigen family B, 16 122 MAGE. lung(3)|ovary(2)|breast(1)|skin(1) 7 0.000 0.56 210 264 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.27 372 136 ASTN1 460 broad.mit.edu 37 1 176845688 176845689 + Frame_Shift_Ins INS - A A KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:176845688_176845689insA uc001glc.2 - 21 3659_3660 c.3447_3448insT c.(3445-3450)GATGATfs p.D1149fs ASTN1_uc001glb.1_Frame_Shift_Ins_p.D1149fs|ASTN1_uc001gld.1_Frame_Shift_Ins_p.D1149fs NM_004319 NP_004310 O14525 ASTN1_HUMAN astrotactin isoform 1 1157_1158 cell migration|neuron cell-cell adhesion integral to membrane ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1) 15 GCCTTGACATCATCCACCACGG 0.574 0.14 158 25 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.29 22 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 73 100 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.44 132 104 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.29 67 27 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.75 153 460 MYST4 23522 broad.mit.edu 37 10 76789970 76789975 + In_Frame_Del DEL GCGAAT - - KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:76789970_76789975delGCGAAT uc001jwn.1 + 18 5881_5886 c.5388_5393delGCGAAT c.(5386-5394)GAGCGAATG>GAG p.RM1797del MYST4_uc001jwo.1_In_Frame_Del_p.RM1505del|MYST4_uc001jwp.1_In_Frame_Del_p.RM1614del NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1797_1798 Interaction with RUNX1 and RUNX2. histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) GCTTATACGAGCGAATGGGTCAGAGT 0.539 0.47 69 62 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.69 4 9 MARK2 2011 broad.mit.edu 37 11 63670237 63670238 + Frame_Shift_Ins INS - C C KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:63670237_63670238insC uc001nxw.2 + 13 1978_1979 c.1399_1400insC c.(1399-1401)ACCfs p.T467fs MARK2_uc001nxx.2_Frame_Shift_Ins_p.T467fs|MARK2_uc001nxy.2_Frame_Shift_Ins_p.T466fs|MARK2_uc001nxv.3_Frame_Shift_Ins_p.T466fs|MARK2_uc001nxz.3_Frame_Shift_Ins_p.T433fs|MARK2_uc009yoy.2_Frame_Shift_Ins_p.T433fs NM_001039469 NP_001034558 Q7KZI7 MARK2_HUMAN MAP/microtubule affinity-regulating kinase 2 467 cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress plasma membrane ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity stomach(1)|ovary(1)|lung(1) 3 0.000 0.17 432 86 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 301 124 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 16 227 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.14 184 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 67 655 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 2 32 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 30 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.40 170 114 CDKL4 344387 broad.mit.edu 37 2 39414801 39414802 + Frame_Shift_Ins INS - AA AA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:39414801_39414802insAA uc002rrm.2 - 6 701_702 c.701_702insTT c.(700-702)TTCfs p.F234fs CDKL4_uc010fal.1_Frame_Shift_Ins_p.F234fs NM_001009565 NP_001009565 Q5MAI5 CDKL4_HUMAN cyclin-dependent kinase-like 4 234 Protein kinase. cytoplasm ATP binding|cyclin-dependent protein kinase activity ovary(1) 1 all_hematologic(82;0.248) TGATGCCATGGAAAAACCCGTT 0.327 0.36 37 21 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.38 10 6 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.46 13 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 90 128 TRIO 7204 broad.mit.edu 37 5 14474148 14474148 + Frame_Shift_Del DEL A - - KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:14474148delA uc003jff.2 + 40 6031 c.6025delA c.(6025-6027)AAAfs p.K2009fs TRIO_uc003jfg.2_RNA|TRIO_uc003jfh.1_Frame_Shift_Del_p.K1658fs NM_007118 NP_009049 O75962 TRIO_HUMAN triple functional domain (PTPRF interacting) 2009 DH 2. apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway cytosol ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1) 18 Lung NSC(4;0.000742) TGATGACATGAAAGGAAAAGA 0.403 0.15 141 24 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.32 39 18 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.64 64 112 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.81 4 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 3 52 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 782 273 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.29 128 52 CCNA1 8900 broad.mit.edu 37 13 37006866 37006866 + Frame_Shift_Del DEL G - - KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:37006866delG uc001uvr.3 + 1 458 c.108delG c.(106-108)CAGfs p.Q36fs CCNA1_uc010teo.1_Intron|CCNA1_uc010abq.2_Intron|CCNA1_uc010abp.2_Intron|CCNA1_uc001uvs.3_Frame_Shift_Del_p.Q36fs|CCNA1_uc010abr.2_RNA NM_003914 NP_003905 P78396 CCNA1_HUMAN cyclin A1 isoform a 36 cell division|G2/M transition of mitotic cell cycle|male meiosis I|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|spermatogenesis cytosol|microtubule cytoskeleton|nucleoplasm protein kinase binding lung(2)|skin(2)|ovary(1) 5 Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242) TCGTCTTCCAGGTAACGTGGG 0.527 0.89 10 77 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 118 73 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 95 415 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KNS42_CENTRAL_NERVOUS_SYSTEM NA KNS42_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 45 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KNS42_CENTRAL_NERVOUS_SYSTEM NA KNS42_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.33 298 149 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KNS42_CENTRAL_NERVOUS_SYSTEM NA KNS42_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.34 67 34 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KNS42_CENTRAL_NERVOUS_SYSTEM NA KNS42_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.39 51 32 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KNS42_CENTRAL_NERVOUS_SYSTEM NA KNS42_CENTRAL_NERVOUS_SYSTEM NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.43 8 6 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KNS42_CENTRAL_NERVOUS_SYSTEM NA KNS42_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.61 231 365 MRE11A 4361 broad.mit.edu 37 11 94209533 94209542 + Frame_Shift_Del DEL ACAAACATTC - - KNS42_CENTRAL_NERVOUS_SYSTEM NA KNS42_CENTRAL_NERVOUS_SYSTEM NA g.chr11:94209533_94209542delACAAACATTC uc001peu.2 - 7 761_770 c.572_581delGAATGTTTGT c.(571-582)CGAATGTTTGTCfs p.R191fs MRE11A_uc001pev.2_Frame_Shift_Del_p.R191fs|MRE11A_uc009ywj.2_Frame_Shift_Del_p.R194fs NM_005591 NP_005582 P49959 MRE11_HUMAN meiotic recombination 11 homolog A isoform 1 191_194 DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase Mre11 complex|nucleoplasm 3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity breast(4)|lung(1) 5 Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824) TTTTTTATTGACAAACATTCGATAGAGCCT 0.305 0.26 92 32 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KNS42_CENTRAL_NERVOUS_SYSTEM NA KNS42_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 328 102 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency KNS42_CENTRAL_NERVOUS_SYSTEM NA KNS42_CENTRAL_NERVOUS_SYSTEM NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.45 18 15 BLM 641 broad.mit.edu 37 15 91293055 91293057 + In_Frame_Del DEL CAA - - KNS42_CENTRAL_NERVOUS_SYSTEM NA KNS42_CENTRAL_NERVOUS_SYSTEM NA g.chr15:91293055_91293057delCAA uc002bpr.2 + 3 654_656 c.557_559delCAA c.(556-561)TCAAAA>TAA p.186_187SK>* BLM_uc010uqh.1_In_Frame_Del_p.186_187SK>*|BLM_uc010uqi.1_5'UTR|BLM_uc010bnx.2_In_Frame_Del_p.186_187SK>* NM_000057 NP_000048 P54132 BLM_HUMAN Bloom syndrome protein 186_187 double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray cytoplasm|lateral element|nuclear matrix|nucleolus|PML body ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding ovary(3)|skin(2)|breast(1) 6 Lung NSC(78;0.0875)|all_lung(78;0.109) Lung(145;0.189) GCTCAGAAATCAAAAAAGGGTAA 0.374 0.44 20 16 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KNS42_CENTRAL_NERVOUS_SYSTEM NA KNS42_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 41 326 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KNS42_CENTRAL_NERVOUS_SYSTEM NA KNS42_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 57 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 38 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.12 349 49 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.36 16 9 MAGI1 9223 broad.mit.edu 37 3 65425561 65425572 + In_Frame_Del DEL CTGCTGCTGCTG - - KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr3:65425561_65425572delCTGCTGCTGCTG uc003dmn.2 - 9 1778_1789 c.1252_1263delCAGCAGCAGCAG c.(1252-1263)CAGCAGCAGCAGdel p.QQQQ418del MAGI1_uc003dmm.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc003dmo.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc003dmp.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc010hny.2_In_Frame_Del_p.QQQQ303del NM_001033057 NP_001028229 Q96QZ7 MAGI1_HUMAN membrane associated guanylate kinase, WW and PDZ 418_421 Poly-Gln. cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly tight junction ATP binding|protein C-terminus binding lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1) 6 Lung NSC(201;0.0016) BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133) AACCTTCTGTctgctgctgctgctgctgctgc 0.368 0.59 26 37 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.39 28 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 86 134 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.37 92 54 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 10 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.10 150 16 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.90 7 66 MAMDC4 158056 broad.mit.edu 37 9 139751886 139751887 + Frame_Shift_Ins INS - G G rs139519920 by1000genomes KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr9:139751886_139751887insG uc004cjs.2 + 18 2224_2225 c.2174_2175insG c.(2173-2175)CCGfs p.P725fs MAMDC4_uc011mej.1_Frame_Shift_Ins_p.P62fs NM_206920 NP_996803 Q6UXC1 AEGP_HUMAN apical early endosomal glycoprotein precursor 804 MAM 4.|Extracellular (Potential). protein transport integral to membrane breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1) 7 all_cancers(76;0.0763)|all_epithelial(76;0.198) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171) GCCGTGCGGCCGGGCCCCTGCT 0.688 0.20 40 10 ADRBK1 156 broad.mit.edu 37 11 67047145 67047146 + In_Frame_Ins INS - AGC AGC KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr11:67047145_67047146insAGC uc009yrn.1 + 5 681_682 c.415_416insAGC c.(415-417)AAG>AAGCAG p.140_141insQ ADRBK1_uc009yrm.1_In_Frame_Ins_p.140_141insQ NM_001619 NP_001610 P25098 ARBK1_HUMAN beta-adrenergic receptor kinase 1 140_141 RGS.|N-terminal. activation of phospholipase C activity|cardiac muscle contraction|desensitization of G-protein coupled receptor protein signaling pathway|muscarinic acetylcholine receptor signaling pathway|negative regulation of striated muscle contraction|negative regulation of the force of heart contraction by chemical signal|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of catecholamine secretion|tachykinin receptor signaling pathway cytosol|soluble fraction alpha-2A adrenergic receptor binding|ATP binding|beta-adrenergic receptor kinase activity|Edg-2 lysophosphatidic acid receptor binding|G-protein coupled receptor kinase activity|signal transducer activity large_intestine(1) 1 BRCA - Breast invasive adenocarcinoma(15;2.26e-06) Adenosine triphosphate(DB00171) CCTGGGGAAGAAGCAGGTGCCT 0.619 0.65 13 24 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.18 317 69 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 90 432 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KNS60_CENTRAL_NERVOUS_SYSTEM NA KNS60_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 7 201 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KNS62_LUNG NA KNS62_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 3 40 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KNS62_LUNG NA KNS62_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.38 245 151 PRRX1 5396 broad.mit.edu 37 1 170633445 170633445 + Frame_Shift_Del DEL A - - KNS62_LUNG NA KNS62_LUNG NA g.chr1:170633445delA uc001ghf.2 + 1 133 c.86delA c.(85-87)CAGfs p.Q29fs PRRX1_uc001ghe.2_Frame_Shift_Del_p.Q29fs NM_022716 NP_073207 P54821 PRRX1_HUMAN paired mesoderm homeobox 1 isoform pmx-1b 29 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity ovary(1) 1 all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181) GACACCCTGCAGGCGAAAAAG 0.672 0.67 12 24 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KNS62_LUNG NA KNS62_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 63 72 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes KNS62_LUNG NA KNS62_LUNG NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.38 604 374 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KNS62_LUNG NA KNS62_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.55 20 24 CSMD3 114788 broad.mit.edu 37 8 113308206 113308207 + Frame_Shift_Ins INS - A A KNS62_LUNG NA KNS62_LUNG NA g.chr8:113308206_113308207insA uc003ynu.2 - 54 8628_8629 c.8469_8470insT c.(8467-8472)ATTGTGfs p.I2823fs CSMD3_uc003yns.2_Frame_Shift_Ins_p.I2025fs|CSMD3_uc003ynt.2_Frame_Shift_Ins_p.I2783fs|CSMD3_uc011lhx.1_Frame_Shift_Ins_p.I2654fs NM_198123 NP_937756 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 isoform 1 2823_2824 Extracellular (Potential).|Sushi 18. integral to membrane|plasma membrane ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1) 63 TGACCATTCACAATCAGTTCTG 0.312 0.62 35 56 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KNS62_LUNG NA KNS62_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 39 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KNS62_LUNG NA KNS62_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.61 661 1047 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KNS62_LUNG NA KNS62_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 423 137 C15orf2 23742 broad.mit.edu 37 15 24921053 24921053 + Frame_Shift_Del DEL C - - KNS62_LUNG NA KNS62_LUNG NA g.chr15:24921053delC uc001ywo.2 + 1 513 c.39delC c.(37-39)CGCfs p.R13fs NM_018958 NP_061831 Q9NZP6 CO002_HUMAN hypothetical protein LOC23742 13 cell differentiation|multicellular organismal development|spermatogenesis ovary(2)|large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1) 8 all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086) all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229) CCGGGTGCCGCCGCCGGCCCC 0.662 0.71 10 24 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KNS62_LUNG NA KNS62_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 30 274 STARD3 10948 broad.mit.edu 37 17 37814105 37814105 + Frame_Shift_Del DEL G - - KNS62_LUNG NA KNS62_LUNG NA g.chr17:37814105delG uc002hsd.2 + 4 499 c.375delG c.(373-375)GCGfs p.A125fs STARD3_uc010weg.1_Intron|STARD3_uc010weh.1_Intron|STARD3_uc002hse.2_Frame_Shift_Del_p.A125fs|STARD3_uc010wei.1_Intron|STARD3_uc002hsf.2_5'UTR|STARD3_uc002hsg.2_5'Flank NM_006804 NP_006795 Q14849 STAR3_HUMAN StAR-related lipid transfer (START) domain 125 Helical; (Potential).|MENTAL. cholesterol metabolic process|mitochondrial transport|steroid biosynthetic process integral to membrane|late endosome membrane cholesterol binding|cholesterol transporter activity 0 Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052) UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171) GGGTGATTGCGGTAAGATGCC 0.642 0.20 262 64 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KNS62_LUNG NA KNS62_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.41 32 22 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KNS62_LUNG NA KNS62_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.34 65 33 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KNS62_LUNG NA KNS62_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 116 443 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KNS62_LUNG NA KNS62_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 7 55 FAM48B1 100130302 broad.mit.edu 37 X 24382374 24382376 + In_Frame_Del DEL TGC - - KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chrX:24382374_24382376delTGC uc011mjx.1 + 1 1497_1499 c.1497_1499delTGC c.(1495-1500)ATTGCT>ATT p.A517del NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 ctgctgctattgctgctgctgct 0.202 0.33 31 15 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 30 PRKAA2 5563 broad.mit.edu 37 1 57173242 57173243 + Frame_Shift_Del DEL AA - - KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr1:57173242_57173243delAA uc001cyk.3 + 9 1586_1587 c.1515_1516delAA c.(1513-1518)ACAACTfs p.T505fs NM_006252 NP_006243 P54646 AAPK2_HUMAN AMP-activated protein kinase alpha 2 catalytic 505_506 carnitine shuttle|cell cycle arrest|cholesterol biosynthetic process|energy reserve metabolic process|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleoplasm ATP binding|metal ion binding p.T506A(2) breast(4)|ovary(1)|stomach(1) 6 TTGATTCCACAACTGCAGAGAG 0.490 0.47 125 109 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 424 120 FMO4 2329 broad.mit.edu 37 1 171289040 171289041 + Frame_Shift_Ins INS - TGGA TGGA KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr1:171289040_171289041insTGGA uc001gho.2 + 3 293_294 c.76_77insTGGA c.(76-78)CTGfs p.L26fs NM_002022 NP_002013 P31512 FMO4_HUMAN flavin containing monooxygenase 4 26 xenobiotic metabolic process integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding kidney(2)|skin(1) 3 all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181) GGATGAGGACCTGGAGCCCACC 0.480 0.43 99 76 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.61 19 30 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.17 69 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.72 93 241 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 98 49 PIK3R1 5295 broad.mit.edu 37 5 67589580 67589582 + In_Frame_Del DEL AAT - - KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr5:67589580_67589582delAAT uc003jva.2 + 11 1903_1905 c.1343_1345delAAT c.(1342-1347)AAATTA>ATA p.448_449KL>I PIK3R1_uc003jvb.2_In_Frame_Del_p.448_449KL>I|PIK3R1_uc003jvc.2_In_Frame_Del_p.148_149KL>I|PIK3R1_uc003jvd.2_In_Frame_Del_p.178_179KL>I|PIK3R1_uc003jve.2_In_Frame_Del_p.127_128KL>I|PIK3R1_uc011crb.1_In_Frame_Del_p.118_119KL>I NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 448_449 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.K448fs*32(2)|p.D434_Q475del(2)|p.L449fs*3(1)|p.?(1)|p.G446_Y452>VI(1)|p.K448_L449>I(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) GTAGGGAAAAAATTACATGAATA 0.281 0.50 6 6 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.52 138 148 ARID1B 57492 broad.mit.edu 37 6 157099402 157099403 + In_Frame_Ins INS - CAG CAG KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr6:157099402_157099403insCAG uc003qqn.2 + 1 317_318 c.165_166insCAG c.(163-168)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) TAAACCAGTTCcagcagcagca 0.124 0.32 104 49 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.10 232 26 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 2 26 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 32 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.51 64 67 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.51 487 497 PRTG 283659 broad.mit.edu 37 15 56035035 56035036 + Splice_Site INS - A A KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr15:56035035_56035036insA uc002adg.2 - 1 142 c.94_splice c.e1+1 p.G32_splice NM_173814 NP_776175 Q2VWP7 PRTG_HUMAN protogenin precursor multicellular organismal development integral to membrane large_intestine(1)|ovary(1)|skin(1) 3 all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135) 0.000 0.40 6 4 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 50 525 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 1.00 0 24 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.86 23 140 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.18 154 33 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 158 566 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KNS81_CENTRAL_NERVOUS_SYSTEM NA KNS81_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 55 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 4 49 XIAP 331 broad.mit.edu 37 X 123025155 123025157 + In_Frame_Del DEL GAG - - KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:123025155_123025157delGAG uc010nqu.2 + 4 1171_1173 c.1045_1047delGAG c.(1045-1047)GAGdel p.E350del XIAP_uc004etx.2_In_Frame_Del_p.E350del|XIAP_uc010nqv.2_5'UTR NM_001167 NP_001158 P98170 XIAP_HUMAN baculoviral IAP repeat-containing protein 4 350 anti-apoptosis|apoptosis|induction of apoptosis by intracellular signals|response to DNA damage stimulus cytosol caspase inhibitor activity|ligase activity|protein binding|zinc ion binding ovary(1)|lung(1) 2 TCATTCACTTGAGGAGTGTCTGG 0.197 0.92 4 47 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.44 244 191 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.12 123 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 116 66 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.28 208 80 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.39 51 32 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 20 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.37 543 321 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.36 7 4 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 190 44 MYH8 4626 broad.mit.edu 37 17 10314206 10314206 + Frame_Shift_Del DEL A - - KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:10314206delA uc002gmm.2 - 15 1570 c.1475delT c.(1474-1476)TTCfs p.F492fs uc002gml.1_Intron NM_002472 NP_002463 P13535 MYH8_HUMAN myosin, heavy chain 8, skeletal muscle, 492 Myosin head-like. muscle filament sliding cytosol|muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle skin(6)|ovary(3)|breast(2) 11 GTGGTGGTTGAAAAACTGTTG 0.443 0.94 4 68 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 18 11 NCOA3 8202 broad.mit.edu 37 20 46279860 46279861 + In_Frame_Ins INS - CAA CAA rs151060280 byFrequency KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:46279860_46279861insCAA uc002xtk.2 + 20 3991_3992 c.3786_3787insCAA c.(3784-3789)insCAA p.1276_1277insQ NCOA3_uc010ght.1_In_Frame_Ins_p.1267_1268insQ|NCOA3_uc002xtl.2_In_Frame_Ins_p.1272_1273insQ|NCOA3_uc002xtm.2_In_Frame_Ins_p.1271_1272insQ|NCOA3_uc002xtn.2_In_Frame_Ins_p.1275_1276insQ|NCOA3_uc010zyc.1_In_Frame_Ins_p.1071_1072insQ NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 1276_1277 Poly-Gln.|Acetyltransferase. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 agcagcagcagcagcaacagca 0.307 0.36 70 40 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.46 149 128 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.95 24 433 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 9 75 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KP2_PANCREAS NA KP2_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 5 68 XIAP 331 broad.mit.edu 37 X 123025155 123025157 + In_Frame_Del DEL GAG - - KP2_PANCREAS NA KP2_PANCREAS NA g.chrX:123025155_123025157delGAG uc010nqu.2 + 4 1171_1173 c.1045_1047delGAG c.(1045-1047)GAGdel p.E350del XIAP_uc004etx.2_In_Frame_Del_p.E350del|XIAP_uc010nqv.2_5'UTR NM_001167 NP_001158 P98170 XIAP_HUMAN baculoviral IAP repeat-containing protein 4 350 anti-apoptosis|apoptosis|induction of apoptosis by intracellular signals|response to DNA damage stimulus cytosol caspase inhibitor activity|ligase activity|protein binding|zinc ion binding ovary(1)|lung(1) 2 TCATTCACTTGAGGAGTGTCTGG 0.197 0.32 116 54 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KP2_PANCREAS NA KP2_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 447 148 RPL14 9045 broad.mit.edu 37 3 40503519 40503521 + In_Frame_Del DEL TAC - - rs111899316;rs147295890 by1000genomes KP2_PANCREAS NA KP2_PANCREAS NA g.chr3:40503519_40503521delTAC uc003ckg.2 + 6 495_497 c.444_446delTAC c.(442-447)GGTACT>GGT p.T149del RPL14_uc003ckh.2_In_Frame_Del_p.T149del|RPL14_uc003cki.2_In_Frame_Del_p.T100del NM_003973 NP_003964 P50914 RL14_HUMAN ribosomal protein L14 149 endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription cytosolic large ribosomal subunit protein binding|RNA binding|structural constituent of ribosome 0 KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065) GTACTAAGGGTActgctgctgct 0.365 0.46 7 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KP2_PANCREAS NA KP2_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.38 93 57 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KP2_PANCREAS NA KP2_PANCREAS NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.26 143 50 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KP2_PANCREAS NA KP2_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 10 UBR5 51366 broad.mit.edu 37 8 103298589 103298589 + Frame_Shift_Del DEL T - - KP2_PANCREAS NA KP2_PANCREAS NA g.chr8:103298589delT uc003ykr.1 - 38 5247 c.5214delA c.(5212-5214)GCAfs p.A1738fs UBR5_uc003yks.1_Frame_Shift_Del_p.A1738fs NM_015902 NP_056986 O95071 UBR5_HUMAN ubiquitin protein ligase E3 component n-recognin 1738 cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus nucleus|soluble fraction protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1) 28 all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05) OV - Ovarian serous cystadenocarcinoma(57;0.000442) CAGACTTGCCTGCTGGTGTAG 0.443 0.31 46 21 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KP2_PANCREAS NA KP2_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.51 167 171 COBRA1 25920 broad.mit.edu 37 9 140158792 140158793 + Frame_Shift_Ins INS - T T KP2_PANCREAS NA KP2_PANCREAS NA g.chr9:140158792_140158793insT uc004cmm.3 + 6 1082_1083 c.879_880insT c.(877-882)GGCCAGfs p.G293fs NM_015456 NP_056271 Q8WX92 NELFB_HUMAN cofactor of BRCA1 293_294 negative regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction cytoplasm|nucleoplasm protein binding 0 all_cancers(76;0.0926) STAD - Stomach adenocarcinoma(284;0.137) OV - Ovarian serous cystadenocarcinoma(145;9.42e-05)|Epithelial(140;0.000766) 0.000 1.00 0 12 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KP2_PANCREAS NA KP2_PANCREAS NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 1.00 0 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KP2_PANCREAS NA KP2_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 306 76 SMAD4 4089 broad.mit.edu 37 18 48593491 48593494 + Frame_Shift_Del DEL AGAC - - rs80338965 KP2_PANCREAS NA KP2_PANCREAS NA g.chr18:48593491_48593494delAGAC uc010xdp.1 + 10 1780_1783 c.1242_1245delAGAC c.(1240-1245)TTAGACfs p.L414fs SMAD4_uc002lfb.3_Frame_Shift_Del_p.L259fs NM_005359 NP_005350 Q13485 SMAD4_HUMAN mothers against decapentaplegic homolog 4 414_415 MH2. BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway activin responsive factor complex|centrosome|cytosol I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity p.0?(35)|p.?(2) pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1) 369 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155) GTTACTACTTAGACAGAGAAGCTG 0.412 0.94 5 72 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KP2_PANCREAS NA KP2_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.69 22 50 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KP2_PANCREAS NA KP2_PANCREAS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.22 136 38 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KP2_PANCREAS NA KP2_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 51 195 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KP2_PANCREAS NA KP2_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 97 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KP3_PANCREAS NA KP3_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.61 21 33 ARID1A 8289 broad.mit.edu 37 1 27106803 27106804 + Frame_Shift_Ins INS - C C KP3_PANCREAS NA KP3_PANCREAS NA g.chr1:27106803_27106804insC uc001bmv.1 + 20 6787_6788 c.6414_6415insC c.(6412-6417)ACACCCfs p.T2138fs ARID1A_uc001bmu.1_Frame_Shift_Ins_p.T1921fs|ARID1A_uc001bmx.1_Frame_Shift_Ins_p.T984fs|ARID1A_uc009vsm.1_Frame_Shift_Ins_p.T466fs|ARID1A_uc009vsn.1_Frame_Shift_Ins_p.T380fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 2138_2139 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.F2141fs*59(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) TTCTGGCCACACCCCCCTTCAG 0.589 0.81 19 82 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KP3_PANCREAS NA KP3_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.47 152 136 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KP3_PANCREAS NA KP3_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.46 7 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KP3_PANCREAS NA KP3_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 38 69 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KP3_PANCREAS NA KP3_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.54 26 31 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 KP3_PANCREAS NA KP3_PANCREAS NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.30 16 7 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KP3_PANCREAS NA KP3_PANCREAS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.93 1 14 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KP3_PANCREAS NA KP3_PANCREAS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.50 5 5 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KP3_PANCREAS NA KP3_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 64 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KP3_PANCREAS NA KP3_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 398 126 TP53 7157 broad.mit.edu 37 17 7578474 7578475 + Frame_Shift_Ins INS - G G KP3_PANCREAS NA KP3_PANCREAS NA g.chr17:7578474_7578475insG uc002gim.2 - 5 649_650 c.455_456insC c.(454-456)CCGfs p.P152fs TP53_uc002gig.1_Frame_Shift_Ins_p.P152fs|TP53_uc002gih.2_Frame_Shift_Ins_p.P152fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Ins_p.P20fs|TP53_uc010cng.1_Frame_Shift_Ins_p.P20fs|TP53_uc002gii.1_Frame_Shift_Ins_p.P20fs|TP53_uc010cnh.1_Frame_Shift_Ins_p.P152fs|TP53_uc010cni.1_Frame_Shift_Ins_p.P152fs|TP53_uc002gij.2_Frame_Shift_Ins_p.P152fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Ins_p.P59fs|TP53_uc002gio.2_Frame_Shift_Ins_p.P20fs|TP53_uc010vug.1_Frame_Shift_Ins_p.P113fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 152 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). P -> R (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|P -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> A (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.P152L(57)|p.P152S(21)|p.P152fs*18(17)|p.P153fs*28(8)|p.P152T(7)|p.0?(7)|p.P152fs*29(5)|p.P152P(5)|p.P152Q(4)|p.P152fs*14(4)|p.P152fs*28(3)|p.P152R(3)|p.T150fs*16(3)|p.P152A(2)|p.P153fs*16(1)|p.P151_V173del23(1)|p.P152_P153del(1)|p.G154fs*16(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.P153fs*20(1)|p.D148fs*23(1)|p.P152del(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.Q144_G154del11(1)|p.G154fs*27(1)|p.P152_P153insXXX(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGGTGCCGGGCGGGGGTGTGGA 0.614 0.85 30 172 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KP3_PANCREAS NA KP3_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.62 18 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KP3_PANCREAS NA KP3_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 108 382 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KP3_PANCREAS NA KP3_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 5 51 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KP4_PANCREAS NA KP4_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 33 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KP4_PANCREAS NA KP4_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.15 496 87 FMO4 2329 broad.mit.edu 37 1 171289040 171289041 + Frame_Shift_Ins INS - TGGA TGGA KP4_PANCREAS NA KP4_PANCREAS NA g.chr1:171289040_171289041insTGGA uc001gho.2 + 3 293_294 c.76_77insTGGA c.(76-78)CTGfs p.L26fs NM_002022 NP_002013 P31512 FMO4_HUMAN flavin containing monooxygenase 4 26 xenobiotic metabolic process integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding kidney(2)|skin(1) 3 all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181) GGATGAGGACCTGGAGCCCACC 0.480 0.50 78 79 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KP4_PANCREAS NA KP4_PANCREAS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.35 17 9 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KP4_PANCREAS NA KP4_PANCREAS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.30 212 91 PLD1 5337 broad.mit.edu 37 3 171431727 171431729 + In_Frame_Del DEL CTT - - KP4_PANCREAS NA KP4_PANCREAS NA g.chr3:171431727_171431729delCTT uc003fhs.2 - 9 981_983 c.865_867delAAG c.(865-867)AAGdel p.K289del PLD1_uc003fht.2_In_Frame_Del_p.K289del NM_002662 NP_002653 Q13393 PLD1_HUMAN phospholipase D1 isoform a 289 PH. cell communication|chemotaxis|Ras protein signal transduction endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity ovary(2)|lung(1) 3 all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186) LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14) Choline(DB00122) TTTCTGTCTCCTTCTTCCCCACC 0.330 0.63 119 203 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KP4_PANCREAS NA KP4_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 72 125 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KP4_PANCREAS NA KP4_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 94 46 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 KP4_PANCREAS NA KP4_PANCREAS NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.61 7 11 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KP4_PANCREAS NA KP4_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KP4_PANCREAS NA KP4_PANCREAS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.30 33 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KP4_PANCREAS NA KP4_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 285 105 ATN1 1822 broad.mit.edu 37 12 7045892 7045915 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633;rs148885085 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes KP4_PANCREAS NA KP4_PANCREAS NA g.chr12:7045892_7045915delCAGCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1722 c.1462_1485delCAGCAGCAGCAGCAGCAGCAGCAG c.(1462-1485)CAGCAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQQ488del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQQ488del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 488_495 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagcagc 0.478 0.28 33 13 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency KP4_PANCREAS NA KP4_PANCREAS NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.24 31 10 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KP4_PANCREAS NA KP4_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 52 490 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KP4_PANCREAS NA KP4_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 100 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KPL1_BREAST NA KPL1_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 7 67 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KPL1_BREAST NA KPL1_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.44 383 302 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KPL1_BREAST NA KPL1_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.48 74 68 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KPL1_BREAST NA KPL1_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 23 37 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KPL1_BREAST NA KPL1_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.31 25 11 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KPL1_BREAST NA KPL1_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 15 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KPL1_BREAST NA KPL1_BREAST NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.95 1 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KPL1_BREAST NA KPL1_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 106 25 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KPL1_BREAST NA KPL1_BREAST NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.58 5 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KPL1_BREAST NA KPL1_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.51 20 21 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KPL1_BREAST NA KPL1_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 49 672 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KPL1_BREAST NA KPL1_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 2 41 MYH9 4627 broad.mit.edu 37 22 36702074 36702091 + In_Frame_Del DEL GAGATGCGGGTCCAGCTT - - rs143801000 byFrequency;by1000genomes KPL1_BREAST NA KPL1_BREAST NA g.chr22:36702074_36702091delGAGATGCGGGTCCAGCTT uc003apg.2 - 17 2275_2292 c.2044_2061delAAGCTGGACCCGCATCTC c.(2044-2061)AAGCTGGACCCGCATCTCdel p.KLDPHL682del MYH9_uc003aph.1_In_Frame_Del_p.KLDPHL546del NM_002473 NP_002464 P35579 MYH9_HUMAN myosin, heavy polypeptide 9, non-muscle 682_687 Myosin head-like. actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity p.H686Y(1) breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1) 11 GGTCCAGCACGAGATGCGGGTCCAGCTTGCCGGCCTGG 0.592 0.25 63 21 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 5 57 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 578 162 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.38 15 9 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.52 29 31 HTT 3064 broad.mit.edu 37 4 3076604 3076612 + In_Frame_Del DEL CAGCAGCAG - - rs10618869 KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr4:3076604_3076612delCAGCAGCAG uc011bvq.1 + 2 203_211 c.58_66delCAGCAGCAG c.(58-66)CAGCAGCAGdel p.QQQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagcagc 0.325 0.26 61 21 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.22 76 21 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 151 345 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 120 75 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.83 2 10 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.49 81 77 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.24 63 20 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.10 328 38 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 22 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.43 12 9 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.18 111 25 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.47 738 647 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.18 154 33 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 57 465 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.10 620 68 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.44 114 91 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 340 45 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 125 532 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KPNRTBM1_AUTONOMIC_GANGLIA NA KPNRTBM1_AUTONOMIC_GANGLIA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 11 161 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KPNSI9S_AUTONOMIC_GANGLIA NA KPNSI9S_AUTONOMIC_GANGLIA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 61 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KPNSI9S_AUTONOMIC_GANGLIA NA KPNSI9S_AUTONOMIC_GANGLIA NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.13 427 63 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KPNSI9S_AUTONOMIC_GANGLIA NA KPNSI9S_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.51 92 95 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KPNSI9S_AUTONOMIC_GANGLIA NA KPNSI9S_AUTONOMIC_GANGLIA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.49 55 52 FOXP2 93986 broad.mit.edu 37 7 114270000 114270001 + In_Frame_Ins INS - CAG CAG KPNSI9S_AUTONOMIC_GANGLIA NA KPNSI9S_AUTONOMIC_GANGLIA NA g.chr7:114270000_114270001insCAG uc003vhb.2 + 5 911_912 c.537_538insCAG c.(535-540)insCAG p.191_192insQ FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_In_Frame_Ins_p.216_217insQ|FOXP2_uc003vha.2_In_Frame_Ins_p.99_100insQ|FOXP2_uc011kmu.1_In_Frame_Ins_p.208_209insQ|FOXP2_uc011kmv.1_In_Frame_Ins_p.191_192insQ|FOXP2_uc010ljz.1_In_Frame_Ins_p.99_100insQ|FOXP2_uc003vgt.1_RNA|FOXP2_uc003vgv.1_In_Frame_Ins_p.191_192insQ|FOXP2_uc003vgx.2_In_Frame_Ins_p.191_192insQ|FOXP2_uc003vhd.2_In_Frame_Ins_p.191_192insQ|FOXP2_uc003vhc.2_In_Frame_Ins_p.216_217insQ NM_014491 NP_055306 O15409 FOXP2_HUMAN forkhead box P2 isoform I 191_192 Gln-rich. camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning cytoplasm|transcription factor complex chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1) 8 agcaacaacagcagcagcagca 0.158 0.25 57 19 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KPNSI9S_AUTONOMIC_GANGLIA NA KPNSI9S_AUTONOMIC_GANGLIA NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.13 47 7 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KPNSI9S_AUTONOMIC_GANGLIA NA KPNSI9S_AUTONOMIC_GANGLIA NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 16 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KPNSI9S_AUTONOMIC_GANGLIA NA KPNSI9S_AUTONOMIC_GANGLIA NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.66 264 502 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KPNSI9S_AUTONOMIC_GANGLIA NA KPNSI9S_AUTONOMIC_GANGLIA NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.92 3 34 CREBBP 1387 broad.mit.edu 37 16 3779071 3779079 + In_Frame_Del DEL TCCCCGGGG - - KPNSI9S_AUTONOMIC_GANGLIA NA KPNSI9S_AUTONOMIC_GANGLIA NA g.chr16:3779071_3779079delTCCCCGGGG uc002cvv.2 - 31 6173_6181 c.5969_5977delCCCCGGGGA c.(5968-5979)ACCCCGGGGAGC>AGC p.TPG1990del CREBBP_uc002cvw.2_In_Frame_Del_p.TPG1952del NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1990_1992 cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) GCCATCTGGCTCCCCGGGGTCCCCATGCC 0.694 0.29 27 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KPNSI9S_AUTONOMIC_GANGLIA NA KPNSI9S_AUTONOMIC_GANGLIA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.85 4 23 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KPNSI9S_AUTONOMIC_GANGLIA NA KPNSI9S_AUTONOMIC_GANGLIA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.91 3 30 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KPNSI9S_AUTONOMIC_GANGLIA NA KPNSI9S_AUTONOMIC_GANGLIA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 78 804 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KPNYN_AUTONOMIC_GANGLIA NA KPNYN_AUTONOMIC_GANGLIA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 4 31 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KPNYN_AUTONOMIC_GANGLIA NA KPNYN_AUTONOMIC_GANGLIA NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 195 63 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KPNYN_AUTONOMIC_GANGLIA NA KPNYN_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.44 92 71 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KPNYN_AUTONOMIC_GANGLIA NA KPNYN_AUTONOMIC_GANGLIA NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.32 185 86 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KPNYN_AUTONOMIC_GANGLIA NA KPNYN_AUTONOMIC_GANGLIA NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.47 20 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KPNYN_AUTONOMIC_GANGLIA NA KPNYN_AUTONOMIC_GANGLIA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 155 63 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KPNYN_AUTONOMIC_GANGLIA NA KPNYN_AUTONOMIC_GANGLIA NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.55 5 6 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KPNYN_AUTONOMIC_GANGLIA NA KPNYN_AUTONOMIC_GANGLIA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 25 244 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KPNYN_AUTONOMIC_GANGLIA NA KPNYN_AUTONOMIC_GANGLIA NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.13 77 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KPNYN_AUTONOMIC_GANGLIA NA KPNYN_AUTONOMIC_GANGLIA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 97 321 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KPNYN_AUTONOMIC_GANGLIA NA KPNYN_AUTONOMIC_GANGLIA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 66 HEPH 9843 broad.mit.edu 37 X 65393494 65393495 + Frame_Shift_Ins INS - C C KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chrX:65393494_65393495insC uc011moz.1 + 4 545_546 c.485_486insC c.(484-486)GGCfs p.G162fs HEPH_uc004dwn.2_Frame_Shift_Ins_p.G162fs|HEPH_uc004dwo.2_5'UTR|HEPH_uc010nkr.2_Frame_Shift_Ins_p.G162fs|HEPH_uc011mpa.1_Frame_Shift_Ins_p.G162fs NM_138737 NP_620074 Q9BQS7 HEPH_HUMAN hephaestin isoform a 159 Extracellular (Potential).|Plastocyanin-like 1. cellular iron ion homeostasis|copper ion transport|transmembrane transport integral to membrane|plasma membrane copper ion binding|oxidoreductase activity lung(5)|ovary(4) 9 CCCCCGGGGGGCAGCCATATCT 0.535 0.17 230 46 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.86 16 102 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.13 1444 209 HOXD13 3239 broad.mit.edu 37 2 176957786 176957797 + In_Frame_Del DEL GGCGGCGGCGGC - - rs3832095 KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr2:176957786_176957797delGGCGGCGGCGGC uc002ukf.1 + 1 255_266 c.168_179delGGCGGCGGCGGC c.(166-180)CGGGCGGCGGCGGCG>CGG p.AAAA65del NM_000523 NP_000514 P35453 HXD13_HUMAN homeobox D13 65_68 Poly-Ala. skeletal system development|transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding lung(1) 1 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0526)|READ - Rectum adenocarcinoma(9;0.0678) 0.000 0.32 828 393 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 1.00 0 15 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.17 80 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 193 166 INPP4B 8821 broad.mit.edu 37 4 143044564 143044564 + Frame_Shift_Del DEL G - - KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr4:143044564delG uc003iix.3 - 21 2493 c.1898delC c.(1897-1899)GCTfs p.A633fs INPP4B_uc003iiw.3_Frame_Shift_Del_p.A633fs|INPP4B_uc011chm.1_RNA|INPP4B_uc011chn.1_Frame_Shift_Del_p.A448fs|INPP4B_uc011cho.1_RNA|INPP4B_uc011chp.1_Frame_Shift_Del_p.A504fs NM_003866 NP_003857 O15327 INP4B_HUMAN inositol polyphosphate-4-phosphatase, type II, 633 signal transduction phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity ovary(1)|lung(1) 2 all_hematologic(180;0.158) AACCAATCCAGCAAGCTGAAA 0.353 0.30 280 120 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.27 221 81 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 2 39 CTSL3 392360 broad.mit.edu 37 9 90388139 90388141 + In_Frame_Del DEL CGT - - KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr9:90388139_90388141delCGT uc004apm.1 + 2 210_212 c.204_206delCGT c.(202-207)TACGTG>TAG p.68_69YV>* NR_027917 RecName: Full=Putative cathepsin L-like protein 3; Short=Cathepsin L-like protein; AltName: Full=HCTSL-s; ovary(1) 1 AGAAAGGCTACGTGACTCCTGTG 0.493 0.41 42 29 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.29 37 15 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.50 5 5 ZFHX3 463 broad.mit.edu 37 16 72831358 72831363 + In_Frame_Del DEL TTGTTG - - KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr16:72831358_72831363delTTGTTG uc002fck.2 - 9 5891_5896 c.5218_5223delCAACAA c.(5218-5223)CAACAAdel p.QQ1740del ZFHX3_uc002fcl.2_In_Frame_Del_p.QQ826del NM_006885 NP_008816 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 isoform A 1740_1741 Poly-Gln. muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation transcription factor complex enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding ovary(2)|skin(2) 4 Ovarian(137;0.13) GCGTTTGTGCttgttgttgttgttgt 0.413 0.28 18 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.85 15 88 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.50 32 32 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 63 734 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KS1_CENTRAL_NERVOUS_SYSTEM NA KS1_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 29 374 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 3 38 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 333 112 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.25 27 9 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.26 49 17 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.48 11 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 107 172 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 21 42 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.79 3 11 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.54 26 31 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 2 30 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.30 16 7 PRKDC 5591 broad.mit.edu 37 8 48711825 48711825 + Frame_Shift_Del DEL T - - KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr8:48711825delT uc003xqi.2 - 73 10300 c.10243delA c.(10243-10245)ACGfs p.T3415fs PRKDC_uc003xqj.2_Frame_Shift_Del_p.T3415fs|PRKDC_uc011ldh.1_Intron NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic 3415 FAT. cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) TCTGCCAGCGTCATGTAAGCA 0.522 0.28 87 34 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 66 CCDC6 8030 broad.mit.edu 37 10 61554344 61554345 + Frame_Shift_Ins INS - A A KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr10:61554344_61554345insA uc001jks.3 - 8 1752_1753 c.1116_1117insT c.(1114-1119)TATGCAfs p.Y372fs NM_005436 NP_005427 Q16204 CCDC6_HUMAN coiled-coil domain containing 6 372_373 cytoplasm|cytoskeleton SH3 domain binding|structural constituent of cytoskeleton ovary(3)|breast(1) 4 Kidney(211;0.0597) GTGTGACTTGCATATGATAGAC 0.406 0.50 79 79 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.48 11 10 ATN1 1822 broad.mit.edu 37 12 7045885 7045886 + In_Frame_Ins INS - CAG CAG KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr12:7045885_7045886insCAG uc001qrw.1 + 5 1692_1693 c.1455_1456insCAG c.(1453-1458)insCAG p.502_503insQ ATN1_uc001qrx.1_In_Frame_Ins_p.502_503insQ|ATN1_uc001qry.1_In_Frame_Ins_p.486_487insQ NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502_503 cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 ACCACcagcaacagcaacagca 0.441 0.35 133 71 KTN1 3895 broad.mit.edu 37 14 56079160 56079161 + Frame_Shift_Ins INS - A A KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr14:56079160_56079161insA uc001xcb.2 + 3 696_697 c.394_395insA c.(394-396)GAAfs p.E132fs KTN1_uc001xce.2_Frame_Shift_Ins_p.E132fs|KTN1_uc001xcc.2_Frame_Shift_Ins_p.E132fs|KTN1_uc001xcd.2_Frame_Shift_Ins_p.E132fs|KTN1_uc010trb.1_Frame_Shift_Ins_p.E132fs|KTN1_uc001xcf.1_Frame_Shift_Ins_p.E132fs NM_182926 NP_891556 Q86UP2 KTN1_HUMAN kinectin 1 isoform a 132 Lumenal (Potential). microtubule-based movement endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction breast(3)|ovary(2)|lung(1)|central_nervous_system(1) 7 GGTCATCAAAGAAAGTGACGCA 0.436 0.62 26 42 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.32 45 21 TTBK2 146057 broad.mit.edu 37 15 43044395 43044395 + Frame_Shift_Del DEL C - - KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr15:43044395delC uc001zqo.2 - 14 3488 c.3049delG c.(3049-3051)GAGfs p.E1017fs TTBK2_uc010bcy.2_Frame_Shift_Del_p.E948fs NM_173500 NP_775771 Q6IQ55 TTBK2_HUMAN tau tubulin kinase 2 1017 cell death ATP binding|protein serine/threonine kinase activity ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1) 7 all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216) GBM - Glioblastoma multiforme(94;3.23e-07) AGCACTTCCTCCTCACAAAAG 0.458 0.25 187 64 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 89 988 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.55 108 131 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.28 59 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 222 601 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KU1919_URINARY_TRACT NA KU1919_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 6 75 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 1 20 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.49 264 250 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 116 29 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.38 16 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.44 93 72 HOXA11 3207 broad.mit.edu 37 7 27224467 27224475 + In_Frame_Del DEL CGCGCTGGG - - KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:27224467_27224475delCGCGCTGGG uc003syx.2 - 1 361_369 c.289_297delCCCAGCGCG c.(289-297)CCCAGCGCGdel p.PSA97del HOXA11_uc003syy.2_RNA|HOXA11AS_uc003syz.1_5'Flank NM_005523 NP_005514 P31270 HXA11_HUMAN homeobox A11 97_99 branching involved in ureteric bud morphogenesis|cartilage development involved in endochondral bone morphogenesis|developmental growth|dorsal/ventral pattern formation|mesodermal cell fate specification|positive regulation of cell development|positive regulation of chondrocyte differentiation protein-DNA complex|transcription factor complex sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity lung(1)|breast(1) 2 0.000 0.23 77 23 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.35 11 6 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.45 35 29 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 36 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 385 116 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.43 8 6 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 41 299 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 15 36 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 163 519 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.84 4 21 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 1 13 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.29 193 78 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 1.00 0 12 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.50 9 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.44 37 29 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 4 10 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.29 20 8 ARID1B 57492 broad.mit.edu 37 6 157099402 157099403 + In_Frame_Ins INS - CAG CAG KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr6:157099402_157099403insCAG uc003qqn.2 + 1 317_318 c.165_166insCAG c.(163-168)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) TAAACCAGTTCcagcagcagca 0.124 0.13 72 11 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.87 4 27 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.31 9 4 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.54 18 21 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 46 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.20 508 127 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 245 97 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.25 38 13 CDH3 1001 broad.mit.edu 37 16 68679613 68679614 + Frame_Shift_Ins INS - A A KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr16:68679613_68679614insA uc002ewf.2 + 2 1252_1253 c.120_121insA c.(118-123)GCGGGAfs p.A40fs CDH3_uc010vli.1_Intron NM_001793 NP_001784 P22223 CADH3_HUMAN cadherin 3, type 1 preproprotein 40_41 adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception integral to membrane calcium ion binding p.?(1) ovary(3)|breast(1)|skin(1) 5 Ovarian(137;0.0564) OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384) 0.000 1.00 0 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.48 84 78 ADCK4 79934 broad.mit.edu 37 19 41209723 41209724 + Frame_Shift_Ins INS - C C KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr19:41209723_41209724insC uc002oor.2 - 8 915_916 c.613_614insG c.(613-615)GCCfs p.A205fs ADCK4_uc002oop.1_5'Flank|ADCK4_uc002ooq.1_Frame_Shift_Ins_p.A164fs NM_024876 NP_079152 Q96D53 ADCK4_HUMAN aarF domain containing kinase 4 isoform a 205 Protein kinase. integral to membrane protein serine/threonine kinase activity 0 Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219) ggccaccttggcctgccagtcc 0.371 0.11 59 7 SLCO4A1 28231 broad.mit.edu 37 20 61297778 61297780 + In_Frame_Del DEL CTT - - KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr20:61297778_61297780delCTT uc002ydb.1 + 7 1528_1530 c.1323_1325delCTT c.(1321-1326)GGCTTC>GGC p.F443del SLCO4A1_uc002ydc.1_RNA|LOC100127888_uc002ydd.2_RNA|SLCO4A1_uc002yde.1_5'Flank NM_016354 NP_057438 Q96BD0 SO4A1_HUMAN solute carrier organic anion transporter family 443 Helical; Name=8; (Potential). sodium-independent organic anion transport integral to membrane|plasma membrane thyroid hormone transmembrane transporter activity ovary(1) 1 Breast(26;3.65e-08) BRCA - Breast invasive adenocarcinoma(19;2.33e-06) TCCTGGGCGGCTTCTTTGTGAAC 0.650 0.68 22 46 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 202 514 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KURAMOCHI_OVARY NA KURAMOCHI_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 28 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 26 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.49 230 225 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.33 20 10 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376116 + In_Frame_Del DEL TGCTGC - - rs143860374;rs62265537 KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr3:113376111_113376116delTGCTGC uc003eam.2 - 7 4824_4829 c.4413_4418delGCAGCA c.(4411-4419)CAGCAGCAA>CAA p.1471_1473QQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1415_1417QQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1471_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgct 0.359 0.35 15 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 143 228 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.30 57 25 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.72 61 156 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.75 4 12 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.42 64 47 ATXN1 6310 broad.mit.edu 37 6 16327907 16327909 + In_Frame_Del DEL TGA - - rs59310777 by1000genomes KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr6:16327907_16327909delTGA uc003nbt.2 - 8 1604_1606 c.633_635delTCA c.(631-636)CATCAG>CAG p.H211del ATXN1_uc010jpi.2_In_Frame_Del_p.H211del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 211 Poly-Gln. H -> HQ (in Ref. 1; CAA55793). cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgctgatgctgatgct 0.384 0.18 92 20 ROS1 6098 broad.mit.edu 37 6 117718231 117718231 + Frame_Shift_Del DEL T - - KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr6:117718231delT uc003pxp.1 - 7 825 c.626delA c.(625-627)GACfs p.D209fs ROS1_uc011ebi.1_RNA|GOPC_uc003pxq.1_Intron NM_002944 NP_002935 P08922 ROS_HUMAN proto-oncogene c-ros-1 protein precursor 209 Fibronectin type-III 2.|Extracellular (Potential). transmembrane receptor protein tyrosine kinase signaling pathway membrane fraction|sodium:potassium-exchanging ATPase complex ATP binding|transmembrane receptor protein tyrosine kinase activity lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1) 25 all_cancers(87;0.00846)|all_epithelial(87;0.0242) GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137) TTCCACAGTGTCGGGACTTGA 0.423 0.50 85 84 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 17 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.53 7 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 3 59 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.37 488 292 NUP214 8021 broad.mit.edu 37 9 134019964 134019969 + In_Frame_Del DEL CCCCCA - - KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr9:134019964_134019969delCCCCCA uc004cag.2 + 12 1703_1708 c.1592_1597delCCCCCA c.(1591-1599)GCCCCCACC>GCC p.PT532del NUP214_uc004cah.2_In_Frame_Del_p.PT532del|NUP214_uc004cai.2_5'UTR|NUP214_uc004caf.1_In_Frame_Del_p.PT532del|NUP214_uc010mzf.2_5'UTR NM_005085 NP_005076 P35658 NU214_HUMAN nucleoporin 214kDa 532_533 11 X 5 AA approximate repeats. carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear pore|nucleoplasm protein binding breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1) 16 all_hematologic(7;0.0028) Myeloproliferative disorder(178;0.204) OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256) GCCTCCCTAGCCCCCACCCCTGCAGC 0.568 0.43 159 118 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.50 8 8 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.31 9 4 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.32 107 51 MINK1 50488 broad.mit.edu 37 17 4799884 4799887 + Splice_Site DEL GTGA - - KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr17:4799884_4799887delGTGA uc010vsl.1 + 30 3971 c.3775_splice c.e30+1 p.A1259_splice MINK1_uc010vsk.1_Splice_Site_p.A1230_splice|MINK1_uc010vsm.1_Splice_Site_p.A1239_splice|MINK1_uc010vsn.1_Splice_Site_p.A1222_splice|MINK1_uc010vso.1_Splice_Site_p.A1167_splice|MINK1_uc010vsp.1_Splice_Site_p.A720_splice NM_153827 NP_722549 Q8N4C8 MINK1_HUMAN misshapen-like kinase 1 isoform 3 JNK cascade cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)|skin(1) 6 ACTTCTGTGGGTGAGTGAGCTGCC 0.627 0.33 106 53 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.23 23 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 59 198 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 99 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 32 400 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KYM1_SOFT_TISSUE NA KYM1_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 9 97 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.68 12 25 DOCK3 1795 broad.mit.edu 37 3 51413196 51413210 + In_Frame_Del DEL AGCCCTGTTCCAGCA - - KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:51413196_51413210delAGCCCTGTTCCAGCA uc011bds.1 + 51 5453_5467 c.5430_5444delAGCCCTGTTCCAGCA c.(5428-5445)CGAGCCCTGTTCCAGCAA>CGA p.ALFQQ1811del NM_004947 NP_004938 Q8IZD9 DOCK3_HUMAN dedicator of cytokinesis 3 1811_1815 cytoplasm GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding 0 BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518) ATTTCCAGCGAGCCCTGTTCCAGCAAGTGGTCGGA 0.530 0.28 91 36 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.50 6 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 73 90 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 71 43 ARID1B 57492 broad.mit.edu 37 6 157099402 157099403 + In_Frame_Ins INS - CAG CAG KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:157099402_157099403insCAG uc003qqn.2 + 1 317_318 c.165_166insCAG c.(163-168)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) TAAACCAGTTCcagcagcagca 0.124 0.23 37 11 RAD21 5885 broad.mit.edu 37 8 117866698 117866699 + Frame_Shift_Ins INS - T T KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:117866698_117866699insT uc003yod.2 - 9 1234_1235 c.946_947insA c.(946-948)ACAfs p.T316fs NM_006265 NP_006256 O60216 RAD21_HUMAN RAD21 homolog 316 Interaction with WAPAL and PDS5B. apoptosis|cell division|chromosome segregation|double-strand break repair|mitotic metaphase/anaphase transition|mitotic prometaphase|protein localization to chromatin|reciprocal meiotic recombination|regulation of transcription from RNA polymerase II promoter chromosome, centromeric region|cohesin complex|nuclear chromosome|nucleoplasm protein binding lung(1)|skin(1) 2 all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172) CTTGGCTTTTGTTTCTTTAACT 0.376 0.39 145 94 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 23 SPI1 6688 broad.mit.edu 37 11 47380501 47380501 + Frame_Shift_Del DEL G - - KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:47380501delG uc001nfc.1 - 4 610 c.387delC c.(385-387)CCCfs p.P129fs SPI1_uc001nfb.1_Frame_Shift_Del_p.P130fs|SLC39A13_uc001nfd.2_Intron|SPI1_uc009ylp.1_Frame_Shift_Del_p.P123fs NM_003120 NP_003111 P17947 SPI1_HUMAN hematopoietic transcription factor PU.1 isoform 129 negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|regulation of erythrocyte differentiation nucleus protein binding|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity lung(1)|central_nervous_system(1) 2 Lung(87;0.0967) 0.000 0.42 7 5 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.61 19 30 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 378 187 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.12 112 15 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 12 90 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.21 137 36 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.67 16 33 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 270 1464 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 92 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 1 21 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.52 307 332 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.23 37 11 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.52 14 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 50 59 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.77 20 67 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.18 182 39 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.85 2 11 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 11 TGFBR1 7046 broad.mit.edu 37 9 101867563 101867564 + Frame_Shift_Ins INS - T T KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chr9:101867563_101867564insT uc004azc.2 + 1 152_153 c.76_77insT c.(76-78)GCGfs p.A26fs TGFBR1_uc004azd.2_Frame_Shift_Ins_p.A26fs NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.40 6 4 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 380 159 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.41 10 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 186 508 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KYSE150_OESOPHAGUS NA KYSE150_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 4 45 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 1 13 TSSK3 81629 broad.mit.edu 37 1 32828383 32828384 + Frame_Shift_Ins INS - T T KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr1:32828383_32828384insT uc001bvf.2 + 1 522_523 c.81_82insT c.(79-84)GCATTTfs p.A27fs uc001bve.1_RNA NM_052841 NP_443073 Q96PN8 TSSK3_HUMAN testis-specific serine kinase 3 27_28 Protein kinase. cell differentiation|multicellular organismal development|spermatogenesis ATP binding|magnesium ion binding|protein serine/threonine kinase activity stomach(1) 1 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.17)|Breast(348;0.212) TCAAAGAAGCATTTTCCAAAAA 0.520 0.83 17 85 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.34 89 46 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 9 4 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.29 54 22 GRK7 131890 broad.mit.edu 37 3 141497729 141497729 + Frame_Shift_Del DEL T - - KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr3:141497729delT uc011bnd.1 + 1 687 c.603delT c.(601-603)GGTfs p.G201fs NM_139209 NP_631948 Q8WTQ7 GRK7_HUMAN G-protein-coupled receptor kinase 7 precursor 201 ATP (By similarity).|Protein kinase. visual perception membrane ATP binding|G-protein coupled receptor kinase activity|signal transducer activity lung(2)|stomach(1)|ovary(1)|skin(1) 5 GGAAAGGTGGTTTTGGGGAGG 0.468 0.59 117 165 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 44 55 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.25 41 14 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.39 110 71 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 40 MASTL 84930 broad.mit.edu 37 10 27447580 27447582 + In_Frame_Del DEL TAT - - KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr10:27447580_27447582delTAT uc001itm.2 + 2 928_930 c.289_291delTAT c.(289-291)TATdel p.Y98del MASTL_uc001itl.2_In_Frame_Del_p.Y98del|MASTL_uc009xkw.1_In_Frame_Del_p.Y98del|MASTL_uc009xkx.1_RNA NM_032844 NP_116233 Q96GX5 GWL_HUMAN microtubule associated serine/threonine 98 Protein kinase. cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus centrosome|cleavage furrow|nucleus ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity stomach(1)|ovary(1)|lung(1) 3 TGTCCATTTGTATTATTCACTGC 0.355 0.53 26 29 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 371 149 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.66 11 21 BCKDK 10295 broad.mit.edu 37 16 31122472 31122473 + Frame_Shift_Ins INS - G G KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr16:31122472_31122473insG uc002eaw.3 + 9 1093_1094 c.777_778insG c.(775-780)GCTGCCfs p.A259fs BCKDK_uc002eav.3_Frame_Shift_Ins_p.A259fs|BCKDK_uc010cah.2_RNA|BCKDK_uc010cai.2_Frame_Shift_Ins_p.A259fs NM_005881 NP_005872 O14874 BCKD_HUMAN branched chain ketoacid dehydrogenase kinase 259_260 Histidine kinase. branched chain family amino acid catabolic process|peptidyl-histidine phosphorylation mitochondrial alpha-ketoglutarate dehydrogenase complex [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity|ATP binding|protein binding|protein serine/threonine kinase activity|two-component sensor activity stomach(1)|breast(1) 2 GCCATGTGGCTGCCCGGTTCCC 0.624 0.20 63 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 13 98 DNMT1 1786 broad.mit.edu 37 19 10273397 10273397 + Frame_Shift_Del DEL T - - KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr19:10273397delT uc002mng.2 - 12 1086 c.906delA c.(904-906)AAAfs p.K302fs DNMT1_uc010xlc.1_Frame_Shift_Del_p.K318fs|DNMT1_uc002mnh.2_Frame_Shift_Del_p.K197fs|DNMT1_uc010xld.1_Frame_Shift_Del_p.K302fs|DNMT1_uc002mnk.2_RNA NM_001379 NP_001370 P26358 DNMT1_HUMAN DNA (cytosine-5-)-methyltransferase 1 isoform b 302 Interaction with the PRC2/EED-EZH2 complex (By similarity). chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent nucleus DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1) 6 OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06) Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035) TTTCAGGTTCTTTTTCTTCGG 0.393 0.69 25 55 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.30 55 24 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 56 412 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KYSE180_OESOPHAGUS NA KYSE180_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 3 47 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KYSE270_OESOPHAGUS NA KYSE270_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.83 8 39 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KYSE270_OESOPHAGUS NA KYSE270_OESOPHAGUS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.30 57 24 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KYSE270_OESOPHAGUS NA KYSE270_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.66 72 138 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KYSE270_OESOPHAGUS NA KYSE270_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.80 11 44 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes KYSE270_OESOPHAGUS NA KYSE270_OESOPHAGUS NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.90 1 9 RGS22 26166 broad.mit.edu 37 8 101076179 101076181 + In_Frame_Del DEL CTT - - KYSE270_OESOPHAGUS NA KYSE270_OESOPHAGUS NA g.chr8:101076179_101076181delCTT uc003yjb.1 - 8 1010_1012 c.815_817delAAG c.(814-819)GAAGGA>GGA p.E272del RGS22_uc003yja.1_In_Frame_Del_p.E91del|RGS22_uc003yjc.1_In_Frame_Del_p.E260del|RGS22_uc011lgz.1_RNA|RGS22_uc010mbo.1_RNA NM_015668 NP_056483 Q8NE09 RGS22_HUMAN regulator of G-protein signaling 22 272 Poly-Glu. negative regulation of signal transduction cytoplasm|plasma membrane GTPase activator activity|signal transducer activity ovary(3)|skin(2)|breast(1)|central_nervous_system(1) 7 Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169) tcttcttctccttcttcttcttc 0.325 0.31 46 21 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KYSE270_OESOPHAGUS NA KYSE270_OESOPHAGUS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.99 1 74 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KYSE270_OESOPHAGUS NA KYSE270_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 578 251 C14orf4 64207 broad.mit.edu 37 14 77493762 77493764 + In_Frame_Del DEL TGC - - KYSE270_OESOPHAGUS NA KYSE270_OESOPHAGUS NA g.chr14:77493762_77493764delTGC uc001xsy.2 - 1 1271_1273 c.372_374delGCA c.(370-375)CAGCAA>CAA p.124_125QQ>Q NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 124_125 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) GAgctgttgttgctgctgctgct 0.236 0.10 71 8 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes KYSE270_OESOPHAGUS NA KYSE270_OESOPHAGUS NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.17 57 12 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KYSE270_OESOPHAGUS NA KYSE270_OESOPHAGUS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 49 119 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KYSE270_OESOPHAGUS NA KYSE270_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.97 8 260 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KYSE270_OESOPHAGUS NA KYSE270_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 4 42 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KYSE30_OESOPHAGUS NA KYSE30_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 5 106 PODN 127435 broad.mit.edu 37 1 53547716 53547721 + In_Frame_Del DEL GGTCTT - - KYSE30_OESOPHAGUS NA KYSE30_OESOPHAGUS NA g.chr1:53547716_53547721delGGTCTT uc001cuv.2 + 10 1876_1881 c.1869_1874delGGTCTT c.(1867-1875)CAGGTCTTG>CAG p.VL624del PODN_uc001cuw.2_In_Frame_Del_p.VL605del|PODN_uc010onr.1_In_Frame_Del_p.VL605del|PODN_uc010ons.1_In_Frame_Del_p.VL482del NM_153703 NP_714914 Q7Z5L7 PODN_HUMAN podocan 576_577 LRR 20. negative regulation of cell migration|negative regulation of cell proliferation cytoplasm|extracellular space|proteinaceous extracellular matrix collagen binding ovary(1)|pancreas(1) 2 AGCACCTGCAGGTCTTGGACATTGAA 0.437 0.91 1 10 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KYSE30_OESOPHAGUS NA KYSE30_OESOPHAGUS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.13 45 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KYSE30_OESOPHAGUS NA KYSE30_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.38 134 83 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KYSE30_OESOPHAGUS NA KYSE30_OESOPHAGUS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.39 267 174 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KYSE30_OESOPHAGUS NA KYSE30_OESOPHAGUS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 22 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KYSE30_OESOPHAGUS NA KYSE30_OESOPHAGUS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.60 132 195 DACH1 1602 broad.mit.edu 37 13 72014811 72014812 + Frame_Shift_Del DEL AT - - KYSE30_OESOPHAGUS NA KYSE30_OESOPHAGUS NA g.chr13:72014811_72014812delAT uc010thn.1 - 12 2519_2520 c.2096_2097delAT c.(2095-2097)TATfs p.Y699fs DACH1_uc010tho.1_Frame_Shift_Del_p.Y551fs|DACH1_uc010thp.1_Frame_Shift_Del_p.Y497fs NM_080759 NP_542937 Q9UI36 DACH1_HUMAN dachshund homolog 1 isoform a 751 multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus DNA binding|nucleotide binding|protein binding breast(1) 1 Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198) GBM - Glioblastoma multiforme(99;0.00032) TAGTTTTCAAATACAGTCTTCC 0.317 0.13 1240 188 MGA 23269 broad.mit.edu 37 15 42059170 42059170 + Frame_Shift_Del DEL C - - KYSE30_OESOPHAGUS NA KYSE30_OESOPHAGUS NA g.chr15:42059170delC uc010ucy.1 + 24 9071 c.8890delC c.(8890-8892)CCCfs p.P2964fs MGA_uc010ucz.1_Frame_Shift_Del_p.P2755fs NM_001164273 NP_001157745 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 1 2925 MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) TGTGTCCTCACCCCCCACCCT 0.498 0.91 47 463 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KYSE30_OESOPHAGUS NA KYSE30_OESOPHAGUS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.34 40 21 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KYSE30_OESOPHAGUS NA KYSE30_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 74 305 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 13 ARID1A 8289 broad.mit.edu 37 1 27102087 27102108 + Frame_Shift_Del DEL GGTAATGATGTCCCTCAAGTCT - - KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr1:27102087_27102108delGGTAATGATGTCCCTCAAGTCT uc001bmv.1 + 19 5386_5407 c.5013_5034delGGTAATGATGTCCCTCAAGTCT c.(5011-5034)CGGGTAATGATGTCCCTCAAGTCTfs p.R1671fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.R1670fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.R1454fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.R517fs|ARID1A_uc009vsm.1_Translation_Start_Site|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1671_1678 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) AGGCATGGCGGGTAATGATGTCCCTCAAGTCTGGTCTCCTGG 0.532 0.16 63 12 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.39 288 181 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.40 28 19 BCL6 604 broad.mit.edu 37 3 187444603 187444604 + Frame_Shift_Del DEL TG - - KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr3:187444603_187444604delTG uc003frp.3 - 7 2080_2081 c.1623_1624delCA c.(1621-1626)CACAGTfs p.H541fs BCL6_uc011bsf.1_Intron|BCL6_uc010hza.2_Frame_Shift_Del_p.H439fs|BCL6_uc003frq.1_Frame_Shift_Del_p.H541fs NM_001130845 NP_001124317 P41182 BCL6_HUMAN B-cell lymphoma 6 protein isoform 1 541_542 negative regulation of B cell apoptosis|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|protein import into nucleus, translocation|regulation of germinal center formation|response to DNA damage stimulus nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|lung(2)|central_nervous_system(1) 5 all_cancers(143;9.45e-12)|Ovarian(172;0.0418) OV - Ovarian serous cystadenocarcinoma(80;1.76e-18) GBM - Glioblastoma multiforme(93;0.0141) GGTTTGTCACTGTGGGTCTGCA 0.604 0.21 111 29 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.62 5 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 64 63 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.45 29 24 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 23 NOTCH1 4851 broad.mit.edu 37 9 139393364 139393365 + Frame_Shift_Del DEL AT - - KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr9:139393364_139393365delAT uc004chz.2 - 33 6166_6167 c.6166_6167delAT c.(6166-6168)ATGfs p.M2056fs NM_017617 NP_060087 P46531 NOTC1_HUMAN notch1 preproprotein 2056 Cytoplasmic (Potential).|ANK 4. aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity p.M2057fs*211(1) haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1) 856 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06) GTTGTTCTGCATATCTTTGTTA 0.609 0.98 4 223 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.60 4 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 430 173 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.35 13 7 ROCK1 6093 broad.mit.edu 37 18 18547866 18547866 + Frame_Shift_Del DEL T - - KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr18:18547866delT uc002kte.2 - 26 3980 c.3039delA c.(3037-3039)AAAfs p.K1013fs NM_005406 NP_005397 Q13464 ROCK1_HUMAN Rho-associated, coiled-coil containing protein 1013 Potential. actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction centriole|cytosol|Golgi membrane ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity lung(2)|breast(2)|central_nervous_system(1) 5 Melanoma(1;0.165) TTTTAAAATCTTTTCGATTCA 0.269 0.38 109 66 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 26 16 GLTSCR1 29998 broad.mit.edu 37 19 48202014 48202015 + Frame_Shift_Del DEL CC - - KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr19:48202014_48202015delCC uc002phh.3 + 12 3566_3567 c.3372_3373delCC c.(3370-3375)CTCCCCfs p.L1124fs GLTSCR1_uc002phi.3_Frame_Shift_Del_p.L882fs NM_015711 NP_056526 Q9NZM4 GSCR1_HUMAN glioma tumor suppressor candidate region gene 1 1124_1125 protein binding pancreas(3) 3 all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086) all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355) AGGGCGCCCTCCCCTCCCCCAG 0.678 0.55 32 39 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 70 339 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KYSE450_OESOPHAGUS NA KYSE450_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 50 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KYSE510_OESOPHAGUS NA KYSE510_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 22 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KYSE510_OESOPHAGUS NA KYSE510_OESOPHAGUS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.45 12 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KYSE510_OESOPHAGUS NA KYSE510_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 57 39 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KYSE510_OESOPHAGUS NA KYSE510_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.40 37 25 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KYSE510_OESOPHAGUS NA KYSE510_OESOPHAGUS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.56 23 29 CUBN 8029 broad.mit.edu 37 10 16962002 16962008 + Frame_Shift_Del DEL GCTGTAT - - rs150035126 KYSE510_OESOPHAGUS NA KYSE510_OESOPHAGUS NA g.chr10:16962002_16962008delGCTGTAT uc001ioo.2 - 44 6827_6833 c.6775_6781delATACAGC c.(6775-6783)ATACAGCTGfs p.I2259fs NM_001081 NP_001072 O60494 CUBN_HUMAN cubilin precursor 2259_2261 CUB 16. cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1) 19 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) TCAAATTGCAGCTGTATGCGTGTTTCC 0.444 0.38 38 23 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KYSE510_OESOPHAGUS NA KYSE510_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 168 57 CHD8 57680 broad.mit.edu 37 14 21860016 21860018 + In_Frame_Del DEL CTT - - KYSE510_OESOPHAGUS NA KYSE510_OESOPHAGUS NA g.chr14:21860016_21860018delCTT uc001was.1 - 35 6116_6118 c.6022_6024delAAG c.(6022-6024)AAGdel p.K2008del CHD8_uc001war.1_In_Frame_Del_p.K1904del NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 2287 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) TTCTGTTCCCCTTCTTCTTATGA 0.414 0.74 104 297 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KYSE510_OESOPHAGUS NA KYSE510_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 85 234 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KYSE510_OESOPHAGUS NA KYSE510_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 49 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.49 27 26 NOTCH2 4853 broad.mit.edu 37 1 120529611 120529612 + Frame_Shift_Ins INS - T T KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr1:120529611_120529612insT uc001eik.2 - 5 1101_1102 c.845_846insA c.(844-846)TACfs p.Y282fs NOTCH2_uc001eil.2_Frame_Shift_Ins_p.Y282fs|NOTCH2_uc001eim.3_Frame_Shift_Ins_p.Y199fs NM_024408 NP_077719 Q04721 NOTC2_HUMAN notch 2 preproprotein 282 EGF-like 7; calcium-binding (Potential).|Extracellular (Potential). anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1) 27 all_neural(166;0.153) all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809) Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133) AGCGGCAGTTGTAAGTGTTGAC 0.475 0.63 109 187 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.15 571 98 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.30 32 14 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.63 13 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.68 57 122 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.82 21 97 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.70 49 112 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 2 14 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.92 1 11 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.15 82 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.89 2 17 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.87 3 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 411 192 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.56 16 20 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.47 80 71 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.18 49 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 41 211 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KYSE520_OESOPHAGUS NA KYSE520_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 9 133 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.83 4 19 ACVR2A 92 broad.mit.edu 37 2 148657349 148657349 + Frame_Shift_Del DEL A - - KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr2:148657349delA uc002twg.2 + 5 679 c.410delA c.(409-411)TACfs p.Y137fs ACVR2A_uc010zbn.1_Frame_Shift_Del_p.Y29fs|ACVR2A_uc002twh.2_Frame_Shift_Del_p.Y137fs NM_001616 NP_001607 P27037 AVR2A_HUMAN activin A receptor, type IIA precursor 137 Helical; (Potential). activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1) 13 BRCA - Breast invasive adenocarcinoma(221;0.0969) CCACCCTATTACAACATCCTG 0.418 0.67 14 29 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.55 5 6 ATP13A5 344905 broad.mit.edu 37 3 193039485 193039485 + Frame_Shift_Del DEL A - - KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr3:193039485delA uc011bsq.1 - 16 1900 c.1900delT c.(1900-1902)TGCfs p.C634fs NM_198505 NP_940907 Q4VNC0 AT135_HUMAN ATPase type 13A5 634 ATP biosynthetic process|cation transport integral to membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding ovary(5)|skin(4)|large_intestine(2) 11 all_cancers(143;1.08e-08)|Ovarian(172;0.0386) OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06) GBM - Glioblastoma multiforme(46;0.000307) TCAGATCTGCAGAACCTGGCC 0.353 0.60 44 65 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 21 35 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 8 18 EGFR 1956 broad.mit.edu 37 7 55210093 55210093 + Frame_Shift_Del DEL C - - KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr7:55210093delC uc003tqk.2 + 2 449 c.203delC c.(202-204)ACCfs p.T68fs EGFR_uc003tqh.2_Frame_Shift_Del_p.T68fs|EGFR_uc003tqi.2_Frame_Shift_Del_p.T68fs|EGFR_uc003tqj.2_Frame_Shift_Del_p.T68fs|EGFR_uc010kzg.1_Frame_Shift_Del_p.T68fs|EGFR_uc011kco.1_Frame_Shift_Del_p.T15fs NM_005228 NP_005219 P00533 EGFR_HUMAN epidermal growth factor receptor isoform a 68 Extracellular (Potential). activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity p.V30_R297>G(5) lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1) 9571 all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318) GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607) Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072) TTGGAAATTACCTATGTGCAG 0.398 0.44 55 43 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 26 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.65 226 422 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 193 76 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.53 7 8 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 1 18 TP53 7157 broad.mit.edu 37 17 7577529 7577530 + Frame_Shift_Ins INS - T T KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr17:7577529_7577530insT uc002gim.2 - 7 945_946 c.751_752insA c.(751-753)ATCfs p.I251fs TP53_uc002gig.1_Frame_Shift_Ins_p.I251fs|TP53_uc002gih.2_Frame_Shift_Ins_p.I251fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Ins_p.I119fs|TP53_uc010cng.1_Frame_Shift_Ins_p.I119fs|TP53_uc002gii.1_Frame_Shift_Ins_p.I119fs|TP53_uc010cnh.1_Frame_Shift_Ins_p.I251fs|TP53_uc010cni.1_Frame_Shift_Ins_p.I251fs|TP53_uc002gij.2_Frame_Shift_Ins_p.I251fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Ins_p.I158fs|TP53_uc002gio.2_Frame_Shift_Ins_p.I119fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 251 |Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). I -> S (in sporadic cancers; somatic mutation).|I -> V (in sporadic cancers; somatic mutation).|I -> M (in LFS; germline mutation).|I -> F (in sporadic cancers; somatic mutation).|I -> T (in sporadic cancers; somatic mutation).|I -> L (in sporadic cancers; somatic mutation).|I -> N (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.I251fs*94(12)|p.I251S(11)|p.I251N(7)|p.0?(7)|p.I251F(6)|p.I251T(4)|p.I251_T253delILT(4)|p.I251I(3)|p.I251L(3)|p.I251del(2)|p.I251V(2)|p.P250_L252delPIL(2)|p.I251fs*13(2)|p.P250_I251insXXXXXX(1)|p.R249_I251delRPI(1)|p.P250_T253delPILT(1)|p.I251fs*12(1)|p.P250_I251insXXXXXXX(1)|p.I251fs*96(1)|p.R249_T256delRPILTIIT(1)|p.P250_I251insX(1)|p.I251_L252insX(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GATGGTGAGGATGGGCCTCCGG 0.579 0.62 30 48 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 10 25 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.36 21 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 45 351 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 KYSE70_OESOPHAGUS NA KYSE70_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.84 6 31 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 4 58 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.16 290 57 MYO3B 140469 broad.mit.edu 37 2 171264254 171264255 + Frame_Shift_Ins INS - A A L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:171264254_171264255insA uc002ufy.2 + 22 2693_2694 c.2550_2551insA c.(2548-2553)GAGAAAfs p.E850fs MYO3B_uc002ufv.2_Frame_Shift_Ins_p.E837fs|MYO3B_uc010fqb.1_Frame_Shift_Ins_p.E837fs|MYO3B_uc002ufz.2_Frame_Shift_Ins_p.E850fs|MYO3B_uc002ufw.2_RNA|MYO3B_uc002ufx.2_RNA|MYO3B_uc002ugb.2_RNA NM_138995 NP_620482 Q8WXR4 MYO3B_HUMAN myosin IIIB isoform 2 850_851 Myosin head-like. response to stimulus|visual perception cytoplasm|myosin complex actin binding|ATP binding|motor activity|protein serine/threonine kinase activity lung(8)|ovary(6)|skin(4)|central_nervous_system(1) 19 GGGTTCTTGAGAAAAATAGAGA 0.460 0.65 54 100 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.18 32 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.51 54 56 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.49 53 51 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 10 PREX2 80243 broad.mit.edu 37 8 69104602 69104609 + Frame_Shift_Del DEL TTACCGAC - - L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:69104602_69104609delTTACCGAC uc003xxv.1 + 37 4473_4480 c.4446_4453delTTACCGAC c.(4444-4455)CTTTACCGACTGfs p.L1482fs NM_024870 NP_079146 Q70Z35 PREX2_HUMAN DEP domain containing 2 isoform a 1482_1485 G-protein coupled receptor protein signaling pathway|intracellular signal transduction intracellular protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1) 17 TGGATGAACTTTACCGACTGGTAGCCTC 0.457 0.16 108 21 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 19 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 241 74 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.32 17 8 SOCS1 8651 broad.mit.edu 37 16 11348971 11348971 + Frame_Shift_Del DEL C - - L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:11348971delC uc002dar.1 - 2 519 c.365delG c.(364-366)GGAfs p.G122fs C16orf75_uc002daq.1_Intron NM_003745 NP_003736 O15524 SOCS1_HUMAN suppressor of cytokine signaling 1 122 SH2. interferon-gamma-mediated signaling pathway|JAK-STAT cascade|negative regulation of insulin receptor signaling pathway|negative regulation of tyrosine phosphorylation of Stat3 protein|regulation of growth|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway cytosol insulin-like growth factor receptor binding|protein kinase binding|protein kinase inhibitor activity p.R107_I126del(1)|p.Y64fs*1(1)|p.K118_P123>T(1) haematopoietic_and_lymphoid_tissue(64)|lung(3)|breast(1)|central_nervous_system(1) 69 0.000 0.54 473 551 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 72 673 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.67 24 48 ZNF217 7764 broad.mit.edu 37 20 52198266 52198266 + Frame_Shift_Del DEL A - - L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:52198266delA uc002xwq.3 - 1 1371 c.1100delT c.(1099-1101)TTAfs p.L367fs ZNF217_uc010gij.1_Frame_Shift_Del_p.L359fs NM_006526 NP_006517 O75362 ZN217_HUMAN zinc finger protein 217 367 negative regulation of transcription, DNA-dependent histone deacetylase complex protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding skin(2)|ovary(1)|large_intestine(1)|lung(1)|breast(1) 6 all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398) BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198) GCTACTGGGTAACTTGGGATC 0.567 0.20 107 27 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 108 341 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 46 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 L33_PANCREAS NA L33_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 2 25 LOC642587 642587 broad.mit.edu 37 1 209605636 209605637 + In_Frame_Ins INS - AGC AGC rs146499758;rs3842530 by1000genomes L33_PANCREAS NA L33_PANCREAS NA g.chr1:209605636_209605637insAGC uc009xcn.2 + 4 634_635 c.251_252insAGC c.(250-252)GTA>GTAGCA p.97_98insA NM_001104548 NP_001098018 hypothetical protein LOC642587 0 OV - Ovarian serous cystadenocarcinoma(81;0.0422) gccaccaccgTagcagcagcag 0.272 0.17 33 7 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes L33_PANCREAS NA L33_PANCREAS NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.55 5 6 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 L33_PANCREAS NA L33_PANCREAS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.39 14 9 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A L33_PANCREAS NA L33_PANCREAS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 113 24 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 L33_PANCREAS NA L33_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 95 139 MAML3 55534 broad.mit.edu 37 4 140810638 140810639 + In_Frame_Ins INS - GCT GCT L33_PANCREAS NA L33_PANCREAS NA g.chr4:140810638_140810639insGCT uc003ihz.1 - 3 2691_2692 c.1939_1940insAGC c.(1939-1941)CCG>CAGCCG p.646_647insQ MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 646_647 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) TGGAGGTGGCGgctgctgctgc 0.416 0.12 164 22 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 L33_PANCREAS NA L33_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 24 39 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 L33_PANCREAS NA L33_PANCREAS NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.81 3 13 DBN1 1627 broad.mit.edu 37 5 176885346 176885347 + Frame_Shift_Ins INS - G G L33_PANCREAS NA L33_PANCREAS NA g.chr5:176885346_176885347insG uc003mgy.2 - 12 1660_1661 c.1488_1489insC c.(1486-1491)CCCACGfs p.P496fs DBN1_uc011dga.1_Frame_Shift_Ins_p.P228fs|DBN1_uc003mgx.2_Frame_Shift_Ins_p.P498fs|DBN1_uc010jkn.1_Frame_Shift_Ins_p.P446fs|DBN1_uc003mgz.1_Frame_Shift_Ins_p.P479fs NM_004395 NP_004386 Q16643 DREB_HUMAN drebrin 1 isoform a 496_497 actin filament organization|regulation of dendrite development|regulation of neuronal synaptic plasticity actomyosin|cytoplasm|dendrite actin binding|profilin binding breast(3)|ovary(1)|lung(1)|skin(1) 6 all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025) all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GAGGGTGGCGTGGGGGCCCTGG 0.683 0.11 139 18 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes L33_PANCREAS NA L33_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 1 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 L33_PANCREAS NA L33_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 67 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency L33_PANCREAS NA L33_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.44 278 216 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - L33_PANCREAS NA L33_PANCREAS NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.40 128 84 ATN1 1822 broad.mit.edu 37 12 7045885 7045886 + In_Frame_Ins INS - CAG CAG L33_PANCREAS NA L33_PANCREAS NA g.chr12:7045885_7045886insCAG uc001qrw.1 + 5 1692_1693 c.1455_1456insCAG c.(1453-1458)insCAG p.502_503insQ ATN1_uc001qrx.1_In_Frame_Ins_p.502_503insQ|ATN1_uc001qry.1_In_Frame_Ins_p.486_487insQ NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502_503 cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 ACCACcagcaacagcaacagca 0.441 0.77 26 86 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency L33_PANCREAS NA L33_PANCREAS NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.47 49 44 TP53 7157 broad.mit.edu 37 17 7579420 7579420 + Frame_Shift_Del DEL G - - L33_PANCREAS NA L33_PANCREAS NA g.chr17:7579420delG uc002gim.2 - 4 461 c.267delC c.(265-267)CCCfs p.P89fs TP53_uc002gig.1_Frame_Shift_Del_p.P89fs|TP53_uc002gih.2_Frame_Shift_Del_p.P89fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.P89fs|TP53_uc010cni.1_Frame_Shift_Del_p.P89fs|TP53_uc002gij.2_Frame_Shift_Del_p.P89fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.P50fs|TP53_uc010cnk.1_Frame_Shift_Del_p.P104fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 89 Interaction with WWOX. P -> L (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.A76_S90del15(3)|p.P89S(3)|p.G59fs*23(3)|p.P89fs*60(1)|p.V73fs*9(1)|p.D48fs*55(1)|p.P85fs*58(1)|p.S33fs*23(1)|p.A86fs*33(1)|p.A86fs*32(1)|p.P87fs*54(1)|p.P13fs*18(1)|p.A88fs*52(1)|p.P89L(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.88 82 593 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 L33_PANCREAS NA L33_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.51 125 131 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 L33_PANCREAS NA L33_PANCREAS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.39 28 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 L33_PANCREAS NA L33_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.95 19 331 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 L33_PANCREAS NA L33_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.77 18 61 EP300 2033 broad.mit.edu 37 22 41556727 41556728 + Splice_Site INS - T T L33_PANCREAS NA L33_PANCREAS NA g.chr22:41556727_41556728insT uc003azl.3 + 20 4066 c.3671_splice c.e20+1 p.T1224_splice NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding p.Y1198_L1243del(1)|p.?(1) haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 AGCCTCAAACGTAAGTAACTGC 0.371 0.95 3 56 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 58 PDE4DIP 9659 broad.mit.edu 37 1 144877148 144877148 + Frame_Shift_Del DEL A - - L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144877148delA uc001elw.3 - 28 4830 c.4539delT c.(4537-4539)TTTfs p.F1513fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.F1469fs|PDE4DIP_uc001elv.3_Frame_Shift_Del_p.F520fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 1513 cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) GGAGATCCTCAAAAGATTTTA 0.493 0.27 196 73 MAPKAPK2 9261 broad.mit.edu 37 1 206858675 206858676 + In_Frame_Ins INS - GCC GCC L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:206858675_206858676insGCC uc001hem.1 + 1 387_388 c.101_102insGCC c.(100-102)CAG>CAGCCG p.40_41insP MAPKAPK2_uc001hel.1_In_Frame_Ins_p.40_41insP NM_032960 NP_116584 P49137 MAPK2_HUMAN mitogen-activated protein kinase-activated 40_41 activation of MAPK activity|hormone biosynthetic process|innate immune response|leukotriene biosynthetic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|prostanoid metabolic process|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|protein binding|protein serine/threonine kinase activity|signal transducer activity 0 Breast(84;0.183) BRCA - Breast invasive adenocarcinoma(75;0.211) cccccggcgcagccgccgccgc 0.267 0.52 14 15 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.32 133 64 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.33 8 4 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 68 94 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 32 70 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 2 19 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.59 31 44 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 19 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 294 145 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.31 18 8 Unknown 0 broad.mit.edu 37 15 20663143 20663144 + Frame_Shift_Ins INS - G G L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:20663143_20663144insG uc001ytg.2 - 9 1177_1178 c.468_469insC c.(466-471)CCCGAGfs p.P156fs uc010tyx.1_RNA|uc001yth.3_Frame_Shift_Ins_p.P156fs|uc010tyy.1_Frame_Shift_Ins_p.P156fs|uc010tyz.1_Frame_Shift_Ins_p.P4fs RecName: Full=Putative HERC2-like protein 3; ACGGGATGCTCGGGGGGAAACA 0.455 0.33 33 16 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 18 89 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 31 211 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 100 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 8 92 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 91 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.49 83 81 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 16 39 MYB 4602 broad.mit.edu 37 6 135516992 135516993 + Frame_Shift_Ins INS - C C L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:135516992_135516993insC uc003qfc.2 + 9 1254_1255 c.1055_1056insC c.(1054-1056)CACfs p.H352fs MYB_uc003qfh.2_Frame_Shift_Ins_p.H352fs|MYB_uc003qfi.2_Frame_Shift_Ins_p.H352fs|MYB_uc010kgi.2_Frame_Shift_Ins_p.H352fs|MYB_uc003qfq.2_Frame_Shift_Ins_p.H349fs|MYB_uc010kgj.2_Frame_Shift_Ins_p.H317fs|MYB_uc003qfo.2_Intron|MYB_uc003qfu.2_Frame_Shift_Ins_p.H349fs|MYB_uc003qfl.2_RNA|MYB_uc003qfv.2_RNA|MYB_uc003qfz.2_RNA|MYB_uc003qfx.2_RNA|MYB_uc003qga.2_RNA|MYB_uc003qgb.2_RNA|MYB_uc010kgk.2_RNA|MYB_uc003qfd.2_RNA|MYB_uc003qfe.2_RNA|MYB_uc003qfg.2_RNA|MYB_uc003qff.2_RNA|MYB_uc003qfj.2_Intron|MYB_uc003qfm.2_RNA|MYB_uc003qfp.2_RNA|MYB_uc003qfn.2_RNA|MYB_uc003qfk.2_RNA|MYB_uc003qfr.2_RNA|MYB_uc003qfs.2_5'UTR|MYB_uc003qft.2_RNA|MYB_uc003qfw.2_Frame_Shift_Ins_p.H164fs|MYB_uc003qfy.2_RNA|MYB_uc003qgc.2_RNA|MYB_uc003qfb.1_Frame_Shift_Ins_p.H352fs|MYB_uc003qge.1_RNA NM_005375 NP_005366 P10242 MYB_HUMAN v-myb myeloblastosis viral oncogene homolog 352 Negative regulatory domain (By similarity). blood coagulation|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of histone H3-K4 methylation|positive regulation of histone H3-K9 methylation|positive regulation of T-helper cell differentiation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear matrix DNA binding|protein binding lung(1) 1 all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221) Lung NSC(302;3.08e-05)|Ovarian(999;0.208) OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117) GGAGAACACCACTCCACTCCAT 0.579 0.94 23 393 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 25 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 346 89 SOCS1 8651 broad.mit.edu 37 16 11348977 11348987 + Frame_Shift_Del DEL GCCATCTTCAC - - L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:11348977_11348987delGCCATCTTCAC uc002dar.1 - 2 503_513 c.349_359delGTGAAGATGGC c.(349-360)GTGAAGATGGCCfs p.V117fs C16orf75_uc002daq.1_Intron NM_003745 NP_003736 O15524 SOCS1_HUMAN suppressor of cytokine signaling 1 117_120 SH2. interferon-gamma-mediated signaling pathway|JAK-STAT cascade|negative regulation of insulin receptor signaling pathway|negative regulation of tyrosine phosphorylation of Stat3 protein|regulation of growth|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway cytosol insulin-like growth factor receptor binding|protein kinase binding|protein kinase inhibitor activity p.V117fs*93(2)|p.R107_I126del(1)|p.Y64fs*1(1)|p.K118_P123>T(1)|p.L115fs*1(1) haematopoietic_and_lymphoid_tissue(64)|lung(3)|breast(1)|central_nervous_system(1) 69 0.000 0.15 1258 223 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.10 104 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 18 133 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.24 90 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 103 451 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.99 1 91 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 4 97 TTN 7273 broad.mit.edu 37 2 179550276 179550278 + In_Frame_Del DEL AAT - - L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179550276_179550278delAAT uc010zfg.1 - 125 28851_28853 c.28627_28629delATT c.(28627-28629)ATTdel p.I9543del TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Del_p.I6204del|TTN_uc010fre.1_Intron NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10470 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CTCTCTTAGAAATAATGTGCAGC 0.355 0.15 113 20 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.29 27 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 105 167 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.81 12 50 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.57 6 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 2 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 28 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.46 394 335 NR4A3 8013 broad.mit.edu 37 9 102590615 102590616 + In_Frame_Ins INS - CAC CAC L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:102590615_102590616insCAC uc004baf.1 + 3 1020_1021 c.291_292insCAC c.(289-294)insCAC p.108_109insH NR4A3_uc004bae.2_In_Frame_Ins_p.108_109insH|NR4A3_uc004bag.1_In_Frame_Ins_p.108_109insH|NR4A3_uc004bai.2_In_Frame_Ins_p.119_120insH NM_006981 NP_008912 Q92570 NR4A3_HUMAN nuclear receptor subfamily 4, group A, member 3 108_109 regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor steroid hormone receptor activity|thyroid hormone receptor activity|zinc ion binding EWSR1/NR4A3(140)|TAF15/NR4A3(33) bone(173) 173 Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189) accatcaccatcaccaccacca 0.485 0.21 26 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 720 234 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.16 88 17 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.61 32 51 HSP90AA1 3320 broad.mit.edu 37 14 102551161 102551163 + In_Frame_Del DEL TCT - - rs55793809 byFrequency;by1000genomes L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:102551161_102551163delTCT uc001yku.3 - 5 1026_1028 c.836_838delAGA c.(835-840)AAGATT>ATT p.K279del HSP90AA1_uc001ykv.3_In_Frame_Del_p.K401del|HSP90AA1_uc001ykw.1_In_Frame_Del_p.K100del|HSP90AA1_uc001ykx.1_In_Frame_Del_p.K268del NM_005348 NP_005339 P07900 HS90A_HUMAN heat shock 90kDa protein 1, alpha isoform 2 279 axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction cytosol|melanosome|plasma membrane ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding ovary(2)|central_nervous_system(2)|prostate(1)|lung(1)|breast(1) 7 Rifabutin(DB00615) ttttccttaatcttcttcttctt 0.256 0.35 191 104 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 33 128 ERG 2078 broad.mit.edu 37 21 39775628 39775628 + Frame_Shift_Del DEL G - - L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:39775628delG uc010gnw.2 - 6 708 c.413delC c.(412-414)CCTfs p.P138fs ERG_uc002yxa.2_Frame_Shift_Del_p.P131fs|ERG_uc011aek.1_Frame_Shift_Del_p.P39fs|ERG_uc010gnv.2_Frame_Shift_Del_p.P39fs|ERG_uc010gnx.2_Frame_Shift_Del_p.P138fs|ERG_uc011ael.1_Frame_Shift_Del_p.P138fs|ERG_uc002yxb.2_Frame_Shift_Del_p.P138fs|ERG_uc011aem.1_Intron|ERG_uc002yxc.3_Frame_Shift_Del_p.P138fs|ERG_uc010gny.1_RNA NM_001136155 NP_001129627 P11308 ERG_HUMAN ets-related isoform 4 138 PNT. cell proliferation|multicellular organismal development|protein phosphorylation cytoplasm|nucleus|ribonucleoprotein complex protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162) prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1) 2828 Prostate(19;3.6e-06) CCATAGCGTAGGATCTGAAAG 0.512 0.23 180 54 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 166 408 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 106 TLR7 51284 broad.mit.edu 37 X 12904316 12904317 + Frame_Shift_Del DEL TA - - LC1F_LUNG NA LC1F_LUNG NA g.chrX:12904316_12904317delTA uc004cvc.2 + 3 828_829 c.689_690delTA c.(688-690)CTAfs p.L230fs NM_016562 NP_057646 Q9NYK1 TLR7_HUMAN toll-like receptor 7 precursor 230 Extracellular (Potential).|LRR 8. cellular response to mechanical stimulus|defense response to virus|I-kappaB phosphorylation|inflammatory response|innate immune response|positive regulation of chemokine production|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus early phagosome|endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosome|plasma membrane double-stranded RNA binding|single-stranded RNA binding|siRNA binding|transmembrane receptor activity ovary(2)|lung(2)|breast(1) 5 Imiquimod(DB00724) TTAACAGAACTATATCTCTACA 0.361 0.32 65 30 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LC1F_LUNG NA LC1F_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 51 PDE4DIP 9659 broad.mit.edu 37 1 144879245 144879246 + Frame_Shift_Ins INS - A A LC1F_LUNG NA LC1F_LUNG NA g.chr1:144879245_144879246insA uc001elw.3 - 27 4495_4496 c.4204_4205insT c.(4204-4206)GGCfs p.G1402fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Ins_p.G1358fs|PDE4DIP_uc001elv.3_Frame_Shift_Ins_p.G409fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 1402 cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) CTCCAAGGTGCCAACAGCTCTC 0.535 0.27 734 267 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - LC1F_LUNG NA LC1F_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.26 412 143 MAGI1 9223 broad.mit.edu 37 3 65425561 65425572 + In_Frame_Del DEL CTGCTGCTGCTG - - LC1F_LUNG NA LC1F_LUNG NA g.chr3:65425561_65425572delCTGCTGCTGCTG uc003dmn.2 - 9 1778_1789 c.1252_1263delCAGCAGCAGCAG c.(1252-1263)CAGCAGCAGCAGdel p.QQQQ418del MAGI1_uc003dmm.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc003dmo.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc003dmp.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc010hny.2_In_Frame_Del_p.QQQQ303del NM_001033057 NP_001028229 Q96QZ7 MAGI1_HUMAN membrane associated guanylate kinase, WW and PDZ 418_421 Poly-Gln. cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly tight junction ATP binding|protein C-terminus binding lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1) 6 Lung NSC(201;0.0016) BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133) AACCTTCTGTctgctgctgctgctgctgctgc 0.368 0.67 4 8 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 LC1F_LUNG NA LC1F_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.50 8 8 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 LC1F_LUNG NA LC1F_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.38 20 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LC1F_LUNG NA LC1F_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 31 51 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LC1F_LUNG NA LC1F_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.32 60 28 NR3C1 2908 broad.mit.edu 37 5 142779253 142779256 + Frame_Shift_Del DEL AGGG - - LC1F_LUNG NA LC1F_LUNG NA g.chr5:142779253_142779256delAGGG uc003lmz.2 - 2 1641_1644 c.1149_1152delCCCT c.(1147-1152)TTCCCTfs p.F383fs NR3C1_uc003lmy.2_Frame_Shift_Del_p.F383fs|NR3C1_uc003lna.2_Frame_Shift_Del_p.F383fs|NR3C1_uc003lnb.2_Frame_Shift_Del_p.F383fs|NR3C1_uc011dbk.1_Intron|NR3C1_uc003lnc.2_Frame_Shift_Del_p.F383fs|NR3C1_uc003lnd.2_Frame_Shift_Del_p.F383fs|NR3C1_uc003lne.2_Frame_Shift_Del_p.F383fs|NR3C1_uc003lnf.2_Frame_Shift_Del_p.F383fs|NR3C1_uc003lng.2_Frame_Shift_Del_p.F383fs|NR3C1_uc003lnh.2_Frame_Shift_Del_p.F383fs|NR3C1_uc003lni.2_Frame_Shift_Del_p.F383fs NM_000176 NP_000167 P04150 GCR_HUMAN glucocorticoid receptor isoform alpha 383_384 Modulating. chromatin modification|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus|transcription from RNA polymerase II promoter mitochondrial matrix|nucleoplasm glucocorticoid receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding ovary(2) 2 Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361) KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176) Amcinonide(DB00288)|Betamethasone(DB00443)|Budesonide(DB01222)|Dexamethasone(DB01234)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluticasone Propionate(DB00588)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol Etabonate(DB00873)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Prednisone(DB00635) CTGTTCGACCAGGGAAGTTCAGAG 0.377 0.51 127 132 DNAH8 1769 broad.mit.edu 37 6 38867601 38867626 + Frame_Shift_Del DEL TTGGTGGTTCCGGAAAACAAAGTCTT - - LC1F_LUNG NA LC1F_LUNG NA g.chr6:38867601_38867626delTTGGTGGTTCCGGAAAACAAAGTCTT uc003ooe.1 + 60 9062_9087 c.8462_8487delTTGGTGGTTCCGGAAAACAAAGTCTT c.(8461-8487)GTTGGTGGTTCCGGAAAACAAAGTCTTfs p.V2821fs NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 CTGGTGGGTGTTGGTGGTTCCGGAAAACAAAGTCTTTCAAGATTGG 0.341 0.14 84 14 CARD11 84433 broad.mit.edu 37 7 2962930 2962930 + Frame_Shift_Del DEL G - - LC1F_LUNG NA LC1F_LUNG NA g.chr7:2962930delG uc003smv.2 - 16 2382 c.1978delC c.(1978-1980)CGGfs p.R660fs NM_032415 NP_115791 Q9BXL7 CAR11_HUMAN caspase recruitment domain family, member 11 660 positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway cytosol|membrane raft|plasma membrane CARD domain binding|guanylate kinase activity haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1) 50 Ovarian(82;0.0115) OV - Ovarian serous cystadenocarcinoma(56;8.44e-14) 0.000 0.12 724 101 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LC1F_LUNG NA LC1F_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 1 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency LC1F_LUNG NA LC1F_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.28 23 9 CDK20 23552 broad.mit.edu 37 9 90582462 90582463 + Frame_Shift_Ins INS - G G rs151084868 LC1F_LUNG NA LC1F_LUNG NA g.chr9:90582462_90582463insG uc004apr.2 - 8 1261_1262 c.955_956insC c.(955-957)CACfs p.H319fs CDK20_uc004aps.2_Frame_Shift_Ins_p.H298fs|CDK20_uc004apt.2_Frame_Shift_Ins_p.H311fs|CDK20_uc004apu.2_3'UTR NM_001039803 NP_001034892 Q8IZL9 CDK20_HUMAN cell cycle related kinase isoform 3 319 cell division|multicellular organismal development cilium|mitochondrion|nucleus ATP binding|cyclin-dependent protein kinase activity skin(1) 1 GTCATGGATGTGGGGGGGCCCT 0.619 0.14 70 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LC1F_LUNG NA LC1F_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 183 84 BCKDK 10295 broad.mit.edu 37 16 31120709 31120716 + Frame_Shift_Del DEL CCAGTCGG - - rs150455286 LC1F_LUNG NA LC1F_LUNG NA g.chr16:31120709_31120716delCCAGTCGG uc002eaw.3 + 2 481_488 c.165_172delCCAGTCGG c.(163-174)AACCAGTCGGCCfs p.N55fs BCKDK_uc002eav.3_Frame_Shift_Del_p.N55fs|BCKDK_uc010cah.2_RNA|BCKDK_uc010cai.2_Frame_Shift_Del_p.N55fs NM_005881 NP_005872 O14874 BCKD_HUMAN branched chain ketoacid dehydrogenase kinase 55_58 branched chain family amino acid catabolic process|peptidyl-histidine phosphorylation mitochondrial alpha-ketoglutarate dehydrogenase complex [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity|ATP binding|protein binding|protein serine/threonine kinase activity|two-component sensor activity stomach(1)|breast(1) 2 CCTTTTACAACCAGTCGGCCATCGACGC 0.683 0.41 33 23 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LC1F_LUNG NA LC1F_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 13 111 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT LC1F_LUNG NA LC1F_LUNG NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.11 536 64 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 LC1F_LUNG NA LC1F_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.37 36 21 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 LC1F_LUNG NA LC1F_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.46 36 31 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LC1F_LUNG NA LC1F_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 81 311 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LC1F_LUNG NA LC1F_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 54 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LCLC103H_LUNG NA LCLC103H_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 4 60 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LCLC103H_LUNG NA LCLC103H_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.51 65 67 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LCLC103H_LUNG NA LCLC103H_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 24 40 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 LCLC103H_LUNG NA LCLC103H_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.17 49 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LCLC103H_LUNG NA LCLC103H_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 152 40 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LCLC103H_LUNG NA LCLC103H_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 6 54 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 LCLC103H_LUNG NA LCLC103H_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 6 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LCLC103H_LUNG NA LCLC103H_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 28 282 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LCLC103H_LUNG NA LCLC103H_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 76 NF2 4771 broad.mit.edu 37 22 30051653 30051667 + Splice_Site DEL GAGGCCGAGCCAGGT - - rs147896582 LCLC103H_LUNG NA LCLC103H_LUNG NA g.chr22:30051653_30051667delGAGGCCGAGCCAGGT uc003age.3 + 6 1042 c.599_splice c.e6+1 p.R200_splice NF2_uc003afy.3_Splice_Site_p.R200_splice|NF2_uc003afz.3_Splice_Site_p.R117_splice|NF2_uc003agf.3_Splice_Site_p.R200_splice|NF2_uc003agb.3_Splice_Site_p.R123_splice|NF2_uc003agc.3_Splice_Site_p.R162_splice|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Splice_Site_p.R200_splice|NF2_uc003aga.3_Splice_Site_p.R158_splice|NF2_uc003agh.3_Splice_Site_p.R159_splice|NF2_uc003agi.3_Splice_Site_p.R117_splice|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Splice_Site_p.R162_splice NM_000268 NP_000259 P35240 MERL_HUMAN neurofibromin 2 isoform 1 actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane cytoskeletal protein binding|protein binding p.?(3)|p.R198*(3)|p.R198fs*4(1)|p.R200fs*7(1)|p.G197C(1) meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1) 728 0.000 0.71 16 40 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LCLC97TM1_LUNG NA LCLC97TM1_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 50 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 LCLC97TM1_LUNG NA LCLC97TM1_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.52 14 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LCLC97TM1_LUNG NA LCLC97TM1_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 139 173 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LCLC97TM1_LUNG NA LCLC97TM1_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 47 68 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LCLC97TM1_LUNG NA LCLC97TM1_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 571 240 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LCLC97TM1_LUNG NA LCLC97TM1_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 49 414 TP53 7157 broad.mit.edu 37 17 7579585 7579585 + Frame_Shift_Del DEL G - - rs11575998 LCLC97TM1_LUNG NA LCLC97TM1_LUNG NA g.chr17:7579585delG uc002gim.2 - 4 296 c.102delC c.(100-102)CCCfs p.P34fs TP53_uc002gig.1_Frame_Shift_Del_p.P34fs|TP53_uc002gih.2_Frame_Shift_Del_p.P34fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.P34fs|TP53_uc010cni.1_Frame_Shift_Del_p.P34fs|TP53_uc002gij.2_Frame_Shift_Del_p.P34fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_5'UTR|TP53_uc010cnk.1_Frame_Shift_Del_p.P49fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 34 Transcription activation (acidic).|Interaction with HRMT1L2. P -> L (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.P34L(2)|p.?(1)|p.S33fs*23(1)|p.P34fs*8(1)|p.P36fs*7(1)|p.P13fs*18(1)|p.S33fs*6(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGGACGGCAAGGGGGACTGTA 0.383 1.00 0 18 MYH4 4622 broad.mit.edu 37 17 10360918 10360918 + Frame_Shift_Del DEL G - - LCLC97TM1_LUNG NA LCLC97TM1_LUNG NA g.chr17:10360918delG uc002gmn.2 - 16 1827 c.1716delC c.(1714-1716)GCCfs p.A572fs uc002gml.1_Intron NM_017533 NP_060003 Q9Y623 MYH4_HUMAN myosin, heavy polypeptide 4, skeletal muscle 572 Myosin head-like. muscle filament sliding muscle myosin complex|myosin filament|sarcomere actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle ovary(10)|skin(2)|central_nervous_system(1) 13 GCTTGCCTTTGGCAGGCTTGG 0.527 0.97 6 174 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 LCLC97TM1_LUNG NA LCLC97TM1_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.13 97 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LCLC97TM1_LUNG NA LCLC97TM1_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 185 611 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LCLC97TM1_LUNG NA LCLC97TM1_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 101 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LI7_LIVER NA LI7_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 2 23 PDE4DIP 9659 broad.mit.edu 37 1 144918891 144918892 + Frame_Shift_Del DEL TG - - rs148279833 LI7_LIVER NA LI7_LIVER NA g.chr1:144918891_144918892delTG uc001elw.3 - 10 1585_1586 c.1294_1295delCA c.(1294-1296)CAGfs p.Q432fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.Q498fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.Q432fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.Q432fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.Q595fs|PDE4DIP_uc001eme.1_5'UTR|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.Q219fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 432 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) GTTTTGTTCCTGGGTTCGAATC 0.441 0.13 160 24 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - LI7_LIVER NA LI7_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.32 129 61 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LI7_LIVER NA LI7_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.28 28 11 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LI7_LIVER NA LI7_LIVER NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 16 28 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes LI7_LIVER NA LI7_LIVER NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.90 1 9 TFR2 7036 broad.mit.edu 37 7 100225010 100225021 + In_Frame_Del DEL CTGGGCCACGGC - - rs80338888 LI7_LIVER NA LI7_LIVER NA g.chr7:100225010_100225021delCTGGGCCACGGC uc003uvv.1 - 16 1902_1913 c.1861_1872delGCCGTGGCCCAG c.(1861-1872)GCCGTGGCCCAGdel p.AVAQ621del TFR2_uc010lhc.1_In_Frame_Del_p.AVAQ162del|TFR2_uc003uvu.1_In_Frame_Del_p.AVAQ450del NM_003227 NP_003218 Q9UP52 TFR2_HUMAN transferrin receptor 2 621_624 Extracellular (Potential). cellular iron ion homeostasis|iron ion transport|proteolysis cytoplasm|integral to plasma membrane peptidase activity|transferrin receptor activity ovary(1)|pancreas(1) 2 Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439) GCCCTGCGAGCTGGGCCACGGCCTGGGCCACG 0.660 0.36 9 5 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - LI7_LIVER NA LI7_LIVER NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.85 2 11 RPGRIP1 57096 broad.mit.edu 37 14 21798427 21798427 + Frame_Shift_Del DEL G - - LI7_LIVER NA LI7_LIVER NA g.chr14:21798427delG uc001wag.2 + 19 3119 c.3119delG c.(3118-3120)TGGfs p.W1040fs RPGRIP1_uc001wah.2_Frame_Shift_Del_p.W682fs|RPGRIP1_uc001wai.2_Frame_Shift_Del_p.W366fs|RPGRIP1_uc001wak.2_Frame_Shift_Del_p.W515fs|RPGRIP1_uc010aim.2_Frame_Shift_Del_p.W423fs|RPGRIP1_uc001wal.2_Frame_Shift_Del_p.W399fs|RPGRIP1_uc001wam.2_Frame_Shift_Del_p.W357fs NM_020366 NP_065099 Q96KN7 RPGR1_HUMAN retinitis pigmentosa GTPase regulator 1040 Interaction with RPGR. response to stimulus|visual perception cilium ovary(4)|breast(2)|pancreas(1) 7 all_cancers(95;0.0017) all_cancers(140;0.0973) Epithelial(56;6.24e-07)|all cancers(55;6.56e-06) GBM - Glioblastoma multiforme(265;0.00888) TACACTGAGTGGAAGTTCTCA 0.323 0.45 48 39 MAPK6 5597 broad.mit.edu 37 15 52338753 52338754 + Frame_Shift_Ins INS - T T LI7_LIVER NA LI7_LIVER NA g.chr15:52338753_52338754insT uc002abp.2 + 2 890_891 c.96_97insT c.(94-99)GGCTTGfs p.G32fs NM_002748 NP_002739 Q16659 MK06_HUMAN mitogen-activated protein kinase 6 32_33 ATP (By similarity).|Protein kinase. cell cycle ATP binding|MAP kinase activity lung(3)|ovary(1) 4 all cancers(107;0.0028) GAGGCAATGGCTTGGTTTTTTC 0.396 0.19 38 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 LI7_LIVER NA LI7_LIVER NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.69 9 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LI7_LIVER NA LI7_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 111 336 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LI7_LIVER NA LI7_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 3 28 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LMSU_STOMACH NA LMSU_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 17 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 LMSU_STOMACH NA LMSU_STOMACH NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.33 10 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LMSU_STOMACH NA LMSU_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.28 117 46 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 LMSU_STOMACH NA LMSU_STOMACH NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.72 21 53 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 LMSU_STOMACH NA LMSU_STOMACH NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.37 47 28 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LMSU_STOMACH NA LMSU_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 28 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency LMSU_STOMACH NA LMSU_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.50 61 61 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 LMSU_STOMACH NA LMSU_STOMACH NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.43 8 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LMSU_STOMACH NA LMSU_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 133 18 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LMSU_STOMACH NA LMSU_STOMACH NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 6 57 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT LMSU_STOMACH NA LMSU_STOMACH NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.12 91 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LMSU_STOMACH NA LMSU_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 20 116 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LMSU_STOMACH NA LMSU_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 5 38 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 3 42 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.40 6 4 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 110 192 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 30 55 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.26 52 18 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 3 23 MLL3 58508 broad.mit.edu 37 7 151935851 151935853 + In_Frame_Del DEL CTT - - rs4024420 by1000genomes LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr7:151935851_151935853delCTT uc003wla.2 - 15 2810_2812 c.2591_2593delAAG c.(2590-2595)GAAGGT>GGT p.E864del MLL3_uc003wkz.2_5'UTR NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 864 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) ATTTCCCGACCTTCTGAAATGTC 0.429 0.39 39 25 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 47 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.82 7 31 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 951 456 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.42 7 5 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.26 141 49 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 32 261 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 25 118 NCOA3 8202 broad.mit.edu 37 20 46279858 46279866 + In_Frame_Del DEL CAGCAGCAA - - rs151060280;rs3092460;rs67218125;rs11472494;rs112826888 byFrequency LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr20:46279858_46279866delCAGCAGCAA uc002xtk.2 + 20 3989_3997 c.3784_3792delCAGCAGCAA c.(3784-3792)CAGCAGCAAdel p.QQQ1274del NCOA3_uc010ght.1_In_Frame_Del_p.QQQ1265del|NCOA3_uc002xtl.2_In_Frame_Del_p.QQQ1270del|NCOA3_uc002xtm.2_In_Frame_Del_p.QQQ1269del|NCOA3_uc002xtn.2_In_Frame_Del_p.QQQ1273del|NCOA3_uc010zyc.1_In_Frame_Del_p.QQQ1069del NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 1274_1276 Poly-Gln.|Acetyltransferase. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 gcagcagcagcagcagcaacagcaacagc 0.321 0.49 225 220 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 237 787 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LN18_CENTRAL_NERVOUS_SYSTEM NA LN18_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 8 117 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 3 97 SOX11 6664 broad.mit.edu 37 2 5833526 5833528 + In_Frame_Del DEL GAC - - LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr2:5833526_5833528delGAC uc002qyj.2 + 1 728_730 c.673_675delGAC c.(673-675)GACdel p.D233del NM_003108 NP_003099 P35716 SOX11_HUMAN SRY-box 11 233 Poly-Asp. cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis cytoplasm|nucleolus enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding central_nervous_system(3) 3 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) OV - Ovarian serous cystadenocarcinoma(76;0.132) 0.000 0.24 350 112 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.43 12 9 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.22 65 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.45 18 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 118 138 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.51 32 33 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 4 47 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.20 423 105 PAPPA 5069 broad.mit.edu 37 9 119158850 119158858 + In_Frame_Del DEL CCAAGAACA - - LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr9:119158850_119158858delCCAAGAACA uc004bjn.2 + 22 5220_5228 c.4839_4847delCCAAGAACA c.(4837-4848)GCCCAAGAACAC>GCC p.QEH1614del PAPPA_uc011lxq.1_In_Frame_Del_p.QEH989del NM_002581 NP_002572 Q13219 PAPP1_HUMAN pregnancy-associated plasma protein A 1614_1616 cell differentiation|female pregnancy cytoplasm|extracellular region|membrane metalloendopeptidase activity|zinc ion binding ovary(4)|skin(4)|pancreas(1) 9 ACCCCCAGGCCCAAGAACACAGCCGGAAA 0.512 0.10 106 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 438 167 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.58 28 38 THAP11 57215 broad.mit.edu 37 16 67876806 67876829 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAACAGCAG - - rs143101373;rs143185886;rs34138555;rs28647874;rs34213159;rs3982383;rs63117363 by1000genomes;byFrequency;byFrequency;byFrequency LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr16:67876806_67876829delCAGCAGCAGCAGCAGCAACAGCAG uc002euo.2 + 1 594_617 c.349_372delCAGCAGCAGCAGCAGCAACAGCAG c.(349-372)CAGCAGCAGCAGCAGCAACAGCAGdel p.QQQQQQQQ125del CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 125_132 Gln-rich. Missing (in Ref. 2; AAH12182). regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) acagcagcaacagcagcagcagcagcaacagcagcagcagcagc 0.335 0.19 239 56 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.29 35 14 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.53 74 84 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 33 218 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LN229_CENTRAL_NERVOUS_SYSTEM NA LN229_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 14 117 FAM123B 139285 broad.mit.edu 37 X 63412647 63412648 + Frame_Shift_Ins INS - A A LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chrX:63412647_63412648insA uc004dvo.2 - 2 792_793 c.519_520insT c.(517-522)TTTAGCfs p.F173fs NM_152424 NP_689637 Q5JTC6 F123B_HUMAN family with sequence similarity 123B 173_174 Wnt receptor signaling pathway cytoplasm|nucleus|plasma membrane p.0?(40)|p.F173fs*36(2) kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1) 112 CGGATACTGCTAAAAAAGCCTT 0.559 0.92 8 89 ATRX 546 broad.mit.edu 37 X 76778785 76778787 + In_Frame_Del DEL TCT - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chrX:76778785_76778787delTCT uc004ecp.3 - 31 7024_7026 c.6792_6794delAGA c.(6790-6795)GAAGAG>GAG p.2264_2265EE>E ATRX_uc004ecq.3_In_Frame_Del_p.2226_2227EE>E|ATRX_uc004eco.3_In_Frame_Del_p.2049_2050EE>E NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 2264_2265 Poly-Glu. DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) TTCAGTCAACTCTTCTTCTTCTT 0.369 0.84 14 72 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.56 21 27 F8 2157 broad.mit.edu 37 X 154157239 154157240 + Frame_Shift_Ins INS - T T LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chrX:154157239_154157240insT uc004fmt.2 - 14 4996_4997 c.4825_4826insA c.(4825-4827)ACAfs p.T1609fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1609 B. acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) CTTAAAAGCTGTTTTTTCTGGT 0.406 0.85 15 83 ARID1A 8289 broad.mit.edu 37 1 27023744 27023744 + Frame_Shift_Del DEL G - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr1:27023744delG uc001bmv.1 + 1 1223 c.850delG c.(850-852)GGGfs p.G284fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.G284fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.G284fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 284 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CGCGGCCGGCGGGGGAACTCC 0.751 0.50 7 7 JAK1 3716 broad.mit.edu 37 1 65339111 65339111 + Frame_Shift_Del DEL T - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr1:65339111delT uc001dbu.1 - 5 674 c.425delA c.(424-426)AAGfs p.K142fs JAK1_uc009wam.1_Frame_Shift_Del_p.K130fs|JAK1_uc001dbv.2_RNA NM_002227 NP_002218 P23458 JAK1_HUMAN janus kinase 1 142 FERM. interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway cytoskeleton|cytosol|endomembrane system|membrane|nucleus ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity p.K142fs*26(3) haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1) 61 BRCA - Breast invasive adenocarcinoma(111;0.0485) ATCTGGAATCTTTTTTTTCTC 0.478 0.45 187 151 BCL9 607 broad.mit.edu 37 1 147092024 147092026 + In_Frame_Del DEL CTT - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr1:147092024_147092026delCTT uc001epq.2 + 8 2803_2805 c.2063_2065delCTT c.(2062-2067)CCTTCT>CCT p.S689del BCL9_uc010ozr.1_In_Frame_Del_p.S615del NM_004326 NP_004317 O00512 BCL9_HUMAN B-cell CLL/lymphoma 9 689 Pro-rich. Wnt receptor signaling pathway nucleus protein binding ovary(2)|large_intestine(2)|breast(1)|skin(1) 6 all_hematologic(923;0.115) CCTCTGAGTCCTTCTAGGGGTGA 0.532 0.34 136 70 FCRL4 83417 broad.mit.edu 37 1 157557655 157557656 + Frame_Shift_Ins INS - T T LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr1:157557655_157557656insT uc001fqw.2 - 4 697_698 c.561_562insA c.(559-564)CAAGAAfs p.Q187fs FCRL4_uc010phy.1_Intron NM_031282 NP_112572 Q96PJ5 FCRL4_HUMAN Fc receptor-like 4 precursor 187_188 Extracellular (Potential). integral to membrane|plasma membrane receptor activity ovary(2)|kidney(1)|skin(1) 4 all_hematologic(112;0.0378)|Hepatocellular(266;0.178) Prostate(1639;0.245) AAAGATTCACCTTGAATTTTAA 0.327 0.49 28 27 RNASEL 6041 broad.mit.edu 37 1 182555468 182555471 + Frame_Shift_Del DEL CTTT - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr1:182555468_182555471delCTTT uc001gpj.1 - 1 638_641 c.471_474delAAAG c.(469-474)ACAAAGfs p.T157fs RNASEL_uc009wxz.1_Frame_Shift_Del_p.T157fs|RNASEL_uc001gpk.2_Frame_Shift_Del_p.T157fs|RNASEL_uc009wya.1_Frame_Shift_Del_p.T157fs NM_021133 NP_066956 Q05823 RN5A_HUMAN ribonuclease L 157_158 mRNA processing|response to virus|type I interferon-mediated signaling pathway mitochondrion ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding ovary(4)|stomach(1) 5 CTTGATCCTCCTTTGTCTTTCGCC 0.480 0.50 186 187 URB2 9816 broad.mit.edu 37 1 229773507 229773507 + Frame_Shift_Del DEL C - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr1:229773507delC uc001hts.1 + 4 3283 c.3147delC c.(3145-3147)AACfs p.N1049fs URB2_uc009xfd.1_Frame_Shift_Del_p.N1049fs NM_014777 NP_055592 Q14146 URB2_HUMAN URB2 ribosome biogenesis 2 homolog 1049 nucleolus central_nervous_system(2)|ovary(1) 3 AAAATCAGAACCCCCAGGGCA 0.507 0.37 130 77 EPAS1 2034 broad.mit.edu 37 2 46607704 46607704 + Frame_Shift_Del DEL G - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr2:46607704delG uc002ruv.2 + 12 2381 c.1893delG c.(1891-1893)ATGfs p.M631fs EPAS1_uc002ruw.2_Frame_Shift_Del_p.M97fs NM_001430 NP_001421 Q99814 EPAS1_HUMAN endothelial PAS domain protein 1 631 angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia transcription factor complex histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding ovary(1)|skin(1) 2 all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18) LUSC - Lung squamous cell carcinoma(58;0.151) 0.000 0.16 941 184 TTN 7273 broad.mit.edu 37 2 179480130 179480130 + Frame_Shift_Del DEL T - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr2:179480130delT uc010zfg.1 - 208 41062 c.40838delA c.(40837-40839)AATfs p.N13613fs TTN_uc010zfh.1_Frame_Shift_Del_p.N7308fs|TTN_uc010zfi.1_Frame_Shift_Del_p.N7241fs|TTN_uc010zfj.1_Frame_Shift_Del_p.N7116fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 14540 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) ACCACCATCATTTTTAGGTGG 0.428 0.65 74 137 TTN 7273 broad.mit.edu 37 2 179595092 179595092 + Frame_Shift_Del DEL G - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr2:179595092delG uc010zfg.1 - 59 14527 c.14303delC c.(14302-14304)CCTfs p.P4768fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.P1429fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 5695 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CACAAAGTAAGGGGGTTCTGA 0.363 0.56 83 106 HDAC4 9759 broad.mit.edu 37 2 240002823 240002823 + Frame_Shift_Del DEL G - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr2:240002823delG uc002vyk.3 - 22 3495 c.2703delC c.(2701-2703)CCCfs p.P901fs HDAC4_uc010fyy.2_Frame_Shift_Del_p.P858fs NM_006037 NP_006028 P56524 HDAC4_HUMAN histone deacetylase 4 901 Histone deacetylase. B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent histone deacetylase complex|transcriptional repressor complex activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding breast(3)|skin(2)|ovary(1) 6 all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159) Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04) CGTCTCCCATGGGGGGGTCCA 0.602 0.31 40 18 SKIL 6498 broad.mit.edu 37 3 170108165 170108165 + Frame_Shift_Del DEL A - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr3:170108165delA uc003fgu.2 + 5 2296 c.1584delA c.(1582-1584)GGAfs p.G528fs SKIL_uc011bps.1_Frame_Shift_Del_p.G508fs|SKIL_uc003fgv.2_Frame_Shift_Del_p.G482fs|SKIL_uc003fgw.2_Frame_Shift_Del_p.G528fs NM_005414 NP_005405 P12757 SKIL_HUMAN SKI-like isoform 1 528 cell cycle arrest|negative regulation of cell differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of axonogenesis|protein heterotrimerization|protein homotrimerization|regulation of apoptosis|regulation of apoptosis|response to antibiotic|response to growth factor stimulus|skeletal muscle tissue development cytoplasm|PML body chromatin binding|nucleotide binding|protein complex binding|protein domain specific binding|SMAD binding|transcription corepressor activity|transcription repressor activity ovary(2)|skin(1) 3 all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137) Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197) ATGATAAGGGAAAAATCATGG 0.358 0.33 48 24 PRKG2 5593 broad.mit.edu 37 4 82061810 82061810 + Frame_Shift_Del DEL T - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr4:82061810delT uc003hmh.2 - 11 1435 c.1421delA c.(1420-1422)AATfs p.N474fs PRKG2_uc011ccf.1_Frame_Shift_Del_p.N54fs|PRKG2_uc011ccg.1_Frame_Shift_Del_p.N54fs|PRKG2_uc011cch.1_Frame_Shift_Del_p.N445fs NM_006259 NP_006250 Q13237 KGP2_HUMAN protein kinase, cGMP-dependent, type II 474 Protein kinase. platelet activation|signal transduction cytosol ATP binding|cGMP binding|cGMP-dependent protein kinase activity breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1) 7 AACATTCTCATTTTTTACTTT 0.338 0.39 41 26 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.12 56 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 117 194 MAML3 55534 broad.mit.edu 37 4 140811911 140811913 + In_Frame_Del DEL AAG - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr4:140811911_140811913delAAG uc003ihz.1 - 2 1429_1431 c.677_679delCTT c.(676-681)TCTTTG>TTG p.S226del MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 226 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) TGCAAGGGCAAAGAAGGTTTCAG 0.483 0.54 34 40 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.36 39 22 CHD1 1105 broad.mit.edu 37 5 98235339 98235340 + Frame_Shift_Ins INS - T T LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr5:98235339_98235340insT uc003knf.2 - 7 1077_1078 c.929_930insA c.(928-930)AACfs p.N310fs NM_001270 NP_001261 O14646 CHD1_HUMAN chromodomain helicase DNA binding protein 1 310 Chromo 1. regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117) COAD - Colon adenocarcinoma(37;0.0717) Epirubicin(DB00445) CTGGTTCTTTGTTTTTTTCAAA 0.411 0.46 79 67 STK32A 202374 broad.mit.edu 37 5 146754724 146754725 + Frame_Shift_Ins INS - A A LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr5:146754724_146754725insA uc010jgn.1 + 11 1255_1256 c.975_976insA c.(973-978)AAGAAAfs p.K325fs STK32A_uc003lom.2_Frame_Shift_Ins_p.K325fs|STK32A_uc011dbw.1_Frame_Shift_Ins_p.K325fs NM_001112724 NP_001106195 Q8WU08 ST32A_HUMAN serine/threonine kinase 32A isoform 1 325_326 ATP binding|metal ion binding|protein serine/threonine kinase activity lung(2)|skin(1) 3 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CTCTACATAAGAAAAAAAAGCG 0.455 0.56 7 9 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.14 69 11 PHF3 23469 broad.mit.edu 37 6 64408416 64408417 + Frame_Shift_Ins INS - T T LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr6:64408416_64408417insT uc003pep.1 + 7 2929_2930 c.2903_2904insT c.(2902-2904)TCTfs p.S968fs PHF3_uc010kah.1_Frame_Shift_Ins_p.S782fs|PHF3_uc003pen.2_Frame_Shift_Ins_p.S880fs|PHF3_uc011dxs.1_Frame_Shift_Ins_p.S237fs NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 968 TFIIS central. multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) GAGCTTTTCTCTTTTTTTCGGG 0.302 0.28 18 7 MLLT4 4301 broad.mit.edu 37 6 168363172 168363172 + Frame_Shift_Del DEL G - - rs141410347 by1000genomes LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr6:168363172delG uc003qwd.2 + 31 5044 c.4902delG c.(4900-4902)GCGfs p.A1634fs MLLT4_uc003qwc.1_Frame_Shift_Del_p.A1622fs|MLLT4_uc003qwg.1_Frame_Shift_Del_p.A933fs NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 1624 Potential. adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) 0.000 0.25 1067 347 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.39 120 77 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 2 15 KCNH2 3757 broad.mit.edu 37 7 150644508 150644508 + Frame_Shift_Del DEL G - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr7:150644508delG uc003wic.2 - 13 3073 c.3060delC c.(3058-3060)CCCfs p.P1020fs KCNH2_uc003wib.2_Frame_Shift_Del_p.P680fs|KCNH2_uc011kux.1_Frame_Shift_Del_p.P924fs NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 1020 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) 0.000 0.39 803 507 MLL3 58508 broad.mit.edu 37 7 151845524 151845524 + Frame_Shift_Del DEL A - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr7:151845524delA uc003wla.2 - 52 13707 c.13488delT c.(13486-13488)TTTfs p.F4496fs MLL3_uc003wkz.2_Frame_Shift_Del_p.F3614fs|MLL3_uc003wkx.2_Frame_Shift_Del_p.F654fs|MLL3_uc003wky.2_Frame_Shift_Del_p.F2060fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 4496 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTTTGTCCTTAAAAAACATGC 0.433 0.44 152 118 MLL3 58508 broad.mit.edu 37 7 151874147 151874148 + Frame_Shift_Ins INS - T T LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr7:151874147_151874148insT uc003wla.2 - 38 8609_8610 c.8390_8391insA c.(8389-8391)AAGfs p.K2797fs MLL3_uc003wkz.2_Frame_Shift_Ins_p.K1858fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.K306fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 2797 K -> R (in Ref. 1; AAK00583). intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding p.K2797fs*26(18) large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTTCTTGTTCCTTTTTTTTTGG 0.347 0.31 133 61 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.73 6 16 BAG4 9530 broad.mit.edu 37 8 38067995 38067995 + Frame_Shift_Del DEL A - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr8:38067995delA uc003xky.1 + 5 1640 c.1358delA c.(1357-1359)GAAfs p.E453fs BAG4_uc003xkz.1_Frame_Shift_Del_p.E417fs NM_004874 NP_004865 O95429 BAG4_HUMAN BCL2-associated athanogene 4 453 BAG. anti-apoptosis|apoptosis|protein folding cytoplasm|nucleus receptor signaling protein activity ovary(1) 1 Colorectal(12;0.000442) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121) 0.000 0.47 322 290 CSPP1 79848 broad.mit.edu 37 8 67998298 67998298 + Frame_Shift_Del DEL A - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr8:67998298delA uc003xxi.2 + 4 395 c.364delA c.(364-366)AAAfs p.K122fs CSPP1_uc003xxg.1_Frame_Shift_Del_p.K122fs|CSPP1_uc003xxh.1_RNA|CSPP1_uc003xxj.2_Frame_Shift_Del_p.K122fs|CSPP1_uc003xxk.2_5'UTR NM_001077204 NP_001070672 Q1MSJ5 CSPP1_HUMAN centrosome spindle pole associated protein 1 122 Potential. centrosome|microtubule|spindle ovary(3)|breast(2) 5 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153) GAAGAAACATAAATTAAAAGA 0.308 0.51 28 29 VPS13B 157680 broad.mit.edu 37 8 100654345 100654346 + Frame_Shift_Ins INS - A A rs141211386 byFrequency LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr8:100654345_100654346insA uc003yiv.2 + 34 5713_5714 c.5602_5603insA c.(5602-5604)GAAfs p.E1868fs VPS13B_uc003yiw.2_Frame_Shift_Ins_p.E1843fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 1868 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) GAAGAATAATGAAAAAACAGAC 0.371 0.49 31 30 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 52 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.18 126 28 SMARCA2 6595 broad.mit.edu 37 9 2119494 2119495 + Frame_Shift_Ins INS - A A LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr9:2119494_2119495insA uc003zhc.2 + 26 3820_3821 c.3721_3722insA c.(3721-3723)CAAfs p.Q1241fs SMARCA2_uc003zhd.2_Frame_Shift_Ins_p.Q1241fs|SMARCA2_uc010mha.2_Frame_Shift_Ins_p.Q1174fs NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 1241 chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.49 302 294 TGFBR1 7046 broad.mit.edu 37 9 101867554 101867555 + Frame_Shift_Ins INS - T T rs67861970 LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr9:101867554_101867555insT uc004azc.2 + 1 143_144 c.67_68insT c.(67-69)GCGfs p.A23fs TGFBR1_uc004azd.2_Frame_Shift_Ins_p.A23fs NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 23 activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.11 120 15 CEP110 11064 broad.mit.edu 37 9 123924208 123924209 + Frame_Shift_Ins INS - T T LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr9:123924208_123924209insT uc004bkx.1 + 31 5195_5196 c.5164_5165insT c.(5164-5166)AGGfs p.R1722fs CEP110_uc004blb.1_Frame_Shift_Ins_p.R391fs|CEP110_uc010mvp.1_Intron NM_007018 NP_008949 Q7Z7A1 CNTRL_HUMAN centrosomal protein 110kDa 1722 Potential. cell division|G2/M transition of mitotic cell cycle centrosome|cytosol protein binding 0 ACATGACCAAAGGGTATCTGAA 0.391 0.49 45 43 NEK6 10783 broad.mit.edu 37 9 127110068 127110068 + Frame_Shift_Del DEL C - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr9:127110068delC uc004bog.2 + 9 947 c.798delC c.(796-798)TACfs p.Y266fs NEK6_uc004bof.2_Frame_Shift_Del_p.Y284fs|NEK6_uc004boh.2_Frame_Shift_Del_p.Y300fs|NEK6_uc010mwj.2_Frame_Shift_Del_p.Y219fs|NEK6_uc010mwk.2_Frame_Shift_Del_p.Y266fs|NEK6_uc004boi.2_Frame_Shift_Del_p.Y266fs NM_014397 NP_055212 Q9HC98 NEK6_HUMAN NIMA-related kinase 6 isoform 2 266 Protein kinase. apoptosis|cell division|chromosome segregation|mitosis|peptidyl-serine phosphorylation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of mitotic metaphase/anaphase transition cytoplasm|nucleus ATP binding|kinesin binding|magnesium ion binding|protein kinase binding|protein serine/threonine kinase activity|signal transducer activity ovary(2)|kidney(1) 3 AGTGTGACTACCCCCCACTCC 0.617 0.40 123 83 PTEN 5728 broad.mit.edu 37 10 89624242 89624243 + Frame_Shift_Del DEL AA - - rs121913290 LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr10:89624242_89624243delAA uc001kfb.2 + 2 1047_1048 c.16_17delAA c.(16-18)AAAfs p.K6fs KILLIN_uc009xti.2_5'Flank NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 6 activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.?(13)|p.0?(12)|p.K6fs*4(10)|p.K6I(1)|p.K6N(1)|p.K6R(1)|p.A3fs*14(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) AGCCATCATCAAAGAGATCGTT 0.485 0.98 1 50 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.53 9 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 1026 222 CNTN1 1272 broad.mit.edu 37 12 41463778 41463779 + Frame_Shift_Ins INS - A A LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr12:41463778_41463779insA uc001rmm.1 + 24 3111_3112 c.2998_2999insA c.(2998-3000)CCAfs p.P1000fs CNTN1_uc001rmn.1_Frame_Shift_Ins_p.P989fs NM_001843 NP_001834 Q12860 CNTN1_HUMAN contactin 1 isoform 1 precursor 1000 axon guidance|cell adhesion|Notch signaling pathway anchored to membrane|membrane fraction|plasma membrane lung(4)|ovary(3)|large_intestine(1)|skin(1) 9 all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716) Lung NSC(34;0.0211)|all_lung(34;0.0294) CACCCTATCCCCAAGTCTTCTC 0.470 0.44 202 160 LGR5 8549 broad.mit.edu 37 12 71950441 71950442 + Frame_Shift_Ins INS - T T rs61737419 byFrequency LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr12:71950441_71950442insT uc001swl.2 + 6 735_736 c.687_688insT c.(685-690)TGCTTTfs p.C229fs LGR5_uc001swm.2_Frame_Shift_Ins_p.C229fs|LGR5_uc001swn.1_RNA NM_003667 NP_003658 O75473 LGR5_HUMAN leucine-rich repeat-containing G protein-coupled 229_230 LRR 7.|Extracellular (Potential). integral to plasma membrane protein-hormone receptor activity lung(4)|skin(3)|ovary(1)|pancreas(1) 9 GAAAGAAATGCTTTGATGGGCT 0.386 0.35 60 32 APAF1 317 broad.mit.edu 37 12 99071206 99071207 + Frame_Shift_Ins INS - A A LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr12:99071206_99071207insA uc001tfz.2 + 13 2374_2375 c.1797_1798insA c.(1795-1800)AACAAAfs p.N599fs APAF1_uc001tfy.2_Frame_Shift_Ins_p.N588fs|APAF1_uc001tga.2_Frame_Shift_Ins_p.N588fs|APAF1_uc001tgb.2_Frame_Shift_Ins_p.N599fs|APAF1_uc001tgc.2_Intron|APAF1_uc009zto.2_Frame_Shift_Ins_p.N8fs NM_181861 NP_863651 O14727 APAF_HUMAN apoptotic peptidase activating factor 1 isoform 599_600 activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development cytosol|Golgi apparatus|nucleus ATP binding|caspase activator activity|protein binding ovary(2)|lung(1) 3 Adenosine triphosphate(DB00171) TATTTAGAAACAAAAAAAACAT 0.347 0.42 31 22 EP400 57634 broad.mit.edu 37 12 132547136 132547138 + In_Frame_Del DEL CAA - - rs60608267;rs111782215 byFrequency LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr12:132547136_132547138delCAA uc001ujn.2 + 46 8259_8261 c.8224_8226delCAA c.(8224-8226)CAAdel p.Q2748del EP400_uc001ujl.2_In_Frame_Del_p.Q2747del|EP400_uc001ujm.2_In_Frame_Del_p.Q2667del|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784 Poly-Gln.|Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) gcagcagcagcaacagcagcagc 0.325 0.10 210 24 EDNRB 1910 broad.mit.edu 37 13 78475267 78475267 + Frame_Shift_Del DEL A - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr13:78475267delA uc001vko.2 - 4 1135 c.877delT c.(877-879)TATfs p.Y293fs EDNRB_uc001vkq.1_Frame_Shift_Del_p.Y293fs|uc001vkn.1_Intron|EDNRB_uc010aez.1_Frame_Shift_Del_p.Y293fs|EDNRB_uc001vkp.1_Frame_Shift_Del_p.Y376fs NM_001122659 NP_001116131 P24530 EDNRB_HUMAN endothelin receptor type B isoform 1 precursor 293 Helical; Name=5; (Potential). activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction integral to plasma membrane endothelin-B receptor activity|peptide hormone binding 0 Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037) GBM - Glioblastoma multiforme(99;0.0933) Bosentan(DB00559) ATTAGTGTATAAAAAAATGCA 0.343 0.46 44 37 NOVA1 4857 broad.mit.edu 37 14 27066542 27066542 + Frame_Shift_Del DEL G - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr14:27066542delG uc001wpy.2 - 1 419 c.101delC c.(100-102)CCTfs p.P34fs NOVA1_uc001wpz.2_Frame_Shift_Del_p.P34fs|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_Frame_Shift_Del_p.P34fs NM_002515 NP_002506 P51513 NOVA1_HUMAN neuro-oncological ventral antigen 1 isoform 1 34 Bipartite nuclear localization signal (Potential). locomotory behavior|RNA splicing|synaptic transmission nucleus RNA binding skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1) 5 GBM - Glioblastoma multiforme(265;0.0135) 0.000 0.40 1440 980 SRP14 6727 broad.mit.edu 37 15 40328564 40328575 + In_Frame_Del DEL TGCTGTTGTTGG - - rs16924521;rs8874;rs7535 by1000genomes LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr15:40328564_40328575delTGCTGTTGTTGG uc001zkq.2 - 5 442_453 c.370_381delCCAACAACAGCA c.(370-381)CCAACAACAGCAdel p.PTTA124del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 124_127 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgttgttgctgctgttgttggtgctgttgct 0.231 0.48 45 42 UNC13C 440279 broad.mit.edu 37 15 54306272 54306273 + Frame_Shift_Ins INS - A A LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr15:54306272_54306273insA uc002ack.2 + 1 1172_1173 c.1172_1173insA c.(1171-1173)TTAfs p.L391fs NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 391 exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) GATTCTGTCTTAAAAAAGTCAT 0.416 0.47 44 39 CIITA 4261 broad.mit.edu 37 16 11001240 11001241 + Frame_Shift_Ins INS - C C LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr16:11001240_11001241insC uc002dai.3 + 11 2024_2025 c.1891_1892insC c.(1891-1893)GCCfs p.A631fs CIITA_uc002daj.3_Frame_Shift_Ins_p.A632fs|CIITA_uc002dak.3_Intron|CIITA_uc002dag.2_Frame_Shift_Ins_p.A631fs|CIITA_uc002dah.2_Frame_Shift_Ins_p.A583fs|CIITA_uc010bup.1_Intron NM_000246 NP_000237 P33076 C2TA_HUMAN class II transactivator 631 NACHT. interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent nucleus activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding central_nervous_system(1) 1 TGGGGAGGACGCCAAGCTGCCC 0.693 0.51 56 58 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.82 10 47 MAP2K3 5606 broad.mit.edu 37 17 21205511 21205512 + Frame_Shift_Ins INS - A A LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr17:21205511_21205512insA uc002gys.2 + 6 721_722 c.456_457insA c.(454-459)CGGAAGfs p.R152fs MAP2K3_uc002gyt.2_Frame_Shift_Ins_p.R123fs|MAP2K3_uc002gyu.2_Frame_Shift_Ins_p.R123fs NM_145109 NP_659731 P46734 MP2K3_HUMAN mitogen-activated protein kinase kinase 3 152_153 Protein kinase. activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity 0 COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553) AGTTCTACCGGAAGGTGCTGGA 0.589 0.17 58 12 GRB7 2886 broad.mit.edu 37 17 37901141 37901142 + Frame_Shift_Ins INS - A A LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr17:37901141_37901142insA uc002hsr.2 + 9 1165_1166 c.915_916insA c.(913-918)CCCAACfs p.P305fs GRB7_uc002hss.2_Frame_Shift_Ins_p.P305fs|GRB7_uc010cwc.2_Frame_Shift_Ins_p.P305fs|GRB7_uc002hst.2_Frame_Shift_Ins_p.P305fs NM_005310 NP_005301 Q14451 GRB7_HUMAN growth factor receptor-bound protein 7 305_306 PH. blood coagulation|epidermal growth factor receptor signaling pathway|leukocyte migration|negative regulation of translation|positive regulation of cell migration|stress granule assembly cytosol|focal adhesion|stress granule phosphatidylinositol binding|protein kinase binding|SH3/SH2 adaptor activity lung(2)|ovary(1)|breast(1)|skin(1) 5 all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052) UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171) CTCTGCAGCCCAACAAGCTTCG 0.554 0.43 87 65 TOP2A 7153 broad.mit.edu 37 17 38546381 38546381 + Frame_Shift_Del DEL T - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr17:38546381delT uc002huq.2 - 34 4429 c.4303delA c.(4303-4305)AGGfs p.R1435fs NM_001067 NP_001058 P11388 TOP2A_HUMAN DNA topoisomerase II, alpha isozyme 1435 apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1) 7 Breast(137;0.00328) STAD - Stomach adenocarcinoma(5;0.00183) Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385) GGGGCAGCCCTTTTTTTGGCA 0.413 0.51 72 76 SOCS3 9021 broad.mit.edu 37 17 76354877 76354878 + Frame_Shift_Ins INS - C C LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr17:76354877_76354878insC uc002jvl.2 - 2 715_716 c.299_300insG c.(298-300)GGCfs p.G100fs NM_003955 NP_003946 O14543 SOCS3_HUMAN suppressor of cytokine signaling 3 100 SH2. anti-apoptosis|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|regulation of growth|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway cytosol protein kinase inhibitor activity ovary(1) 1 BRCA - Breast invasive adenocarcinoma(99;0.000688)|OV - Ovarian serous cystadenocarcinoma(97;0.0554) GAGAGAAGCTGCCCCCCTCACA 0.649 0.35 31 17 RBBP8 5932 broad.mit.edu 37 18 20572852 20572853 + Frame_Shift_Ins INS - A A LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr18:20572852_20572853insA uc002ktw.2 + 11 1393_1394 c.1062_1063insA c.(1060-1065)GGGAAAfs p.G354fs RBBP8_uc002kty.2_Frame_Shift_Ins_p.G354fs|RBBP8_uc002ktz.2_Frame_Shift_Ins_p.G354fs|RBBP8_uc002kua.2_Frame_Shift_Ins_p.G354fs|RBBP8_uc002ktx.1_Frame_Shift_Ins_p.G354fs NM_002894 NP_002885 Q99708 COM1_HUMAN retinoblastoma binding protein 8 isoform a 354_355 cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter nucleus damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity ovary(1)|lung(1)|skin(1) 3 all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19) OV - Ovarian serous cystadenocarcinoma(1;0.00196) TACAGCCTGGGAAAAAAAAACA 0.361 0.46 35 30 TLE2 7089 broad.mit.edu 37 19 3005855 3005855 + Frame_Shift_Del DEL G - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr19:3005855delG uc002lww.2 - 16 1875 c.1612delC c.(1612-1614)CGTfs p.R538fs TLE2_uc010xhb.1_Frame_Shift_Del_p.R205fs|TLE2_uc010dth.2_Frame_Shift_Del_p.R539fs|TLE2_uc010xhc.1_Frame_Shift_Del_p.R416fs|TLE2_uc010dti.2_Frame_Shift_Del_p.R552fs NM_003260 NP_003251 Q04725 TLE2_HUMAN transducin-like enhancer protein 2 isoform 1 538 WD 2. negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway nucleus protein binding|transcription corepressor activity 0 UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) GCCTTGATACGGGGGGTGGGC 0.642 0.62 5 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 80 192 CLPTM1 1209 broad.mit.edu 37 19 45490501 45490501 + Frame_Shift_Del DEL C - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr19:45490501delC uc002pai.2 + 8 873 c.858delC c.(856-858)AACfs p.N286fs CLPTM1_uc010ejv.1_Frame_Shift_Del_p.N184fs|CLPTM1_uc010xxf.1_Frame_Shift_Del_p.N184fs|CLPTM1_uc010xxg.1_Frame_Shift_Del_p.N272fs NM_001294 NP_001285 O96005 CLPT1_HUMAN cleft lip and palate associated transmembrane 286 Extracellular (Potential). cell differentiation|multicellular organismal development|regulation of T cell differentiation in thymus external side of plasma membrane|integral to plasma membrane ovary(1) 1 all_neural(266;0.224)|Ovarian(192;0.231) OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187) ACTACTGGAACCTGCAGAAGG 0.597 0.96 7 162 AURKC 6795 broad.mit.edu 37 19 57746647 57746647 + Frame_Shift_Del DEL G - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr19:57746647delG uc002qoe.2 + 7 981 c.792delG c.(790-792)CTGfs p.L264fs AURKC_uc002qoc.2_Frame_Shift_Del_p.L245fs|AURKC_uc002qod.2_Frame_Shift_Del_p.L230fs|AURKC_uc010etv.2_Frame_Shift_Del_p.L261fs NM_001015878 NP_001015878 Q9UQB9 AURKC_HUMAN aurora kinase C isoform 1 264 Protein kinase. cell cycle|cytokinesis condensed chromosome|cytoplasm|midbody|spindle midzone ATP binding|protein serine/threonine kinase activity lung(4)|ovary(2) 6 Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157) UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122) CAATGCCTCTGGGGGCCCGGG 0.532 0.43 8 6 PTPRT 11122 broad.mit.edu 37 20 40790090 40790090 + Frame_Shift_Del DEL G - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr20:40790090delG uc002xkg.2 - 17 2768 c.2584delC c.(2584-2586)CGGfs p.R862fs PTPRT_uc010ggj.2_Frame_Shift_Del_p.R881fs|PTPRT_uc010ggi.2_Frame_Shift_Del_p.R65fs NM_007050 NP_008981 O14522 PTPRT_HUMAN protein tyrosine phosphatase, receptor type, T 862 Cytoplasmic (Potential). homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway cell surface|integral to membrane|plasma membrane alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity skin(8)|ovary(7)|lung(5) 20 Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783) AACTGGTCCCGGGGGTAGCTC 0.612 0.43 84 64 NCOA3 8202 broad.mit.edu 37 20 46264693 46264694 + Frame_Shift_Del DEL CT - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr20:46264693_46264694delCT uc002xtk.2 + 12 1768_1769 c.1563_1564delCT c.(1561-1566)AGCTCTfs p.S521fs NCOA3_uc010ght.1_Frame_Shift_Del_p.S531fs|NCOA3_uc002xtl.2_Frame_Shift_Del_p.S521fs|NCOA3_uc002xtm.2_Frame_Shift_Del_p.S521fs|NCOA3_uc002xtn.2_Frame_Shift_Del_p.S521fs|NCOA3_uc010zyc.1_Frame_Shift_Del_p.S316fs NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 521_522 Ser-rich. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 TTTCCAGCAGCTCTCTCAGTGC 0.455 0.48 87 81 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 113 701 COL18A1 80781 broad.mit.edu 37 21 46925058 46925059 + Frame_Shift_Del DEL GA - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr21:46925058_46925059delGA uc011afs.1 + 35 4136_4137 c.4115_4116delGA c.(4114-4116)GGAfs p.G1372fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.G957fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.G1137fs|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1375 Triple-helical region 9 (COL9). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.43 295 221 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 10 76 MN1 4330 broad.mit.edu 37 22 28193004 28193004 + Frame_Shift_Del DEL C - - LNCAPCLONEFGC_PROSTATE NA LNCAPCLONEFGC_PROSTATE NA g.chr22:28193004delC uc003adj.2 - 1 4483 c.3528delG c.(3526-3528)GGGfs p.G1176fs NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 1176 binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 CACCCTTCAGCCCCAGAGGCT 0.677 0.54 38 44 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 37 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.40 6 4 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 87 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 60 101 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 23 36 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 12 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.36 27 15 HSF1 3297 broad.mit.edu 37 8 145537675 145537675 + Frame_Shift_Del DEL C - - LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145537675delC uc003zbt.3 + 12 1512 c.1342delC c.(1342-1344)CCCfs p.P448fs HSF1_uc003zbu.3_RNA NM_005526 NP_005517 Q00613 HSF1_HUMAN heat shock transcription factor 1 448 Transactivation domain. cytoplasm protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055) 0.000 0.12 53 7 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.88 2 15 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.33 8 4 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 270 67 CDKN1B 1027 broad.mit.edu 37 12 12871060 12871070 + Frame_Shift_Del DEL AAGGTGCCTGC - - LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:12871060_12871070delAAGGTGCCTGC uc001rat.2 + 1 759_769 c.287_297delAAGGTGCCTGC c.(286-297)AAAGGTGCCTGCfs p.K96fs NM_004064 NP_004055 P46527 CDN1B_HUMAN cyclin-dependent kinase inhibitor 1B 96_99 autophagic cell death|cell cycle arrest|cellular response to lithium ion|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of transcription, DNA-dependent|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process|S phase of mitotic cell cycle cytosol|endosome|nucleoplasm cyclin-dependent protein kinase inhibitor activity|protein phosphatase binding|transforming growth factor beta receptor, cytoplasmic mediator activity ovary(1)|lung(1) 2 Prostate(47;0.0322)|all_epithelial(100;0.159) BRCA - Breast invasive adenocarcinoma(232;0.0336) CGGCCCCCCAAAGGTGCCTGCAAGGTGCCGG 0.621 0.85 5 29 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.58 5 7 GLG1 2734 broad.mit.edu 37 16 74640666 74640667 + Frame_Shift_Ins INS - C C LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:74640666_74640667insC uc002fcy.3 - 1 376_377 c.326_327insG c.(325-327)GGCfs p.G109fs GLG1_uc002fcx.2_Frame_Shift_Ins_p.G109fs|GLG1_uc002fcw.3_Frame_Shift_Ins_p.G109fs|GLG1_uc002fcz.3_5'UTR NM_001145667 NP_001139139 Q92896 GSLG1_HUMAN golgi apparatus protein 1 isoform 3 109 Extracellular (Potential). Golgi membrane|integral to membrane receptor binding ovary(1)|breast(1) 2 CCAGCTTCCAGCCCCCACCAGC 0.569 0.38 10 6 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 5 30 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.40 26 17 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.23 49 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 89 527 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 69 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LOXIMVI_SKIN NA LOXIMVI_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.68 12 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LOXIMVI_SKIN NA LOXIMVI_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.39 59 38 TBP 6908 broad.mit.edu 37 6 170871038 170871046 + In_Frame_Del DEL CAACAGCAA - - rs145348820;rs71010672;rs10592950;rs62430309 LOXIMVI_SKIN NA LOXIMVI_SKIN NA g.chr6:170871038_170871046delCAACAGCAA uc003qxt.2 + 3 446_454 c.214_222delCAACAGCAA c.(214-222)CAACAGCAAdel p.QQQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_95 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding p.Q72del(1) ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcagcagcagcaacagcaacagcagcagc 0.177 0.32 21 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 LOXIMVI_SKIN NA LOXIMVI_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.22 66 19 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LOXIMVI_SKIN NA LOXIMVI_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 1 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency LOXIMVI_SKIN NA LOXIMVI_SKIN NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.71 304 730 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 LOXIMVI_SKIN NA LOXIMVI_SKIN NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.35 11 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LOXIMVI_SKIN NA LOXIMVI_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 447 115 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LOXIMVI_SKIN NA LOXIMVI_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 27 308 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 LOXIMVI_SKIN NA LOXIMVI_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.64 20 36 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LOXIMVI_SKIN NA LOXIMVI_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 229 756 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LOXIMVI_SKIN NA LOXIMVI_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 2 23 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 53 TTN 7273 broad.mit.edu 37 2 179542390 179542392 + In_Frame_Del DEL CTT - - LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179542390_179542392delCTT uc010zfg.1 - 143 30739_30741 c.30515_30517delAAG c.(30514-30519)GAAGTC>GTC p.E10172del TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Del_p.E6833del|TTN_uc010fre.1_Intron|TTN_uc002una.1_RNA|TTN_uc010frf.1_RNA NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 11099 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCTGGAAGGACTTCTTCTTCAGG 0.443 0.94 6 88 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.38 15 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 121 183 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.26 101 35 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 24 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 507 244 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 87 1075 RBBP8 5932 broad.mit.edu 37 18 20572852 20572853 + Frame_Shift_Ins INS - A A LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr18:20572852_20572853insA uc002ktw.2 + 11 1393_1394 c.1062_1063insA c.(1060-1065)GGGAAAfs p.G354fs RBBP8_uc002kty.2_Frame_Shift_Ins_p.G354fs|RBBP8_uc002ktz.2_Frame_Shift_Ins_p.G354fs|RBBP8_uc002kua.2_Frame_Shift_Ins_p.G354fs|RBBP8_uc002ktx.1_Frame_Shift_Ins_p.G354fs NM_002894 NP_002885 Q99708 COM1_HUMAN retinoblastoma binding protein 8 isoform a 354_355 cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter nucleus damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity ovary(1)|lung(1)|skin(1) 3 all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19) OV - Ovarian serous cystadenocarcinoma(1;0.00196) TACAGCCTGGGAAAAAAAAACA 0.361 0.36 141 79 PSENEN 55851 broad.mit.edu 37 19 36237741 36237741 + Frame_Shift_Del DEL C - - LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:36237741delC uc002obi.1 + 4 503 c.299delC c.(298-300)ACCfs p.T100fs TMEM149_uc010eej.2_5'Flank|U2AF1L4_uc002obh.1_5'Flank|U2AF1L4_uc002obe.2_5'Flank|U2AF1L4_uc002obf.2_5'Flank|U2AF1L4_uc002obg.2_5'Flank|PSENEN_uc002obj.1_Frame_Shift_Del_p.T100fs|PSENEN_uc002obk.1_Intron|LIN37_uc002obm.2_5'Flank NM_172341 NP_758844 Q9NZ42 PEN2_HUMAN presenilin enhancer 2 100 Lumenal (Potential). amyloid precursor protein catabolic process|apoptosis|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing endoplasmic reticulum membrane|Golgi cisterna membrane|integral to plasma membrane aspartic-type endopeptidase activity|protein binding ovary(2) 2 all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) 0.000 0.24 90 28 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.56 33 42 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 182 472 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 6 109 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 4 158 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 270 80 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.47 16 14 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.13 88 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 103 142 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 29 55 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 16 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 2 100 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 326 38 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.64 8 14 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 12 84 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.20 44 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 91 361 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 79 279 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LS123_LARGE_INTESTINE NA LS123_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 9 79 KDM6A 7403 broad.mit.edu 37 X 44966717 44966718 + Frame_Shift_Ins INS - A A LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chrX:44966717_44966718insA uc004dge.3 + 27 4316_4317 c.3941_3942insA c.(3940-3942)GGAfs p.G1314fs KDM6A_uc011mkz.1_Frame_Shift_Ins_p.G1366fs|KDM6A_uc011mla.1_Frame_Shift_Ins_p.G1269fs|KDM6A_uc011mlb.1_Frame_Shift_Ins_p.G1321fs|KDM6A_uc011mlc.1_Frame_Shift_Ins_p.G1018fs|KDM6A_uc011mld.1_Frame_Shift_Ins_p.G953fs NM_021140 NP_066963 O15550 KDM6A_HUMAN ubiquitously transcribed tetratricopeptide 1314 histone H3-K4 methylation metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2) 84 ATTGCTGCAGGAAAAGAGATTA 0.386 1.00 0 11 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 25 ARID1A 8289 broad.mit.edu 37 1 27097688 27097688 + Frame_Shift_Del DEL A - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr1:27097688delA uc001bmv.1 + 12 3650 c.3277delA c.(3277-3279)AAAfs p.K1093fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.K1093fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.K1093fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.K710fs|ARID1A_uc001bmx.1_5'UTR|ARID1A_uc009vsm.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1093 ARID. androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CAGCTCCTTGAAAAAGCAGTA 0.473 0.45 54 45 TIE1 7075 broad.mit.edu 37 1 43778141 43778141 + Frame_Shift_Del DEL C - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr1:43778141delC uc001ciu.2 + 12 1875 c.1796delC c.(1795-1797)TCCfs p.S599fs TIE1_uc010okd.1_Frame_Shift_Del_p.S599fs|TIE1_uc010oke.1_Frame_Shift_Del_p.S554fs|TIE1_uc009vwq.2_Frame_Shift_Del_p.S555fs|TIE1_uc010okf.1_Frame_Shift_Del_p.S244fs|TIE1_uc010okg.1_Frame_Shift_Del_p.S244fs NM_005424 NP_005415 P35590 TIE1_HUMAN tyrosine kinase with immunoglobulin-like and 599 Fibronectin type-III 2.|Extracellular (Potential). mesoderm development integral to plasma membrane ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity lung(3)|stomach(1)|salivary_gland(1)|ovary(1)|skin(1) 7 Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0505) AACGTCTCATCCCCCCAGGCC 0.706 0.51 17 18 CDC7 8317 broad.mit.edu 37 1 91977242 91977242 + Frame_Shift_Del DEL T - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr1:91977242delT uc001doe.2 + 5 589 c.424delT c.(424-426)TTTfs p.F142fs CDC7_uc001dof.2_Frame_Shift_Del_p.F142fs|CDC7_uc010osw.1_Frame_Shift_Del_p.F114fs|CDC7_uc009wdc.2_Frame_Shift_Del_p.F142fs NM_003503 NP_003494 O00311 CDC7_HUMAN cell division cycle 7 142 Protein kinase. cell cycle checkpoint|cell division|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|positive regulation of cell proliferation|regulation of S phase cytoplasm|nucleoplasm ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity stomach(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 5 all_lung(203;0.0165)|Lung NSC(277;0.0562) all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124) GCATGAGTCGTTTTTGGTAGG 0.303 0.45 141 116 BCL9 607 broad.mit.edu 37 1 147092681 147092681 + Frame_Shift_Del DEL C - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr1:147092681delC uc001epq.2 + 8 3460 c.2720delC c.(2719-2721)TCCfs p.S907fs BCL9_uc010ozr.1_Frame_Shift_Del_p.S833fs NM_004326 NP_004317 O00512 BCL9_HUMAN B-cell CLL/lymphoma 9 907 Pro-rich. Wnt receptor signaling pathway nucleus protein binding ovary(2)|large_intestine(2)|breast(1)|skin(1) 6 all_hematologic(923;0.115) TCCATTAAGTCCCCCCCTGTT 0.622 0.41 42 29 HORMAD1 84072 broad.mit.edu 37 1 150676776 150676776 + Frame_Shift_Del DEL T - - rs45439605 LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr1:150676776delT uc001evk.1 - 11 954 c.848delA c.(847-849)AACfs p.N283fs HORMAD1_uc001evl.1_Frame_Shift_Del_p.N276fs|HORMAD1_uc001evm.1_Frame_Shift_Del_p.N203fs NM_032132 NP_115508 Q86X24 HORM1_HUMAN HORMA domain containing 1 283 blastocyst development|cell differentiation|meiotic DNA double-strand break formation|meiotic recombination checkpoint|meiotic sister chromatid cohesion|mitosis|oogenesis|regulation of homologous chromosome segregation|spermatogenesis|synaptonemal complex assembly chromosome|nucleus ovary(2)|central_nervous_system(1) 3 all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171) UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171) AGATGCAGGGTTTTTTTCCTG 0.289 0.39 67 42 PIP5K1A 8394 broad.mit.edu 37 1 151209155 151209155 + Frame_Shift_Del DEL C - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr1:151209155delC uc001exj.2 + 9 1513 c.1061delC c.(1060-1062)GCCfs p.A354fs PIP5K1A_uc001exi.2_Frame_Shift_Del_p.A341fs|PIP5K1A_uc010pcu.1_Frame_Shift_Del_p.A342fs|PIP5K1A_uc001exk.2_Frame_Shift_Del_p.A341fs|PIP5K1A_uc010pcv.1_Frame_Shift_Del_p.A111fs NM_001135638 NP_001129110 Q99755 PI51A_HUMAN phosphatidylinositol-4-phosphate 5-kinase, type 354 PIPK. phospholipid biosynthetic process|signal transduction endomembrane system|Golgi stack|lamellipodium|nuclear speck 1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|kinase binding ovary(1)|central_nervous_system(1)|skin(1) 3 Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.181) CGAAGACCGGCCCCCCAAAAG 0.507 0.42 33 24 AAK1 22848 broad.mit.edu 37 2 69706110 69706111 + Frame_Shift_Ins INS - G G LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr2:69706110_69706111insG uc002sfp.2 - 20 3157_3158 c.2652_2653insC c.(2650-2655)CCCACAfs p.P884fs NM_014911 NP_055726 Q2M2I8 AAK1_HUMAN AP2 associated kinase 1 884_885 coated pit|mitochondrion|plasma membrane ATP binding|protein serine/threonine kinase activity 0 GAGATTGCTGTGGGGGCAAACT 0.455 0.31 51 23 LRP2 4036 broad.mit.edu 37 2 169997025 169997025 + Frame_Shift_Del DEL G - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr2:169997025delG uc002ues.2 - 72 13352 c.13139delC c.(13138-13140)CCAfs p.P4380fs NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 4380 EGF-like 17.|Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) 0.000 0.57 124 164 TTN 7273 broad.mit.edu 37 2 179598102 179598102 + Frame_Shift_Del DEL T - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr2:179598102delT uc010zfg.1 - 51 12410 c.12186delA c.(12184-12186)AAAfs p.K4062fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.K723fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 4989 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTATTCGGTATTTTTTACTGG 0.468 0.45 153 125 IRS1 3667 broad.mit.edu 37 2 227661341 227661341 + Frame_Shift_Del DEL C - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr2:227661341delC uc002voh.3 - 1 2166 c.2114delG c.(2113-2115)GGCfs p.G705fs NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 705 fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) AGAGTGGTGGCCCCCTACCCC 0.517 0.39 118 77 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.36 7 4 EPHB3 2049 broad.mit.edu 37 3 184280039 184280041 + In_Frame_Del DEL CCG - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr3:184280039_184280041delCCG uc003foz.2 + 1 453_455 c.16_18delCCG c.(16-18)CCGdel p.P10del NM_004443 NP_004434 P54753 EPHB3_HUMAN ephrin receptor EphB3 precursor 10 integral to plasma membrane ATP binding|ephrin receptor activity lung(5)|breast(2)|upper_aerodigestive_tract(1)|stomach(1)|skin(1)|ovary(1) 11 all_cancers(143;1.89e-10)|Ovarian(172;0.0339) Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22) 0.000 0.27 205 75 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.18 56 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 59 68 NKD2 85409 broad.mit.edu 37 5 1038292 1038292 + Frame_Shift_Del DEL A - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr5:1038292delA uc003jbt.1 + 10 1165 c.1160delA c.(1159-1161)CAAfs p.Q387fs NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 387 exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.53 255 286 CLPTM1L 81037 broad.mit.edu 37 5 1325892 1325892 + Frame_Shift_Del DEL A - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr5:1325892delA uc003jch.2 - 10 1166 c.1120delT c.(1120-1122)TGGfs p.W374fs CLPTM1L_uc003jcg.2_Frame_Shift_Del_p.W205fs NM_030782 NP_110409 Q96KA5 CLP1L_HUMAN CLPTM1-like 374 Cytoplasmic (Potential). apoptosis integral to membrane breast(1)|central_nervous_system(1) 2 Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09) Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181) KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208) AGGCCTCTCCAAAAAATAGTC 0.448 0.42 30 22 RASA1 5921 broad.mit.edu 37 5 86658452 86658452 + Frame_Shift_Del DEL A - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr5:86658452delA uc003kiw.2 + 10 1535 c.1417delA c.(1417-1419)AAAfs p.K473fs RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_Frame_Shift_Del_p.K296fs|RASA1_uc011ctv.1_Frame_Shift_Del_p.K306fs|RASA1_uc011ctw.1_Frame_Shift_Del_p.K307fs|RASA1_uc010jaw.2_Frame_Shift_Del_p.K295fs NM_002890 NP_002881 P20936 RASA1_HUMAN RAS p21 protein activator 1 isoform 1 473 cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis cytosol|intrinsic to internal side of plasma membrane glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding upper_aerodigestive_tract(3)|ovary(1)|lung(1) 5 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) 0.000 0.52 32 34 CHD1 1105 broad.mit.edu 37 5 98236745 98236745 + Frame_Shift_Del DEL T - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr5:98236745delT uc003knf.2 - 6 777 c.629delA c.(628-630)AAGfs p.K210fs NM_001270 NP_001261 O14646 CHD1_HUMAN chromodomain helicase DNA binding protein 1 210 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117) COAD - Colon adenocarcinoma(37;0.0717) Epirubicin(DB00445) AATCTGTCTCTTTTTTTGTCC 0.313 0.40 88 58 FER 2241 broad.mit.edu 37 5 108290522 108290522 + Frame_Shift_Del DEL A - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr5:108290522delA uc003kop.1 + 12 1806 c.1422delA c.(1420-1422)TTAfs p.L474fs FER_uc011cvf.1_RNA|FER_uc011cvg.1_Frame_Shift_Del_p.L299fs NM_005246 NP_005237 P16591 FER_HUMAN fer (fps/fes related) tyrosine kinase 474 SH2. intracellular signal transduction|peptidyl-tyrosine phosphorylation cytoplasm|nucleus ATP binding|non-membrane spanning protein tyrosine kinase activity lung(2)|stomach(1)|ovary(1)|kidney(1) 5 all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152) OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174) AAGAACTGTTAAAAAAACAAG 0.408 0.55 33 40 RAD50 10111 broad.mit.edu 37 5 131931451 131931452 + Frame_Shift_Ins INS - A A LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr5:131931451_131931452insA uc003kxi.2 + 13 2543_2544 c.2156_2157insA c.(2155-2157)CTAfs p.L719fs RAD50_uc003kxh.2_Frame_Shift_Ins_p.L580fs NM_005732 NP_005723 Q92878 RAD50_HUMAN RAD50 homolog isoform 1 719 Zinc-hook.|Potential. DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding lung(2)|ovary(1)|skin(1) 4 all_cancers(142;0.0368)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GAATCAGAGCTAAAAAAAAAGG 0.416 0.33 16 8 PTK7 5754 broad.mit.edu 37 6 43106964 43106965 + Frame_Shift_Ins INS - C C LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr6:43106964_43106965insC uc003oub.1 + 9 1651_1652 c.1453_1454insC c.(1453-1455)ACCfs p.T485fs PTK7_uc003ouc.1_Frame_Shift_Ins_p.T485fs|PTK7_uc003oud.1_Frame_Shift_Ins_p.T485fs|PTK7_uc003oue.1_Intron|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Frame_Shift_Ins_p.T493fs|PTK7_uc010jyj.1_Intron NM_002821 NP_002812 Q13308 PTK7_HUMAN PTK7 protein tyrosine kinase 7 isoform a 485 Ig-like C2-type 5.|Extracellular (Potential). actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration cell-cell junction|integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ovary(2)|large_intestine(1) 3 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423) TATGAGCAGCACCCCAGCCGGC 0.599 0.47 9 8 MLLT4 4301 broad.mit.edu 37 6 168272982 168272982 + Frame_Shift_Del DEL A - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr6:168272982delA uc003qwd.2 + 4 642 c.500delA c.(499-501)GAAfs p.E167fs MLLT4_uc003qwb.1_Frame_Shift_Del_p.E167fs|MLLT4_uc003qwc.1_Frame_Shift_Del_p.E168fs NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 168 Glu/Lys-rich.|Potential. adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) gaaaagaaggaaaaaaagaag 0.343 0.40 6 4 TRIM24 8805 broad.mit.edu 37 7 138262329 138262329 + Frame_Shift_Del DEL A - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr7:138262329delA uc003vuc.2 + 14 2467 c.2252delA c.(2251-2253)CAAfs p.Q751fs TRIM24_uc003vub.2_Frame_Shift_Del_p.Q717fs NM_015905 NP_056989 O15164 TIF1A_HUMAN transcriptional intermediary factor 1 alpha 751 cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter cytoplasm chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1) 8 TCTAGGCCTCAAAATGTAATT 0.348 0.69 5 11 KIAA1549 57670 broad.mit.edu 37 7 138536987 138536987 + Frame_Shift_Del DEL G - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr7:138536987delG uc011kql.1 - 17 5325 c.5276delC c.(5275-5277)CCGfs p.P1759fs KIAA1549_uc011kqi.1_Frame_Shift_Del_p.P543fs|KIAA1549_uc003vuk.3_Frame_Shift_Del_p.P1709fs|KIAA1549_uc011kqj.1_Frame_Shift_Del_p.P1759fs|KIAA1549_uc011kqk.1_Frame_Shift_Del_p.P543fs NM_020910 NP_065961 Q9HCM3 K1549_HUMAN hypothetical protein LOC57670 isoform 1 1759 integral to membrane KIAA1549/BRAF(229) central_nervous_system(229)|pancreas(1) 230 TGGACCCGTCGGGGGAGTCAT 0.323 0.46 34 29 KCNH2 3757 broad.mit.edu 37 7 150656679 150656679 + Frame_Shift_Del DEL G - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr7:150656679delG uc003wic.2 - 3 466 c.453delC c.(451-453)CCCfs p.P151fs KCNH2_uc011kux.1_Frame_Shift_Del_p.P55fs|KCNH2_uc003wie.2_Frame_Shift_Del_p.P151fs NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 151 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) GCCAGCTGGTGGGGGGGCCCC 0.587 0.44 58 45 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.88 2 14 EXT1 2131 broad.mit.edu 37 8 118831974 118831975 + Frame_Shift_Del DEL GA - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr8:118831974_118831975delGA uc003yok.1 - 6 2249_2250 c.1476_1477delTC c.(1474-1479)TCTCAGfs p.S492fs NM_000127 NP_000118 Q16394 EXT1_HUMAN exostosin 1 492_493 Lumenal (Potential). glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development Golgi membrane|integral to endoplasmic reticulum membrane glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity ovary(2)|lung(2) 4 all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173) STAD - Stomach adenocarcinoma(47;0.012) GGCTGGGACTGAGAGACCAGGG 0.554 0.25 40 13 TNFRSF11B 4982 broad.mit.edu 37 8 119936895 119936896 + Frame_Shift_Ins INS - C C LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr8:119936895_119936896insC uc003yon.3 - 5 1246_1247 c.923_924insG c.(922-924)GGAfs p.G308fs NM_002546 NP_002537 O00300 TR11B_HUMAN osteoprotegerin precursor 308 Death 2. apoptosis|skeletal system development cytokine activity|receptor activity central_nervous_system(2) 2 all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234) STAD - Stomach adenocarcinoma(47;0.00193) TGTCTTCTGCTCCCACTTTCTT 0.480 0.43 181 136 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 2 22 WNK2 65268 broad.mit.edu 37 9 96051830 96051831 + Frame_Shift_Ins INS - G G LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr9:96051830_96051831insG uc004ati.1 + 20 4905_4906 c.4905_4906insG c.(4903-4908)TGCGGGfs p.C1635fs WNK2_uc011lud.1_Frame_Shift_Ins_p.C1598fs|WNK2_uc004atj.2_Frame_Shift_Ins_p.C1598fs|WNK2_uc004atk.2_Frame_Shift_Ins_p.C1235fs|WNK2_uc004atl.1_Frame_Shift_Ins_p.C193fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 1635_1636 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 CAGAGGTCTGCGGGGGGGACCT 0.683 0.33 16 8 FOXE1 2304 broad.mit.edu 37 9 100616763 100616763 + Frame_Shift_Del DEL C - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr9:100616763delC uc004axu.2 + 1 1227 c.567delC c.(565-567)CGCfs p.R189fs NM_004473 NP_004464 O00358 FOXE1_HUMAN forkhead box E1 189 Pro-rich.|Ala-rich. cell migration|embryonic organ morphogenesis|hair follicle morphogenesis|hard palate development|lens morphogenesis in camera-type eye|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|peripheral nervous system development|pharynx development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|soft palate development|thymus development|thyroid gland development|thyroid hormone generation transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding 0 Acute lymphoblastic leukemia(62;0.158) 0.000 0.73 15 40 ABL1 25 broad.mit.edu 37 9 133760264 133760264 + Frame_Shift_Del DEL G - - rs67129258 LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr9:133760264delG uc004bzw.2 + 11 2590 c.2587delG c.(2587-2589)GGGfs p.G863fs ABL1_uc004bzv.2_Frame_Shift_Del_p.G882fs NM_005157 NP_005148 P00519 ABL1_HUMAN c-abl oncogene 1, receptor tyrosine kinase 863 Pro-rich. G -> R (in Ref. 1; AAA51561). actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1) 817 all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204) OV - Ovarian serous cystadenocarcinoma(145;5.4e-05) Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619) 0.000 0.42 359 262 ADK 132 broad.mit.edu 37 10 76429988 76429990 + In_Frame_Del DEL ATT - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr10:76429988_76429990delATT uc001jwi.2 + 10 997_999 c.925_927delATT c.(925-927)ATTdel p.I310del ADK_uc010qlb.1_In_Frame_Del_p.I253del|ADK_uc001jwj.2_In_Frame_Del_p.I293del|ADK_uc010qlc.1_In_Frame_Del_p.I275del|ADK_uc001jwl.2_In_Frame_Del_p.I80del NM_006721 NP_006712 P55263 ADK_HUMAN adenosine kinase isoform b 310 purine base metabolic process|purine ribonucleoside salvage cytosol adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor ovary(1)|skin(1) 2 Prostate(51;0.0112)|Ovarian(15;0.148) Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811) CCAGAAAGAAATTATTGATACCA 0.355 0.49 73 69 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.42 53 39 MRE11A 4361 broad.mit.edu 37 11 94192633 94192633 + Frame_Shift_Del DEL T - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr11:94192633delT uc001peu.2 - 13 1630 c.1441delA c.(1441-1443)ACAfs p.T481fs MRE11A_uc001pev.2_Frame_Shift_Del_p.T481fs|MRE11A_uc009ywj.2_Frame_Shift_Del_p.T484fs NM_005591 NP_005582 P49959 MRE11_HUMAN meiotic recombination 11 homolog A isoform 1 481 DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase Mre11 complex|nucleoplasm 3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity breast(4)|lung(1) 5 Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824) AATCGCTGTGTTTTTTCCAAC 0.388 0.46 113 95 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 307 70 DDX10 1662 broad.mit.edu 37 11 108562720 108562720 + Frame_Shift_Del DEL A - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr11:108562720delA uc001pkm.2 + 8 1158 c.1093delA c.(1093-1095)AGAfs p.R365fs DDX10_uc001pkl.1_Frame_Shift_Del_p.R365fs NM_004398 NP_004389 Q13206 DDX10_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 10 365 Helicase C-terminal. ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity breast(2)|lung(1)|prostate(1) 4 all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729) BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133) TGTCCGTAAGAGAGCTGCAGT 0.428 0.52 28 30 GRIN2B 2904 broad.mit.edu 37 12 13769540 13769540 + Frame_Shift_Del DEL G - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr12:13769540delG uc001rbt.2 - 5 1356 c.1177delC c.(1177-1179)CGAfs p.R393fs NM_000834 NP_000825 Q13224 NMDE2_HUMAN N-methyl-D-aspartate receptor subunit 2B 393 Extracellular (Potential). response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding central_nervous_system(4)|ovary(3)|skin(3)|lung(2) 12 Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043) GGACACATTCGGGGCCACACA 0.507 0.35 134 71 ACACB 32 broad.mit.edu 37 12 109661678 109661681 + Frame_Shift_Del DEL CAAA - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr12:109661678_109661681delCAAA uc001tob.2 + 27 3970_3973 c.3851_3854delCAAA c.(3850-3855)GCAAACfs p.A1284fs ACACB_uc001toc.2_Frame_Shift_Del_p.A1284fs NM_001093 NP_001084 O00763 ACACB_HUMAN acetyl-Coenzyme A carboxylase beta 1284_1285 acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation cytosol|endomembrane system|Golgi apparatus|membrane acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1) 8 Biotin(DB00121) TTCTATCACGCAAACAAAGTCGTG 0.368 0.47 57 51 FOS 2353 broad.mit.edu 37 14 75746736 75746737 + Frame_Shift_Ins INS - C C rs66753615 LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr14:75746736_75746737insC uc001xrn.2 + 2 503_504 c.298_299insC c.(298-300)GCCfs p.A100fs FOS_uc010tva.1_Frame_Shift_Ins_p.A100fs|FOS_uc010asi.2_5'UTR|FOS_uc001xro.2_5'Flank NM_005252 NP_005243 P01100 FOS_HUMAN v-fos FBJ murine osteosarcoma viral oncogene 100 cellular response to reactive oxygen species|DNA methylation|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|SMAD protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter|transforming growth factor beta receptor signaling pathway protein dimerization activity|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding lung(2)|ovary(1) 3 all_lung(585;0.0138)|all_epithelial(191;0.0263)|all_neural(303;0.112) BRCA - Breast invasive adenocarcinoma(234;0.0117) CGGAGTCCCCGCCCCCTCCGCT 0.673 0.40 98 65 TRIP11 9321 broad.mit.edu 37 14 92454634 92454634 + Frame_Shift_Del DEL T - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr14:92454634delT uc001xzy.2 - 16 6042 c.5254delA c.(5254-5256)AGAfs p.R1752fs TRIP11_uc010auf.1_Frame_Shift_Del_p.R1488fs NM_004239 NP_004230 Q15643 TRIPB_HUMAN thyroid hormone receptor interactor 11 1752 Potential. transcription from RNA polymerase II promoter cytoskeleton|Golgi apparatus|membrane|nucleus protein binding|transcription coactivator activity ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1) 13 COAD - Colon adenocarcinoma(157;0.223) CTACTTTGTCTTTTAAGTTCT 0.333 0.42 37 27 SGK269 79834 broad.mit.edu 37 15 77471473 77471475 + In_Frame_Del DEL GAA - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr15:77471473_77471475delGAA uc002bcm.2 - 3 3102_3104 c.2794_2796delTTC c.(2794-2796)TTCdel p.F932del SGK269_uc002bcn.2_In_Frame_Del_p.F932del NM_024776 NP_079052 Q9H792 PEAK1_HUMAN NKF3 kinase family member 932 cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading actin cytoskeleton|cytoplasm|focal adhesion ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding 0 STAD - Stomach adenocarcinoma(199;0.124) TCCGACGGCGGAAGAAGCTTTTA 0.512 0.40 85 56 TAOK2 9344 broad.mit.edu 37 16 29998225 29998226 + Frame_Shift_Del DEL GA - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr16:29998225_29998226delGA uc002dva.1 + 16 3415_3416 c.2632_2633delGA c.(2632-2634)GAGfs p.E878fs uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TAOK2_uc002dvb.1_Intron|TAOK2_uc002dvc.1_Intron|TAOK2_uc010bzm.1_Frame_Shift_Del_p.E885fs|TAOK2_uc002dvd.1_Frame_Shift_Del_p.E705fs NM_016151 NP_057235 Q9UL54 TAOK2_HUMAN TAO kinase 2 isoform 2 878 Glu-rich. actin cytoskeleton organization|activation of MAPKK activity|apoptosis|cell migration|focal adhesion assembly|positive regulation of JNK cascade|protein targeting to membrane|regulation of cell growth|regulation of cell shape|response to stress cytoplasmic vesicle membrane|cytoskeleton|dendrite|integral to membrane|nucleolus ATP binding|protein serine/threonine kinase activity ovary(1) 1 GAAGGAGGATGAGAGTCTTCTG 0.599 0.50 5 5 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 76 616 NLRP1 22861 broad.mit.edu 37 17 5463340 5463341 + Frame_Shift_Del DEL TC - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr17:5463340_5463341delTC uc002gci.2 - 4 1230_1231 c.675_676delGA c.(673-678)GAGAAAfs p.E225fs NLRP1_uc002gcg.1_Frame_Shift_Del_p.E225fs|NLRP1_uc002gck.2_Frame_Shift_Del_p.E225fs|NLRP1_uc002gcj.2_Frame_Shift_Del_p.E225fs|NLRP1_uc002gcl.2_Frame_Shift_Del_p.E225fs|NLRP1_uc002gch.3_Frame_Shift_Del_p.E225fs|NLRP1_uc010clh.2_Frame_Shift_Del_p.E225fs NM_033004 NP_127497 Q9C000 NALP1_HUMAN NLR family, pyrin domain containing 1 isoform 1 225_226 defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide cytoplasm|NALP1 inflammasome complex|nucleus ATP binding|caspase activator activity|enzyme binding|protein domain specific binding lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1) 9 Colorectal(1115;3.48e-05) TTCTCTGATTTCTCTCTCTCTC 0.480 0.10 95 10 MYH1 4619 broad.mit.edu 37 17 10406224 10406224 + Frame_Shift_Del DEL T - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr17:10406224delT uc002gmo.2 - 24 3036 c.2942delA c.(2941-2943)AACfs p.N981fs uc002gml.1_Intron NM_005963 NP_005954 P12882 MYH1_HUMAN myosin, heavy chain 1, skeletal muscle, adult 981 Potential. muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1) 21 TTCTGTGAGGTTTTTCACCTA 0.483 0.42 158 114 KSR1 8844 broad.mit.edu 37 17 25910015 25910016 + Frame_Shift_Ins INS - CC CC LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr17:25910015_25910016insCC uc010crg.2 + 5 898_899 c.453_454insCC c.(451-456)ACGCCCfs p.T151fs KSR1_uc002gzj.1_RNA NM_014238 NP_055053 Q8IVT5 KSR1_HUMAN kinase suppressor of ras 286_287 Poly-Pro. Ras protein signal transduction cytoplasm|membrane ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity lung(3)|central_nervous_system(1) 4 Lung NSC(42;0.00836) BRCA - Breast invasive adenocarcinoma(3;0.00122) UCEC - Uterine corpus endometrioid carcinoma (53;0.168) CACCACGGACGCCCCCCCCACC 0.678 0.27 43 16 STAT5A 6776 broad.mit.edu 37 17 40453399 40453399 + Frame_Shift_Del DEL C - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr17:40453399delC uc002hzj.1 + 10 1738 c.1096delC c.(1096-1098)CCCfs p.P366fs STAT5A_uc010cya.1_Frame_Shift_Del_p.P366fs|STAT5A_uc010cyb.1_Frame_Shift_Del_p.P366fs|STAT5A_uc010cyc.1_Frame_Shift_Del_p.P336fs NM_003152 NP_003143 P42229 STA5A_HUMAN signal transducer and activator of transcription 366 2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|oxaloacetate metabolic process|succinate metabolic process|taurine metabolic process|valine metabolic process cytosol|nucleoplasm calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity lung(1) 1 all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.128) GCACATGAATCCCCCCCAGGT 0.567 0.41 86 60 RPTOR 57521 broad.mit.edu 37 17 78854262 78854262 + Frame_Shift_Del DEL G - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr17:78854262delG uc002jyt.1 + 14 2362 c.1557delG c.(1555-1557)CTGfs p.L519fs RPTOR_uc010wug.1_Intron NM_020761 NP_065812 Q8N122 RPTOR_HUMAN raptor isoform 1 519 cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade cytosol|lysosome|TORC1 complex protein complex binding lung(4)|urinary_tract(1)|ovary(1) 6 AGTACTTCCTGTCGGTCCTGG 0.632 0.40 206 138 TCF3 6929 broad.mit.edu 37 19 1615487 1615487 + Frame_Shift_Del DEL G - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr19:1615487delG uc002ltr.2 - 18 1686 c.1619delC c.(1618-1620)CCAfs p.P540fs TCF3_uc002ltn.2_Intron|TCF3_uc002lto.2_Frame_Shift_Del_p.P301fs|TCF3_uc002ltt.3_Intron|TCF3_uc002ltq.2_Frame_Shift_Del_p.P544fs|TCF3_uc002lts.1_Intron NM_003200 NP_003191 P15923 TFE2_HUMAN transcription factor 3 isoform E12 540 B cell lineage commitment|B cell lineage commitment|G1 phase of mitotic cell cycle|immunoglobulin V(D)J recombination|muscle cell differentiation|positive regulation of B cell proliferation|positive regulation of cell cycle|positive regulation of muscle cell differentiation|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter cytoplasm|nucleus|protein complex|transcription factor complex bHLH transcription factor binding|DNA binding|E-box binding|identical protein binding|mitogen-activated protein kinase kinase kinase binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|vitamin D response element binding lung(2)|breast(2)|ovary(1)|large_intestine(1)|skin(1) 7 Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) CTTCTGCTCTGGGGGGAGAAG 0.697 0.38 10 6 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.69 12 27 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 184 425 TSSK2 23617 broad.mit.edu 37 22 19119732 19119732 + Frame_Shift_Del DEL C - - LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr22:19119732delC uc002zow.2 + 1 1412 c.820delC c.(820-822)CCCfs p.P274fs DGCR14_uc002zot.2_3'UTR|DGCR14_uc002zou.2_3'UTR|DGCR14_uc002zov.2_RNA NM_053006 NP_443732 Q96PF2 TSSK2_HUMAN testis-specific serine kinase 2 274 cell differentiation|multicellular organismal development|spermatogenesis cytoplasm ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity stomach(1) 1 Colorectal(54;0.0993) GTGGCTGCAGCCCCCCAAGCC 0.627 0.48 53 49 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LS180_LARGE_INTESTINE NA LS180_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 59 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.59 28 40 SRPK3 26576 broad.mit.edu 37 X 153049488 153049488 + Frame_Shift_Del DEL G - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chrX:153049488delG uc004fil.2 + 10 999 c.967delG c.(967-969)GGGfs p.G323fs SRPK3_uc004fik.2_Frame_Shift_Del_p.G389fs|SRPK3_uc010nul.2_Intron|SRPK3_uc004fin.2_Frame_Shift_Del_p.G322fs|SRPK3_uc004fim.2_Intron NM_014370 NP_055185 Q9UPE1 SRPK3_HUMAN serine arginine rich protein-specific kinase 3 323 Protein kinase. cell differentiation|muscle organ development|muscle tissue development ATP binding|protein serine/threonine kinase activity pancreas(2)|lung(1) 3 all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05) 0.000 0.18 843 190 EPHA2 1969 broad.mit.edu 37 1 16474977 16474977 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr1:16474977delC uc001aya.1 - 3 856 c.719delG c.(718-720)GGTfs p.G240fs EPHA2_uc010oca.1_Frame_Shift_Del_p.G240fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 240 Extracellular (Potential).|Cys-rich. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) GGGCTCTTCACCCCCCGGTGG 0.667 0.25 24 8 ARID1A 8289 broad.mit.edu 37 1 27100176 27100176 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr1:27100176delC uc001bmv.1 + 16 4345 c.3972delC c.(3970-3972)TACfs p.Y1324fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.Y1323fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.Y1324fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.Y941fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.Y170fs|ARID1A_uc009vsm.1_5'UTR|ARID1A_uc009vsn.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1324 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.Y1324fs*1(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CTAGCCGCTACCCCCCgcagc 0.517 0.49 32 31 TSSK3 81629 broad.mit.edu 37 1 32829677 32829677 + Frame_Shift_Del DEL T - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr1:32829677delT uc001bvf.2 + 2 1068 c.627delT c.(625-627)CCTfs p.P209fs uc001bve.1_5'Flank NM_052841 NP_443073 Q96PN8 TSSK3_HUMAN testis-specific serine kinase 3 209 Protein kinase. cell differentiation|multicellular organismal development|spermatogenesis ATP binding|magnesium ion binding|protein serine/threonine kinase activity stomach(1) 1 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.17)|Breast(348;0.212) CCAGCCTACCTTTTGACGACA 0.577 0.37 85 50 ZFYVE9 9372 broad.mit.edu 37 1 52729482 52729483 + Frame_Shift_Del DEL TG - - rs142799022 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr1:52729482_52729483delTG uc001cto.2 + 5 2388_2389 c.2216_2217delTG c.(2215-2217)CTGfs p.L739fs ZFYVE9_uc001ctn.2_Frame_Shift_Del_p.L739fs|ZFYVE9_uc001ctp.2_Frame_Shift_Del_p.L739fs NM_004799 NP_004790 O95405 ZFYV9_HUMAN zinc finger, FYVE domain containing 9 isoform 3 739 FYVE-type. endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway early endosome membrane metal ion binding|protein binding|receptor activity|serine-type peptidase activity ovary(2)|lung(2)|central_nervous_system(2)|skin(2) 8 AAATGTAAACTGTTATACATGG 0.426 0.28 125 48 NFIA 4774 broad.mit.edu 37 1 61553917 61553917 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr1:61553917delA uc001czw.2 + 2 608 c.124delA c.(124-126)AAAfs p.K42fs NFIA_uc001czy.2_Frame_Shift_Del_p.K34fs|NFIA_uc010oos.1_Frame_Shift_Del_p.K87fs|NFIA_uc001czv.2_Frame_Shift_Del_p.K42fs NM_001134673 NP_001128145 Q12857 NFIA_HUMAN nuclear factor I/A isoform 1 42 CTF/NF-I. DNA replication|viral genome replication cell junction|nucleus DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding pancreas(1)|skin(1) 2 AAAATACTTCAAAAAACATGA 0.453 0.11 103 13 WLS 79971 broad.mit.edu 37 1 68697982 68697982 + Frame_Shift_Del DEL T - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr1:68697982delT uc001def.1 - 1 272 c.1delA c.(1-3)ATGfs p.M1fs WLS_uc001dee.2_Frame_Shift_Del_p.M1fs|WLS_uc001deg.1_Frame_Shift_Del_p.M1fs|WLS_uc001deh.1_Frame_Shift_Del_p.M1fs NM_024911 NP_079187 Q5T9L3 WLS_HUMAN G protein-coupled receptor 177 isoform 1 1 multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Wnt receptor signaling pathway cytoplasmic vesicle membrane|Golgi membrane|integral to membrane signal transducer activity 0 GCCCCAGCCATTTTTGCGCCC 0.483 0.25 131 44 HIPK1 204851 broad.mit.edu 37 1 114514512 114514512 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr1:114514512delC uc001eem.2 + 15 3241 c.3080delC c.(3079-3081)ACCfs p.T1027fs HIPK1_uc001eel.2_Frame_Shift_Del_p.T1027fs|HIPK1_uc001een.2_Frame_Shift_Del_p.T1027fs|HIPK1_uc001eeo.2_Frame_Shift_Del_p.T653fs|HIPK1_uc001eep.2_Frame_Shift_Del_p.T633fs|HIPK1_uc001eeq.2_Frame_Shift_Del_p.T319fs NM_198268 NP_938009 Q86Z02 HIPK1_HUMAN homeodomain-interacting protein kinase 1 isoform 1027 Interaction with TP53. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus ATP binding|protein binding|protein serine/threonine kinase activity ovary(4) 4 Lung SC(450;0.184) all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05) Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133) TGCTGTATCACCCCCACAGGG 0.522 0.28 113 43 THBS3 7059 broad.mit.edu 37 1 155165845 155165845 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr1:155165845delC uc001fix.2 - 22 2768 c.2745delG c.(2743-2745)GGGfs p.G915fs RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Frame_Shift_Del_p.G906fs|THBS3_uc001fiz.2_Frame_Shift_Del_p.G878fs|THBS3_uc001fiy.2_Frame_Shift_Del_p.G444fs|THBS3_uc010pfu.1_Frame_Shift_Del_p.G795fs NM_007112 NP_009043 P49746 TSP3_HUMAN thrombospondin 3 precursor 915 TSP C-terminal. cell-matrix adhesion extracellular region|perinuclear region of cytoplasm calcium ion binding|heparin binding|structural molecule activity breast(3)|ovary(2) 5 all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) CACCAAGACGCCCCCCTCGCA 0.498 0.32 253 120 ALK 238 broad.mit.edu 37 2 29451843 29451843 + Frame_Shift_Del DEL G - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr2:29451843delG uc002rmy.2 - 16 3629 c.2722delC c.(2722-2724)CAGfs p.Q908fs NM_004304 NP_004295 Q9UM73 ALK_HUMAN anaplastic lymphoma kinase precursor 908 Gly-rich.|Extracellular (Potential). protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2) haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1) 1218 Acute lymphoblastic leukemia(172;0.155) Adenosine triphosphate(DB00171) TTCATGGCCTGGGGGCAGGAA 0.597 0.28 23 9 BIRC6 57448 broad.mit.edu 37 2 32820101 32820101 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr2:32820101delA uc010ezu.2 + 68 13636 c.13502delA c.(13501-13503)GAAfs p.E4501fs NM_016252 NP_057336 Q9NR09 BIRC6_HUMAN baculoviral IAP repeat-containing 6 4501 anti-apoptosis|apoptosis intracellular acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1) 14 Acute lymphoblastic leukemia(172;0.155) taaataaCAGAAAAAAAACTG 0.244 0.60 24 36 BCL11A 53335 broad.mit.edu 37 2 60688969 60688969 + Frame_Shift_Del DEL G - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr2:60688969delG uc002sae.1 - 4 1306 c.1078delC c.(1078-1080)CTCfs p.L360fs BCL11A_uc002sab.2_Frame_Shift_Del_p.L360fs|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Frame_Shift_Del_p.L326fs|BCL11A_uc002sad.1_Frame_Shift_Del_p.L208fs|BCL11A_uc002saf.1_Frame_Shift_Del_p.L326fs NM_022893 NP_075044 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A isoform 1 360 Pro-rich. negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|cytoplasm|nucleus|nucleus nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding central_nervous_system(6)|breast(3)|ovary(2)|skin(2) 13 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) 0.000 0.34 444 225 LRP1B 53353 broad.mit.edu 37 2 141032034 141032034 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr2:141032034delC uc002tvj.1 - 85 14073 c.13101delG c.(13099-13101)GGGfs p.G4367fs NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 4367 Extracellular (Potential). protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) TAATGCAGTGCCCCCCATGGC 0.418 0.33 154 75 RIF1 55183 broad.mit.edu 37 2 152320159 152320160 + Frame_Shift_Ins INS - A A LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr2:152320159_152320160insA uc002txm.2 + 30 4255_4256 c.4125_4126insA c.(4123-4128)GAGAAAfs p.E1375fs RIF1_uc002txl.2_Frame_Shift_Ins_p.E1375fs|RIF1_uc002txn.2_Frame_Shift_Ins_p.E1375fs|RIF1_uc002txo.2_Frame_Shift_Ins_p.E1375fs|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1375_1376 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) CTGTAGAGGAGAAAAATGTAGA 0.356 0.32 130 61 TLK1 9874 broad.mit.edu 37 2 171854244 171854246 + In_Frame_Del DEL AAG - - rs1128335 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr2:171854244_171854246delAAG uc002ugn.2 - 19 2464_2466 c.1992_1994delCTT c.(1990-1995)TTCTTT>TTT p.664_665FF>F TLK1_uc002ugo.2_In_Frame_Del_p.685_686FF>F|TLK1_uc002ugp.2_In_Frame_Del_p.616_617FF>F|TLK1_uc002ugq.2_RNA|TLK1_uc010zdn.1_In_Frame_Del_p.568_569FF>F NM_012290 NP_036422 Q9UKI8 TLK1_HUMAN tousled-like kinase 1 isoform 1 664_665 Protein kinase. F -> Y (in Ref. 1; BAA20562). cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus nucleus ATP binding|protein binding|protein serine/threonine kinase activity central_nervous_system(1) 1 AAGACACTGAAAGAAGATGACTC 0.355 0.24 79 25 CASP8 841 broad.mit.edu 37 2 202137379 202137380 + Frame_Shift_Del DEL AT - - rs142688117 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr2:202137379_202137380delAT uc002uxr.1 + 5 639_640 c.430_431delAT c.(430-432)ATAfs p.I144fs CASP8_uc010ftc.1_Frame_Shift_Del_p.I144fs|CASP8_uc002uxo.1_Frame_Shift_Del_p.I144fs|CASP8_uc002uxp.1_Frame_Shift_Del_p.I176fs|CASP8_uc002uxq.1_Frame_Shift_Del_p.I144fs|CASP8_uc002uxs.1_Frame_Shift_Del_p.I144fs|CASP8_uc002uxt.1_Frame_Shift_Del_p.I203fs|CASP8_uc002uxu.1_RNA|CASP8_uc010ftd.1_Frame_Shift_Del_p.I41fs|CASP8_uc002uxv.1_Frame_Shift_Del_p.I144fs|CASP8_uc002uxw.1_Frame_Shift_Del_p.I144fs|CASP8_uc002uxy.1_Frame_Shift_Del_p.I144fs|CASP8_uc002uxx.1_Frame_Shift_Del_p.I144fs|CASP8_uc010ftf.2_Frame_Shift_Del_p.I144fs|CASP8_uc010fte.1_Frame_Shift_Del_p.I41fs NM_033355 NP_203519 Q14790 CASP8_HUMAN caspase 8 isoform B precursor 144 DED 2. activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor centrosome|cytosol|mitochondrial outer membrane cysteine-type endopeptidase activity|protein binding|protein binding upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1) 5 GGATATTTTCATAGAGATGGAG 0.396 0.38 34 21 PASK 23178 broad.mit.edu 37 2 242054497 242054497 + Frame_Shift_Del DEL G - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr2:242054497delG uc002wao.1 - 14 3386 c.3294delC c.(3292-3294)CCCfs p.P1098fs PASK_uc010zol.1_Frame_Shift_Del_p.P912fs|PASK_uc010zom.1_Frame_Shift_Del_p.P1063fs|PASK_uc010fzl.1_Frame_Shift_Del_p.P1098fs|PASK_uc010zon.1_Frame_Shift_Del_p.P879fs|PASK_uc002wap.2_Frame_Shift_Del_p.P641fs|PASK_uc002waq.2_Frame_Shift_Del_p.P1098fs NM_015148 NP_055963 Q96RG2 PASK_HUMAN PAS domain containing serine/threonine kinase 1098 Protein kinase. regulation of transcription, DNA-dependent Golgi apparatus ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity ovary(4)|lung(1)|skin(1) 6 all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968) CATCCAGCCTGGGGTGGCGGT 0.582 0.22 116 32 RARB 5915 broad.mit.edu 37 3 25542672 25542672 + Splice_Site DEL G - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr3:25542672delG uc011awl.1 + 3 394 c.328_splice c.e3-1 p.G110_splice RARB_uc003cdi.1_Splice_Site|RARB_uc003cdh.2_Splice_Site_p.G103_splice NM_016152 NP_057236 P10826 RARB_HUMAN retinoic acid receptor, beta isoform 2 embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor cytoplasm|nucleoplasm protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding ovary(1)|large_intestine(1)|pancreas(1) 3 Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799) CTTGCTTGCAGGGCTTTTTCC 0.358 0.32 153 71 TGFBR2 7048 broad.mit.edu 37 3 30691872 30691873 + Frame_Shift_Del DEL AA - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr3:30691872_30691873delAA uc003ceo.2 + 3 756_757 c.374_375delAA c.(373-375)GAAfs p.E125fs TGFBR2_uc003cen.2_Frame_Shift_Del_p.E150fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 125 Extracellular (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 ATTATGAAGGAAAAAAAAAAGC 0.426 0.92 26 319 SMARCC1 6599 broad.mit.edu 37 3 47718258 47718258 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr3:47718258delA uc003crq.2 - 17 1704 c.1586delT c.(1585-1587)TTAfs p.L529fs SMARCC1_uc011bbc.1_RNA|SMARCC1_uc011bbd.1_Frame_Shift_Del_p.L420fs NM_003074 NP_003065 Q92922 SMRC1_HUMAN SWI/SNF-related matrix-associated 529 SWIRM. FL -> GG (in Ref. 1; AAC50693). chromatin remodeling|nervous system development|transcription, DNA-dependent nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex DNA binding|protein N-terminus binding|transcription coactivator activity skin(2)|lung(1) 3 BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01) 0.000 0.26 578 202 FLNB 2317 broad.mit.edu 37 3 58081881 58081882 + Frame_Shift_Ins INS - A A LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr3:58081881_58081882insA uc003djj.2 + 6 1085_1086 c.920_921insA c.(919-921)CCTfs p.P307fs FLNB_uc010hne.2_Frame_Shift_Ins_p.P307fs|FLNB_uc003djk.2_Frame_Shift_Ins_p.P307fs|FLNB_uc010hnf.2_Frame_Shift_Ins_p.P307fs|FLNB_uc003djl.2_Frame_Shift_Ins_p.P138fs|FLNB_uc003djm.2_Frame_Shift_Ins_p.P138fs NM_001457 NP_001448 O75369 FLNB_HUMAN filamin B isoform 2 307 Filamin 1. actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction cell cortex|integral to membrane|nucleus|sarcomere actin binding breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1) 19 BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898) CAAGTGACCCCTGACAGTGACA 0.550 0.39 25 16 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.32 25 12 GATA2 2624 broad.mit.edu 37 3 128204873 128204873 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr3:128204873delC uc003ekm.3 - 4 1003 c.568delG c.(568-570)GCTfs p.A190fs GATA2_uc003ekn.3_Frame_Shift_Del_p.A190fs|GATA2_uc003eko.2_Frame_Shift_Del_p.A190fs NM_001145661 NP_001139133 P23769 GATA2_HUMAN GATA binding protein 2 isoform 1 190 blood coagulation|negative regulation of fat cell differentiation|negative regulation of fat cell proliferation|negative regulation of neural precursor cell proliferation|negative regulation of Notch signaling pathway|phagocytosis|positive regulation of angiogenesis|positive regulation of phagocytosis|positive regulation of transcription from RNA polymerase II promoter nucleoplasm C2H2 zinc finger domain binding|chromatin binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding haematopoietic_and_lymphoid_tissue(13)|lung(1)|skin(1) 15 GBM - Glioblastoma multiforme(114;0.173) GGAGACGCAGCCCCCGTGGTG 0.632 0.12 76 10 PIK3CB 5291 broad.mit.edu 37 3 138413710 138413710 + Frame_Shift_Del DEL G - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr3:138413710delG uc011bmq.1 - 12 1810 c.1810delC c.(1810-1812)CGGfs p.R604fs PIK3CB_uc011bmn.1_Frame_Shift_Del_p.R116fs|PIK3CB_uc011bmo.1_Frame_Shift_Del_p.R50fs|PIK3CB_uc011bmp.1_Frame_Shift_Del_p.R191fs NM_006219 NP_006210 P42338 PK3CB_HUMAN catalytic phosphatidylinositol 3-kinase beta 604 PI3K helical. activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway phosphatidylinositol 3-kinase complex 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity breast(2)|ovary(1)|lung(1)|skin(1) 5 AGGGCCTCCCGGGGGGGCAGT 0.468 0.38 75 45 WHSC1 7468 broad.mit.edu 37 4 1902973 1902973 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr4:1902973delA uc003gdz.3 + 2 768 c.592delA c.(592-594)AAAfs p.K198fs WHSC1_uc003geb.3_Frame_Shift_Del_p.K198fs|WHSC1_uc003gec.3_Frame_Shift_Del_p.K198fs|WHSC1_uc003ged.3_Frame_Shift_Del_p.K198fs|WHSC1_uc003gee.3_RNA|WHSC1_uc003gef.3_RNA|WHSC1_uc003gdx.2_Frame_Shift_Del_p.K198fs|WHSC1_uc003gdy.1_Frame_Shift_Del_p.K198fs|WHSC1_uc010icd.1_Frame_Shift_Del_p.K198fs|WHSC1_uc003gea.1_Frame_Shift_Del_p.K198fs|WHSC1_uc010ice.1_Frame_Shift_Del_p.K198fs|WHSC1_uc003geg.1_Frame_Shift_Del_p.K198fs|WHSC1_uc003geh.1_Frame_Shift_Del_p.K198fs NM_001042424 NP_001035889 O96028 NSD2_HUMAN Wolf-Hirschhorn syndrome candidate 1 protein 198 anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|cytoplasm|nuclear membrane|nucleolus DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding ovary(3)|lung(3)|skin(2)|pancreas(1) 9 all_epithelial(65;1.34e-05) OV - Ovarian serous cystadenocarcinoma(23;0.00606) STAD - Stomach adenocarcinoma(129;0.232) TCCTTCAGATAAAAAGGTATT 0.522 0.31 40 18 BMP2K 55589 broad.mit.edu 37 4 79792115 79792116 + In_Frame_Ins INS - CAG CAG LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr4:79792115_79792116insCAG uc003hlk.2 + 11 1576_1577 c.1410_1411insCAG c.(1408-1413)insCAG p.486_487insQ BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Ins_p.486_487insQ|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486_487 Gln/His-rich. nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 agcaacagcaacagcagcagca 0.213 0.24 86 27 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.11 57 7 TET2 54790 broad.mit.edu 37 4 106155778 106155779 + Frame_Shift_Ins INS - A A LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr4:106155778_106155779insA uc003hxk.2 + 3 1065_1066 c.679_680insA c.(679-681)GAAfs p.E227fs TET2_uc011cez.1_Frame_Shift_Ins_p.E248fs|TET2_uc003hxj.2_RNA|TET2_uc010ilp.1_Frame_Shift_Ins_p.E227fs|TET2_uc003hxi.1_Frame_Shift_Ins_p.E227fs NM_001127208 NP_001120680 Q6N021 TET2_HUMAN tet oncogene family member 2 isoform a 227 cell cycle|myeloid cell differentiation metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen haematopoietic_and_lymphoid_tissue(732)|pancreas(1) 733 Myeloproliferative disorder(5;0.0393) OV - Ovarian serous cystadenocarcinoma(123;7.18e-08) TGAACTCCTGGAAAAAACACTG 0.406 0.55 133 160 ALPK1 80216 broad.mit.edu 37 4 113353696 113353697 + Frame_Shift_Ins INS - T T LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr4:113353696_113353697insT uc003iap.3 + 11 3272_3273 c.2993_2994insT c.(2992-2994)AATfs p.N998fs ALPK1_uc003ian.3_Frame_Shift_Ins_p.N998fs|ALPK1_uc011cfx.1_Frame_Shift_Ins_p.N920fs|ALPK1_uc003iao.3_Intron|ALPK1_uc010imo.2_Frame_Shift_Ins_p.N826fs NM_025144 NP_079420 Q96QP1 ALPK1_HUMAN alpha-kinase 1 998 ATP binding|protein serine/threonine kinase activity ovary(5) 5 Ovarian(17;0.0446)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.00325) AGACTAGAGAATACGGGGGTTT 0.485 0.29 30 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.69 65 144 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.88 17 122 APC 324 broad.mit.edu 37 5 112175951 112175952 + Frame_Shift_Ins INS - A A LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr5:112175951_112175952insA uc010jby.2 + 16 5040_5041 c.4660_4661insA c.(4660-4662)GAAfs p.E1554fs APC_uc011cvt.1_Frame_Shift_Ins_p.E1536fs|APC_uc003kpz.3_Frame_Shift_Ins_p.E1554fs|APC_uc003kpy.3_Frame_Shift_Ins_p.E1554fs|APC_uc010jbz.2_Frame_Shift_Ins_p.E1271fs|APC_uc010jca.2_Frame_Shift_Ins_p.E854fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1554 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.T1556fs*3(35)|p.E1554fs*5(2)|p.E1554*(2)|p.?(1)|p.T1556fs*9(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1554fs*11(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GAAAGAGGCAGAAAAAACTATT 0.342 0.17 71 15 RAD50 10111 broad.mit.edu 37 5 131931451 131931452 + Frame_Shift_Ins INS - A A LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr5:131931451_131931452insA uc003kxi.2 + 13 2543_2544 c.2156_2157insA c.(2155-2157)CTAfs p.L719fs RAD50_uc003kxh.2_Frame_Shift_Ins_p.L580fs NM_005732 NP_005723 Q92878 RAD50_HUMAN RAD50 homolog isoform 1 719 Zinc-hook.|Potential. DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding lung(2)|ovary(1)|skin(1) 4 all_cancers(142;0.0368)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GAATCAGAGCTAAAAAAAAAGG 0.416 0.25 131 43 CDC25C 995 broad.mit.edu 37 5 137627689 137627690 + Frame_Shift_Ins INS - T T LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr5:137627689_137627690insT uc003lcp.1 - 8 1002_1003 c.731_732insA c.(730-732)AAGfs p.K244fs CDC25C_uc003lcq.1_Frame_Shift_Ins_p.K171fs|CDC25C_uc003lcr.1_Frame_Shift_Ins_p.K244fs|CDC25C_uc011cyp.1_Frame_Shift_Ins_p.K261fs|CDC25C_uc003lcs.1_Frame_Shift_Ins_p.K322fs NM_001790 NP_001781 P30307 MPIP3_HUMAN cell division cycle 25C isoform a 244 cell cycle checkpoint|cell division|cell proliferation|DNA replication|G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis|traversing start control point of mitotic cell cycle cytosol|nucleoplasm protein tyrosine phosphatase activity|WW domain binding lung(3) 3 KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592) CAGAAAAATACTTTTTTTTAAC 0.386 0.18 249 55 HNRNPH1 3187 broad.mit.edu 37 5 179044916 179044916 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr5:179044916delA uc003mkf.3 - 8 911 c.805delT c.(805-807)TCAfs p.S269fs HNRNPH1_uc011dgn.1_5'UTR|HNRNPH1_uc003mkg.3_Frame_Shift_Del_p.S177fs|HNRNPH1_uc003mke.3_Frame_Shift_Del_p.S269fs|HNRNPH1_uc003mkh.3_Frame_Shift_Del_p.S269fs NM_005520 NP_005511 P31943 HNRH1_HUMAN heterogeneous nuclear ribonucleoprotein H1 269 2 X 16 AA Gly-rich approximate repeats. regulation of RNA splicing actin cytoskeleton|catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm nucleotide binding|poly(U) RNA binding|protein binding 0 GACATTCCTGAAAAACAGTAA 0.433 0.23 295 87 SRPK1 6732 broad.mit.edu 37 6 35803222 35803222 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr6:35803222delA uc003olj.2 - 16 1950 c.1827delT c.(1825-1827)TTTfs p.F609fs SRPK1_uc011dtg.1_Frame_Shift_Del_p.F593fs|SRPK1_uc003olh.2_Frame_Shift_Del_p.F502fs|SRPK1_uc003oli.2_Frame_Shift_Del_p.F502fs NM_003137 NP_003128 Q96SB4 SRPK1_HUMAN SFRS protein kinase 1 609 Protein kinase. cell differentiation|chromosome segregation|interspecies interaction between organisms|intracellular protein kinase cascade|mRNA processing|negative regulation of viral genome replication|positive regulation of viral genome replication|regulation of mRNA processing|RNA splicing cytoplasm|nucleus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity ovary(1) 1 CTAGAACCTCAAAAAGGCCCC 0.478 0.63 108 182 CDC5L 988 broad.mit.edu 37 6 44394456 44394456 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr6:44394456delA uc003oxl.2 + 13 2147 c.1888delA c.(1888-1890)AAAfs p.K630fs NM_001253 NP_001244 Q99459 CDC5L_HUMAN CDC5-like 630 Interaction with DAPK3 (By similarity). cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus DNA binding|RNA binding lung(3)|ovary(1)|kidney(1)|skin(1) 6 all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208) Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536) AGAAGAGCTGAAAAAGGTATG 0.343 0.41 32 22 PHF3 23469 broad.mit.edu 37 6 64408152 64408152 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr6:64408152delA uc003pep.1 + 6 2746 c.2720delA c.(2719-2721)GAAfs p.E907fs PHF3_uc010kag.1_Frame_Shift_Del_p.E819fs|PHF3_uc010kah.1_Frame_Shift_Del_p.E721fs|PHF3_uc003pen.2_Frame_Shift_Del_p.E819fs|PHF3_uc011dxs.1_Frame_Shift_Del_p.E176fs NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 907 multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) AAGAAAGTTGAAAAAGGAGTG 0.343 0.16 139 27 MLLT4 4301 broad.mit.edu 37 6 168299041 168299041 + Frame_Shift_Del DEL G - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr6:168299041delG uc003qwd.2 + 11 1613 c.1471delG c.(1471-1473)GGGfs p.G491fs MLLT4_uc003qwb.1_Frame_Shift_Del_p.G476fs|MLLT4_uc003qwc.1_Frame_Shift_Del_p.G492fs|MLLT4_uc003qwf.2_Frame_Shift_Del_p.G177fs NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 492 FHA. adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) AGTGCAGTTTGGGGCGTCCCA 0.517 0.67 38 76 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.37 160 95 ITGB8 3696 broad.mit.edu 37 7 20438535 20438536 + Frame_Shift_Ins INS - T T LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr7:20438535_20438536insT uc003suu.2 + 9 1904_1905 c.1199_1200insT c.(1198-1200)TATfs p.Y400fs ITGB8_uc011jyh.1_Frame_Shift_Ins_p.Y265fs|ITGB8_uc003sut.2_Frame_Shift_Ins_p.Y400fs NM_002214 NP_002205 P26012 ITB8_HUMAN integrin, beta 8 precursor 400 Extracellular (Potential). cell-matrix adhesion|integrin-mediated signaling pathway|placenta blood vessel development integrin complex protein binding|receptor activity skin(3) 3 CAAGGCATCTATTTTAACATTA 0.411 0.39 158 102 PTPN12 5782 broad.mit.edu 37 7 77256504 77256507 + Frame_Shift_Del DEL CAAA - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr7:77256504_77256507delCAAA uc003ugh.2 + 13 1599_1602 c.1508_1511delCAAA c.(1507-1512)TCAAACfs p.S503fs PTPN12_uc011kgp.1_Frame_Shift_Del_p.S384fs|PTPN12_uc011kgq.1_Frame_Shift_Del_p.S373fs|PTPN12_uc010lds.2_Frame_Shift_Del_p.S235fs NM_002835 NP_002826 Q05209 PTN12_HUMAN protein tyrosine phosphatase, non-receptor type 503_504 soluble fraction non-membrane spanning protein tyrosine phosphatase activity|SH3 domain binding ovary(1)|breast(1)|pancreas(1) 3 0.000 0.57 162 219 ING3 54556 broad.mit.edu 37 7 120595626 120595627 + Frame_Shift_Ins INS - T T LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr7:120595626_120595627insT uc003vjn.2 + 4 349_350 c.215_216insT c.(214-216)GCTfs p.A72fs ING3_uc011knr.1_Frame_Shift_Ins_p.A72fs|ING3_uc003vjl.2_Frame_Shift_Ins_p.A72fs|ING3_uc003vjm.1_Frame_Shift_Ins_p.A72fs|ING3_uc003vjo.2_5'UTR|ING3_uc003vjp.2_Frame_Shift_Ins_p.A72fs|ING3_uc011kns.1_Frame_Shift_Ins_p.A57fs NM_019071 NP_061944 Q9NXR8 ING3_HUMAN inhibitor of growth family, member 3 isoform 1 72 histone H2A acetylation|histone H4 acetylation|positive regulation of apoptosis|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent NuA4 histone acetyltransferase complex|Piccolo NuA4 histone acetyltransferase complex zinc ion binding ovary(1) 1 all_neural(327;0.117) 0.000 0.28 113 44 LRGUK 136332 broad.mit.edu 37 7 133906656 133906656 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr7:133906656delA uc003vrm.1 + 16 1985 c.1969delA c.(1969-1971)AAAfs p.K657fs NM_144648 NP_653249 Q96M69 LRGUK_HUMAN leucine-rich repeats and guanylate kinase domain 657 ATP binding|kinase activity lung(2)|skin(2)|kidney(1) 5 ACTTTCAGCCAAAAAAACACC 0.388 0.49 133 126 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 15 SCARA5 286133 broad.mit.edu 37 8 27729504 27729504 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr8:27729504delC uc003xgj.2 - 9 1875 c.1435delG c.(1435-1437)GTGfs p.V479fs SCARA5_uc010luz.2_Frame_Shift_Del_p.V254fs NM_173833 NP_776194 Q6ZMJ2 SCAR5_HUMAN scavenger receptor class A, member 5 479 SRCR.|Extracellular (Potential). cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization integral to plasma membrane ferritin receptor activity|scavenger receptor activity central_nervous_system(1)|skin(1) 2 Ovarian(32;0.0218) UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228) CAGTTTGTCACCCCCCATTTG 0.567 0.26 225 78 VPS13B 157680 broad.mit.edu 37 8 100866037 100866038 + Frame_Shift_Ins INS - A A LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr8:100866037_100866038insA uc003yiv.2 + 56 10606_10607 c.10495_10496insA c.(10495-10497)GAAfs p.E3499fs VPS13B_uc003yiw.2_Frame_Shift_Ins_p.E3474fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 3499 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) AGAATACAAGGAAAAATGTTTT 0.386 0.40 77 52 RGS22 26166 broad.mit.edu 37 8 101014478 101014478 + Frame_Shift_Del DEL T - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr8:101014478delT uc003yjb.1 - 18 2937 c.2742delA c.(2740-2742)AAAfs p.K914fs RGS22_uc003yja.1_Frame_Shift_Del_p.K733fs|RGS22_uc003yjc.1_Frame_Shift_Del_p.K902fs|RGS22_uc011lgz.1_RNA NM_015668 NP_056483 Q8NE09 RGS22_HUMAN regulator of G-protein signaling 22 914 RGS 1. negative regulation of signal transduction cytoplasm|plasma membrane GTPase activator activity|signal transducer activity ovary(3)|skin(2)|breast(1)|central_nervous_system(1) 7 Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169) CAAAGAAATATTTTTTATTAA 0.343 0.17 174 36 RIMS2 9699 broad.mit.edu 37 8 104831783 104831783 + Frame_Shift_Del DEL T - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr8:104831783delT uc003ylw.2 + 1 368 c.48delT c.(46-48)CATfs p.H16fs RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylq.2_Frame_Shift_Del_p.H16fs|RIMS2_uc003ylr.2_Frame_Shift_Del_p.H16fs NM_014677 NP_055492 Q9UQ26 RIMS2_HUMAN regulating synaptic membrane exocytosis 2 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment intracellular protein transport cell junction|presynaptic membrane metal ion binding|Rab GTPase binding ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1) 15 OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229) TTTTATCTCATTTTCATGGGG 0.358 0.27 94 35 COL14A1 7373 broad.mit.edu 37 8 121209133 121209134 + Frame_Shift_Ins INS - T T LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr8:121209133_121209134insT uc003yox.2 + 6 805_806 c.540_541insT c.(538-543)TTCTTGfs p.F180fs COL14A1_uc003yoy.2_5'UTR|COL14A1_uc010mde.1_5'UTR NM_021110 NP_066933 Q05707 COEA1_HUMAN collagen, type XIV, alpha 1 precursor 180_181 VWFA 1. cell-cell adhesion|collagen fibril organization collagen type XIV|extracellular space collagen binding|extracellular matrix structural constituent|protein binding, bridging ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1) 12 Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503) TTCGGCATTTCTTGGAAAACCT 0.411 0.18 160 35 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 ENHO 375704 broad.mit.edu 37 9 34521668 34521669 + Frame_Shift_Ins INS - C C LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr9:34521668_34521669insC uc003zun.1 - 2 449_450 c.25_26insG c.(25-27)GCCfs p.A9fs ENHO_uc003zuo.2_RNA NM_198573 NP_940975 Q6UWT2 ENHO_HUMAN adropin precursor 9 extracellular region 0 0.000 0.48 305 284 DAPK1 1612 broad.mit.edu 37 9 90321802 90321802 + Frame_Shift_Del DEL G - - rs56169226 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr9:90321802delG uc004apc.2 + 26 3954 c.3816delG c.(3814-3816)ATGfs p.M1272fs DAPK1_uc004apd.2_Frame_Shift_Del_p.M1272fs|DAPK1_uc011ltg.1_Frame_Shift_Del_p.M1206fs|DAPK1_uc011lth.1_Frame_Shift_Del_p.M1009fs|DAPK1_uc004apg.2_Frame_Shift_Del_p.M249fs NM_004938 NP_004929 P53355 DAPK1_HUMAN death-associated protein kinase 1 1272 apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade actin cytoskeleton|cytoplasm ATP binding|calmodulin binding|protein serine/threonine kinase activity ovary(1)|breast(1) 2 CCAACACCATGGGGGGGTACA 0.582 0.33 18 9 PTCH1 5727 broad.mit.edu 37 9 98209617 98209617 + Frame_Shift_Del DEL G - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr9:98209617delG uc004avk.3 - 23 4109 c.3921delC c.(3919-3921)CCCfs p.P1307fs PTCH1_uc010mrn.2_Frame_Shift_Del_p.P99fs|PTCH1_uc010mro.2_Frame_Shift_Del_p.P1156fs|PTCH1_uc010mrp.2_Frame_Shift_Del_p.P1156fs|PTCH1_uc010mrq.2_Frame_Shift_Del_p.P1156fs|PTCH1_uc004avl.3_Frame_Shift_Del_p.P1156fs|PTCH1_uc010mrr.2_Frame_Shift_Del_p.P1241fs|PTCH1_uc004avm.3_Frame_Shift_Del_p.P1306fs NM_000264 NP_000255 Q13635 PTC1_HUMAN patched isoform L 1307 Cytoplasmic (Potential). embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway integral to plasma membrane hedgehog receptor activity skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1) 379 Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136) 0.000 0.38 323 200 SPTAN1 6709 broad.mit.edu 37 9 131389702 131389704 + In_Frame_Del DEL AGG - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr9:131389702_131389704delAGG uc004bvl.3 + 49 6712_6714 c.6599_6601delAGG c.(6598-6603)CAGGAG>CAG p.E2202del SPTAN1_uc004bvm.3_In_Frame_Del_p.E2207del|SPTAN1_uc004bvn.3_In_Frame_Del_p.E2182del|SPTAN1_uc010mye.1_In_Frame_Del_p.R90del|SPTAN1_uc010myf.1_In_Frame_Del_p.E31del|SPTAN1_uc004bvo.3_5'Flank NM_003127 NP_003118 Q13813 SPTA2_HUMAN spectrin, alpha, non-erythrocytic 1 2202 Missing (in EIEE5; could form a heterodimer with SPTBN1 but the heterodimer is thermally instable; suggests a dominant negative effect). actin filament capping|axon guidance|cellular component disassembly involved in apoptosis cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton breast(5)|ovary(4)|pancreas(1) 10 0.000 0.16 1287 248 PKN3 29941 broad.mit.edu 37 9 131468151 131468151 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr9:131468151delC uc004bvw.2 + 3 797 c.404delC c.(403-405)ACCfs p.T135fs PKN3_uc010myh.2_Frame_Shift_Del_p.T135fs|PKN3_uc011mbk.1_5'UTR NM_013355 NP_037487 Q6P5Z2 PKN3_HUMAN protein kinase PKNbeta 135 REM 2. signal transduction Golgi apparatus|nucleus|perinuclear region of cytoplasm ATP binding|protein binding|protein kinase C activity stomach(2)|lung(2) 4 GCCAGTGGCACCCCCAAGGTA 0.617 0.34 33 17 CACNB2 783 broad.mit.edu 37 10 18439797 18439810 + Splice_Site DEL TTTTTTTTTTTTTA - - rs74120235;rs71402148 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr10:18439797_18439810delTTTTTTTTTTTTTA uc001ipr.2 + 2 181 c.121_splice c.e2-2 p.S41_splice CACNB2_uc009xjz.1_Splice_Site_p.S41_splice|CACNB2_uc001ips.2_Splice_Site_p.S41_splice|CACNB2_uc001ipt.2_Splice_Site_p.S41_splice|CACNB2_uc010qcl.1_Splice_Site|CACNB2_uc001ipu.2_Splice_Site_p.S13_splice|CACNB2_uc001ipv.2_Splice_Site_p.S13_splice|CACNB2_uc009xka.1_Splice_Site_p.S13_splice NM_201596 NP_963890 Q08289 CACB2_HUMAN calcium channel, voltage-dependent, beta 2 axon guidance|neuromuscular junction development integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity large_intestine(1)|central_nervous_system(1)|skin(1) 3 Magnesium Sulfate(DB00653)|Verapamil(DB00661) tttttttttttttttttttttttAGTCATATGGA 0.327 0.12 107 15 ABI1 10006 broad.mit.edu 37 10 27044586 27044586 + Frame_Shift_Del DEL T - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr10:27044586delT uc001isx.2 - 10 1330 c.1163delA c.(1162-1164)AACfs p.N388fs ABI1_uc001ite.2_Intron|ABI1_uc010qdh.1_Intron|ABI1_uc010qdi.1_Intron|ABI1_uc001isy.2_Frame_Shift_Del_p.N361fs|ABI1_uc001ita.2_Intron|ABI1_uc001isz.2_Frame_Shift_Del_p.N356fs|ABI1_uc001itb.2_Intron|ABI1_uc001itc.2_Frame_Shift_Del_p.N360fs|ABI1_uc010qdj.1_Frame_Shift_Del_p.N302fs|ABI1_uc001itd.2_Intron|ABI1_uc010qdk.1_Intron|ABI1_uc010qdg.1_Intron NM_005470 NP_005461 Q8IZP0 ABI1_HUMAN abl-interactor 1 isoform a 388 Pro-rich. actin polymerization or depolymerization|cellular component movement|negative regulation of cell proliferation|peptidyl-tyrosine phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway cell junction|cytoskeleton|cytosol|endoplasmic reticulum|filopodium|growth cone|lamellipodium|nucleus|soluble fraction|synapse|synaptosome cytoskeletal protein binding central_nervous_system(1) 1 AAACTTACTGTTTTCCTGCAC 0.478 0.45 106 86 RET 5979 broad.mit.edu 37 10 43622119 43622120 + Frame_Shift_Ins INS - C C LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr10:43622119_43622120insC uc001jal.2 + 19 3326_3327 c.3136_3137insC c.(3136-3138)GCCfs p.A1046fs RET_uc001jak.1_Frame_Shift_Ins_p.A1046fs|RET_uc010qez.1_Frame_Shift_Ins_p.A792fs NM_020975 NP_066124 P07949 RET_HUMAN ret proto-oncogene isoform a 1046 Cytoplasmic (Potential). homophilic cell adhesion|positive regulation of metanephric glomerulus development|positive regulation of transcription, DNA-dependent|posterior midgut development integral to membrane ATP binding|calcium ion binding|transmembrane receptor protein tyrosine kinase activity thyroid(404)|adrenal_gland(20)|lung(9)|large_intestine(5)|breast(4)|ovary(4)|central_nervous_system(3)|urinary_tract(1)|NS(1) 451 Ovarian(717;0.0423) Sunitinib(DB01268) CTGTAATAATGCCCCCCTCCCT 0.530 0.38 113 69 PTEN 5728 broad.mit.edu 37 10 89692826 89692826 + Frame_Shift_Del DEL T - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr10:89692826delT uc001kfb.2 + 6 1341 c.310delT c.(310-312)TTTfs p.F104fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 104 Phosphatase tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R55fs*1(4)|p.?(2)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.F56fs*2(1)|p.P103fs*3(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) TATCAAACCCTTTTGTGAAGA 0.383 0.49 239 226 PTEN 5728 broad.mit.edu 37 10 89693003 89693003 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr10:89693003delA uc001kfb.2 + 6 1518 c.487delA c.(487-489)AAAfs p.K163fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 163 Phosphatase tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R55fs*1(4)|p.?(2)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.K163_V166>NKGE(1)|p.F56fs*2(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GACCAGAGACAAAAAGGTAAG 0.328 0.45 83 68 CTBP2 1488 broad.mit.edu 37 10 126692032 126692032 + Frame_Shift_Del DEL G - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr10:126692032delG uc009yak.2 - 4 375 c.88delC c.(88-90)CTGfs p.L30fs CTBP2_uc009yal.2_Frame_Shift_Del_p.L30fs|CTBP2_uc001lif.3_Frame_Shift_Del_p.L30fs|CTBP2_uc001lih.3_Frame_Shift_Del_p.L30fs|CTBP2_uc001lid.3_Frame_Shift_Del_p.L98fs|CTBP2_uc001lie.3_Frame_Shift_Del_p.L570fs NM_001329 NP_001320 P56545 CTBP2_HUMAN C-terminal binding protein 2 isoform 1 30 negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation cell junction|synapse|transcriptional repressor complex NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding 0 all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173) Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147) CGGGGGTGCAGGGGGCCGTTC 0.697 0.16 49 9 RELA 5970 broad.mit.edu 37 11 65422151 65422151 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr11:65422151delC uc001ofg.2 - 11 1494 c.1354delG c.(1354-1356)GCCfs p.A452fs RELA_uc001ofh.2_Frame_Shift_Del_p.A449fs|RELA_uc010ron.1_Frame_Shift_Del_p.A463fs|RELA_uc009yqr.2_Frame_Shift_Del_p.A399fs|RELA_uc001ofe.2_3'UTR|RELA_uc001off.2_Intron NM_021975 NP_068810 Q04206 TF65_HUMAN v-rel reticuloendotheliosis viral oncogene 452 Activation domain. anti-apoptosis|cellular defense response|cytokine-mediated signaling pathway|defense response to virus|inflammatory response|innate immune response|interspecies interaction between organisms|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription, DNA-dependent|nerve growth factor receptor signaling pathway|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of inflammatory response|response to interleukin-1|response to UV-B|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|transcription factor complex activating transcription factor binding|chromatin binding|identical protein binding|NF-kappaB binding|phosphate binding|protein kinase binding|protein N-terminus binding|repressing transcription factor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|ubiquitin protein ligase binding lung(3)|ovary(1) 4 ccaagcaaggcccccaggtct 0.393 0.24 133 43 MRE11A 4361 broad.mit.edu 37 11 94197308 94197308 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr11:94197308delA uc001peu.2 - 11 1385 c.1196delT c.(1195-1197)TTCfs p.F399fs MRE11A_uc001pev.2_Frame_Shift_Del_p.F399fs|MRE11A_uc009ywj.2_Frame_Shift_Del_p.F402fs NM_005591 NP_005582 P49959 MRE11_HUMAN meiotic recombination 11 homolog A isoform 1 399 DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase Mre11 complex|nucleoplasm 3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity breast(4)|lung(1) 5 Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824) TCTATGCCTGAAAAAATGGAT 0.338 0.51 57 59 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 395 138 CASP4 837 broad.mit.edu 37 11 104825475 104825475 + Frame_Shift_Del DEL T - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr11:104825475delT uc001pid.1 - 2 334 c.261delA c.(259-261)AAAfs p.K87fs CASP4_uc001pib.1_Frame_Shift_Del_p.K31fs|CASP4_uc009yxg.1_5'UTR|CASP4_uc010rux.1_Frame_Shift_Del_p.K87fs|CASP4_uc010ruy.1_Frame_Shift_Del_p.K87fs NM_001225 NP_001216 P49662 CASP4_HUMAN caspase 4 isoform alpha precursor 87 CARD. apoptosis|induction of apoptosis|proteolysis intracellular cysteine-type endopeptidase activity|protein binding lung(2)|ovary(1)|skin(1) 4 Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047) BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357) CAGTCTTACCTTTTTTATTGG 0.393 0.26 172 59 MLL 4297 broad.mit.edu 37 11 118344186 118344186 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr11:118344186delC uc001pta.2 + 3 2335 c.2312delC c.(2311-2313)ACCfs p.T771fs MLL_uc001ptb.2_Frame_Shift_Del_p.T771fs|MLL_uc001psz.1_Frame_Shift_Del_p.T804fs|MLL_uc001ptd.1_Intron NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 771 apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) TCACCTCTCACCCCCCCGTCT 0.453 0.24 334 103 MLL 4297 broad.mit.edu 37 11 118391565 118391565 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr11:118391565delA uc001pta.2 + 34 11492 c.11469delA c.(11467-11469)TTAfs p.L3823fs MLL_uc001ptb.2_Frame_Shift_Del_p.L3826fs NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3823 apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) TCCGGCACTTAAAAAAGACTT 0.378 0.28 97 38 LRRK2 120892 broad.mit.edu 37 12 40707828 40707829 + Frame_Shift_Ins INS - A A LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr12:40707828_40707829insA uc001rmg.3 + 32 4712_4713 c.4591_4592insA c.(4591-4593)GAAfs p.E1531fs LRRK2_uc009zjw.2_Frame_Shift_Ins_p.E369fs|LRRK2_uc001rmi.2_Frame_Shift_Ins_p.E364fs NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 1531 activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) TGTAGAACTTGAAAAAATCATT 0.356 0.22 232 66 LRRK2 120892 broad.mit.edu 37 12 40761539 40761539 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr12:40761539delA uc001rmg.3 + 51 7677 c.7556delA c.(7555-7557)GAAfs p.E2519fs LRRK2_uc009zjw.2_Frame_Shift_Del_p.E1357fs|LRRK2_uc001rmi.2_3'UTR NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 2519 activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) GAATTAGCTGAAAAAATGAGA 0.308 0.12 113 16 ADAMTS20 80070 broad.mit.edu 37 12 43833808 43833808 + Frame_Shift_Del DEL T - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr12:43833808delT uc010skx.1 - 17 2355 c.2355delA c.(2353-2355)AAAfs p.K785fs ADAMTS20_uc001rno.1_5'Flank|ADAMTS20_uc001rnp.1_5'Flank NM_025003 NP_079279 P59510 ATS20_HUMAN a disintegrin-like and metalloprotease with 785 Spacer. proteinaceous extracellular matrix zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1) 19 all_cancers(12;2.6e-05)|Lung SC(27;0.184) Lung NSC(34;0.0569)|all_lung(34;0.129) GBM - Glioblastoma multiforme(48;0.0473) CATTGATTTCTTTTTTTGACG 0.303 0.52 111 121 CCNT1 904 broad.mit.edu 37 12 49099623 49099623 + Frame_Shift_Del DEL T - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr12:49099623delT uc001rse.1 - 3 623 c.300delA c.(298-300)AAAfs p.K100fs CCNT1_uc009zkz.1_5'UTR NM_001240 NP_001231 O60563 CCNT1_HUMAN cyclin T1 100 cell cycle|cell division|interspecies interaction between organisms|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction nucleoplasm DNA binding|protein kinase binding ovary(3)|lung(1)|breast(1)|skin(1) 6 CATGTTCCAATTTTTTGGGCT 0.388 0.47 197 177 GLI1 2735 broad.mit.edu 37 12 57860075 57860075 + Frame_Shift_Del DEL G - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr12:57860075delG uc001snx.2 + 8 893 c.815delG c.(814-816)TGGfs p.W272fs GLI1_uc009zpq.2_Frame_Shift_Del_p.W144fs NM_005269 NP_005260 P08151 GLI1_HUMAN GLI family zinc finger 1 isoform 1 272 C2H2-type 2. epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter cytosol|nucleus transcription regulatory region DNA binding|zinc ion binding skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1) 15 GBM - Glioblastoma multiforme(3;3.99e-32) GTGTGCCACTGGGGGGGCTGC 0.597 0.24 261 84 CYP27B1 1594 broad.mit.edu 37 12 58160653 58160654 + Frame_Shift_Ins INS - C C LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr12:58160653_58160654insC uc001spz.1 - 1 323_324 c.171_172insG c.(169-174)GGGCTGfs p.G57fs CYP27B1_uc001sqa.1_5'UTR|CYP27B1_uc001sqb.1_5'Flank|CYP27B1_uc001sqc.1_5'Flank NM_000785 NP_000776 O15528 CP27B_HUMAN cytochrome P450, family 27, subfamily B, 57_58 bone mineralization|calcium ion homeostasis|calcium ion transport|decidualization|G1 to G0 transition|hormone biosynthetic process|negative regulation of calcidiol 1-monooxygenase activity|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of keratinocyte differentiation|positive regulation of vitamin D 24-hydroxylase activity|positive regulation of vitamin D receptor signaling pathway|regulation of bone mineralization|response to estrogen stimulus|response to interferon-gamma|response to lipopolysaccharide|response to tumor necrosis factor|response to vitamin D|vitamin D biosynthetic process|xenobiotic metabolic process mitochondrial outer membrane calcidiol 1-monooxygenase activity|electron carrier activity|heme binding central_nervous_system(3) 3 all_cancers(7;8.09e-80)|Lung NSC(6;2.26e-27)|all_lung(6;1.99e-25)|all_epithelial(6;3.62e-18)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122) GBM - Glioblastoma multiforme(5;1.97e-113)|all cancers(5;1.54e-78)|BRCA - Breast invasive adenocarcinoma(9;0.0294) Calcidiol(DB00146)|Calcitriol(DB00136)|Ergocalciferol(DB00153) AGCCTCGACAGCCCCCCCTTGC 0.599 0.17 82 17 MDM2 4193 broad.mit.edu 37 12 69233090 69233090 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr12:69233090delC uc001sui.2 + 11 1242 c.955delC c.(955-957)CCCfs p.P319fs MDM2_uc009zri.2_Frame_Shift_Del_p.P274fs|MDM2_uc009zqx.2_Frame_Shift_Del_p.P264fs|MDM2_uc009zqw.2_Intron|MDM2_uc001suk.2_Intron|MDM2_uc001sun.3_Frame_Shift_Del_p.P138fs|MDM2_uc009zqz.2_Frame_Shift_Del_p.P266fs|MDM2_uc009zra.2_Frame_Shift_Del_p.P117fs|MDM2_uc001sum.1_Intron|MDM2_uc009zrd.2_Frame_Shift_Del_p.P3fs|MDM2_uc009zrc.2_Frame_Shift_Del_p.P3fs|MDM2_uc009zre.2_Frame_Shift_Del_p.P60fs|MDM2_uc009zrf.2_Frame_Shift_Del_p.P3fs|MDM2_uc001suo.2_Frame_Shift_Del_p.P113fs|MDM2_uc009zrg.2_Frame_Shift_Del_p.P35fs|MDM2_uc009zrh.2_Frame_Shift_Del_p.P87fs NM_002392 NP_002383 Q00987 MDM2_HUMAN mouse double minute 2 homolog isoform MDM2 313 RanBP2-type.|Necessary for interaction with USP2.|Region II. cellular response to hypoxia|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|establishment of protein localization|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein complex assembly|protein destabilization|protein localization to nucleus|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to antibiotic|synaptic transmission cytosol|endocytic vesicle membrane|insoluble fraction|nucleolus|nucleoplasm|plasma membrane|protein complex enzyme binding|identical protein binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding lung(2)|central_nervous_system(1) 3 all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684) all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143) TGAAATGAATCCCCCCCTTCC 0.428 0.25 173 59 CIT 11113 broad.mit.edu 37 12 120288067 120288068 + Frame_Shift_Ins INS - A A LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr12:120288067_120288068insA uc001txi.1 - 5 479_480 c.426_427insT c.(424-429)TTTGAGfs p.F142fs CIT_uc001txj.1_Frame_Shift_Ins_p.F142fs NM_007174 NP_009105 O14578 CTRO_HUMAN citron 142_143 Protein kinase. intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) CGCTCTTCCTCAAAAAATGAAA 0.391 0.27 212 80 FLT3 2322 broad.mit.edu 37 13 28578215 28578216 + Frame_Shift_Del DEL GA - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr13:28578215_28578216delGA uc001urw.2 - 24 3037_3038 c.2955_2956delTC c.(2953-2958)TCTCCGfs p.S985fs FLT3_uc010aao.2_RNA|FLT3_uc010tdn.1_Frame_Shift_Del_p.S944fs NM_004119 NP_004110 P36888 FLT3_HUMAN fms-related tyrosine kinase 3 precursor 985_986 Cytoplasmic (Potential). positive regulation of cell proliferation integral to plasma membrane ATP binding|vascular endothelial growth factor receptor activity haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1) 8549 Acute lymphoblastic leukemia(6;0.04) Lung SC(185;0.0156)|Ovarian(182;0.0392) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212) Sorafenib(DB00398)|Sunitinib(DB01268) TGAGCCTGCGGAGAGAGTAGCC 0.460 0.54 138 160 LHFP 10186 broad.mit.edu 37 13 40175234 40175235 + Frame_Shift_Ins INS - T T LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr13:40175234_40175235insT uc001uxf.2 - 2 630_631 c.119_120insA c.(118-120)AAGfs p.K40fs NM_005780 NP_005771 Q9Y693 LHFP_HUMAN lipoma HMGIC fusion partner precursor 40 integral to membrane DNA binding HMGA2/LHFP(2) soft_tissue(2)|lung(1)|breast(1) 4 Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114) OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105) AGGACACAGGCTTGCCCAGCTG 0.545 0.27 181 66 LCP1 3936 broad.mit.edu 37 13 46733797 46733797 + Frame_Shift_Del DEL T - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr13:46733797delT uc001vaz.3 - 2 127 c.1delA c.(1-3)ATGfs p.M1fs LCP1_uc001vba.3_Frame_Shift_Del_p.M1fs NM_002298 NP_002289 P13796 PLSL_HUMAN L-plastin 1 regulation of intracellular protein transport|T cell activation involved in immune response cell junction|cytosol|ruffle membrane calcium ion binding lung(4)|ovary(3) 7 Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262) KIRC - Kidney renal clear cell carcinoma(16;0.234) GBM - Glioblastoma multiforme(144;5.39e-05) CCTCTGGCCATTTTTTATTGC 0.398 0.17 69 14 NIN 51199 broad.mit.edu 37 14 51237214 51237215 + Frame_Shift_Del DEL CT - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr14:51237214_51237215delCT uc001wym.2 - 12 1516_1517 c.1325_1326delAG c.(1324-1326)GAGfs p.E442fs NIN_uc001wyi.2_Frame_Shift_Del_p.E442fs|NIN_uc001wyj.2_RNA|NIN_uc001wyk.2_Frame_Shift_Del_p.E442fs|NIN_uc010tqp.1_Frame_Shift_Del_p.E448fs|NIN_uc001wyo.2_Frame_Shift_Del_p.E442fs|NIN_uc001wyp.1_Frame_Shift_Del_p.E404fs NM_182946 NP_891991 Q8N4C6 NIN_HUMAN ninein isoform 5 442 Potential. centrosome localization centrosome|microtubule calcium ion binding|GTP binding|protein binding skin(3)|ovary(1)|kidney(1)|central_nervous_system(1) 6 all_epithelial(31;0.00244)|Breast(41;0.127) GCAGGATCTGCTCTCTCTCTTT 0.460 0.31 316 145 CASC5 57082 broad.mit.edu 37 15 40914353 40914353 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr15:40914353delA uc010bbs.1 + 11 2130 c.1969delA c.(1969-1971)AAAfs p.K657fs CASC5_uc010ucq.1_Frame_Shift_Del_p.K481fs|CASC5_uc001zme.2_Frame_Shift_Del_p.K631fs|CASC5_uc010bbt.1_Frame_Shift_Del_p.K631fs NM_170589 NP_733468 Q8NG31 CASC5_HUMAN cancer susceptibility candidate 5 isoform 1 657 Interaction with BUB1 and BUB1B. acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm protein binding breast(3)|central_nervous_system(1)|skin(1) 5 all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946) GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211) CATAATAGCCAAAAACAGCTT 0.388 0.32 138 64 TP53BP1 7158 broad.mit.edu 37 15 43748186 43748186 + Frame_Shift_Del DEL T - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr15:43748186delT uc001zrs.2 - 12 2753 c.2605delA c.(2605-2607)ATGfs p.M869fs TP53BP1_uc010udp.1_Frame_Shift_Del_p.M869fs|TP53BP1_uc001zrq.3_Frame_Shift_Del_p.M874fs|TP53BP1_uc001zrr.3_Frame_Shift_Del_p.M874fs|TP53BP1_uc010udq.1_Frame_Shift_Del_p.M874fs NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 869 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) GCATTAGCCATTTTTGAGTCT 0.468 0.17 304 61 LRRK1 79705 broad.mit.edu 37 15 101550745 101550745 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr15:101550745delA uc002bwr.2 + 8 1399 c.1080delA c.(1078-1080)TCAfs p.S360fs LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA NM_024652 NP_078928 Q38SD2 LRRK1_HUMAN leucine-rich repeat kinase 1 360 LRR 4. small GTPase mediated signal transduction mitochondrion ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1) 12 Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094) OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23) TGACAGCTTCAAAAAATTGTT 0.368 0.33 61 30 GRIN2A 2903 broad.mit.edu 37 16 9943709 9943709 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr16:9943709delA uc002czo.3 - 5 1780 c.1232delT c.(1231-1233)CTGfs p.L411fs GRIN2A_uc010uym.1_Frame_Shift_Del_p.L411fs|GRIN2A_uc010uyn.1_Frame_Shift_Del_p.L254fs|GRIN2A_uc002czr.3_Frame_Shift_Del_p.L411fs NM_001134407 NP_001127879 Q12879 NMDE1_HUMAN N-methyl-D-aspartate receptor subunit 2A isoform 411 Extracellular (Potential). response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1) 45 Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043) 0.000 0.10 652 72 CHD9 80205 broad.mit.edu 37 16 53358016 53358016 + Frame_Shift_Del DEL A - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr16:53358016delA uc002ehb.2 + 38 8067 c.7903delA c.(7903-7905)AAAfs p.K2635fs CHD9_uc002egy.2_Frame_Shift_Del_p.K2619fs|CHD9_uc002ehc.2_Frame_Shift_Del_p.K2620fs|CHD9_uc002ehf.2_Frame_Shift_Del_p.K1733fs|CHD9_uc010cbw.2_Frame_Shift_Del_p.K701fs NM_025134 NP_079410 Q3L8U1 CHD9_HUMAN chromodomain helicase DNA binding protein 9 2635 cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleoplasm ATP binding|DNA binding|helicase activity|protein binding lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1) 7 all_cancers(37;0.0212) GAGACGGCCTAAAAGTGGAAT 0.493 0.33 197 95 THAP11 57215 broad.mit.edu 37 16 67876824 67876829 + In_Frame_Del DEL CAGCAG - - rs34213159;rs3982383;rs63117363 byFrequency LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr16:67876824_67876829delCAGCAG uc002euo.2 + 1 612_617 c.367_372delCAGCAG c.(367-372)CAGCAGdel p.QQ131del CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 131_132 Gln-rich. Missing (in Ref. 2; AAH12182). regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) gcagcagcaacagcagcagcagcagc 0.311 0.38 48 30 MLKL 197259 broad.mit.edu 37 16 74709590 74709591 + Frame_Shift_Del DEL CT - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr16:74709590_74709591delCT uc002fdb.2 - 8 1551_1552 c.1110_1111delAG c.(1108-1113)AGAGTCfs p.R370fs MLKL_uc002fdc.2_Intron NM_152649 NP_689862 Q8NB16 MLKL_HUMAN mixed lineage kinase domain-like isoform 1 370_371 Protein kinase. ATP binding|protein binding|protein kinase activity stomach(2) 2 GTAGATTTGACTCTGTCTGTCT 0.391 0.31 262 119 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 6 54 FANCA 2175 broad.mit.edu 37 16 89831344 89831345 + Frame_Shift_Ins INS - AG AG LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr16:89831344_89831345insAG uc002fou.1 - 28 2773_2774 c.2731_2732insCT c.(2731-2733)TGGfs p.W911fs FANCA_uc010vpn.1_Frame_Shift_Ins_p.W911fs|FANCA_uc010vpo.1_Frame_Shift_Ins_p.W40fs NM_000135 NP_000126 O15360 FANCA_HUMAN Fanconi anemia, complementation group A isoform 911 DNA repair|protein complex assembly cytoplasm|nucleoplasm protein binding ovary(2)|breast(2)|central_nervous_system(1)|skin(1) 6 Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194) BRCA - Breast invasive adenocarcinoma(80;0.028) TCTGTGTGTCCAGAGAGAGAGG 0.554 0.48 59 54 PER1 5187 broad.mit.edu 37 17 8050889 8050889 + Frame_Shift_Del DEL G - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr17:8050889delG uc002gkd.2 - 12 1634 c.1396delC c.(1396-1398)CTGfs p.L466fs PER1_uc010vuq.1_RNA|PER1_uc010vur.1_Frame_Shift_Del_p.L450fs NM_002616 NP_002607 O15534 PER1_HUMAN period 1 466 circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus signal transducer activity lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1) 9 TCCTCATTCAGGGGGGCCCTG 0.657 0.15 50 9 CSF3 1440 broad.mit.edu 37 17 38171944 38171944 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr17:38171944delC uc002htp.2 + 2 81 c.41delC c.(40-42)GCCfs p.A14fs CSF3_uc002hto.2_Frame_Shift_Del_p.A14fs|CSF3_uc002htq.2_Frame_Shift_Del_p.A10fs|CSF3_uc010wep.1_Frame_Shift_Del_p.A10fs NM_000759 NP_000750 P09919 CSF3_HUMAN colony stimulating factor 3 isoform a precursor 14 cytokine-mediated signaling pathway|granulocyte differentiation|immune response|positive regulation of cell proliferation extracellular space cytokine activity|enzyme binding|granulocyte colony-stimulating factor receptor binding|growth factor activity ovary(1) 1 Colorectal(19;0.000442) Myeloproliferative disorder(1115;0.0255) Filgrastim(DB00099)|Pegfilgrastim(DB00019) CTGTCCCCAGCCCTGCAGCTG 0.647 0.33 14 7 STAT3 6774 broad.mit.edu 37 17 40490767 40490767 + Frame_Shift_Del DEL T - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr17:40490767delT uc002hzl.1 - 6 772 c.532delA c.(532-534)ACCfs p.T178fs STAT3_uc002hzk.1_Frame_Shift_Del_p.T178fs|STAT3_uc002hzm.1_Frame_Shift_Del_p.T178fs|STAT3_uc010wgh.1_Frame_Shift_Del_p.T80fs|STAT3_uc002hzn.1_Frame_Shift_Del_p.T178fs NM_139276 NP_644805 P40763 STAT3_HUMAN signal transducer and activator of transcription 178 cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis cytosol|nucleus|plasma membrane calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding ovary(1)|lung(1)|breast(1)|central_nervous_system(1) 4 all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135) BRCA - Breast invasive adenocarcinoma(366;0.139) CTCTTGAGGGTTTTATAGTTG 0.333 0.98 2 112 RNF43 54894 broad.mit.edu 37 17 56435161 56435161 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr17:56435161delC uc002iwf.2 - 8 3932 c.1976delG c.(1975-1977)GGTfs p.G659fs RNF43_uc010wnv.1_Frame_Shift_Del_p.G618fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.G659fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.G659fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.G532fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 659 Pro-rich.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.22 277 78 MAP3K3 4215 broad.mit.edu 37 17 61766917 61766918 + Frame_Shift_Ins INS - C C LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr17:61766917_61766918insC uc002jbg.2 + 11 1204_1205 c.885_886insC c.(883-888)TTTCCCfs p.F295fs MAP3K3_uc002jbe.2_Frame_Shift_Ins_p.F326fs|MAP3K3_uc002jbf.2_Frame_Shift_Ins_p.F326fs|MAP3K3_uc002jbh.2_Frame_Shift_Ins_p.F322fs|MAP3K3_uc010wpo.1_Frame_Shift_Ins_p.F210fs|MAP3K3_uc010wpp.1_Frame_Shift_Ins_p.F291fs NM_002401 NP_002392 Q99759 M3K3_HUMAN mitogen-activated protein kinase kinase kinase 3 295_296 MAPKKK cascade|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autophosphorylation cytosol ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding lung(3)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1) 6 GAAGAACATTTCCCCGAATACG 0.584 0.76 4 13 SOCS3 9021 broad.mit.edu 37 17 76354878 76354878 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr17:76354878delC uc002jvl.2 - 2 715 c.299delG c.(298-300)GGCfs p.G100fs NM_003955 NP_003946 O14543 SOCS3_HUMAN suppressor of cytokine signaling 3 100 SH2. anti-apoptosis|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|regulation of growth|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway cytosol protein kinase inhibitor activity ovary(1) 1 BRCA - Breast invasive adenocarcinoma(99;0.000688)|OV - Ovarian serous cystadenocarcinoma(97;0.0554) AGAGAAGCTGCCCCCCTCACA 0.647 0.97 1 29 FBN3 84467 broad.mit.edu 37 19 8171074 8171075 + Frame_Shift_Ins INS - C C LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr19:8171074_8171075insC uc002mjf.2 - 37 4751_4752 c.4730_4731insG c.(4729-4731)GGTfs p.G1577fs NM_032447 NP_115823 Q75N90 FBN3_HUMAN fibrillin 3 precursor 1577 EGF-like 24; calcium-binding. proteinaceous extracellular matrix calcium ion binding|extracellular matrix structural constituent ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1) 11 TGACGCAGTCACCCCCCTGACA 0.564 0.37 24 14 MAP3K10 4294 broad.mit.edu 37 19 40720945 40720945 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr19:40720945delC uc002ona.2 + 10 2899 c.2611delC c.(2611-2613)CCCfs p.P871fs MAP3K10_uc002onb.2_Frame_Shift_Del_p.P260fs NM_002446 NP_002437 Q02779 M3K10_HUMAN mitogen-activated protein kinase kinase kinase 871 activation of JUN kinase activity|induction of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of JNK cascade|protein autophosphorylation|smoothened signaling pathway cytoplasm ATP binding|bHLH transcription factor binding|JUN kinase kinase kinase activity|protein homodimerization activity|transcription corepressor activity ovary(2)|lung(2)|skin(1)|pancreas(1) 6 CCGCCGCCGGCCCCCTGAGTT 0.701 0.33 8 4 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.64 37 66 NCOA3 8202 broad.mit.edu 37 20 46279858 46279866 + In_Frame_Del DEL CAGCAGCAA - - rs151060280;rs3092460;rs67218125;rs11472494;rs112826888 byFrequency LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr20:46279858_46279866delCAGCAGCAA uc002xtk.2 + 20 3989_3997 c.3784_3792delCAGCAGCAA c.(3784-3792)CAGCAGCAAdel p.QQQ1274del NCOA3_uc010ght.1_In_Frame_Del_p.QQQ1265del|NCOA3_uc002xtl.2_In_Frame_Del_p.QQQ1270del|NCOA3_uc002xtm.2_In_Frame_Del_p.QQQ1269del|NCOA3_uc002xtn.2_In_Frame_Del_p.QQQ1273del|NCOA3_uc010zyc.1_In_Frame_Del_p.QQQ1069del NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 1274_1276 Poly-Gln.|Acetyltransferase. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 gcagcagcagcagcagcaacagcaacagc 0.321 0.39 95 60 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.40 21 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.67 81 167 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 63 MYH9 4627 broad.mit.edu 37 22 36690293 36690293 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr22:36690293delC uc003apg.2 - 28 3913 c.3682delG c.(3682-3684)GAGfs p.E1228fs NM_002473 NP_002464 P35579 MYH9_HUMAN myosin, heavy polypeptide 9, non-muscle 1228 Potential. actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1) 11 TTGGCCAGCTCCCCCCGCTCG 0.592 0.32 237 113 GTSE1 51512 broad.mit.edu 37 22 46712114 46712114 + Frame_Shift_Del DEL C - - LS411N_LARGE_INTESTINE NA LS411N_LARGE_INTESTINE NA g.chr22:46712114delC uc011aqy.1 + 7 1449 c.1237delC c.(1237-1239)CCCfs p.P413fs GTSE1_uc011aqz.1_Frame_Shift_Del_p.P260fs|GTSE1_uc003bhl.1_Frame_Shift_Del_p.P38fs|GTSE1_uc003bhm.1_Frame_Shift_Del_p.P38fs NM_016426 NP_057510 Q9NYZ3 GTSE1_HUMAN G-2 and S-phase expressed 1 394 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G2 phase of mitotic cell cycle|microtubule-based process cytoplasmic microtubule ovary(1) 1 Ovarian(80;0.00965)|all_neural(38;0.0416) UCEC - Uterine corpus endometrioid carcinoma (28;0.00462) GCTCACGGCACCCCCCTCAGC 0.632 0.35 45 24 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LS513_LARGE_INTESTINE NA LS513_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 24 PRKD3 23683 broad.mit.edu 37 2 37483801 37483803 + Splice_Site DEL TTA - - rs56389006 LS513_LARGE_INTESTINE NA LS513_LARGE_INTESTINE NA g.chr2:37483801_37483803delTTA uc002rqd.2 - 16 2968 c.2413_splice c.e16+1 p.A805_splice NM_005813 NP_005804 O94806 KPCD3_HUMAN protein kinase D3 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction cytoplasm|membrane|nucleus ATP binding|metal ion binding|protein binding|protein kinase C activity lung(2)|ovary(1)|central_nervous_system(1) 4 all_hematologic(82;0.21) ttttttttttttACCTTCACCAG 0.305 0.17 34 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LS513_LARGE_INTESTINE NA LS513_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.71 28 69 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LS513_LARGE_INTESTINE NA LS513_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.26 29 10 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - LS513_LARGE_INTESTINE NA LS513_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.83 2 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LS513_LARGE_INTESTINE NA LS513_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LS513_LARGE_INTESTINE NA LS513_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 210 43 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 LS513_LARGE_INTESTINE NA LS513_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.20 59 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LS513_LARGE_INTESTINE NA LS513_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 118 413 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LS513_LARGE_INTESTINE NA LS513_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 3 28 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LU65_LUNG NA LU65_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 66 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - LU65_LUNG NA LU65_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 600 130 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 LU65_LUNG NA LU65_LUNG NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.41 10 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 LU65_LUNG NA LU65_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.48 24 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LU65_LUNG NA LU65_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 75 126 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes LU65_LUNG NA LU65_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 18 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 LU65_LUNG NA LU65_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.57 37 49 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LU65_LUNG NA LU65_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 15 TET1 80312 broad.mit.edu 37 10 70451160 70451161 + Frame_Shift_Ins INS - T T LU65_LUNG NA LU65_LUNG NA g.chr10:70451160_70451161insT uc001jok.3 + 12 6505_6506 c.6000_6001insT c.(5998-6003)ATCTTTfs p.I2000fs NM_030625 NP_085128 Q8NFU7 TET1_HUMAN CXXC finger 6 2000_2001 F -> L (in Ref. 4; CAD28467). DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding ovary(5)|lung(2)|prostate(1)|breast(1) 9 GTGAGCACATCTTTTTGGATGC 0.535 0.12 486 64 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 LU65_LUNG NA LU65_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.33 10 5 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LU65_LUNG NA LU65_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 300 133 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LU65_LUNG NA LU65_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 194 628 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LU65_LUNG NA LU65_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 5 47 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LU99_LUNG NA LU99_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 35 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - LU99_LUNG NA LU99_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.32 359 166 ALS2 57679 broad.mit.edu 37 2 202609085 202609087 + In_Frame_Del DEL ATA - - LU99_LUNG NA LU99_LUNG NA g.chr2:202609085_202609087delATA uc002uyo.2 - 10 2420_2422 c.2064_2066delTAT c.(2062-2067)ATTATG>ATG p.I688del ALS2_uc002uyp.3_In_Frame_Del_p.I688del|ALS2_uc002uyq.2_In_Frame_Del_p.I688del|ALS2_uc010ftl.2_RNA NM_020919 NP_065970 Q96Q42 ALS2_HUMAN alsin isoform 1 688 cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity skin(5)|lung(1)|breast(1) 7 AATATACCCCATAATGTTTTTAT 0.365 0.49 111 107 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A LU99_LUNG NA LU99_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.15 162 28 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 LU99_LUNG NA LU99_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.50 15 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LU99_LUNG NA LU99_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 77 112 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LU99_LUNG NA LU99_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.25 96 32 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 LU99_LUNG NA LU99_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.31 256 115 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 LU99_LUNG NA LU99_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.32 13 6 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 LU99_LUNG NA LU99_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.22 69 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LU99_LUNG NA LU99_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 3 51 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency LU99_LUNG NA LU99_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.28 28 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LU99_LUNG NA LU99_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 511 172 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 LU99_LUNG NA LU99_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.81 6 26 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LU99_LUNG NA LU99_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 17 148 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LU99_LUNG NA LU99_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 206 554 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LU99_LUNG NA LU99_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 9 84 EP300 2033 broad.mit.edu 37 22 41547916 41547916 + Frame_Shift_Del DEL C - - LU99_LUNG NA LU99_LUNG NA g.chr22:41547916delC uc003azl.3 + 15 3292 c.2897delC c.(2896-2898)GCCfs p.A966fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 966 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 AATTCTCAGGCCATTGCTGAG 0.478 0.99 1 99 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LUDLU1_LUNG NA LUDLU1_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 3 37 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - LUDLU1_LUNG NA LUDLU1_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 425 96 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LUDLU1_LUNG NA LUDLU1_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 71 49 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LUDLU1_LUNG NA LUDLU1_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 13 35 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 LUDLU1_LUNG NA LUDLU1_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.31 18 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LUDLU1_LUNG NA LUDLU1_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 39 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 LUDLU1_LUNG NA LUDLU1_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 284 89 BRCA2 675 broad.mit.edu 37 13 32893309 32893309 + Frame_Shift_Del DEL A - - LUDLU1_LUNG NA LUDLU1_LUNG NA g.chr13:32893309delA uc001uub.1 + 3 390 c.163delA c.(163-165)AACfs p.N55fs BRCA2_uc001uua.1_5'UTR NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 55 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) ACATAAAAACAACAATTACGA 0.353 0.68 26 54 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 LUDLU1_LUNG NA LUDLU1_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.38 16 10 ERN1 2081 broad.mit.edu 37 17 62133220 62133221 + In_Frame_Ins INS - GCT GCT LUDLU1_LUNG NA LUDLU1_LUNG NA g.chr17:62133220_62133221insGCT uc002jdz.2 - 13 1599_1600 c.1486_1487insAGC c.(1486-1488)CTG>CAGCTG p.495_496insQ NM_001433 NP_001424 O75460 ERN1_HUMAN endoplasmic reticulum to nucleus signalling 1 495_496 Cytoplasmic (Potential). activation of signaling protein activity involved in unfolded protein response|apoptosis|cell cycle arrest|induction of apoptosis|mRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent integral to endoplasmic reticulum membrane ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(4)|lung(2)|stomach(1)|ovary(1)|kidney(1) 9 0.000 0.25 486 159 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 LUDLU1_LUNG NA LUDLU1_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.43 50 37 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LUDLU1_LUNG NA LUDLU1_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 97 272 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 LUDLU1_LUNG NA LUDLU1_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 1 22 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 LXF289_LUNG NA LXF289_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 LXF289_LUNG NA LXF289_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 55 31 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 LXF289_LUNG NA LXF289_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 12 35 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes LXF289_LUNG NA LXF289_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 1 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 LXF289_LUNG NA LXF289_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 34 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C LXF289_LUNG NA LXF289_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 27 187 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 LXF289_LUNG NA LXF289_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.72 43 109 NTSR1 4923 broad.mit.edu 37 20 61340864 61340864 + Frame_Shift_Del DEL A - - LXF289_LUNG NA LXF289_LUNG NA g.chr20:61340864delA uc002ydf.2 + 1 676 c.305delA c.(304-306)CATfs p.H102fs NM_002531 NP_002522 P30989 NTR1_HUMAN neurotensin receptor 1 102 Helical; Name=2; (Potential). endoplasmic reticulum|Golgi apparatus|integral to plasma membrane neurotensin receptor activity, G-protein coupled skin(2)|lung(1)|central_nervous_system(1) 4 Breast(26;3.65e-08) BRCA - Breast invasive adenocarcinoma(19;3.63e-06) 0.000 0.58 627 862 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 LXF289_LUNG NA LXF289_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.19 46 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 LXF289_LUNG NA LXF289_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 76 387 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 49 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.44 22 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 124 190 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.36 7 4 POU3F2 5454 broad.mit.edu 37 6 99283172 99283173 + In_Frame_Ins INS - CAG CAG M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr6:99283172_99283173insCAG uc003ppe.2 + 1 593_594 c.423_424insCAG c.(421-426)insCAG p.149_150insQ NM_005604 NP_005595 P20265 PO3F2_HUMAN POU domain, class 3, transcription factor 2 149_150 positive regulation of cell proliferation identical protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197) BRCA - Breast invasive adenocarcinoma(108;0.0355) aacagcagcaacagcagcagca 0.465 0.45 83 69 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 2 29 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.10 249 29 MLLT3 4300 broad.mit.edu 37 9 20414376 20414377 + In_Frame_Ins INS - CTG CTG rs1761445 M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr9:20414376_20414377insCTG uc003zoe.2 - 5 726_727 c.467_468insCAG c.(466-468)AGT>AGCAGT p.156_156S>SS MLLT3_uc011lne.1_In_Frame_Ins_p.124_124S>SS|MLLT3_uc011lnf.1_In_Frame_Ins_p.153_153S>SS|MLLT3_uc003zof.2_5'UTR|MLLT3_uc011lng.1_Splice_Site_p.T124_splice NM_004529 NP_004520 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia 156 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding lung(2)|ovary(1) 3 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) tgctgctgctactgctgctgct 0.144 0.39 230 144 PTEN 5728 broad.mit.edu 37 10 89711992 89711992 + Frame_Shift_Del DEL C - - M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr10:89711992delC uc001kfb.2 + 7 1641 c.610delC c.(610-612)CCAfs p.P204fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 204 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R55fs*1(4)|p.?(3)|p.G165fs*9(3)|p.P204T(2)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.G165_K342del(1)|p.G165_*404del(1)|p.P204S(1)|p.P204fs*17(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) TGAAACTATTCCAATGTTCAG 0.358 1.00 0 124 ZNF384 171017 broad.mit.edu 37 12 6777070 6777084 + In_Frame_Del DEL TGCTGCTGCTGCTGC - - rs151322806;rs111332695;rs78573212;rs1052680;rs149757410;rs72393318 M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr12:6777070_6777084delTGCTGCTGCTGCTGC uc010sfh.1 - 11 1738_1752 c.1530_1544delGCAGCAGCAGCAGCA c.(1528-1545)CAGCAGCAGCAGCAGCAA>CAA p.510_515QQQQQQ>Q ZNF384_uc001qpz.2_In_Frame_Del_p.449_454QQQQQQ>Q|ZNF384_uc001qqa.2_In_Frame_Del_p.449_454QQQQQQ>Q|ZNF384_uc001qqb.2_In_Frame_Del_p.433_438QQQQQQ>Q|ZNF384_uc001qqc.2_In_Frame_Del_p.449_454QQQQQQ>Q|ZNF384_uc001qqd.2_In_Frame_Del_p.394_399QQQQQQ>Q|ZNF384_uc001qqe.2_In_Frame_Del_p.433_438QQQQQQ>Q NM_001135734 NP_001129206 Q8TF68 ZN384_HUMAN nuclear matrix transcription factor 4 isoform d 510_515 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding EWSR1/ZNF384(4) haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1) 8 TGGTGgctgttgctgctgctgctgctgctgctgct 0.321 0.27 229 86 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 35 229 JUNB 3726 broad.mit.edu 37 19 12903092 12903093 + Frame_Shift_Ins INS - G G M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr19:12903092_12903093insG uc002mvc.2 + 1 783_784 c.507_508insG c.(505-510)CCCGGGfs p.P169fs JUNB_uc002mvb.2_RNA NM_002229 NP_002220 P17275 JUNB_HUMAN jun B proto-oncogene 169_170 chromatin|nucleus protein dimerization activity|transcription coactivator activity|transcription corepressor activity lung(2)|central_nervous_system(1) 3 cggctgggcccgggggcgTCTA 0.564 0.10 87 10 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.15 129 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 151 519 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 M059K_CENTRAL_NERVOUS_SYSTEM NA M059K_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 108 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 76 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.46 161 138 GATA2 2624 broad.mit.edu 37 3 128205090 128205097 + Frame_Shift_Del DEL GGTCCAGG - - M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:128205090_128205097delGGTCCAGG uc003ekm.3 - 4 779_786 c.344_351delCCTGGACC c.(343-351)CCCTGGACCfs p.P115fs GATA2_uc003ekn.3_Frame_Shift_Del_p.P115fs|GATA2_uc003eko.2_Frame_Shift_Del_p.P115fs|uc003ekp.2_5'Flank NM_001145661 NP_001139133 P23769 GATA2_HUMAN GATA binding protein 2 isoform 1 115_117 blood coagulation|negative regulation of fat cell differentiation|negative regulation of fat cell proliferation|negative regulation of neural precursor cell proliferation|negative regulation of Notch signaling pathway|phagocytosis|positive regulation of angiogenesis|positive regulation of phagocytosis|positive regulation of transcription from RNA polymerase II promoter nucleoplasm C2H2 zinc finger domain binding|chromatin binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding haematopoietic_and_lymphoid_tissue(13)|lung(1)|skin(1) 15 GBM - Glioblastoma multiforme(114;0.173) 0.000 0.50 729 729 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 94 19 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.35 15 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.49 100 96 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 17 39 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.32 258 122 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 1 21 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 263 65 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.14 113 18 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 10 33 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.26 73 25 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 51 559 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 82 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MALME3M_SKIN NA MALME3M_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 6 119 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MALME3M_SKIN NA MALME3M_SKIN NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 1295 386 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MALME3M_SKIN NA MALME3M_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.28 72 28 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MALME3M_SKIN NA MALME3M_SKIN NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.31 299 137 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MALME3M_SKIN NA MALME3M_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.46 62 53 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MALME3M_SKIN NA MALME3M_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 220 312 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MALME3M_SKIN NA MALME3M_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 27 73 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MALME3M_SKIN NA MALME3M_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.97 1 35 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MALME3M_SKIN NA MALME3M_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 41 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MALME3M_SKIN NA MALME3M_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 243 105 DUSP6 1848 broad.mit.edu 37 12 89743180 89743190 + Frame_Shift_Del DEL TAGGGGATATG - - MALME3M_SKIN NA MALME3M_SKIN NA g.chr12:89743180_89743190delTAGGGGATATG uc001tay.2 - 3 1467_1477 c.987_997delCATATCCCCTA c.(985-999)AACATATCCCCTAACfs p.N329fs DUSP6_uc001taz.2_Frame_Shift_Del_p.N183fs NM_001946 NP_001937 Q16828 DUS6_HUMAN dual specificity phosphatase 6 isoform a 329_333 Tyrosine-protein phosphatase. dorsal/ventral pattern formation|inactivation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|nerve growth factor receptor signaling pathway|positive regulation of apoptosis|regulation of endodermal cell fate specification|regulation of fibroblast growth factor receptor signaling pathway|regulation of heart growth|response to nitrosative stress|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity 0 AAGTTGAAGTTAGGGGATATGTTGGATTTTT 0.488 0.12 1104 157 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 MALME3M_SKIN NA MALME3M_SKIN NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.53 21 24 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes MALME3M_SKIN NA MALME3M_SKIN NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.52 10 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MALME3M_SKIN NA MALME3M_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 62 406 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MALME3M_SKIN NA MALME3M_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 30 608 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes MALME3M_SKIN NA MALME3M_SKIN NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.23 416 125 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 1 21 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 523 154 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.26 121 42 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 69 83 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.35 68 36 CCND3 896 broad.mit.edu 37 6 41903683 41903689 + Frame_Shift_Del DEL GGTGTAT - - MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:41903683_41903689delGGTGTAT uc003orn.2 - 5 1033_1039 c.868_874delATACACC c.(868-876)ATACACCTGfs p.I290fs CCND3_uc003orp.2_Frame_Shift_Del_p.I209fs|CCND3_uc011duk.1_Frame_Shift_Del_p.I94fs|CCND3_uc003orm.2_Frame_Shift_Del_p.I240fs|CCND3_uc003oro.2_Frame_Shift_Del_p.I218fs NM_001760 NP_001751 P30281 CCND3_HUMAN cyclin D3 isoform 2 290_292 cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus protein kinase binding 0 Colorectal(47;0.121) Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152) CAGGGCTACAGGTGTATGGCTGTGACA 0.652 0.38 13 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.82 3 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 1 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 277 128 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.43 8 6 SMARCA4 6597 broad.mit.edu 37 19 11144179 11144190 + In_Frame_Del DEL GAGGAGCAGGAT - - MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:11144179_11144190delGAGGAGCAGGAT uc002mqf.3 + 26 4044_4055 c.3760_3771delGAGGAGCAGGAT c.(3760-3771)GAGGAGCAGGATdel p.EEQD1254del SMARCA4_uc010dxp.2_In_Frame_Del_p.EEQD1254del|SMARCA4_uc010dxo.2_In_Frame_Del_p.EEQD1254del|SMARCA4_uc010dxq.2_In_Frame_Del_p.EEQD1254del|SMARCA4_uc010dxr.2_In_Frame_Del_p.EEQD1254del|SMARCA4_uc002mqj.3_In_Frame_Del_p.EEQD1254del|SMARCA4_uc010dxs.2_In_Frame_Del_p.EEQD1254del|SMARCA4_uc010dxt.1_In_Frame_Del_p.EEQD474del|SMARCA4_uc002mqh.3_In_Frame_Del_p.EEQD377del|SMARCA4_uc002mqi.1_In_Frame_Del_p.EEQD457del NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 1254_1257 chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) CCTGGAGCACGAGGAGCAGGATGAGGTGAGCC 0.580 0.38 20 12 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.19 62 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 143 654 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 77 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MCAS_OVARY NA MCAS_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 37 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MCAS_OVARY NA MCAS_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.45 200 162 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes MCAS_OVARY NA MCAS_OVARY NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.56 8 10 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MCAS_OVARY NA MCAS_OVARY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 63 14 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MCAS_OVARY NA MCAS_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.26 32 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MCAS_OVARY NA MCAS_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.67 79 160 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MCAS_OVARY NA MCAS_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.21 64 17 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 MCAS_OVARY NA MCAS_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.60 146 222 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 MCAS_OVARY NA MCAS_OVARY NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.25 54 18 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 MCAS_OVARY NA MCAS_OVARY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.71 4 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MCAS_OVARY NA MCAS_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 51 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MCAS_OVARY NA MCAS_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 907 460 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MCAS_OVARY NA MCAS_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.73 4 11 RNF43 54894 broad.mit.edu 37 17 56438166 56438167 + Frame_Shift_Del DEL AG - - MCAS_OVARY NA MCAS_OVARY NA g.chr17:56438166_56438167delAG uc002iwf.2 - 6 2782_2783 c.826_827delCT c.(826-828)CTGfs p.L276fs RNF43_uc010wnv.1_Frame_Shift_Del_p.L235fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.L276fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.L276fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.L149fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 276 RING-type; atypical.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.54 1261 1487 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MCAS_OVARY NA MCAS_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 34 95 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MCAS_OVARY NA MCAS_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.95 30 613 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MCAS_OVARY NA MCAS_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.86 15 96 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MDAMB134VI_BREAST NA MDAMB134VI_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 46 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MDAMB134VI_BREAST NA MDAMB134VI_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 264 69 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MDAMB134VI_BREAST NA MDAMB134VI_BREAST NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 125 28 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MDAMB134VI_BREAST NA MDAMB134VI_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.49 83 79 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MDAMB134VI_BREAST NA MDAMB134VI_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.57 26 34 MYST3 7994 broad.mit.edu 37 8 41790713 41790714 + In_Frame_Ins INS - GGT GGT MDAMB134VI_BREAST NA MDAMB134VI_BREAST NA g.chr8:41790713_41790714insGGT uc010lxb.2 - 18 5568_5569 c.5024_5025insACC c.(5023-5025)CCC>CCACCC p.1675_1675P>PP MYST3_uc010lxc.2_In_Frame_Ins_p.1675_1675P>PP|MYST3_uc003xon.3_In_Frame_Ins_p.1675_1675P>PP NM_001099412 NP_001092882 Q92794 MYST3_HUMAN MYST histone acetyltransferase (monocytic 1675 Gln/Pro-rich. histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1) 7 all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211) all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983) Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171) gctgctgctggggtggtggagg 0.119 0.65 66 124 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 MDAMB134VI_BREAST NA MDAMB134VI_BREAST NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.47 10 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MDAMB134VI_BREAST NA MDAMB134VI_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 86 21 EIF4B 1975 broad.mit.edu 37 12 53433983 53433984 + Frame_Shift_Del DEL TG - - MDAMB134VI_BREAST NA MDAMB134VI_BREAST NA g.chr12:53433983_53433984delTG uc001sbh.3 + 15 2018_2019 c.1812_1813delTG c.(1810-1815)AATGAGfs p.N604fs EIF4B_uc010snu.1_Frame_Shift_Del_p.N609fs|EIF4B_uc010snv.1_Frame_Shift_Del_p.N565fs|EIF4B_uc001sbi.2_Frame_Shift_Del_p.N357fs|uc001sbj.1_RNA NM_001417 NP_001408 P23588 IF4B_HUMAN eukaryotic translation initiation factor 4B 604_605 insulin receptor signaling pathway|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation cytosol|eukaryotic translation initiation factor 4F complex nucleotide binding|translation initiation factor activity breast(1)|kidney(1) 2 AAGATGAAAATGAGGGAGAAGA 0.436 0.15 256 45 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MDAMB134VI_BREAST NA MDAMB134VI_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 2 30 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MDAMB134VI_BREAST NA MDAMB134VI_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 6 24 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MDAMB134VI_BREAST NA MDAMB134VI_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 86 444 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MDAMB134VI_BREAST NA MDAMB134VI_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 75 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.31 130 59 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 75 ARID1A 8289 broad.mit.edu 37 1 27101214 27101215 + Frame_Shift_Ins INS - G G MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr1:27101214_27101215insG uc001bmv.1 + 18 4869_4870 c.4496_4497insG c.(4495-4497)CAGfs p.Q1499fs ARID1A_uc001bmt.1_Frame_Shift_Ins_p.Q1498fs|ARID1A_uc001bmu.1_Intron|ARID1A_uc001bmw.1_Frame_Shift_Ins_p.Q1116fs|ARID1A_uc001bmx.1_Frame_Shift_Ins_p.Q345fs|ARID1A_uc009vsm.1_Intron|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1499 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) ACCATGTGGCAGGGGCGTAATG 0.584 0.88 19 145 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.73 4 11 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.22 56 16 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.10 176 20 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.67 97 199 NKD2 85409 broad.mit.edu 37 5 1038446 1038447 + In_Frame_Ins INS - CAC CAC rs3840989 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr5:1038446_1038447insCAC uc003jbt.1 + 10 1319_1320 c.1314_1315insCAC c.(1312-1317)insCAC p.447_448insH NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 447_448 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.39 259 163 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.37 81 48 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.37 175 102 NRG2 9542 broad.mit.edu 37 5 139422564 139422565 + In_Frame_Ins INS - GCT GCT MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr5:139422564_139422565insGCT uc003lex.1 - 1 315_316 c.90_91insAGC c.(88-93)insAGC p.30_31insS NRG2_uc003lev.1_In_Frame_Ins_p.30_31insS|NRG2_uc003lew.1_In_Frame_Ins_p.30_31insS|NRG2_uc003ley.1_In_Frame_Ins_p.30_31insS NM_004883 NP_004874 O14511 NRG2_HUMAN neuregulin 2 isoform 1 30_31 embryo development extracellular region|integral to membrane|plasma membrane growth factor activity pancreas(2)|breast(2)|ovary(1)|skin(1) 6 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) ctgctcctctcgctgctgctgc 0.322 0.27 35 13 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.59 16 23 PHKG1 5260 broad.mit.edu 37 7 56149336 56149337 + Frame_Shift_Ins INS - G G MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr7:56149336_56149337insG uc003trz.1 - 9 1099_1100 c.904_905insC c.(904-906)CGGfs p.R302fs PSPH_uc003trj.2_Intron|PHKG1_uc003try.1_Frame_Shift_Ins_p.R196fs|PHKG1_uc011kdb.1_Frame_Shift_Ins_p.R334fs|PHKG1_uc011kdc.1_Frame_Shift_Ins_p.R293fs|PHKG1_uc011kdd.1_Frame_Shift_Ins_p.R248fs NM_006213 NP_006204 Q16816 PHKG1_HUMAN phosphorylase kinase gamma subunit 1 302 glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process cytosol ATP binding|calmodulin binding|phosphorylase kinase activity large_intestine(1) 1 Breast(14;0.214) Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099) GAACTTCCCCCGGGGGCTGAAG 0.614 0.37 150 88 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 24 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 62 SMARCA2 6595 broad.mit.edu 37 9 2039774 2039776 + In_Frame_Del DEL CAA - - rs13296987 byFrequency MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr9:2039774_2039776delCAA uc003zhc.2 + 4 763_765 c.664_666delCAA c.(664-666)CAAdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) acagcagcagcaacagcagcagc 0.266 0.13 94 14 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.13 506 74 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.52 274 295 NCOR2 9612 broad.mit.edu 37 12 124887058 124887059 + In_Frame_Ins INS - GCTGCT GCTGCT rs35831183;rs67031864 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr12:124887058_124887059insGCTGCT uc010tba.1 - 14 1648_1649 c.1531_1532insAGCAGC c.(1531-1533)CCC>CAGCAGCCC p.510_511insQQ NCOR2_uc010tay.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010taz.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbb.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbc.1_In_Frame_Ins_p.509_510insQQ|NCOR2_uc001ugj.1_In_Frame_Ins_p.510_511insQQ NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 510_511 cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) GCGGGGCATGGgctgctgctgc 0.312 0.18 94 20 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.33 132 66 EP400 57634 broad.mit.edu 37 12 132547094 132547105 + In_Frame_Del DEL CAGCAGCAGCAG - - rs34444665;rs113304321;rs74479394;rs145603866;rs138126821;rs148607006 byFrequency;byFrequency MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr12:132547094_132547105delCAGCAGCAGCAG uc001ujn.2 + 46 8217_8228 c.8182_8193delCAGCAGCAGCAG c.(8182-8193)CAGCAGCAGCAGdel p.QQQQ2744del EP400_uc001ujl.2_In_Frame_Del_p.QQQQ2743del|EP400_uc001ujm.2_In_Frame_Del_p.QQQQ2663del|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2780_2783 Poly-Gln.|Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) gcagcaacaacagcagcagcagcagcagcagc 0.321 0.21 204 55 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 19 189 NF1 4763 broad.mit.edu 37 17 29665752 29665755 + Frame_Shift_Del DEL ACTT - - MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr17:29665752_29665755delACTT uc002hgg.2 + 46 7183_7186 c.6850_6853delACTT c.(6850-6855)ACTTACfs p.T2284fs NF1_uc002hgh.2_Frame_Shift_Del_p.T2263fs|NF1_uc010cso.2_Frame_Shift_Del_p.T472fs|NF1_uc010wbt.1_Intron|NF1_uc010wbu.1_RNA NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 2284_2285 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.Y2285fs*5(4) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) AGGACCTGACACTTACAACAGTCA 0.319 0.40 79 53 TRIM37 4591 broad.mit.edu 37 17 57141768 57141769 + Splice_Site INS - A A rs147621691 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr17:57141768_57141769insA uc002iwy.3 - 10 1254 c.810_splice c.e10-1 p.S270_splice TRIM37_uc002iwz.3_Splice_Site_p.S270_splice|TRIM37_uc002ixa.3_Splice_Site_p.S148_splice|TRIM37_uc010woc.1_Splice_Site_p.S236_splice NM_001005207 NP_001005207 O94972 TRI37_HUMAN tripartite motif-containing 37 protein perinuclear region of cytoplasm|peroxisome ligase activity|protein binding|zinc ion binding lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1) 7 Medulloblastoma(34;0.0922)|all_neural(34;0.101) ACTAATTCACTAAAAAAAAAAA 0.272 0.30 26 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 32 139 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 322 40 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 112 467 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 116 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 MDAMB175VII_BREAST NA MDAMB175VII_BREAST NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.40 262 173 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MDAMB231_BREAST NA MDAMB231_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 42 GAK 2580 broad.mit.edu 37 4 860791 860791 + Frame_Shift_Del DEL G - - MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr4:860791delG uc003gbm.3 - 21 3024 c.2825delC c.(2824-2826)CCTfs p.P942fs GAK_uc003gbn.3_Frame_Shift_Del_p.P863fs|GAK_uc010ibk.1_Frame_Shift_Del_p.P836fs|GAK_uc010ibi.2_Frame_Shift_Del_p.P123fs|GAK_uc010ibj.2_RNA|GAK_uc003gbl.3_Frame_Shift_Del_p.P806fs NM_005255 NP_005246 O14976 GAK_HUMAN cyclin G associated kinase 942 cell cycle focal adhesion|Golgi apparatus|perinuclear region of cytoplasm ATP binding|heat shock protein binding|protein serine/threonine kinase activity lung(2)|central_nervous_system(1)|skin(1) 4 Colorectal(103;0.219) 0.000 0.60 456 690 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.23 27 8 FGF2 2247 broad.mit.edu 37 4 123748258 123748259 + Frame_Shift_Ins INS - G G MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr4:123748258_123748259insG uc003iev.1 + 1 396_397 c.328_329insG c.(328-330)CGGfs p.R110fs NM_002006 NP_001997 P09038 FGF2_HUMAN fibroblast growth factor 2 110 activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing extracellular space fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity ovary(1)|lung(1)|central_nervous_system(1) 3 Pentosan Polysulfate(DB00686) 0.000 0.10 93 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 67 73 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.22 43 12 HMMR 3161 broad.mit.edu 37 5 162917425 162917426 + Frame_Shift_Ins INS - A A MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr5:162917425_162917426insA uc003lzf.2 + 17 2171_2172 c.1989_1990insA c.(1987-1992)GCTAAAfs p.A663fs HMMR_uc003lzh.2_Frame_Shift_Ins_p.A664fs|HMMR_uc003lzg.2_Frame_Shift_Ins_p.A648fs|HMMR_uc011dem.1_Frame_Shift_Ins_p.A577fs|uc003lzi.2_Intron NM_012484 NP_036616 O75330 HMMR_HUMAN hyaluronan-mediated motility receptor isoform b 663_664 Hyaluronic acid-binding (Potential). cell surface|cytoplasm hyaluronic acid binding 0 Renal(175;0.000281) Medulloblastoma(196;0.00853)|all_neural(177;0.0408) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848) GTCAGCTTGCTAAAAAAAAACA 0.307 0.55 14 17 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.17 1232 255 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.45 12 10 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.12 87 12 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.63 38 64 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 222 75 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 29 292 NF1 4763 broad.mit.edu 37 17 29541474 29541475 + Frame_Shift_Ins INS - C C MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr17:29541474_29541475insC uc002hgg.2 + 13 1731_1732 c.1398_1399insC c.(1396-1401)CTTACAfs p.L466fs NF1_uc002hge.1_Frame_Shift_Ins_p.L466fs|NF1_uc002hgf.1_Frame_Shift_Ins_p.L466fs|NF1_uc002hgh.2_Frame_Shift_Ins_p.L466fs|NF1_uc010csn.1_Frame_Shift_Ins_p.L326fs NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 466_467 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) TTTAGAGTCTTACATTTAAAGA 0.287 1.00 0 15 TRIM37 4591 broad.mit.edu 37 17 57141768 57141769 + Splice_Site INS - A A rs147621691 MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr17:57141768_57141769insA uc002iwy.3 - 10 1254 c.810_splice c.e10-1 p.S270_splice TRIM37_uc002iwz.3_Splice_Site_p.S270_splice|TRIM37_uc002ixa.3_Splice_Site_p.S148_splice|TRIM37_uc010woc.1_Splice_Site_p.S236_splice NM_001005207 NP_001005207 O94972 TRI37_HUMAN tripartite motif-containing 37 protein perinuclear region of cytoplasm|peroxisome ligase activity|protein binding|zinc ion binding lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1) 7 Medulloblastoma(34;0.0922)|all_neural(34;0.101) ACTAATTCACTAAAAAAAAAAA 0.272 0.62 5 8 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.13 976 147 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.20 33 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 130 679 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MDAMB231_BREAST NA MDAMB231_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 4 38 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MDAMB361_BREAST NA MDAMB361_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 4 46 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MDAMB361_BREAST NA MDAMB361_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 219 73 ARNT 405 broad.mit.edu 37 1 150785729 150785737 + In_Frame_Del DEL CTGCTGGCC - - MDAMB361_BREAST NA MDAMB361_BREAST NA g.chr1:150785729_150785737delCTGCTGGCC uc001evr.1 - 21 2334_2342 c.2191_2199delGGCCAGCAG c.(2191-2199)GGCCAGCAGdel p.GQQ731del ARNT_uc010pck.1_In_Frame_Del_p.GQQ219del|ARNT_uc001evs.1_In_Frame_Del_p.GQQ716del|ARNT_uc009wmb.1_In_Frame_Del_p.GQQ717del|ARNT_uc009wmc.1_In_Frame_Del_p.GQQ729del|ARNT_uc009wmd.1_In_Frame_Del_p.GQQ715del NM_001668 NP_001659 P27540 ARNT_HUMAN aryl hydrocarbon receptor nuclear translocator 731_733 Gln-rich. positive regulation of hormone biosynthetic process|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|response to hypoxia aryl hydrocarbon receptor binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity skin(4)|lung(3)|central_nervous_system(1)|kidney(1) 9 all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211) GATGATGAGGCTGCTGGCCCTGCCACTGT 0.531 0.38 58 36 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MDAMB361_BREAST NA MDAMB361_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 76 123 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MDAMB361_BREAST NA MDAMB361_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.45 63 51 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MDAMB361_BREAST NA MDAMB361_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 1 10 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MDAMB361_BREAST NA MDAMB361_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.38 8 5 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MDAMB361_BREAST NA MDAMB361_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 266 28 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - MDAMB361_BREAST NA MDAMB361_BREAST NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.12 98 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MDAMB361_BREAST NA MDAMB361_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 181 81 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MDAMB361_BREAST NA MDAMB361_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 61 768 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MDAMB361_BREAST NA MDAMB361_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.64 18 32 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MDAMB361_BREAST NA MDAMB361_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 52 192 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MDAMB361_BREAST NA MDAMB361_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 106 ELK1 2002 broad.mit.edu 37 X 47496437 47496437 + Frame_Shift_Del DEL C - - MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chrX:47496437delC uc004dik.3 - 6 1485 c.1163delG c.(1162-1164)CGTfs p.R388fs ELK1_uc010nhv.2_Frame_Shift_Del_p.R388fs|ELK1_uc010nhw.2_Frame_Shift_Del_p.R278fs|ELK1_uc004dil.3_RNA NM_001114123 NP_001107595 P19419 ELK1_HUMAN ELK1 protein 388 Sufficient for interaction with MAD2L2. innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity ovary(2) 2 0.000 0.38 10 6 Unknown 0 broad.mit.edu 37 X 80185320 80185321 + Frame_Shift_Ins INS - A A MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chrX:80185320_80185321insA uc004eec.1 + 1 393_394 c.219_220insA c.(217-222)GGGAAAfs p.G73fs SubName: Full=cDNA FLJ16670 fis, clone THYMU3001133, highly similar to Voltage-dependent anion-selective channel protein 1; SubName: Full=Voltage-dependent anion channel 1, isoform CRA_a; CTAACACTGGGAAAAAAAATGC 0.485 0.37 114 66 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.53 28 32 HORMAD1 84072 broad.mit.edu 37 1 150672622 150672622 + Frame_Shift_Del DEL T - - MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr1:150672622delT uc001evk.1 - 14 1176 c.1070delA c.(1069-1071)AATfs p.N357fs GOLPH3L_uc001evj.2_5'Flank|GOLPH3L_uc010pci.1_5'Flank|HORMAD1_uc001evl.1_Frame_Shift_Del_p.N350fs|HORMAD1_uc001evm.1_Frame_Shift_Del_p.N277fs NM_032132 NP_115508 Q86X24 HORM1_HUMAN HORMA domain containing 1 357 blastocyst development|cell differentiation|meiotic DNA double-strand break formation|meiotic recombination checkpoint|meiotic sister chromatid cohesion|mitosis|oogenesis|regulation of homologous chromosome segregation|spermatogenesis|synaptonemal complex assembly chromosome|nucleus ovary(2)|central_nervous_system(1) 3 all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171) UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171) TCTCTTCCGATTTTCTTTGGA 0.318 0.55 51 62 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.30 61 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.73 61 164 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.84 12 64 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.72 5 13 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.81 6 25 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.35 15 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 3 77 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.17 221 45 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.31 11 5 HERC2 8924 broad.mit.edu 37 15 28501091 28501092 + Frame_Shift_Del DEL AG - - MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr15:28501091_28501092delAG uc001zbj.2 - 19 2903_2904 c.2797_2798delCT c.(2797-2799)CTTfs p.L933fs HERC2_uc001zbl.1_Frame_Shift_Del_p.L628fs NM_004667 NP_004658 O95714 HERC2_HUMAN hect domain and RLD 2 933 DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process nucleus guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1) 13 all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227) all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199) GCCCACCAGAAGATCAATCATG 0.490 0.10 108 12 MEF2A 4205 broad.mit.edu 37 15 100252710 100252712 + In_Frame_Del DEL CAG - - MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr15:100252710_100252712delCAG uc010urw.1 + 11 1617_1619 c.1258_1260delCAG c.(1258-1260)CAGdel p.Q430del MEF2A_uc010urv.1_In_Frame_Del_p.Q360del|MEF2A_uc010bos.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvf.2_In_Frame_Del_p.Q422del|MEF2A_uc002bve.2_In_Frame_Del_p.Q428del|MEF2A_uc002bvg.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvi.2_In_Frame_Del_p.Q420del|MEF2A_uc010bot.2_In_Frame_Del_p.Q352del NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 430 Gln/Pro-rich. Missing (in Ref. 4; AAB17195/AAB17196). apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) ATCGGGCTTCcagcagcagcagc 0.493 0.29 17 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 33 397 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.15 56 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 149 92 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.54 12 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 77 200 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MDAMB435S_SKIN NA MDAMB435S_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 4 39 BTK 695 broad.mit.edu 37 X 100617657 100617672 + Frame_Shift_Del DEL GATCACTGTTGTACCG - - rs141567416 MDAMB436_BREAST NA MDAMB436_BREAST NA g.chrX:100617657_100617672delGATCACTGTTGTACCG uc004ehg.2 - 6 590_605 c.397_412delCGGTACAACAGTGATC c.(397-414)CGGTACAACAGTGATCTGfs p.R133fs BTK_uc010nnn.2_Frame_Shift_Del_p.R133fs|BTK_uc010nno.2_Frame_Shift_Del_p.R167fs|BTK_uc004ehi.2_Frame_Shift_Del_p.R133fs NM_000061 NP_000052 Q06187 BTK_HUMAN Bruton agammaglobulinemia tyrosine kinase 133_138 Btk-type. calcium-mediated signaling|induction of apoptosis by extracellular signals|mesoderm development cytosol|membrane raft|nucleus|plasma membrane ATP binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol-3,4,5-trisphosphate binding lung(3)|central_nervous_system(2)|ovary(1) 6 TTCTGAACCAGATCACTGTTGTACCGGATTACTGTA 0.458 0.45 142 115 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MDAMB436_BREAST NA MDAMB436_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.46 45 38 OBSCN 84033 broad.mit.edu 37 1 228463615 228463617 + In_Frame_Del DEL CGC - - MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr1:228463615_228463617delCGC uc009xez.1 + 21 6152_6154 c.6108_6110delCGC c.(6106-6111)CACGCC>CAC p.A2037del OBSCN_uc001hsn.2_In_Frame_Del_p.A2037del|OBSCN_uc001hsp.1_5'Flank NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 2037 Ig-like 20. apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) 0.000 0.35 389 207 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.50 12 12 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.11 54 7 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.23 53 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 87 76 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.77 25 83 CDKL3 51265 broad.mit.edu 37 5 133655167 133655185 + Frame_Shift_Del DEL TGCAAGTGAGGTGACAAAT - - MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr5:133655167_133655185delTGCAAGTGAGGTGACAAAT uc003kzf.3 - 6 775_793 c.656_674delATTTGTCACCTCACTTGCA c.(655-675)AATTTGTCACCTCACTTGCAGfs p.N219fs CDKL3_uc011cxm.1_Frame_Shift_Del_p.N26fs|CDKL3_uc011cxn.1_Intron|CDKL3_uc010jdw.2_5'UTR|CDKL3_uc011cxo.1_5'UTR|CDKL3_uc011cxp.1_Intron|CDKL3_uc011cxq.1_Frame_Shift_Del_p.N26fs|CDKL3_uc003kzg.3_Frame_Shift_Del_p.N219fs|CDKL3_uc011cxr.1_Frame_Shift_Del_p.N219fs NM_001113575 NP_001107047 Q8IVW4 CDKL3_HUMAN cyclin-dependent kinase-like 3 isoform 1 219_225 Protein kinase. cytoplasm ATP binding|cyclin-dependent protein kinase activity breast(1) 1 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) AAAGATATTCTGCAAGTGAGGTGACAAATTGCCTGAAAA 0.320 0.56 36 45 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.77 3 10 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.91 1 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 30 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.38 10 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 294 66 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.55 25 31 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 41 206 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MDAMB436_BREAST NA MDAMB436_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 4 46 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MDAMB453_BREAST NA MDAMB453_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 72 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MDAMB453_BREAST NA MDAMB453_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.20 107 26 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MDAMB453_BREAST NA MDAMB453_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.55 62 77 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MDAMB453_BREAST NA MDAMB453_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.92 1 12 WHSC1L1 54904 broad.mit.edu 37 8 38176449 38176458 + Frame_Shift_Del DEL CTGTTTCAAC - - MDAMB453_BREAST NA MDAMB453_BREAST NA g.chr8:38176449_38176458delCTGTTTCAAC uc003xli.2 - 9 2328_2337 c.1810_1819delGTTGAAACAG c.(1810-1821)GTTGAAACAGTTfs p.V604fs WHSC1L1_uc011lbm.1_Frame_Shift_Del_p.V604fs|WHSC1L1_uc010lwe.2_Frame_Shift_Del_p.V604fs|WHSC1L1_uc003xlj.2_Frame_Shift_Del_p.V604fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 604_607 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) GCCTGAGGAACTGTTTCAACCTGTTTGGAC 0.300 0.16 689 133 CASC5 57082 broad.mit.edu 37 15 40939253 40939253 + Frame_Shift_Del DEL C - - MDAMB453_BREAST NA MDAMB453_BREAST NA g.chr15:40939253delC uc010bbs.1 + 18 6314 c.6153delC c.(6151-6153)TGCfs p.C2051fs CASC5_uc010bbt.1_Frame_Shift_Del_p.C2025fs NM_170589 NP_733468 Q8NG31 CASC5_HUMAN cancer susceptibility candidate 5 isoform 1 2051 Necessary for kinetochore localization and for interaction with NSL1 and DSN1.|Potential. acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm protein binding breast(3)|central_nervous_system(1)|skin(1) 5 all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946) GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211) TCGATAACTGCCTCACTGAGA 0.303 0.14 522 85 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MDAMB453_BREAST NA MDAMB453_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 42 210 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.20 28 7 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.53 38 42 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.26 324 114 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.33 41 20 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.64 60 108 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.38 8 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.75 40 118 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.84 7 38 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.69 4 9 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.33 35 17 ARID1B 57492 broad.mit.edu 37 6 157099402 157099403 + In_Frame_Ins INS - CAG CAG MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr6:157099402_157099403insCAG uc003qqn.2 + 1 317_318 c.165_166insCAG c.(163-168)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) TAAACCAGTTCcagcagcagca 0.124 0.45 75 62 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.83 2 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 2 36 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.81 5 21 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.52 11 12 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.65 43 79 CSNK1G1 53944 broad.mit.edu 37 15 64497132 64497135 + Frame_Shift_Del DEL TCTT - - MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr15:64497132_64497135delTCTT uc002anf.2 - 8 1259_1262 c.779_782delAAGA c.(778-783)AAAGAGfs p.K260fs CSNK1G1_uc002ane.2_RNA|CSNK1G1_uc002ang.1_Frame_Shift_Del_p.K260fs|CSNK1G1_uc002anh.1_Frame_Shift_Del_p.K260fs|CSNK1G1_uc002anj.2_Frame_Shift_Del_p.K242fs NM_022048 NP_071331 Q9HCP0 KC1G1_HUMAN casein kinase 1, gamma 1 260_261 Protein kinase. Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity 0 TTGATATCTCTCTTTTAATGTGTC 0.382 0.98 2 97 ERBB2 2064 broad.mit.edu 37 17 37865585 37865585 + Frame_Shift_Del DEL G - - MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr17:37865585delG uc002hso.2 + 4 692 c.454delG c.(454-456)GGGfs p.G152fs ERBB2_uc002hsm.2_Frame_Shift_Del_p.G122fs|ERBB2_uc010cwa.2_Frame_Shift_Del_p.G137fs|ERBB2_uc002hsp.2_5'UTR|ERBB2_uc010cwb.2_Frame_Shift_Del_p.G152fs|ERBB2_uc010wek.1_Intron|ERBB2_uc002hsl.2_Frame_Shift_Del_p.G122fs|ERBB2_uc002hsn.1_Frame_Shift_Del_p.G152fs NM_004448 NP_004439 P04626 ERBB2_HUMAN erbB-2 isoform a 152 Extracellular (Potential). cell proliferation|heart development|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of cell adhesion|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|protein autophosphorylation|regulation of angiogenesis|regulation of microtubule-based process|regulation of transcription, DNA-dependent|transcription, DNA-dependent|wound healing integral to membrane|nucleus|perinuclear region of cytoplasm|receptor complex ATP binding|DNA binding|epidermal growth factor receptor activity|ErbB-3 class receptor binding|identical protein binding|protein C-terminus binding|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity lung(73)|central_nervous_system(16)|ovary(16)|stomach(14)|breast(9)|upper_aerodigestive_tract(5)|large_intestine(3)|liver(3)|endometrium(2)|skin(1)|pancreas(1) 143 all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052) Ovarian(249;0.0547)|Colorectal(1115;0.234) UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171) UCEC - Uterine corpus endometrioid carcinoma (308;0.0767) Lapatinib(DB01259)|Letrozole(DB01006)|Trastuzumab(DB00072) CTTGAAAGGAGGGGTCTTGAT 0.532 0.93 3 41 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.38 40 25 NOTCH3 4854 broad.mit.edu 37 19 15272336 15272337 + Frame_Shift_Ins INS - G G rs114887570 by1000genomes MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr19:15272336_15272337insG uc002nan.2 - 33 6178_6179 c.6102_6103insC c.(6100-6105)CCCGGTfs p.P2034fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 2034_2035 Cytoplasmic (Potential). Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.21 675 183 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 91 224 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.15 67 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.67 31 62 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 47 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 MDAMB468_BREAST NA MDAMB468_BREAST NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.55 151 183 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.25 42 14 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.63 16 27 PRDM16 63976 broad.mit.edu 37 1 3102984 3102984 + Frame_Shift_Del DEL C - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr1:3102984delC uc001akf.2 + 2 413 c.333delC c.(331-333)GGCfs p.G111fs PRDM16_uc001akc.2_Frame_Shift_Del_p.G111fs|PRDM16_uc001akd.2_Frame_Shift_Del_p.G111fs|PRDM16_uc001ake.2_Frame_Shift_Del_p.G111fs|PRDM16_uc009vlh.2_5'UTR NM_022114 NP_071397 Q9HAZ2 PRD16_HUMAN PR domain containing 16 isoform 1 111 SET. brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent transcriptional repressor complex protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1) 7 all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111) all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134) Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137) AGAGGCTGGGCCCCTGCGTGG 0.637 0.65 12 22 SPEN 23013 broad.mit.edu 37 1 16257322 16257322 + Frame_Shift_Del DEL T - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr1:16257322delT uc001axk.1 + 11 4791 c.4587delT c.(4585-4587)CGTfs p.R1529fs SPEN_uc010obp.1_Frame_Shift_Del_p.R1488fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 1529 Potential. interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) TTGCTTCTCGTTTTTTACACA 0.383 0.26 59 21 NFIA 4774 broad.mit.edu 37 1 61553917 61553917 + Frame_Shift_Del DEL A - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr1:61553917delA uc001czw.2 + 2 608 c.124delA c.(124-126)AAAfs p.K42fs NFIA_uc001czy.2_Frame_Shift_Del_p.K34fs|NFIA_uc010oos.1_Frame_Shift_Del_p.K87fs|NFIA_uc001czv.2_Frame_Shift_Del_p.K42fs NM_001134673 NP_001128145 Q12857 NFIA_HUMAN nuclear factor I/A isoform 1 42 CTF/NF-I. DNA replication|viral genome replication cell junction|nucleus DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding pancreas(1)|skin(1) 2 AAAATACTTCAAAAAACATGA 0.453 0.41 17 12 RIF1 55183 broad.mit.edu 37 2 152319553 152319553 + Frame_Shift_Del DEL A - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr2:152319553delA uc002txm.2 + 30 3649 c.3519delA c.(3517-3519)AGAfs p.R1173fs RIF1_uc002txl.2_Frame_Shift_Del_p.R1173fs|RIF1_uc002txn.2_Frame_Shift_Del_p.R1173fs|RIF1_uc002txo.2_Frame_Shift_Del_p.R1173fs|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1173 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) ATGATGAAAGAAAAAAAGCTT 0.353 0.42 21 15 TTN 7273 broad.mit.edu 37 2 179505993 179505993 + Frame_Shift_Del DEL T - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr2:179505993delT uc010zfg.1 - 169 33128 c.32904delA c.(32902-32904)AAAfs p.K10968fs TTN_uc010zfh.1_Frame_Shift_Del_p.K4663fs|TTN_uc010zfi.1_Frame_Shift_Del_p.K4596fs|TTN_uc010zfj.1_Frame_Shift_Del_p.K4471fs|TTN_uc010fre.1_Frame_Shift_Del_p.K846fs|TTN_uc002umw.1_Intron|TTN_uc002umx.1_Intron NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 11895 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CTTTTTCTAGTTTTTTAGGTT 0.284 0.39 28 18 ERBB4 2066 broad.mit.edu 37 2 212568865 212568866 + Frame_Shift_Ins INS - A A MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr2:212568865_212568866insA uc002veg.1 - 11 1350_1351 c.1252_1253insT c.(1252-1254)TCTfs p.S418fs ERBB4_uc002veh.1_Frame_Shift_Ins_p.S418fs|ERBB4_uc010zji.1_Frame_Shift_Ins_p.S418fs|ERBB4_uc010zjj.1_Frame_Shift_Ins_p.S418fs|ERBB4_uc010fut.1_Frame_Shift_Ins_p.S418fs NM_005235 NP_005226 Q15303 ERBB4_HUMAN v-erb-a erythroblastic leukemia viral oncogene 418 Extracellular (Potential). cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway basolateral plasma membrane|cytoplasm|integral to membrane|nucleus ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 33 Renal(323;0.06)|Lung NSC(271;0.197) UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266) CACCAGGTTAGAAAAAACACTG 0.391 0.54 17 20 DCLK3 85443 broad.mit.edu 37 3 36779824 36779824 + Frame_Shift_Del DEL G - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr3:36779824delG uc003cgi.2 - 2 818 c.327delC c.(325-327)CCCfs p.P109fs NM_033403 NP_208382 Q9C098 DCLK3_HUMAN doublecortin-like kinase 3 109 cytoplasm|nucleus ATP binding|protein serine/threonine kinase activity lung(3)|large_intestine(2)|breast(1)|skin(1)|ovary(1)|kidney(1) 9 TGGCTTCCCTGGGGGGCTTGC 0.562 0.46 192 161 PBRM1 55193 broad.mit.edu 37 3 52682399 52682400 + Frame_Shift_Ins INS - T T MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr3:52682399_52682400insT uc003des.2 - 7 785_786 c.773_774insA c.(772-774)AATfs p.N258fs PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Ins_p.N258fs|PBRM1_uc003der.2_Frame_Shift_Ins_p.N258fs|PBRM1_uc003det.2_Frame_Shift_Ins_p.N258fs|PBRM1_uc003deu.2_Frame_Shift_Ins_p.N258fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Ins_p.N258fs|PBRM1_uc010hmk.1_Frame_Shift_Ins_p.N258fs|PBRM1_uc003dey.2_Frame_Shift_Ins_p.N258fs|PBRM1_uc003dez.1_Frame_Shift_Ins_p.N258fs|PBRM1_uc003dfb.1_Frame_Shift_Ins_p.N156fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 258 Bromo 2. chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.44 154 119 FLNB 2317 broad.mit.edu 37 3 58140654 58140654 + Frame_Shift_Del DEL T - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr3:58140654delT uc003djj.2 + 40 6936 c.6771delT c.(6769-6771)CCTfs p.P2257fs FLNB_uc010hne.2_Frame_Shift_Del_p.P2288fs|FLNB_uc003djk.2_Frame_Shift_Del_p.P2246fs|FLNB_uc010hnf.2_Frame_Shift_Del_p.P2233fs|FLNB_uc003djl.2_Frame_Shift_Del_p.P2077fs|FLNB_uc003djm.2_Frame_Shift_Del_p.P2064fs NM_001457 NP_001448 O75369 FLNB_HUMAN filamin B isoform 2 2257 Interaction with INPPL1.|Filamin 21. actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction cell cortex|integral to membrane|nucleus|sarcomere actin binding breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1) 19 BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898) CCCAAGAGCCTGGTATGTATT 0.353 0.56 7 9 FOXP1 27086 broad.mit.edu 37 3 71021797 71021798 + Frame_Shift_Del DEL TG - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr3:71021797_71021798delTG uc003dol.2 - 14 1883_1884 c.1560_1561delCA c.(1558-1563)CACAAGfs p.H520fs FOXP1_uc003dom.2_Frame_Shift_Del_p.H444fs|FOXP1_uc003don.2_RNA|FOXP1_uc003doo.2_Frame_Shift_Del_p.H519fs|FOXP1_uc003dop.2_Frame_Shift_Del_p.H520fs|FOXP1_uc003doq.1_Intron|FOXP1_uc003doi.2_Frame_Shift_Del_p.H420fs|FOXP1_uc003doj.2_Frame_Shift_Del_p.H420fs|FOXP1_uc003dok.2_Frame_Shift_Del_p.H333fs|FOXP1_uc003dor.1_Frame_Shift_Del_p.H297fs NM_032682 NP_116071 Q9H334 FOXP1_HUMAN forkhead box P1 isoform 1 520_521 Fork-head. cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development cytoplasm|transcription factor complex chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding ovary(1)|lung(1) 2 Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209) BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05) ACAAAACACTTGTGAAGACTAA 0.386 0.45 129 107 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.58 5 7 TNK2 10188 broad.mit.edu 37 3 195595228 195595229 + Frame_Shift_Ins INS - G G MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr3:195595228_195595229insG uc003fvu.1 - 12 2438_2439 c.1895_1896insC c.(1894-1896)CCGfs p.P632fs TNK2_uc003fvq.1_Frame_Shift_Ins_p.P39fs|TNK2_uc003fvr.1_Frame_Shift_Ins_p.P157fs|TNK2_uc003fvs.1_Frame_Shift_Ins_p.P664fs|TNK2_uc003fvt.1_Frame_Shift_Ins_p.P710fs|TNK2_uc010hzw.1_RNA|TNK2_uc003fvv.1_3'UTR NM_005781 NP_005772 Q07912 ACK1_HUMAN tyrosine kinase, non-receptor, 2 isoform 1 632 Required for interaction with SRC.|Required for interaction with NEDD4 (By similarity).|Pro-rich. Missing (in Ref. 4; AAH08884). positive regulation of peptidyl-tyrosine phosphorylation|protein ubiquitination|small GTPase mediated signal transduction adherens junction|cytoplasmic vesicle membrane|endosome|nucleus ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1) 10 all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206) Lung NSC(153;0.191) Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05) GBM - Glioblastoma multiforme(46;0.000757) Adenosine triphosphate(DB00171) CATAGGCGGGCGGGGGGGGCAG 0.728 0.38 21 13 BMP2K 55589 broad.mit.edu 37 4 79792082 79792083 + In_Frame_Ins INS - CAG CAG rs5859654;rs35071794 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr4:79792082_79792083insCAG uc003hlk.2 + 11 1543_1544 c.1377_1378insCAG c.(1375-1380)insCAG p.486_487insQ BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Ins_p.486_487insQ|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486_487 Gln/His-rich. nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 GTCATCCTCACcagcagcagca 0.262 0.23 267 81 AFF1 4299 broad.mit.edu 37 4 88036342 88036343 + Frame_Shift_Ins INS - G G MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr4:88036342_88036343insG uc003hqj.3 + 11 2743_2744 c.2336_2337insG c.(2335-2337)AAGfs p.K779fs AFF1_uc011ccz.1_Frame_Shift_Ins_p.K786fs|AFF1_uc003hqk.3_Frame_Shift_Ins_p.K779fs|AFF1_uc011cda.1_Frame_Shift_Ins_p.K417fs NM_005935 NP_005926 P51825 AFF1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 779 nucleus sequence-specific DNA binding transcription factor activity breast(1) 1 Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114) OV - Ovarian serous cystadenocarcinoma(123;0.000233) CCTCCCGGGAAGGGGAGCCGCC 0.579 0.25 24 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 86 202 MAML3 55534 broad.mit.edu 37 4 140811064 140811096 + Splice_Site DEL TGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC - - rs72203913;rs13108712;rs12506879;rs67877726;rs72161425;rs79090010 by1000genomes;by1000genomes MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr4:140811064_140811096delTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC uc003ihz.1 - 2 2264 c.1512_splice c.e2+1 p.Q504_splice MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) TGAGtgctgttgctgctgctgctgctgctgctgctgctgctgctgctgctgct 0.288 0.21 496 134 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 45 28 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.50 6 6 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.17 86 18 FANCE 2178 broad.mit.edu 37 6 35425715 35425715 + Frame_Shift_Del DEL C - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr6:35425715delC uc003oko.1 + 4 1108 c.923delC c.(922-924)GCCfs p.A308fs FANCE_uc010jvw.1_Frame_Shift_Del_p.A308fs NM_021922 NP_068741 Q9HB96 FANCE_HUMAN Fanconi anemia, complementation group E 308 Interaction with FANCC. DNA repair nucleoplasm protein binding ovary(1)|lung(1)|skin(1) 3 TTGGAGGATGCCCCCCCAGTT 0.542 0.35 44 24 PHF3 23469 broad.mit.edu 37 6 64395267 64395267 + Frame_Shift_Del DEL A - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr6:64395267delA uc003pep.1 + 3 1670 c.1644delA c.(1642-1644)AGAfs p.R548fs PHF3_uc010kaf.1_Frame_Shift_Del_p.R548fs|PHF3_uc003pem.2_Frame_Shift_Del_p.R501fs|PHF3_uc010kag.1_Frame_Shift_Del_p.R460fs|PHF3_uc010kah.1_Frame_Shift_Del_p.R362fs|PHF3_uc003pen.2_Frame_Shift_Del_p.R460fs|PHF3_uc011dxs.1_Intron|PHF3_uc003peo.2_Frame_Shift_Del_p.R548fs NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 548 multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) TCAAAGTCAGAAAAAAACAAA 0.333 0.50 9 9 PRKAR1B 5575 broad.mit.edu 37 7 720281 720281 + Frame_Shift_Del DEL G - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr7:720281delG uc003siu.1 - 4 366 c.260delC c.(259-261)CCGfs p.P87fs PRKAR1B_uc003siv.2_Frame_Shift_Del_p.P87fs|PRKAR1B_uc003siw.1_Frame_Shift_Del_p.P87fs NM_002735 NP_002726 P31321 KAP1_HUMAN protein kinase, cAMP-dependent, regulatory, type 87 Dimerization and phosphorylation. activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport cAMP-dependent protein kinase complex|cytosol cAMP binding|cAMP-dependent protein kinase regulator activity 0 Ovarian(82;0.0779) UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152) CACAGGGTTCGGGGGGGTGGG 0.617 0.29 165 68 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 22 MLL3 58508 broad.mit.edu 37 7 151842355 151842355 + Frame_Shift_Del DEL T - - rs141106704 by1000genomes MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr7:151842355delT uc003wla.2 - 54 14276 c.14057delA c.(14056-14058)AATfs p.N4686fs MLL3_uc003wkz.2_Frame_Shift_Del_p.N3804fs|MLL3_uc003wkx.2_Frame_Shift_Del_p.N844fs|MLL3_uc003wky.2_Frame_Shift_Del_p.N2250fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 4686 FYR C-terminal. intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) GAAGGTATAATTTTCACATGC 0.483 0.39 46 29 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.88 3 23 ERLIN2 11160 broad.mit.edu 37 8 37611633 37611633 + Frame_Shift_Del DEL A - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr8:37611633delA uc003xke.3 + 12 1135 c.1020delA c.(1018-1020)TGAfs p.*340fs NM_007175 NP_009106 O94905 ERLN2_HUMAN ER lipid raft associated 2 isoform 1 340 ER-associated protein catabolic process endoplasmic reticulum membrane|integral to membrane|plasma membrane protein binding 0 Lung NSC(58;0.174) BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10) AGGAGAATTGAAAAAAACTTG 0.438 0.75 3 9 ADHFE1 137872 broad.mit.edu 37 8 67356834 67356834 + Frame_Shift_Del DEL A - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr8:67356834delA uc003xwb.3 + 5 238 c.204delA c.(202-204)CTAfs p.L68fs ADHFE1_uc003xwd.3_RNA|ADHFE1_uc003xwc.3_Frame_Shift_Del_p.L20fs|ADHFE1_uc003xwe.3_RNA|ADHFE1_uc003xwf.3_RNA|ADHFE1_uc011les.1_5'UTR|ADHFE1_uc011leq.1_RNA|ADHFE1_uc011ler.1_RNA NM_144650 NP_653251 Q8IWW8 HOT_HUMAN alcohol dehydrogenase, iron containing, 1 68 2-oxoglutarate metabolic process|molecular hydrogen transport mitochondrial matrix hydroxyacid-oxoacid transhydrogenase activity|metal ion binding ovary(1)|lung(1)|breast(1)|skin(1) 4 Lung NSC(129;0.197) Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226) TGTAGGACCTAAAAAACATGG 0.408 0.61 75 115 VPS13B 157680 broad.mit.edu 37 8 100654474 100654474 + Frame_Shift_Del DEL A - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr8:100654474delA uc003yiv.2 + 34 5842 c.5731delA c.(5731-5733)AAAfs p.K1911fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.K1886fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 1911 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TCCTTCAGGGAAAAAAATAGG 0.458 0.35 84 46 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 2 86 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) agcagcagcaacagcagcagca 0.267 0.25 206 69 FANCG 2189 broad.mit.edu 37 9 35074203 35074203 + Frame_Shift_Del DEL G - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr9:35074203delG uc003zwb.1 - 14 2263 c.1771delC c.(1771-1773)CTGfs p.L591fs VCP_uc003zvy.2_5'Flank|VCP_uc003zvz.2_5'Flank|VCP_uc010mkh.1_5'Flank|VCP_uc010mki.1_5'Flank|FANCG_uc003zwa.1_Frame_Shift_Del_p.L333fs|FANCG_uc010mkj.1_Frame_Shift_Del_p.L333fs NM_004629 NP_004620 O15287 FANCG_HUMAN Fanconi anemia, complementation group G 591 cell cycle checkpoint|DNA repair|mitochondrion organization mitochondrion|nucleoplasm damaged DNA binding|protein binding ovary(2)|large_intestine(1)|lung(1) 4 LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778) TCTAGGTACAGGGGGAGAGAC 0.512 0.50 23 23 ILK 3611 broad.mit.edu 37 11 6629392 6629392 + Frame_Shift_Del DEL C - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr11:6629392delC uc001mee.2 + 3 341 c.206delC c.(205-207)ACCfs p.T69fs ILK_uc001mef.2_Frame_Shift_Del_p.T69fs|ILK_uc010rap.1_Intron|ILK_uc010raq.1_Frame_Shift_Del_p.T69fs|ILK_uc001meg.2_5'UTR|ILK_uc001meh.2_Frame_Shift_Del_p.T69fs|ILK_uc001mei.2_5'Flank NM_001014794 NP_001014794 Q13418 ILK_HUMAN integrin-linked kinase 69 Interaction with LIMS1.|ANK 3. cell junction assembly|cell proliferation|cell-matrix adhesion|integrin-mediated signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of transcription, DNA-dependent cytosol|focal adhesion ATP binding|protein serine/threonine kinase activity central_nervous_system(1) 1 Breast(177;7.61e-05)|Medulloblastoma(188;0.00263)|all_neural(188;0.026)|all_lung(207;0.152) Epithelial(150;5.49e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00012)|Lung(200;0.00942)|LUSC - Lung squamous cell carcinoma(625;0.0163) GGGGATGACACCCCCCTGCAT 0.557 0.33 10 5 PIK3C2A 5286 broad.mit.edu 37 11 17156697 17156699 + In_Frame_Del DEL AAG - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr11:17156697_17156699delAAG uc001mmq.3 - 9 1922_1924 c.1856_1858delCTT c.(1855-1860)TCTTTG>TTG p.S619del PIK3C2A_uc009ygu.1_Intron|PIK3C2A_uc010rcw.1_In_Frame_Del_p.S239del|PIK3C2A_uc001mmr.3_Intron|PIK3C2A_uc010rcx.1_In_Frame_Del_p.S619del NM_002645 NP_002636 O00443 P3C2A_HUMAN phosphoinositide-3-kinase, class 2 alpha 619 cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity lung(4)|central_nervous_system(4)|stomach(1)|ovary(1) 10 Phosphatidylserine(DB00144) CCTCCAAACAAAGAAGTCACCTA 0.365 0.39 25 16 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 1.00 0 11 MAP3K11 4296 broad.mit.edu 37 11 65365835 65365835 + Frame_Shift_Del DEL C - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr11:65365835delC uc001oew.2 - 10 2964 c.2471delG c.(2470-2472)GGCfs p.G824fs KCNK7_uc001oeq.2_5'Flank|KCNK7_uc001oer.2_5'Flank|KCNK7_uc001oes.2_5'Flank|KCNK7_uc001oeu.2_5'Flank|MAP3K11_uc001oev.2_Frame_Shift_Del_p.G240fs|MAP3K11_uc010rol.1_Frame_Shift_Del_p.G567fs|MAP3K11_uc001oex.1_Frame_Shift_Del_p.G313fs NM_002419 NP_002410 Q16584 M3K11_HUMAN mitogen-activated protein kinase kinase kinase 824 Pro-rich. activation of JUN kinase activity|cell proliferation|G1 phase of mitotic cell cycle|microtubule-based process|positive regulation of JNK cascade|protein autophosphorylation centrosome|microtubule ATP binding|JUN kinase kinase kinase activity|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity breast(3)|lung(1)|central_nervous_system(1)|skin(1) 6 GTCCTGGGGGCCCCCCTGGAA 0.701 0.51 56 59 MAML2 84441 broad.mit.edu 37 11 95825375 95825377 + In_Frame_Del DEL TGC - - rs11277537 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr11:95825375_95825377delTGC uc001pfw.1 - 2 3103_3105 c.1818_1820delGCA c.(1816-1821)CAGCAA>CAA p.606_607QQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 606_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgct 0.113 0.16 1368 251 ARHGEF12 23365 broad.mit.edu 37 11 120351043 120351043 + Frame_Shift_Del DEL T - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr11:120351043delT uc001pxl.1 + 38 4148 c.4141delT c.(4141-4143)TTTfs p.F1381fs ARHGEF12_uc009zat.2_Frame_Shift_Del_p.F1362fs|ARHGEF12_uc009zau.1_Frame_Shift_Del_p.F1278fs NM_015313 NP_056128 Q9NZN5 ARHGC_HUMAN Rho guanine nucleotide exchange factor (GEF) 12 1381 apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|membrane G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity lung(2)|breast(2)|skin(2)|ovary(1) 7 Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231) TGGAGAGCACTTTTTTGATGC 0.453 0.48 111 103 WNT1 7471 broad.mit.edu 37 12 49374348 49374348 + Frame_Shift_Del DEL G - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr12:49374348delG uc001rsu.2 + 3 698 c.500delG c.(499-501)TGGfs p.W167fs NM_005430 NP_005421 P04628 WNT1_HUMAN wingless-type MMTV integration site family, 167 brain segmentation|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|central nervous system morphogenesis|cerebellum formation|dermatome development|diencephalon development|embryonic axis specification|forebrain anterior/posterior pattern formation|fourth ventricle development|hemopoietic stem cell proliferation|hepatocyte differentiation|inner ear morphogenesis|mesoderm morphogenesis|midbrain development|midbrain-hindbrain boundary maturation during brain development|negative regulation of cell-cell adhesion|negative regulation of cell-substrate adhesion|negative regulation of DNA damage checkpoint|negative regulation of fat cell differentiation|neuron fate determination|positive regulation of fibroblast proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of lamellipodium assembly|positive regulation of Notch signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to wounding|signal transduction in response to DNA damage|Spemann organizer formation|T cell differentiation in thymus|Wnt receptor signaling pathway, calcium modulating pathway early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix cytokine activity|frizzled-2 binding|transcription regulatory region DNA binding kidney(1) 1 BRCA - Breast invasive adenocarcinoma(357;0.244) gACTGGCACTGGGGGGGCTGC 0.552 0.45 22 18 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.15 206 37 NOVA1 4857 broad.mit.edu 37 14 27066542 27066542 + Frame_Shift_Del DEL G - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr14:27066542delG uc001wpy.2 - 1 419 c.101delC c.(100-102)CCTfs p.P34fs NOVA1_uc001wpz.2_Frame_Shift_Del_p.P34fs|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_Frame_Shift_Del_p.P34fs NM_002515 NP_002506 P51513 NOVA1_HUMAN neuro-oncological ventral antigen 1 isoform 1 34 Bipartite nuclear localization signal (Potential). locomotory behavior|RNA splicing|synaptic transmission nucleus RNA binding skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1) 5 GBM - Glioblastoma multiforme(265;0.0135) 0.000 0.51 703 725 SIX4 51804 broad.mit.edu 37 14 61190487 61190488 + In_Frame_Ins INS - GCG GCG MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr14:61190487_61190488insGCG uc001xfc.2 - 1 305_306 c.305_306insCGC c.(304-306)GCG>GCCGCG p.102_102A>AA SIX4_uc010app.1_In_Frame_Ins_p.94_94A>AA NM_017420 NP_059116 Q9UIU6 SIX4_HUMAN sine oculis homeobox homolog 4 102 Ala-rich. nucleus breast(3)|ovary(1) 4 OV - Ovarian serous cystadenocarcinoma(108;0.0275) 0.000 0.37 398 232 TRIP11 9321 broad.mit.edu 37 14 92505926 92505926 + Frame_Shift_Del DEL T - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr14:92505926delT uc001xzy.2 - 1 892 c.104delA c.(103-105)AAGfs p.K35fs TRIP11_uc001xzz.3_RNA NM_004239 NP_004230 Q15643 TRIPB_HUMAN thyroid hormone receptor interactor 11 35 transcription from RNA polymerase II promoter cytoskeleton|Golgi apparatus|membrane|nucleus protein binding|transcription coactivator activity ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1) 13 COAD - Colon adenocarcinoma(157;0.223) CAGCATATCCTTTGTAAAGTT 0.587 0.12 205 29 HSP90AA1 3320 broad.mit.edu 37 14 102550781 102550782 + Frame_Shift_Del DEL CT - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr14:102550781_102550782delCT uc001yku.3 - 6 1291_1292 c.1101_1102delAG c.(1099-1104)AGAGTTfs p.R367fs HSP90AA1_uc001ykv.3_Frame_Shift_Del_p.R489fs|HSP90AA1_uc001ykw.1_Frame_Shift_Del_p.R188fs|HSP90AA1_uc001ykx.1_Frame_Shift_Del_p.R356fs NM_005348 NP_005339 P07900 HS90A_HUMAN heat shock 90kDa protein 1, alpha isoform 2 367_368 axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction cytosol|melanosome|plasma membrane ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding ovary(2)|central_nervous_system(2)|prostate(1)|lung(1)|breast(1) 7 Rifabutin(DB00615) ATGATGAAAACTCTGCGTACAT 0.366 0.23 62 19 MEF2A 4205 broad.mit.edu 37 15 100252709 100252710 + In_Frame_Ins INS - CAGCAG CAGCAG MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr15:100252709_100252710insCAGCAG uc010urw.1 + 11 1616_1617 c.1257_1258insCAGCAG c.(1255-1260)insCAGCAG p.429_430insQQ MEF2A_uc010urv.1_In_Frame_Ins_p.359_360insQQ|MEF2A_uc010bos.2_In_Frame_Ins_p.419_420insQQ|MEF2A_uc002bvf.2_In_Frame_Ins_p.421_422insQQ|MEF2A_uc002bve.2_In_Frame_Ins_p.427_428insQQ|MEF2A_uc002bvg.2_In_Frame_Ins_p.419_420insQQ|MEF2A_uc002bvi.2_In_Frame_Ins_p.419_420insQQ|MEF2A_uc010bot.2_In_Frame_Ins_p.351_352insQQ NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 429_430 Gln/Pro-rich. Missing (in Ref. 4; AAB17195/AAB17196). apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) CATCGGGCTTCcagcagcagca 0.485 0.29 20 8 MYH11 4629 broad.mit.edu 37 16 15818186 15818188 + In_Frame_Del DEL CTT - - rs113302393 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr16:15818186_15818188delCTT uc002ddy.2 - 31 4302_4304 c.4195_4197delAAG c.(4195-4197)AAGdel p.K1399del MYH11_uc002ddv.2_In_Frame_Del_p.K1406del|MYH11_uc002ddw.2_In_Frame_Del_p.K1399del|MYH11_uc002ddx.2_In_Frame_Del_p.K1406del|MYH11_uc010bvg.2_In_Frame_Del_p.K1231del|NDE1_uc010uzy.1_3'UTR|NDE1_uc002dds.2_3'UTR|MYH11_uc010bvh.2_In_Frame_Del_p.K105del|NDE1_uc002ddz.1_RNA NM_002474 NP_002465 P35749 MYH11_HUMAN smooth muscle myosin heavy chain 11 isoform 1399 Potential. axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction cytosol|melanosome|muscle myosin complex|myosin filament actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1) 15 TCTCGATCTCCTTCTGGAACCTC 0.557 0.45 196 160 PALB2 79728 broad.mit.edu 37 16 23646533 23646533 + Frame_Shift_Del DEL T - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr16:23646533delT uc002dlx.1 - 4 1534 c.1334delA c.(1333-1335)AAGfs p.K445fs NM_024675 NP_078951 Q86YC2 PALB2_HUMAN partner and localizer of BRCA2 445 double-strand break repair via homologous recombination nucleoplasm DNA binding|protein binding lung(3)|breast(3)|ovary(2)|skin(1)|kidney(1)|pancreas(1) 11 GBM - Glioblastoma multiforme(48;0.0167) ACTTGCATCCTTATTTTTATT 0.393 0.53 52 59 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.21 30 8 AATK 9625 broad.mit.edu 37 17 79094440 79094441 + Frame_Shift_Del DEL TG - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr17:79094440_79094441delTG uc010dia.2 - 11 3375_3376 c.3295_3296delCA c.(3295-3297)CAGfs p.Q1099fs AATK_uc010dhz.2_Intron NM_001080395 NP_001073864 Q6ZMQ8 LMTK1_HUMAN apoptosis-associated tyrosine kinase 1099 Pro-rich. integral to membrane|mitochondrion|perinuclear region of cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1) 9 all_neural(118;0.101) BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524) 0.000 0.52 699 753 PRKACA 5566 broad.mit.edu 37 19 14218178 14218178 + Frame_Shift_Del DEL T - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr19:14218178delT uc002myc.2 - 2 290 c.90delA c.(88-90)AAAfs p.K30fs PRKACA_uc002myb.2_Frame_Shift_Del_p.K22fs|PRKACA_uc010xnm.1_Translation_Start_Site|PRKACA_uc002myd.2_Translation_Start_Site NM_002730 NP_002721 P17612 KAPCA_HUMAN cAMP-dependent protein kinase catalytic subunit 30 activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|G2/M transition of mitotic cell cycle|gluconeogenesis|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|regulation of insulin secretion|transmembrane transport|triglyceride catabolic process|water transport cAMP-dependent protein kinase complex|centrosome|cytosol|nucleoplasm|plasma membrane ATP binding|cAMP-dependent protein kinase activity|cAMP-dependent protein kinase inhibitor activity|protein kinase binding lung(1) 1 GACTTTCCCATTTTTTAAGAA 0.552 0.36 35 20 CIC 23152 broad.mit.edu 37 19 42795075 42795075 + Frame_Shift_Del DEL G - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr19:42795075delG uc002otf.1 + 10 2195 c.2155delG c.(2155-2157)GGGfs p.G719fs NM_015125 NP_055940 Q96RK0 CIC_HUMAN capicua homolog 719 Pro-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1) 11 Prostate(69;0.00682) TCGGGTGCCTGGGGGCTCCCC 0.642 0.95 2 42 STK35 140901 broad.mit.edu 37 20 2083470 2083471 + Frame_Shift_Ins INS - G G MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr20:2083470_2083471insG uc010gak.2 + 2 351_352 c.351_352insG c.(349-354)GCAGGGfs p.A117fs STK35_uc010zpu.1_5'UTR|STK35_uc002wfw.3_5'Flank NM_080836 NP_543026 Q8TDR2 STK35_HUMAN serine/threonine kinase 35 117_118 Ala-rich. cytoplasm|nucleolus ATP binding|protein serine/threonine kinase activity ovary(1) 1 0.000 0.49 186 178 REM1 28954 broad.mit.edu 37 20 30070121 30070122 + Frame_Shift_Ins INS - G G MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr20:30070121_30070122insG uc002wwa.2 + 4 739_740 c.455_456insG c.(454-456)CAGfs p.Q152fs NM_014012 NP_054731 O75628 REM1_HUMAN RAS-like GTP-binding protein REM 152 small GTPase mediated signal transduction membrane calmodulin binding|GTP binding|GTPase activity p.Q152H(1) lung(2)|pancreas(2) 4 all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198) Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347) TCATGCCTGCAGGGGGGCAGTG 0.604 0.39 103 66 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 77 10 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 132 380 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 77 MED15 51586 broad.mit.edu 37 22 20918817 20918819 + In_Frame_Del DEL CAG - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr22:20918817_20918819delCAG uc002zsp.2 + 6 612_614 c.532_534delCAG c.(532-534)CAGdel p.Q188del MED15_uc002zsn.1_In_Frame_Del_p.Q107del|MED15_uc002zso.2_In_Frame_Del_p.Q117del|MED15_uc002zsq.2_In_Frame_Del_p.Q188del|MED15_uc010gso.2_In_Frame_Del_p.Q188del|MED15_uc002zsr.2_In_Frame_Del_p.Q162del|MED15_uc011ahs.1_In_Frame_Del_p.Q162del|MED15_uc011aht.1_In_Frame_Del_p.Q162del|MED15_uc002zss.2_In_Frame_Del_p.Q107del|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 188 Poly-Gln. regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) ggcggcgctacagcagcagcagc 0.148 0.36 149 83 PI4KA 5297 broad.mit.edu 37 22 21105629 21105629 + Frame_Shift_Del DEL G - - MDAPCA2B_PROSTATE NA MDAPCA2B_PROSTATE NA g.chr22:21105629delG uc002zsz.3 - 27 3162 c.2931delC c.(2929-2931)CCCfs p.P977fs NM_058004 NP_477352 P42356 PI4KA_HUMAN phosphatidylinositol 4-kinase type 3 alpha 977 phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission Golgi-associated vesicle 1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1) 4 all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196) AGGGGGCGTCGGGGATGTCAT 0.552 0.41 201 142 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.76 20 65 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.14 410 66 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 79 20 PPP3CA 5530 broad.mit.edu 37 4 101947030 101947041 + In_Frame_Del DEL TATTGCTGCTAT - - MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chr4:101947030_101947041delTATTGCTGCTAT uc011cen.1 - 14 2222_2233 c.1547_1558delATAGCAGCAATA c.(1546-1560)AATAGCAGCAATATT>ATT p.NSSN516del PPP3CA_uc003hvu.2_In_Frame_Del_p.NSSN506del|PPP3CA_uc010ilj.2_In_Frame_Del_p.NSSN464del|PPP3CA_uc003hvt.2_In_Frame_Del_p.NSSN493del|PPP3CA_uc003hvs.2_In_Frame_Del_p.NSSN449del|PPP3CA_uc010ilk.2_In_Frame_Del_p.NSSN284del NM_000944 NP_000935 Q08209 PP2BA_HUMAN protein phosphatase 3, catalytic subunit, alpha 516_519 protein dephosphorylation calcineurin complex|cytosol|nucleus calcium ion binding|calmodulin binding ovary(1)|skin(1) 2 OV - Ovarian serous cystadenocarcinoma(123;6.79e-08) GGTCACTGAATATTGCTGCTATTACTGCCATT 0.458 0.25 165 55 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 91 125 APC 324 broad.mit.edu 37 5 112175951 112175952 + Frame_Shift_Ins INS - A A MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chr5:112175951_112175952insA uc010jby.2 + 16 5040_5041 c.4660_4661insA c.(4660-4662)GAAfs p.E1554fs APC_uc011cvt.1_Frame_Shift_Ins_p.E1536fs|APC_uc003kpz.3_Frame_Shift_Ins_p.E1554fs|APC_uc003kpy.3_Frame_Shift_Ins_p.E1554fs|APC_uc010jbz.2_Frame_Shift_Ins_p.E1271fs|APC_uc010jca.2_Frame_Shift_Ins_p.E854fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1554 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.T1556fs*3(35)|p.E1554fs*5(2)|p.E1554*(2)|p.?(1)|p.T1556fs*9(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1554fs*11(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GAAAGAGGCAGAAAAAACTATT 0.342 0.71 12 29 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.13 331 51 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.77 5 17 TRAF2 7186 broad.mit.edu 37 9 139815582 139815582 + Frame_Shift_Del DEL T - - MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chr9:139815582delT uc010nbu.2 + 10 1226 c.1053delT c.(1051-1053)GATfs p.D351fs TRAF2_uc004cjv.2_Frame_Shift_Del_p.D351fs|TRAF2_uc011mek.1_Frame_Shift_Del_p.D340fs|TRAF2_uc010nbw.2_Frame_Shift_Del_p.D326fs NM_021138 NP_066961 Q12933 TRAF2_HUMAN TNF receptor-associated factor 2 351 MATH. LEMEASTYDGVFIWKISDFARKR -> RPFQAQCGHRYCSF CLASILRKL (in Ref. 1; AAA87706). activation of caspase activity|activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cellular protein complex assembly|induction of apoptosis by extracellular signals|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|protein autoubiquitination|protein homotrimerization|protein K63-linked ubiquitination|tumor necrosis factor-mediated signaling pathway CD40 receptor complex|cytosol|internal side of plasma membrane CD40 receptor binding|enzyme binding|protein binding|signal transducer activity|sphingolipid binding|ubiquitin-protein ligase activity|zinc ion binding ovary(1)|lung(1)|breast(1)|skin(1) 4 all_cancers(76;0.11) Myeloproliferative disorder(178;0.0511) STAD - Stomach adenocarcinoma(284;0.229) OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06) CCACCTACGATGGGGTCTTCA 0.602 0.20 152 38 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 619 268 STRADA 92335 broad.mit.edu 37 17 61781369 61781369 + Frame_Shift_Del DEL T - - MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chr17:61781369delT uc002jbm.2 - 12 1298 c.1139delA c.(1138-1140)AAGfs p.K380fs STRADA_uc002jbn.2_Frame_Shift_Del_p.K322fs|STRADA_uc002jbo.2_Frame_Shift_Del_p.K343fs|STRADA_uc002jbp.2_3'UTR|STRADA_uc002jbq.2_Frame_Shift_Del_p.K322fs|STRADA_uc010wpq.1_3'UTR|STRADA_uc010wpr.1_3'UTR|STRADA_uc010ddw.2_Frame_Shift_Del_p.K351fs|STRADA_uc002jbr.2_3'UTR NM_001003787 NP_001003787 Q7RTN6 STRAA_HUMAN STE20-related kinase adaptor alpha isoform 1 380 activation of protein kinase activity|cell cycle arrest|insulin receptor signaling pathway|protein export from nucleus|regulation of fatty acid oxidation cytosol|nucleus ATP binding|kinase binding|protein kinase activity ovary(1) 1 0.000 0.26 811 283 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 63 38 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 156 412 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MDST8_LARGE_INTESTINE NA MDST8_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.83 17 83 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.47 39 34 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.29 22 9 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.47 47 41 HCLS1 3059 broad.mit.edu 37 3 121351315 121351316 + In_Frame_Ins INS - GGCTCAGGCTCA GGCTCAGGCTCA rs150627065 by1000genomes MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:121351315_121351316insGGCTCAGGCTCA uc003eeh.3 - 12 1228_1229 c.1103_1104insTGAGCCTGAGCC c.(1102-1104)CCC>CCTGAGCCTGAGCCC p.368_368P>PEPEP HCLS1_uc011bjj.1_In_Frame_Ins_p.331_331P>PEPEP|HCLS1_uc011bjk.1_RNA NM_005335 NP_005326 P14317 HCLS1_HUMAN hematopoietic cell-specific Lyn substrate 1 368 erythrocyte differentiation|intracellular signal transduction|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of STAT protein|response to hormone stimulus mitochondrion|nucleus|plasma membrane DNA binding|sequence-specific DNA binding transcription factor activity 0 GBM - Glioblastoma multiforme(114;0.0912) gctcaggctcgggctcaggctc 0.465 0.50 5 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 151 263 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.90 21 183 CAMK2A 815 broad.mit.edu 37 5 149631618 149631618 + Frame_Shift_Del DEL C - - MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:149631618delC uc003lru.2 - 8 740 c.525delG c.(523-525)GGGfs p.G175fs CAMK2A_uc003lrt.2_Frame_Shift_Del_p.G175fs|CAMK2A_uc010jhe.2_Frame_Shift_Del_p.G155fs|CAMK2A_uc010jhf.1_Frame_Shift_Del_p.G13fs NM_171825 NP_741960 Q9UQM7 KCC2A_HUMAN calcium/calmodulin-dependent protein kinase II 175 Protein kinase. interferon-gamma-mediated signaling pathway|positive regulation of NF-kappaB transcription factor activity|synaptic transmission cell junction|cytosol|endocytic vesicle membrane|nucleoplasm|presynaptic membrane ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity large_intestine(1) 1 all_hematologic(541;0.224) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) 0.000 0.20 66 17 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.22 28 8 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.22 202 58 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.13 292 44 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.79 10 37 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 19 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.33 164 82 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 50 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.56 7 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 1300 443 ATN1 1822 broad.mit.edu 37 12 7045892 7045894 + In_Frame_Del DEL CAG - - rs66756893;rs67074116 MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:7045892_7045894delCAG uc001qrw.1 + 5 1699_1701 c.1462_1464delCAG c.(1462-1464)CAGdel p.Q502del ATN1_uc001qrx.1_In_Frame_Del_p.Q502del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagc 0.458 0.19 227 52 TP53 7157 broad.mit.edu 37 17 7576896 7576897 + Frame_Shift_Ins INS - G G MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:7576896_7576897insG uc002gim.2 - 9 1143_1144 c.949_950insC c.(949-951)CAGfs p.Q317fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Frame_Shift_Ins_p.Q317fs|TP53_uc010cne.1_RNA|TP53_uc010cnf.1_Frame_Shift_Ins_p.Q185fs|TP53_uc010cng.1_Frame_Shift_Ins_p.Q185fs|TP53_uc002gii.1_Frame_Shift_Ins_p.Q185fs|TP53_uc010cnh.1_Frame_Shift_Ins_p.Q317fs|TP53_uc010cni.1_Frame_Shift_Ins_p.Q317fs|TP53_uc002gij.2_Frame_Shift_Ins_p.Q317fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 317 Bipartite nuclear localization signal.|Interaction with HIPK1 (By similarity).|Interaction with CARM1. Q -> H (in a kidney cancer with no family history; germline mutation and in a sporadic cancer; somatic mutation).|Q -> P (in a sporadic cancer; somatic mutation).|Q -> K (in sporadic cancers; somatic mutation).|Q -> L (in a sporadic cancer; somatic mutation).|Q -> R (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.Q317*(19)|p.0?(7)|p.Q317K(3)|p.Q317R(2)|p.S315fs*22(1)|p.?(1)|p.S314fs*25(1)|p.L308fs*15(1)|p.Q317P(1)|p.Q317fs*28(1)|p.Q317fs*45(1)|p.Q317fs*19(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) CTTCTTTGGCTGGGGAGAGGAG 0.470 0.91 14 149 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.59 38 54 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 88 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 15 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.31 220 101 RIF1 55183 broad.mit.edu 37 2 152320713 152320715 + In_Frame_Del DEL AAG - - MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:152320713_152320715delAAG uc002txm.2 + 30 4809_4811 c.4679_4681delAAG c.(4678-4683)AAAGAA>AAA p.E1562del RIF1_uc002txl.2_In_Frame_Del_p.E1562del|RIF1_uc002txn.2_In_Frame_Del_p.E1562del|RIF1_uc002txo.2_In_Frame_Del_p.E1562del|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1562 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) TCGGAGGCAAAAGAAGAAGGTTC 0.404 0.42 11 8 PPARG 5468 broad.mit.edu 37 3 12434181 12434182 + Frame_Shift_Ins INS - A A MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:12434181_12434182insA uc003bwx.2 + 4 640_641 c.549_550insA c.(547-552)CACAAAfs p.H183fs PPARG_uc003bwr.2_Frame_Shift_Ins_p.H155fs|PPARG_uc003bws.2_Frame_Shift_Ins_p.H155fs|PPARG_uc003bwu.2_Frame_Shift_Ins_p.H155fs|PPARG_uc003bwv.2_Frame_Shift_Ins_p.H155fs|PPARG_uc010hea.1_RNA|PPARG_uc003bwq.1_Frame_Shift_Ins_p.H155fs|PPARG_uc003bwt.1_Frame_Shift_Ins_p.H155fs|PPARG_uc003bww.1_Frame_Shift_Ins_p.H183fs NM_015869 NP_056953 P37231 PPARG_HUMAN peroxisome proliferative activated receptor 183_184 NR C4-type.|Nuclear receptor. activation of caspase activity|cell fate commitment|cell maturation|cellular response to insulin stimulus|epithelial cell differentiation|glucose homeostasis|induction of apoptosis|innate immune response|lipid homeostasis|lipoprotein transport|long-chain fatty acid transport|low-density lipoprotein particle receptor biosynthetic process|monocyte differentiation|negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|placenta development|positive regulation of fat cell differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to lipid|response to low-density lipoprotein particle stimulus|white fat cell differentiation cytosol|nucleoplasm activating transcription factor binding|arachidonic acid binding|drug binding|enzyme binding|prostaglandin receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding ovary(1)|kidney(1) 2 Atorvastatin(DB01076)|Icosapent(DB00159)|Pioglitazone(DB01132)|Rosiglitazone(DB00412)|Troglitazone(DB00197) GTCGGATCCACAAAAAAAGTAG 0.361 0.46 30 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 74 51 NUP153 9972 broad.mit.edu 37 6 17633077 17633078 + Splice_Site INS - A A rs36027788;rs147103527 MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:17633077_17633078insA uc003ncd.1 - 17 2665 c.2465_splice c.e17-1 p.G822_splice NUP153_uc011dje.1_Splice_Site_p.G853_splice|NUP153_uc010jpl.1_Splice_Site_p.G780_splice NM_005124 NP_005115 P49790 NU153_HUMAN nucleoporin 153kDa carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm DNA binding|protein binding|transporter activity|zinc ion binding lung(4)|ovary(2)|breast(2)|skin(1) 9 Breast(50;0.0259)|Ovarian(93;0.0584) all_hematologic(90;0.125) all cancers(50;0.0981)|Epithelial(50;0.112) CTGAACTTCCTAAAAAAAAAAA 0.406 0.28 34 13 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.33 8 4 FADD 8772 broad.mit.edu 37 11 70049816 70049817 + Frame_Shift_Ins INS - G G MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:70049816_70049817insG uc001opm.2 + 1 548_549 c.251_252insG c.(250-252)GCGfs p.A84fs NM_003824 NP_003815 Q13158 FADD_HUMAN Fas-associated via death domain 84 activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction cytosol death receptor binding|identical protein binding ovary(1)|lung(1)|pancreas(1) 3 Esophageal squamous(2;1.19e-45) LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) 0.000 0.10 729 78 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 171 51 TP53 7157 broad.mit.edu 37 17 7577582 7577584 + In_Frame_Del DEL GTG - - MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:7577582_7577584delGTG uc002gim.2 - 7 891_893 c.697_699delCAC c.(697-699)CACdel p.H233del TP53_uc002gig.1_In_Frame_Del_p.H233del|TP53_uc002gih.2_In_Frame_Del_p.H233del|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_In_Frame_Del_p.H101del|TP53_uc010cng.1_In_Frame_Del_p.H101del|TP53_uc002gii.1_In_Frame_Del_p.H101del|TP53_uc010cnh.1_In_Frame_Del_p.H233del|TP53_uc010cni.1_In_Frame_Del_p.H233del|TP53_uc002gij.2_In_Frame_Del_p.H233del|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_In_Frame_Del_p.H140del|TP53_uc002gio.2_In_Frame_Del_p.H101del NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 233 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). H -> Y (in sporadic cancers; somatic mutation).|H -> R (in sporadic cancers; somatic mutation).|H -> D (in LFS; germline mutation and in a sporadic cancer; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> P (in a sporadic cancer; somatic mutation).|H -> L (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.H233Y(4)|p.H233fs*6(3)|p.H233L(2)|p.T230fs*6(2)|p.H233Q(2)|p.H233D(2)|p.C229_H233delCTTIH(2)|p.I232_Y236delIHYNY(1)|p.Y234fs*2(1)|p.H233del(1)|p.H233fs*14(1)|p.H233R(1)|p.T230_Y234delTTIHY(1)|p.H233fs*7(1)|p.V225fs*23(1)|p.D228fs*12(1)|p.I232fs*5(1)|p.H233_C242del10(1)|p.H233P(1)|p.Y234fs*6(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) TGTAGTTGTAGTGGATGGTGGTA 0.562 0.97 2 78 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 25 16 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 94 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 78 461 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 3 33 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MELHO_SKIN NA MELHO_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 64 PSEN2 5664 broad.mit.edu 37 1 227069751 227069760 + Splice_Site DEL TAGGTCCCAC - - MELHO_SKIN NA MELHO_SKIN NA g.chr1:227069751_227069760delTAGGTCCCAC uc009xeo.1 + 4 568 c.141_splice c.e4+2 p.W47_splice PSEN2_uc009xep.1_Splice_Site_p.W47_splice|PSEN2_uc001hqk.2_Splice_Site NM_000447 NP_000438 P49810 PSN2_HUMAN presenilin 2 isoform 1 amyloid precursor protein catabolic process|anti-apoptosis|apoptosis|beta-amyloid metabolic process|calcium ion transport|induction of apoptosis by extracellular signals|intracellular signal transduction|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity apical plasma membrane|axon|cell cortex|cell surface|centrosome|ciliary rootlet|dendritic shaft|endoplasmic reticulum membrane|Golgi membrane|growth cone|integral to plasma membrane|kinetochore|lysosomal membrane|membrane raft|mitochondrial inner membrane|neuromuscular junction|neuronal cell body|nuclear inner membrane|perinuclear region of cytoplasm|Z disc aspartic-type endopeptidase activity|protein binding lung(2) 2 Prostate(94;0.0771) GCCCAGTGGGTAGGTCCCACCAGCAGCTGG 0.605 0.24 147 47 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes MELHO_SKIN NA MELHO_SKIN NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.14 74 12 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MELHO_SKIN NA MELHO_SKIN NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 108 29 TNK2 10188 broad.mit.edu 37 3 195597064 195597065 + Frame_Shift_Ins INS - C C MELHO_SKIN NA MELHO_SKIN NA g.chr3:195597064_195597065insC uc003fvu.1 - 11 2006_2007 c.1463_1464insG c.(1462-1464)GGAfs p.G488fs TNK2_uc003fvq.1_5'Flank|TNK2_uc003fvr.1_5'UTR|TNK2_uc003fvs.1_Frame_Shift_Ins_p.G520fs|TNK2_uc003fvt.1_Frame_Shift_Ins_p.G551fs|TNK2_uc010hzw.1_RNA|TNK2_uc003fvv.1_Frame_Shift_Ins_p.G318fs NM_005781 NP_005772 Q07912 ACK1_HUMAN tyrosine kinase, non-receptor, 2 isoform 1 488 Missing (in Ref. 4; AAH08884). positive regulation of peptidyl-tyrosine phosphorylation|protein ubiquitination|small GTPase mediated signal transduction adherens junction|cytoplasmic vesicle membrane|endosome|nucleus ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1) 10 all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206) Lung NSC(153;0.191) Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05) GBM - Glioblastoma multiforme(46;0.000757) Adenosine triphosphate(DB00171) CCATGGGGTTTCCCAGATACAG 0.619 0.47 140 124 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MELHO_SKIN NA MELHO_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.18 50 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MELHO_SKIN NA MELHO_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 114 206 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 MELHO_SKIN NA MELHO_SKIN NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.17 53 11 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 MELHO_SKIN NA MELHO_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.29 25 10 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MELHO_SKIN NA MELHO_SKIN NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.17 49 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MELHO_SKIN NA MELHO_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 499 174 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency MELHO_SKIN NA MELHO_SKIN NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.18 93 20 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 MELHO_SKIN NA MELHO_SKIN NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.65 17 31 BUB1B 701 broad.mit.edu 37 15 40488855 40488857 + In_Frame_Del DEL GAG - - rs1017842 byFrequency;by1000genomes MELHO_SKIN NA MELHO_SKIN NA g.chr15:40488855_40488857delGAG uc001zkx.3 + 9 1380_1382 c.1168_1170delGAG c.(1168-1170)GAGdel p.E391del BUB1B_uc010ucl.1_In_Frame_Del_p.E254del NM_001211 NP_001202 O60566 BUB1B_HUMAN budding uninhibited by benzimidazoles 1 beta 391 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone ATP binding|protein binding|protein serine/threonine kinase activity stomach(2)|ovary(1)|kidney(1) 4 all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556) GCAAGCGTCTGAGGAGAAGAAAG 0.419 0.30 52 22 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MELHO_SKIN NA MELHO_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 56 326 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MELHO_SKIN NA MELHO_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 14 245 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MELJUSO_SKIN NA MELJUSO_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 5 89 MERTK 10461 broad.mit.edu 37 2 112767569 112767575 + Frame_Shift_Del DEL GTAATTT - - MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr2:112767569_112767575delGTAATTT uc002thk.1 + 15 2127_2133 c.2005_2011delGTAATTT c.(2005-2013)GTAATTTTAfs p.V669fs MERTK_uc002thl.1_Frame_Shift_Del_p.V493fs NM_006343 NP_006334 Q12866 MERTK_HUMAN MER receptor tyrosine kinase precursor 669_671 Protein kinase.|Cytoplasmic (Potential). cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration integral to plasma membrane|soluble fraction ATP binding|transmembrane receptor protein tyrosine kinase activity lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1) 9 AAAGCCCATGGTAATTTTACCCTTCAT 0.415 0.29 177 72 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.58 10 14 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 154 40 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 22 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 105 116 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 58 28 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.16 414 76 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 16 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.32 42 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 5 49 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.22 292 82 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 405 190 SORL1 6653 broad.mit.edu 37 11 121477667 121477668 + Splice_Site INS - TT TT MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr11:121477667_121477668insTT uc001pxx.2 + 36 5141 c.5061_splice c.e36+1 p.I1687_splice SORL1_uc010rzp.1_Splice_Site_p.I533_splice|SORL1_uc010rzq.1_Splice_Site_p.I302_splice NM_003105 NP_003096 Q92673 SORL_HUMAN sortilin-related receptor containing LDLR class cholesterol metabolic process|lipid transport|receptor-mediated endocytosis integral to plasma membrane|low-density lipoprotein particle low-density lipoprotein particle binding|transmembrane receptor activity ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1) 15 Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113) BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108) TGAGTACATTGTAAGTACCTTC 0.510 0.41 17 12 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.39 14 9 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 15 161 STAC2 342667 broad.mit.edu 37 17 37371427 37371427 + Frame_Shift_Del DEL C - - MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr17:37371427delC uc002hrs.2 - 5 862 c.643delG c.(643-645)GCAfs p.A215fs STAC2_uc010cvt.2_Frame_Shift_Del_p.A73fs NM_198993 NP_945344 Q6ZMT1 STAC2_HUMAN SH3 and cysteine rich domain 2 215 intracellular signal transduction metal ion binding pancreas(1) 1 TTCATCAGTGCCAGGGAGGTG 0.607 0.46 113 95 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.24 99 32 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 105 455 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 9 146 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes MELJUSO_SKIN NA MELJUSO_SKIN NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.16 203 40 HEPH 9843 broad.mit.edu 37 X 65423347 65423347 + Frame_Shift_Del DEL A - - MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chrX:65423347delA uc011moz.1 + 13 2288 c.2228delA c.(2227-2229)GAAfs p.E743fs HEPH_uc004dwn.2_Frame_Shift_Del_p.E743fs|HEPH_uc004dwo.2_Frame_Shift_Del_p.E473fs|HEPH_uc010nkr.2_Frame_Shift_Del_p.E551fs|HEPH_uc011mpa.1_Frame_Shift_Del_p.E743fs|HEPH_uc010nks.2_Frame_Shift_Del_p.E32fs NM_138737 NP_620074 Q9BQS7 HEPH_HUMAN hephaestin isoform a 740 Extracellular (Potential).|Plastocyanin-like 5. cellular iron ion homeostasis|copper ion transport|transmembrane transport integral to membrane|plasma membrane copper ion binding|oxidoreductase activity lung(5)|ovary(4) 9 ATCATGGCAGAAGAAGTAGAG 0.517 0.42 73 52 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 4 88 ARID1A 8289 broad.mit.edu 37 1 27101543 27101544 + Frame_Shift_Ins INS - C C MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr1:27101543_27101544insC uc001bmv.1 + 18 5198_5199 c.4825_4826insC c.(4825-4827)TCTfs p.S1609fs ARID1A_uc001bmt.1_Frame_Shift_Ins_p.S1608fs|ARID1A_uc001bmu.1_Frame_Shift_Ins_p.S1392fs|ARID1A_uc001bmw.1_Frame_Shift_Ins_p.S1226fs|ARID1A_uc001bmx.1_Frame_Shift_Ins_p.S455fs|ARID1A_uc009vsm.1_Intron|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1609 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) ATTCCTGCACTCTGGGATGAAA 0.589 0.46 174 150 ARID1A 8289 broad.mit.edu 37 1 27102141 27102142 + Frame_Shift_Ins INS - A A MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr1:27102141_27102142insA uc001bmv.1 + 19 5440_5441 c.5067_5068insA c.(5065-5070)GATACCfs p.D1689fs ARID1A_uc001bmt.1_Frame_Shift_Ins_p.D1688fs|ARID1A_uc001bmu.1_Frame_Shift_Ins_p.D1472fs|ARID1A_uc001bmx.1_Frame_Shift_Ins_p.D535fs|ARID1A_uc009vsm.1_Frame_Shift_Ins_p.D17fs|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1689_1690 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GGGCATTAGATACCATCAACAT 0.500 0.46 156 131 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 546 153 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.52 37 40 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.48 28 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 155 359 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 30 52 PIK3R1 5295 broad.mit.edu 37 5 67589628 67589629 + In_Frame_Ins INS - TAGATT TAGATT MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr5:67589628_67589629insTAGATT uc003jva.2 + 11 1951_1952 c.1391_1392insTAGATT c.(1390-1392)GAT>GATAGATTT p.464_465insRF PIK3R1_uc003jvb.2_In_Frame_Ins_p.464_465insRF|PIK3R1_uc003jvc.2_In_Frame_Ins_p.164_165insRF|PIK3R1_uc003jvd.2_In_Frame_Ins_p.194_195insRF|PIK3R1_uc003jve.2_In_Frame_Ins_p.143_144insRF|PIK3R1_uc011crb.1_In_Frame_Ins_p.134_135insRF NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 464_465 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.D434_Q475del(2)|p.D464fs*2(1)|p.?(1)|p.D464H(1)|p.Y463_L466del(1)|p.T454_D464del(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) 0.000 0.16 207 38 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 27 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.36 72 40 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 53 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.11 112 14 PTEN 5728 broad.mit.edu 37 10 89720660 89720660 + Frame_Shift_Del DEL T - - MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr10:89720660delT uc001kfb.2 + 9 1842 c.811delT c.(811-813)TTTfs p.F271fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 271 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.F271S(2)|p.D268_F279>VGQNVSLLGKYI(2)|p.F271fs*5(1)|p.G165_*404del(1)|p.F271L(1)|p.G165_K342del(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GGACAAAATGTTTCACTTTTG 0.244 0.44 85 66 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.53 547 608 POLE 5426 broad.mit.edu 37 12 133252037 133252039 + In_Frame_Del DEL CTT - - MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr12:133252037_133252039delCTT uc001uks.1 - 12 1215_1217 c.1171_1173delAAG c.(1171-1173)AAGdel p.K391del POLE_uc010tbq.1_RNA|POLE_uc009zyu.1_In_Frame_Del_p.K364del NM_006231 NP_006222 Q07864 DPOE1_HUMAN DNA-directed DNA polymerase epsilon 391 base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair nucleoplasm chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding ovary(3)|skin(3)|lung(1)|central_nervous_system(1) 8 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.0416) OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05) 0.000 0.55 282 351 C14orf4 64207 broad.mit.edu 37 14 77493648 77493650 + In_Frame_Del DEL GCG - - MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr14:77493648_77493650delGCG uc001xsy.2 - 1 1385_1387 c.486_488delCGC c.(484-489)GCCGCT>GCT p.162_163AA>A NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 162_163 Poly-Ala. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) TTCCACCgcagcggcggcggcgg 0.581 0.32 15 7 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.14 59 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 161 98 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.23 320 94 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 36 272 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MESSA_SOFT_TISSUE NA MESSA_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 9 131 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MEWO_SKIN NA MEWO_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 3 35 F8 2157 broad.mit.edu 37 X 154156923 154156924 + Frame_Shift_Ins INS - G G MEWO_SKIN NA MEWO_SKIN NA g.chrX:154156923_154156924insG uc004fmt.2 - 14 5312_5313 c.5141_5142insC c.(5140-5142)ACAfs p.T1714fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1714 F5/8 type A 3.|Plastocyanin-like 5. T -> S (in HEMA; moderate). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AATAGTGTCGTGTTTTCTTTTG 0.396 0.20 44 11 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes MEWO_SKIN NA MEWO_SKIN NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.52 10 11 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MEWO_SKIN NA MEWO_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 25 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MEWO_SKIN NA MEWO_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.50 15 15 MAML3 55534 broad.mit.edu 37 4 140641185 140641186 + Frame_Shift_Ins INS - G G MEWO_SKIN NA MEWO_SKIN NA g.chr4:140641185_140641186insG uc003ihz.1 - 7 3445_3446 c.2693_2694insC c.(2692-2694)CCTfs p.P898fs MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_Frame_Shift_Ins_p.P366fs NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 899 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) GCCCAGAGGCAGGTTGCCTCGG 0.530 0.12 476 63 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MEWO_SKIN NA MEWO_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 110 155 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MEWO_SKIN NA MEWO_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 23 47 COL4A3BP 10087 broad.mit.edu 37 5 74685425 74685425 + Frame_Shift_Del DEL C - - MEWO_SKIN NA MEWO_SKIN NA g.chr5:74685425delC uc011csu.1 - 12 1698 c.1276delG c.(1276-1278)GAAfs p.E426fs COL4A3BP_uc003kds.2_Frame_Shift_Del_p.E400fs|COL4A3BP_uc003kdt.2_Frame_Shift_Del_p.E554fs|COL4A3BP_uc003kdu.2_Frame_Shift_Del_p.E426fs NM_005713 NP_005704 Q9Y5P4 C43BP_HUMAN alpha 3 type IV collagen binding protein isoform 426 START. ER to Golgi ceramide transport|immune response cytosol|endoplasmic reticulum membrane|Golgi apparatus ceramide binding|phosphatidylinositol-4-phosphate binding|protein binding|protein kinase activity skin(1) 1 all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174) OV - Ovarian serous cystadenocarcinoma(47;1e-53) ACCTTCATTTCTCCTTCTTCT 0.408 0.36 7 4 AFF4 27125 broad.mit.edu 37 5 132232802 132232803 + Frame_Shift_Ins INS - A A MEWO_SKIN NA MEWO_SKIN NA g.chr5:132232802_132232803insA uc003kyd.2 - 11 1927_1928 c.1519_1520insT c.(1519-1521)CGAfs p.R507fs AFF4_uc011cxk.1_Frame_Shift_Ins_p.R185fs|AFF4_uc003kye.1_Frame_Shift_Ins_p.R507fs NM_014423 NP_055238 Q9UHB7 AFF4_HUMAN ALL1 fused gene from 5q31 507 transcription from RNA polymerase II promoter mitochondrion|nucleolus protein binding|sequence-specific DNA binding transcription factor activity ovary(2)|kidney(2)|skin(1) 5 all_cancers(142;0.145)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GCCCTGCTCTCGGCCTTCCTTT 0.475 0.49 243 238 DST 667 broad.mit.edu 37 6 56497798 56497799 + Frame_Shift_Del DEL AG - - MEWO_SKIN NA MEWO_SKIN NA g.chr6:56497798_56497799delAG uc003pdf.2 - 27 3587_3588 c.3559_3560delCT c.(3559-3561)CTAfs p.L1187fs DST_uc003pcz.3_Frame_Shift_Del_p.L1009fs|DST_uc011dxj.1_Frame_Shift_Del_p.L1038fs|DST_uc011dxk.1_Frame_Shift_Del_p.L1049fs|DST_uc003pcy.3_Frame_Shift_Del_p.L683fs|DST_uc003pdb.2_Frame_Shift_Del_p.L683fs|DST_uc003pdc.3_Frame_Shift_Del_p.L683fs|DST_uc003pdd.3_Frame_Shift_Del_p.L683fs NM_001144769 NP_001138241 Q03001 DYST_HUMAN dystonin isoform 2 1009 cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1) 14 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) TAGATTACTTAGAACTTGCTGA 0.366 0.51 42 44 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 MEWO_SKIN NA MEWO_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.46 7 6 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MEWO_SKIN NA MEWO_SKIN NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.26 37 13 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 MEWO_SKIN NA MEWO_SKIN NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.86 2 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MEWO_SKIN NA MEWO_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.37 382 221 SIK2 23235 broad.mit.edu 37 11 111571668 111571668 + Frame_Shift_Del DEL C - - MEWO_SKIN NA MEWO_SKIN NA g.chr11:111571668delC uc001plt.2 + 5 655 c.537delC c.(535-537)AGCfs p.S179fs NM_015191 NP_056006 Q9H0K1 SIK2_HUMAN SNF1-like kinase 2 179 Protein kinase. intracellular protein kinase cascade|regulation of insulin receptor signaling pathway Golgi apparatus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|skin(1) 3 GGTGTGGCAGCCCCCCTTATG 0.433 0.90 8 73 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes MEWO_SKIN NA MEWO_SKIN NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.58 5 7 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency MEWO_SKIN NA MEWO_SKIN NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.16 93 18 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MEWO_SKIN NA MEWO_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.30 112 47 BRSK1 84446 broad.mit.edu 37 19 55820004 55820005 + Splice_Site INS - A A MEWO_SKIN NA MEWO_SKIN NA g.chr19:55820004_55820005insA uc002qkg.2 + 18 2367 c.2090_splice c.e18-2 p.G697_splice BRSK1_uc002qkf.2_Splice_Site_p.G713_splice|BRSK1_uc002qkh.2_Splice_Site_p.G392_splice NM_032430 NP_115806 Q8TDC3 BRSK1_HUMAN BR serine/threonine kinase 1 establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV cell junction|cytoplasm|nucleus magnesium ion binding|protein serine/threonine kinase activity ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1) 6 Renal(1328;0.245) BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.0474) CCTGTGCCTCTAGGTCCCAGCC 0.599 0.42 7 5 SULF2 55959 broad.mit.edu 37 20 46331407 46331407 + Frame_Shift_Del DEL G - - MEWO_SKIN NA MEWO_SKIN NA g.chr20:46331407delG uc002xto.2 - 4 753 c.423delC c.(421-423)TTCfs p.F141fs SULF2_uc002xtr.2_Frame_Shift_Del_p.F141fs|SULF2_uc002xtq.2_Frame_Shift_Del_p.F141fs|SULF2_uc010ghv.1_Frame_Shift_Del_p.F141fs NM_018837 NP_061325 Q8IWU5 SULF2_HUMAN sulfatase 2 isoform a precursor 141 bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway cell surface|endoplasmic reticulum|extracellular space|Golgi stack arylsulfatase activity|calcium ion binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 GATACTTCCCGAAGAAAGCTG 0.507 0.38 49 30 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 MEWO_SKIN NA MEWO_SKIN NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.10 102 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MEWO_SKIN NA MEWO_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 45 197 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MEWO_SKIN NA MEWO_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 99 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.52 29 31 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 1 18 PHOX2B 8929 broad.mit.edu 37 4 41748168 41748173 + In_Frame_Del DEL TGGGAC - - MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chr4:41748168_41748173delTGGGAC uc003gwf.3 - 3 956_961 c.596_601delGTCCCA c.(595-603)GGTCCCAAT>GAT p.199_201GPN>D NM_003924 NP_003915 Q99453 PHX2B_HUMAN paired-like homeobox 2b 199_201 positive regulation of transcription from RNA polymerase II promoter nuclear chromatin RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity autonomic_ganglia(7)|lung(2)|ovary(2)|central_nervous_system(1) 12 0.000 0.10 74 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 85 72 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 27 73 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.77 225 735 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 220 90 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.38 13 8 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.15 90 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.97 2 56 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.70 25 59 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 154 1173 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 51 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes MFE280_ENDOMETRIUM NA MFE280_ENDOMETRIUM NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.11 77 10 KDM6A 7403 broad.mit.edu 37 X 44922929 44922930 + Frame_Shift_Del DEL AT - - rs145117943;rs138994395 MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chrX:44922929_44922930delAT uc004dge.3 + 16 2165_2166 c.1790_1791delAT c.(1789-1791)CATfs p.H597fs KDM6A_uc010nhk.2_Frame_Shift_Del_p.H563fs|KDM6A_uc011mkz.1_Frame_Shift_Del_p.H649fs|KDM6A_uc011mla.1_Frame_Shift_Del_p.H552fs|KDM6A_uc011mlb.1_Frame_Shift_Del_p.H604fs|KDM6A_uc011mlc.1_Frame_Shift_Del_p.H301fs|KDM6A_uc011mld.1_Frame_Shift_Del_p.H236fs NM_021140 NP_066963 O15550 KDM6A_HUMAN ubiquitously transcribed tetratricopeptide 597 histone H3-K4 methylation metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2) 84 GGCAATAATCATATAACAGGAA 0.500 0.54 77 90 RPS6KA6 27330 broad.mit.edu 37 X 83403063 83403063 + Frame_Shift_Del DEL T - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chrX:83403063delT uc004eej.1 - 4 404 c.327delA c.(325-327)AAAfs p.K109fs RPS6KA6_uc011mqt.1_Frame_Shift_Del_p.K109fs|RPS6KA6_uc011mqu.1_Frame_Shift_Del_p.K6fs|RPS6KA6_uc010nmo.1_RNA NM_014496 NP_055311 Q9UK32 KS6A6_HUMAN ribosomal protein S6 kinase polypeptide 6 109 Protein kinase 1. axon guidance|central nervous system development|intracellular protein kinase cascade|synaptic transmission cytosol|nucleoplasm ATP binding|magnesium ion binding|protein serine/threonine kinase activity lung(5)|stomach(1)|central_nervous_system(1)|skin(1) 8 TTAAAGAGGCTTTTTTTAACA 0.303 0.46 31 26 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.54 33 38 PDE4DIP 9659 broad.mit.edu 37 1 144917591 144917592 + Frame_Shift_Ins INS - T T MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr1:144917591_144917592insT uc001elw.3 - 12 1803_1804 c.1512_1513insA c.(1510-1515)AAAGAAfs p.K504fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Ins_p.K570fs|PDE4DIP_uc001emc.1_Frame_Shift_Ins_p.K504fs|PDE4DIP_uc001emd.1_Frame_Shift_Ins_p.K504fs|PDE4DIP_uc001emb.1_Frame_Shift_Ins_p.K667fs|PDE4DIP_uc001eme.1_Frame_Shift_Ins_p.K33fs|PDE4DIP_uc001emf.1_Frame_Shift_Ins_p.K291fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 504_505 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TGGCGCAGTTCTTTTTCTTTCT 0.450 0.21 315 83 MYO3B 140469 broad.mit.edu 37 2 171509587 171509587 + Frame_Shift_Del DEL T - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr2:171509587delT uc002ufy.2 + 35 4125 c.3982delT c.(3982-3984)TTTfs p.F1328fs MYO3B_uc002ufz.2_Frame_Shift_Del_p.F1301fs|MYO3B_uc002ufw.2_RNA|MYO3B_uc002ufx.2_RNA|MYO3B_uc002ugb.2_RNA|uc002ugc.1_Intron NM_138995 NP_620482 Q8WXR4 MYO3B_HUMAN myosin IIIB isoform 2 1328 response to stimulus|visual perception cytoplasm|myosin complex actin binding|ATP binding|motor activity|protein serine/threonine kinase activity lung(8)|ovary(6)|skin(4)|central_nervous_system(1) 19 CCACCCTTCCTTTTTTTCTTC 0.413 0.46 115 97 TTN 7273 broad.mit.edu 37 2 179398170 179398170 + Frame_Shift_Del DEL G - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr2:179398170delG uc010zfg.1 - 307 95692 c.95468delC c.(95467-95469)CCAfs p.P31823fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.P25518fs|TTN_uc010zfi.1_Frame_Shift_Del_p.P25451fs|TTN_uc010zfj.1_Frame_Shift_Del_p.P25326fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 32750 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TAATGTTGGTGGGGGGATGCC 0.458 0.47 67 59 ITGAV 3685 broad.mit.edu 37 2 187521085 187521085 + Frame_Shift_Del DEL G - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr2:187521085delG uc002upq.2 + 17 1952 c.1676delG c.(1675-1677)AGGfs p.R559fs ITGAV_uc010frs.2_Frame_Shift_Del_p.R523fs|ITGAV_uc010zfv.1_Frame_Shift_Del_p.R513fs NM_002210 NP_002201 P06756 ITAV_HUMAN integrin alpha-V isoform 1 precursor 559 Extracellular (Potential). angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance integrin complex receptor activity|transforming growth factor beta binding ovary(2)|kidney(1)|skin(1) 4 OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189) STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108) ACTATTTCAAGGGGGGGACTG 0.428 0.42 51 37 SPEG 10290 broad.mit.edu 37 2 220347922 220347922 + Frame_Shift_Del DEL C - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr2:220347922delC uc010fwg.2 + 30 5737 c.5737delC c.(5737-5739)CCCfs p.P1913fs NM_005876 NP_005867 Q15772 SPEG_HUMAN SPEG complex locus 1913 muscle organ development|negative regulation of cell proliferation nucleus ATP binding|protein serine/threonine kinase activity stomach(9)|ovary(4)|central_nervous_system(1) 14 Renal(207;0.0183) Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163) CAGAAGGCCACCCCCCAGTGG 0.667 0.64 4 7 STK25 10494 broad.mit.edu 37 2 242438136 242438138 + In_Frame_Del DEL AGG - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr2:242438136_242438138delAGG uc002wbm.2 - 7 1104_1106 c.833_835delCCT c.(832-837)TCCTTC>TTC p.S278del STK25_uc002wbk.2_In_Frame_Del_p.S97del|STK25_uc002wbl.2_3'UTR|STK25_uc002wbn.2_In_Frame_Del_p.S278del|STK25_uc002wbo.2_In_Frame_Del_p.S201del|STK25_uc010zos.1_In_Frame_Del_p.S184del|STK25_uc010zot.1_In_Frame_Del_p.S204del|STK25_uc002wbp.2_In_Frame_Del_p.S278del|STK25_uc010fzo.2_In_Frame_Del_p.S201del|STK25_uc010zou.1_In_Frame_Del_p.S184del|STK25_uc010zov.1_In_Frame_Del_p.S184del NM_006374 NP_006365 O00506 STK25_HUMAN serine/threonine kinase 25 278 response to oxidative stress|signal transduction Golgi apparatus ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity 0 all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2) Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839) TCCGTGAGGAAGGAGGTCTTCTT 0.591 0.47 57 51 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.60 4 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 54 66 LIFR 3977 broad.mit.edu 37 5 38502761 38502761 + Frame_Shift_Del DEL T - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr5:38502761delT uc010ive.1 - 11 1910 c.1578delA c.(1576-1578)AAAfs p.K526fs LIFR_uc003jli.2_Frame_Shift_Del_p.K526fs NM_001127671 NP_001121143 P42702 LIFR_HUMAN leukemia inhibitory factor receptor precursor 526 Extracellular (Potential).|Fibronectin type-III 3. positive regulation of cell proliferation extracellular region|integral to plasma membrane ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity ovary(3)|large_intestine(1) 4 all_lung(31;0.00021) TTAAATGTTGTTTTTTATTGC 0.318 0.31 67 30 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.52 46 50 APC 324 broad.mit.edu 37 5 112178376 112178377 + Frame_Shift_Ins INS - A A MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr5:112178376_112178377insA uc010jby.2 + 16 7465_7466 c.7085_7086insA c.(7084-7086)GGAfs p.G2362fs APC_uc011cvt.1_Frame_Shift_Ins_p.G2344fs|APC_uc003kpz.3_Frame_Shift_Ins_p.G2362fs|APC_uc003kpy.3_Frame_Shift_Ins_p.G2362fs|APC_uc010jbz.2_Frame_Shift_Ins_p.G2079fs|APC_uc010jca.2_Frame_Shift_Ins_p.G1662fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 2362 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.?(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) TCAGGTTCTGGAAAAATGTCAT 0.406 0.44 70 56 FBN2 2201 broad.mit.edu 37 5 127713452 127713453 + Frame_Shift_Ins INS - T T MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr5:127713452_127713453insT uc003kuu.2 - 13 2280_2281 c.1841_1842insA c.(1840-1842)AACfs p.N614fs FBN2_uc003kuv.2_Frame_Shift_Ins_p.N581fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 614 EGF-like 8; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) TACCAACACAGTTTTTTCCATC 0.386 0.43 131 100 RAD50 10111 broad.mit.edu 37 5 131925448 131925449 + Frame_Shift_Ins INS - A A MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr5:131925448_131925449insA uc003kxi.2 + 9 1758_1759 c.1371_1372insA c.(1369-1374)CTGAAAfs p.L457fs RAD50_uc003kxh.2_Frame_Shift_Ins_p.L318fs NM_005732 NP_005723 Q92878 RAD50_HUMAN RAD50 homolog isoform 1 457_458 Potential. DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding lung(2)|ovary(1)|skin(1) 4 all_cancers(142;0.0368)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) AGAATGAGCTGAAAAATGTGAA 0.342 0.51 85 87 NOTCH4 4855 broad.mit.edu 37 6 32163217 32163217 + Frame_Shift_Del DEL T - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr6:32163217delT uc003obb.2 - 30 6148 c.6009delA c.(6007-6009)AAAfs p.K2003fs GPSM3_uc003oax.3_5'Flank|GPSM3_uc003oay.3_5'Flank|GPSM3_uc003oaz.2_5'UTR|NOTCH4_uc011dpt.1_3'UTR|NOTCH4_uc003oba.2_Frame_Shift_Del_p.K663fs|NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 2003 Cytoplasmic (Potential). cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 0.000 0.49 177 171 TTK 7272 broad.mit.edu 37 6 80751897 80751898 + Frame_Shift_Del DEL AA - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr6:80751897_80751898delAA uc003pjc.2 + 22 2626_2627 c.2552_2553delAA c.(2551-2553)GAAfs p.E851fs TTK_uc003pjb.3_Frame_Shift_Del_p.E850fs NM_003318 NP_003309 P33981 TTK_HUMAN TTK protein kinase 851 mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation spindle ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity p.R838fs*4(3) ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1) 11 all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2) BRCA - Breast invasive adenocarcinoma(397;0.0321) AAGACTTTTGAAAAAAAAAGGG 0.297 0.37 66 39 SLC22A3 6581 broad.mit.edu 37 6 160829931 160829931 + Frame_Shift_Del DEL T - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr6:160829931delT uc003qti.2 + 4 862 c.835delT c.(835-837)TTTfs p.F279fs SLC22A3_uc011efx.1_RNA NM_021977 NP_068812 O75751 S22A3_HUMAN solute carrier family 22 member 3 279 Helical; (Potential). integral to plasma membrane|membrane fraction protein binding|quaternary ammonium group transmembrane transporter activity skin(2)|ovary(1)|central_nervous_system(1) 4 Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218) OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06) GCTGCCCAGCTTTCTCTTCCT 0.398 0.50 96 95 MAP3K4 4216 broad.mit.edu 37 6 161469829 161469829 + Frame_Shift_Del DEL A - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr6:161469829delA uc003qtn.2 + 3 667 c.525delA c.(523-525)CCAfs p.P175fs MAP3K4_uc010kkc.1_Frame_Shift_Del_p.P175fs|MAP3K4_uc003qto.2_Frame_Shift_Del_p.P175fs|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_5'UTR NM_005922 NP_005913 Q9Y6R4 M3K4_HUMAN mitogen-activated protein kinase kinase kinase 4 175 activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity perinuclear region of cytoplasm ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding ovary(3)|lung(3)|skin(2)|stomach(1) 9 Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771) OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05) GATCTTTGCCAAAAAAATCAA 0.438 0.42 190 137 TRPS1 7227 broad.mit.edu 37 8 116631427 116631428 + Frame_Shift_Del DEL AC - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr8:116631427_116631428delAC uc003ynz.2 - 2 1317_1318 c.858_859delGT c.(856-861)GTGTTTfs p.V286fs TRPS1_uc011lhy.1_Frame_Shift_Del_p.V290fs|TRPS1_uc003yny.2_Frame_Shift_Del_p.V299fs|TRPS1_uc010mcy.2_Frame_Shift_Del_p.V286fs NM_014112 NP_054831 Q9UHF7 TRPS1_HUMAN zinc finger transcription factor TRPS1 286_287 negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) ACACCAGAAAACACAGAACGGT 0.450 0.44 134 105 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.28 469 182 WNK2 65268 broad.mit.edu 37 9 96051651 96051651 + Frame_Shift_Del DEL C - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr9:96051651delC uc004ati.1 + 20 4726 c.4726delC c.(4726-4728)CCCfs p.P1576fs WNK2_uc011lud.1_Frame_Shift_Del_p.P1539fs|WNK2_uc004atj.2_Frame_Shift_Del_p.P1539fs|WNK2_uc004atk.2_Frame_Shift_Del_p.P1176fs|WNK2_uc004atl.1_Frame_Shift_Del_p.P134fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 1576 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 GGAAGGGCCGCCCCCCAGGGT 0.701 0.45 17 14 RXRA 6256 broad.mit.edu 37 9 137300040 137300040 + Frame_Shift_Del DEL C - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr9:137300040delC uc004cfb.2 + 3 487 c.325delC c.(325-327)CCCfs p.P109fs RXRA_uc004cfc.1_Frame_Shift_Del_p.P12fs NM_002957 NP_002948 P19793 RXRA_HUMAN retinoid X receptor, alpha 109 Modulating (By similarity). cellular lipid metabolic process|cholesterol metabolic process|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid|vitamin metabolic process nuclear chromatin|nucleoplasm enzyme binding|ligand-regulated transcription factor activity|protein heterodimerization activity|retinoic acid-responsive element binding|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|transcription coactivator activity|vitamin D receptor binding|zinc ion binding upper_aerodigestive_tract(1)|ovary(1) 2 OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07) Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926) GGACATCAAGCCCCCCCTGGG 0.632 0.32 30 14 MYO3A 53904 broad.mit.edu 37 10 26417377 26417378 + Frame_Shift_Ins INS - A A MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr10:26417377_26417378insA uc001isn.2 + 20 2532_2533 c.2172_2173insA c.(2170-2175)TTCAAAfs p.F724fs MYO3A_uc009xko.1_Frame_Shift_Ins_p.F724fs|MYO3A_uc009xkp.1_RNA|MYO3A_uc009xkq.1_Intron NM_017433 NP_059129 Q8NEV4 MYO3A_HUMAN myosin IIIA 724_725 Myosin head-like. protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception cytoplasm|filamentous actin|filopodium|myosin complex actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 18 TTGAAAATTTCAAAAAAAATTC 0.342 0.43 110 84 PTEN 5728 broad.mit.edu 37 10 89720812 89720812 + Frame_Shift_Del DEL A - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr10:89720812delA uc001kfb.2 + 9 1994 c.963delA c.(961-963)ACAfs p.T321fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 321 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.T321fs*23(9)|p.T321fs*3(7)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.N323fs*2(2)|p.T319_K332del(1)|p.T321fs*22(1)|p.G165_*404del(1)|p.G165_K342del(1)|p.L316fs*1(1)|p.W274_F341del(1)|p.V317_K322del(1)|p.T321fs*4(1)|p.T321fs*6(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) TTACTTTAACAAAAAATGATC 0.323 0.46 147 125 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.70 3 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 282 100 WNK1 65125 broad.mit.edu 37 12 970296 970297 + Frame_Shift_Ins INS - A A MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr12:970296_970297insA uc001qio.3 + 7 2245_2246 c.1738_1739insA c.(1738-1740)GAAfs p.E580fs WNK1_uc001qip.3_Frame_Shift_Ins_p.E580fs|WNK1_uc001qir.3_Frame_Shift_Ins_p.E27fs NM_018979 NP_061852 Q9H4A3 WNK1_HUMAN WNK lysine deficient protein kinase 1 580 intracellular protein kinase cascade|ion transport|neuron development cytoplasm ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1) 23 all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632) Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197) GGAGGAGCAAGAAAAAAAAAAG 0.470 0.14 237 39 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.38 8 5 HSP90AA1 3320 broad.mit.edu 37 14 102551263 102551264 + In_Frame_Ins INS - CTT CTT rs3208445 MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr14:102551263_102551264insCTT uc001yku.3 - 5 925_926 c.735_736insAAG c.(733-738)insAAG p.245_246insK HSP90AA1_uc001ykv.3_In_Frame_Ins_p.367_368insK|HSP90AA1_uc001ykw.1_In_Frame_Ins_p.66_67insK|HSP90AA1_uc001ykx.1_In_Frame_Ins_p.234_235insK NM_005348 NP_005339 P07900 HS90A_HUMAN heat shock 90kDa protein 1, alpha isoform 2 245_246 axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction cytosol|melanosome|plasma membrane ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding ovary(2)|central_nervous_system(2)|prostate(1)|lung(1)|breast(1) 7 Rifabutin(DB00615) tcttctttttctttttcttctt 0.218 0.40 272 185 PAK6 56924 broad.mit.edu 37 15 40564460 40564460 + Frame_Shift_Del DEL C - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr15:40564460delC uc010bbl.2 + 6 1334 c.894delC c.(892-894)AACfs p.N298fs PAK6_uc010bbm.2_Frame_Shift_Del_p.N298fs|PAK6_uc001zky.3_Frame_Shift_Del_p.N298fs|PAK6_uc010bbn.2_Frame_Shift_Del_p.N298fs|PAK6_uc001zlb.2_Frame_Shift_Del_p.N298fs NM_001128628 NP_001122100 Q9NQU5 PAK6_HUMAN p21-activated kinase 6 298 Linker. ATP binding|protein binding|protein serine/threonine kinase activity lung(5)|large_intestine(1)|ovary(1)|skin(1) 8 all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544) AGAAAGACAACCCCCCAAGCC 0.622 0.38 83 50 TRPM7 54822 broad.mit.edu 37 15 50926659 50926660 + Frame_Shift_Ins INS - G G MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr15:50926659_50926660insG uc001zyt.3 - 8 1190_1191 c.926_927insC c.(925-927)CCTfs p.P309fs TRPM7_uc010bew.1_Frame_Shift_Ins_p.P309fs NM_017672 NP_060142 Q96QT4 TRPM7_HUMAN transient receptor potential cation channel, 309 Cytoplasmic (Potential). cell death integral to membrane ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity ovary(4)|stomach(3)|breast(1)|central_nervous_system(1)|skin(1) 10 all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045) CTACTGGAACAGGGGGGCTTTC 0.455 0.46 50 43 FASN 2194 broad.mit.edu 37 17 80051614 80051615 + Frame_Shift_Del DEL GT - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr17:80051614_80051615delGT uc002kdu.2 - 4 430_431 c.313_314delAC c.(313-315)ACTfs p.T105fs NM_004104 NP_004095 P49327 FAS_HUMAN fatty acid synthase 105 Beta-ketoacyl synthase (By similarity). energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process cytosol|Golgi apparatus|melanosome|plasma membrane 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding central_nervous_system(1) 1 all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246) OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237) Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339) CCAGACGCCAGTGTGTGTTCCT 0.678 0.41 27 19 SMAD7 4092 broad.mit.edu 37 18 46474795 46474795 + Frame_Shift_Del DEL G - - MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr18:46474795delG uc002ldg.2 - 2 913 c.626delC c.(625-627)CCTfs p.P209fs SMAD7_uc010xde.1_5'UTR NM_005904 NP_005895 O15105 SMAD7_HUMAN SMAD family member 7 209 Poly-Pro.|PY-motif.|Important for interaction with SMURF2. Missing: Diminishes interaction with SMURF2. adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding 0 Colorectal(1;0.0518) GGAGTAAGGAGGGGGGGGAGA 0.388 0.26 42 15 ATP8B1 5205 broad.mit.edu 37 18 55365039 55365040 + Frame_Shift_Ins INS - T T MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr18:55365039_55365040insT uc002lgw.2 - 6 614_615 c.614_615insA c.(613-615)AATfs p.N205fs uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 205 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) GAACAAAATCATTTTTTTTCAG 0.386 0.31 9 4 MAP3K10 4294 broad.mit.edu 37 19 40721103 40721104 + Frame_Shift_Ins INS - C C MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr19:40721103_40721104insC uc002ona.2 + 10 3057_3058 c.2769_2770insC c.(2767-2772)GGGCCCfs p.G923fs MAP3K10_uc002onb.2_Frame_Shift_Ins_p.G312fs NM_002446 NP_002437 Q02779 M3K10_HUMAN mitogen-activated protein kinase kinase kinase 923_924 activation of JUN kinase activity|induction of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of JNK cascade|protein autophosphorylation|smoothened signaling pathway cytoplasm ATP binding|bHLH transcription factor binding|JUN kinase kinase kinase activity|protein homodimerization activity|transcription corepressor activity ovary(2)|lung(2)|skin(1)|pancreas(1) 6 0.000 0.45 704 566 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 44 319 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MFE296_ENDOMETRIUM NA MFE296_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 6 48 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.61 16 25 RPL22 6146 broad.mit.edu 37 1 6257793 6257794 + Frame_Shift_Ins INS - C C MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr1:6257793_6257794insC uc001amd.2 - 2 81_82 c.35_36insG c.(34-36)GGCfs p.G12fs RPL22_uc001ame.2_Frame_Shift_Ins_p.G12fs NM_000983 NP_000974 P35268 RL22_HUMAN ribosomal protein L22 proprotein 12 endocrine pancreas development|translational elongation|translational termination|viral transcription cytosolic large ribosomal subunit heparin binding|RNA binding|structural constituent of ribosome 0 Ovarian(185;0.0634) all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211) Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182) TCTTTTTTTTGCCCCCCTTCAC 0.386 0.44 72 56 MTOR 2475 broad.mit.edu 37 1 11294234 11294235 + Frame_Shift_Ins INS - G G MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr1:11294234_11294235insG uc001asd.2 - 14 2417_2418 c.2296_2297insC c.(2296-2298)CGAfs p.R766fs NM_004958 NP_004949 P42345 MTOR_HUMAN FK506 binding protein 12-rapamycin associated 766 cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex ATP binding|phosphoprotein binding|protein serine/threonine kinase activity central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2) 29 GCGGATGAGTCGGGGGGCATTG 0.535 0.38 404 245 EPHA2 1969 broad.mit.edu 37 1 16462199 16462199 + Frame_Shift_Del DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr1:16462199delG uc001aya.1 - 6 1516 c.1379delC c.(1378-1380)CCGfs p.P460fs EPHA2_uc010oca.1_Frame_Shift_Del_p.P460fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 460 Extracellular (Potential).|Fibronectin type-III 2. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) 0.000 0.35 659 358 PAX7 5081 broad.mit.edu 37 1 18961629 18961629 + Frame_Shift_Del DEL A - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr1:18961629delA uc001bay.2 + 3 944 c.346delA c.(346-348)AAAfs p.K116fs PAX7_uc001baz.2_Frame_Shift_Del_p.K116fs|PAX7_uc010oct.1_Frame_Shift_Del_p.K116fs NM_002584 NP_002575 P23759 PAX7_HUMAN paired box 7 isoform 1 116 Paired. anti-apoptosis nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity PAX7/FOXO1(197) soft_tissue(197)|lung(3)|prostate(1)|ovary(1)|breast(1) 203 Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576) GGATGTAGAGAAAAAGATTGA 0.527 0.64 5 9 ARID1A 8289 broad.mit.edu 37 1 27105606 27105633 + Frame_Shift_Del DEL AGGACAGAGAACGCTACTGGATCCTGGG - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr1:27105606_27105633delAGGACAGAGAACGCTACTGGATCCTGGG uc001bmv.1 + 20 5590_5617 c.5217_5244delAGGACAGAGAACGCTACTGGATCCTGGG c.(5215-5244)CCAGGACAGAGAACGCTACTGGATCCTGGGfs p.P1739fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.P1522fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.P585fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.P67fs|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1739_1748 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) TGGGTGACCCAGGACAGAGAACGCTACTGGATCCTGGGAGGTTCAGCA 0.482 0.10 74 8 CLSPN 63967 broad.mit.edu 37 1 36228779 36228780 + Frame_Shift_Ins INS - T T MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr1:36228779_36228780insT uc001bzi.2 - 4 805_806 c.725_726insA c.(724-726)AACfs p.N242fs CLSPN_uc009vux.2_Frame_Shift_Ins_p.N242fs NM_022111 NP_071394 Q9HAW4 CLSPN_HUMAN claspin 242 activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation nucleoplasm anaphase-promoting complex binding|DNA binding breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1) 8 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887) 0.000 0.42 129 93 EPS15 2060 broad.mit.edu 37 1 51829633 51829633 + Frame_Shift_Del DEL T - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr1:51829633delT uc001csq.1 - 23 2356 c.2264delA c.(2263-2265)AATfs p.N755fs EPS15_uc009vyz.1_Frame_Shift_Del_p.N621fs|EPS15_uc001csp.3_Frame_Shift_Del_p.N441fs NM_001981 NP_001972 P42566 EPS15_HUMAN epidermal growth factor receptor pathway 755 15 X 3 AA repeats of D-P-F. cell proliferation|clathrin coat assembly|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|protein transport cytosol|early endosome membrane calcium ion binding|SH3 domain binding lung(1)|kidney(1) 2 CTCAAATACATTTTTTGTAAT 0.433 0.46 133 115 ZFYVE9 9372 broad.mit.edu 37 1 52810442 52810443 + Frame_Shift_Ins INS - T T MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr1:52810442_52810443insT uc001cto.2 + 18 4114_4115 c.3942_3943insT c.(3940-3945)GTGTTTfs p.V1314fs ZFYVE9_uc001ctp.2_Frame_Shift_Ins_p.V1255fs NM_004799 NP_004790 O95405 ZFYV9_HUMAN zinc finger, FYVE domain containing 9 isoform 3 1314_1315 endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway early endosome membrane metal ion binding|protein binding|receptor activity|serine-type peptidase activity ovary(2)|lung(2)|central_nervous_system(2)|skin(2) 8 GGGAACAGGTGTTTTTCCTAGA 0.431 0.46 80 68 JAK1 3716 broad.mit.edu 37 1 65339110 65339111 + Frame_Shift_Ins INS - T T MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr1:65339110_65339111insT uc001dbu.1 - 5 674_675 c.425_426insA c.(424-426)AAGfs p.K142fs JAK1_uc009wam.1_Frame_Shift_Ins_p.K130fs|JAK1_uc001dbv.2_RNA NM_002227 NP_002218 P23458 JAK1_HUMAN janus kinase 1 142 FERM. interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway cytoskeleton|cytosol|endomembrane system|membrane|nucleus ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity p.K142fs*26(3) haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1) 61 BRCA - Breast invasive adenocarcinoma(111;0.0485) CATCTGGAATCTTTTTTTTCTC 0.480 0.41 157 110 BRDT 676 broad.mit.edu 37 1 92446865 92446866 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr1:92446865_92446866insA uc001dok.3 + 11 2140_2141 c.1791_1792insA c.(1789-1794)CAGAAAfs p.Q597fs BRDT_uc001dol.3_Frame_Shift_Ins_p.Q597fs|BRDT_uc010osz.1_Frame_Shift_Ins_p.Q601fs|BRDT_uc009wdf.2_Frame_Shift_Ins_p.Q524fs|BRDT_uc010ota.1_Frame_Shift_Ins_p.Q551fs|BRDT_uc010otb.1_Frame_Shift_Ins_p.Q551fs|BRDT_uc001dom.3_Frame_Shift_Ins_p.Q597fs NM_207189 NP_997072 Q58F21 BRDT_HUMAN testis-specific bromodomain protein 597_598 Potential. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein serine/threonine kinase activity|transcription coactivator activity stomach(2)|ovary(1)|lung(1) 4 all_lung(203;0.00531)|Lung NSC(277;0.0194) all cancers(265;0.0228)|Epithelial(280;0.133) TTCACTCACAGAAAAAACAGGA 0.317 0.51 33 34 RBM15 64783 broad.mit.edu 37 1 110882873 110882873 + Frame_Shift_Del DEL C - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr1:110882873delC uc001dzl.1 + 1 929 c.846delC c.(844-846)CACfs p.H282fs RBM15_uc001dzm.1_Frame_Shift_Del_p.H282fs|uc001dzj.2_5'Flank NM_022768 NP_073605 Q96T37 RBM15_HUMAN RNA binding motif protein 15 282 interspecies interaction between organisms nucleus nucleotide binding|protein binding|RNA binding ovary(3) 3 all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634) BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135) 0.000 0.50 190 190 DDR2 4921 broad.mit.edu 37 1 162735841 162735841 + Frame_Shift_Del DEL C - - rs137924775 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr1:162735841delC uc001gcf.2 + 11 1615 c.1150delC c.(1150-1152)CCCfs p.P384fs DDR2_uc001gcg.2_Frame_Shift_Del_p.P384fs NM_001014796 NP_001014796 Q16832 DDR2_HUMAN discoidin domain receptor family, member 2 384 Extracellular (Potential). cell adhesion integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(2)|central_nervous_system(2)|ovary(1)|kidney(1) 6 all_hematologic(112;0.115) BRCA - Breast invasive adenocarcinoma(70;0.113) TCCTATGGCACCCACAACCTA 0.468 0.45 93 76 PRKD3 23683 broad.mit.edu 37 2 37506994 37506994 + Frame_Shift_Del DEL C - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr2:37506994delC uc002rqd.2 - 7 1622 c.1067delG c.(1066-1068)GGTfs p.G356fs PRKD3_uc002rqe.1_5'Flank|PRKD3_uc002rqf.1_Frame_Shift_Del_p.G356fs NM_005813 NP_005804 O94806 KPCD3_HUMAN protein kinase D3 356 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction cytoplasm|membrane|nucleus ATP binding|metal ion binding|protein binding|protein kinase C activity lung(2)|ovary(1)|central_nervous_system(1) 4 all_hematologic(82;0.21) GTCATCCAAACCCCGACTACT 0.388 0.42 123 89 ZAK 51776 broad.mit.edu 37 2 174062830 174062830 + Frame_Shift_Del DEL A - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr2:174062830delA uc002uhz.2 + 8 859 c.659delA c.(658-660)GAAfs p.E220fs ZAK_uc002uhx.2_Frame_Shift_Del_p.E220fs|ZAK_uc002uhy.2_Frame_Shift_Del_p.E220fs|ZAK_uc010zei.1_Frame_Shift_Del_p.E119fs|ZAK_uc002uia.1_Frame_Shift_Del_p.E220fs|uc002uib.2_RNA NM_016653 NP_057737 Q9NYL2 MLTK_HUMAN MLK-related kinase isoform 1 220 Protein kinase. activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation cytoplasm|nucleus ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding lung(3)|stomach(1)|ovary(1)|skin(1) 6 OV - Ovarian serous cystadenocarcinoma(117;0.176) CTTGTAGTGGAAAAAAACGAG 0.383 0.48 62 57 NFE2L2 4780 broad.mit.edu 37 2 178095913 178095914 + Frame_Shift_Ins INS - T T MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr2:178095913_178095914insT uc002ulh.3 - 5 1972_1973 c.1417_1418insA c.(1417-1419)ATCfs p.I473fs NFE2L2_uc002ulg.3_Frame_Shift_Ins_p.I457fs|NFE2L2_uc010zfa.1_Frame_Shift_Ins_p.I450fs|NFE2L2_uc002uli.3_Frame_Shift_Ins_p.I457fs NM_006164 NP_006155 Q16236 NF2L2_HUMAN nuclear factor erythroid 2-like 2 isoform 1 473 transcription from RNA polymerase II promoter centrosome|cytosol|nucleus|plasma membrane protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity central_nervous_system(1) 1 Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935) 0.000 0.43 567 428 TTN 7273 broad.mit.edu 37 2 179419377 179419378 + Frame_Shift_Ins INS - T T MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr2:179419377_179419378insT uc010zfg.1 - 281 81216_81217 c.80992_80993insA c.(80992-80994)ATCfs p.I26998fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Ins_p.I20693fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.I20626fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.I20501fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 27925 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GTAGTGAGTGATTTTTGCACCA 0.470 0.40 179 118 TTN 7273 broad.mit.edu 37 2 179646985 179646985 + Frame_Shift_Del DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr2:179646985delG uc010zfg.1 - 20 3558 c.3334delC c.(3334-3336)CATfs p.H1112fs TTN_uc010zfh.1_Frame_Shift_Del_p.H1066fs|TTN_uc010zfi.1_Frame_Shift_Del_p.H1066fs|TTN_uc010zfj.1_Frame_Shift_Del_p.H1066fs|TTN_uc002unb.2_Frame_Shift_Del_p.H1112fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 1112 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CAGTATACATGGGGCTTTGGG 0.463 0.55 38 47 COL3A1 1281 broad.mit.edu 37 2 189850464 189850465 + Frame_Shift_Ins INS - C C MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr2:189850464_189850465insC uc002uqj.1 + 4 524_525 c.407_408insC c.(406-408)GGCfs p.G136fs NM_000090 NP_000081 P02461 CO3A1_HUMAN collagen type III alpha 1 preproprotein 136 axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway collagen type III|extracellular space extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding central_nervous_system(7)|ovary(4)|large_intestine(2) 13 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141) Collagenase(DB00048)|Palifermin(DB00039) GGTTCTCCTGGCCCCCCTGGAA 0.431 0.44 97 75 ALS2 57679 broad.mit.edu 37 2 202590151 202590153 + In_Frame_Del DEL TTG - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr2:202590151_202590153delTTG uc002uyo.2 - 20 3629_3631 c.3273_3275delCAA c.(3271-3276)AACAAG>AAG p.N1091del ALS2_uc002uyp.3_In_Frame_Del_p.N1091del|ALS2_uc010ftl.2_RNA NM_020919 NP_065970 Q96Q42 ALS2_HUMAN alsin isoform 1 1091 MORN 2. cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity skin(5)|lung(1)|breast(1) 7 GTTCATTGCCTTGTTTGGGATTC 0.379 0.34 155 79 FN1 2335 broad.mit.edu 37 2 216269207 216269208 + Frame_Shift_Ins INS - G G MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr2:216269207_216269208insG uc002vfa.2 - 20 3423_3424 c.3157_3158insC c.(3157-3159)CTGfs p.L1053fs FN1_uc002vfb.2_Frame_Shift_Ins_p.L1053fs|FN1_uc002vfc.2_Frame_Shift_Ins_p.L1053fs|FN1_uc002vfd.2_Frame_Shift_Ins_p.L1053fs|FN1_uc002vfe.2_Frame_Shift_Ins_p.L1053fs|FN1_uc002vff.2_Frame_Shift_Ins_p.L1053fs|FN1_uc002vfg.2_Frame_Shift_Ins_p.L1053fs|FN1_uc002vfh.2_Frame_Shift_Ins_p.L1053fs|FN1_uc002vfi.2_Frame_Shift_Ins_p.L1053fs|FN1_uc002vfj.2_Frame_Shift_Ins_p.L1053fs NM_212482 NP_997647 P02751 FINC_HUMAN fibronectin 1 isoform 1 preproprotein 1053 |Fibronectin type-III 5. acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix collagen binding|extracellular matrix structural constituent|heparin binding central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1) 13 Renal(323;0.127) Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) CAGATTCCTCAGTGGGTACTTG 0.564 0.30 100 43 CNTN6 27255 broad.mit.edu 37 3 1427472 1427472 + Frame_Shift_Del DEL A - - rs35763173 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr3:1427472delA uc003boz.2 + 20 2962 c.2695delA c.(2695-2697)AAAfs p.K899fs CNTN6_uc011asj.1_Frame_Shift_Del_p.K827fs|CNTN6_uc003bpa.2_Frame_Shift_Del_p.K899fs NM_014461 NP_055276 Q9UQ52 CNTN6_HUMAN contactin 6 precursor 899 axon guidance|cell adhesion|central nervous system development|Notch signaling pathway anchored to membrane|plasma membrane skin(3)|lung(2)|breast(2)|pancreas(1) 8 all_cancers(2;0.000164)|all_epithelial(2;0.107) Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139) TGTTACCACCAAAAAGTCTCG 0.458 0.47 28 25 TOP2B 7155 broad.mit.edu 37 3 25673949 25673949 + Frame_Shift_Del DEL T - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr3:25673949delT uc011awn.1 - 10 1297 c.1254delA c.(1252-1254)AAAfs p.K418fs TOP2B_uc003cdj.2_Frame_Shift_Del_p.K413fs NM_001068 NP_001059 Q02880 TOP2B_HUMAN DNA topoisomerase II, beta isozyme 418 DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|resolution of meiotic recombination intermediates|sister chromatid segregation cytosol|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex|WINAC complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity breast(2)|ovary(1)|lung(1)|skin(1) 5 CTTTAAAAAATTTTTCTGACA 0.294 0.51 48 49 ULK4 54986 broad.mit.edu 37 3 41860984 41860985 + In_Frame_Ins INS - TTT TTT MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr3:41860984_41860985insTTT uc003ckv.3 - 19 1979_1980 c.1778_1779insAAA c.(1777-1779)AAG>AAAAAG p.593_593K>KK ULK4_uc003ckw.2_In_Frame_Ins_p.593_593K>KK NM_017886 NP_060356 Q96C45 ULK4_HUMAN unc-51-like kinase 4 593 ATP binding|protein serine/threonine kinase activity 0 KIRC - Kidney renal clear cell carcinoma(284;0.214) CTCTAGGGTTCTTTTTTTTTTC 0.450 0.27 59 22 PBRM1 55193 broad.mit.edu 37 3 52678768 52678768 + Frame_Shift_Del DEL T - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr3:52678768delT uc003des.2 - 8 863 c.851delA c.(850-852)AAGfs p.K284fs PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.K284fs|PBRM1_uc003der.2_Frame_Shift_Del_p.K284fs|PBRM1_uc003det.2_Frame_Shift_Del_p.K284fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.K284fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.K284fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.K284fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.K284fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.K284fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.K182fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 284 chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding p.K284fs*16(1) kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.38 159 98 FLNB 2317 broad.mit.edu 37 3 58089788 58089788 + Frame_Shift_Del DEL G - - rs145086495 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr3:58089788delG uc003djj.2 + 10 1751 c.1586delG c.(1585-1587)TGGfs p.W529fs FLNB_uc010hne.2_Frame_Shift_Del_p.W529fs|FLNB_uc003djk.2_Frame_Shift_Del_p.W529fs|FLNB_uc010hnf.2_Frame_Shift_Del_p.W529fs|FLNB_uc003djl.2_Frame_Shift_Del_p.W360fs|FLNB_uc003djm.2_Frame_Shift_Del_p.W360fs NM_001457 NP_001448 O75369 FLNB_HUMAN filamin B isoform 2 529 Filamin 3. actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction cell cortex|integral to membrane|nucleus|sarcomere actin binding breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1) 19 BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898) 0.000 0.46 504 437 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.32 13 6 GATA2 2624 broad.mit.edu 37 3 128204992 128204992 + Frame_Shift_Del DEL C - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr3:128204992delC uc003ekm.3 - 4 884 c.449delG c.(448-450)GGAfs p.G150fs GATA2_uc003ekn.3_Frame_Shift_Del_p.G150fs|GATA2_uc003eko.2_Frame_Shift_Del_p.G150fs NM_001145661 NP_001139133 P23769 GATA2_HUMAN GATA binding protein 2 isoform 1 150 blood coagulation|negative regulation of fat cell differentiation|negative regulation of fat cell proliferation|negative regulation of neural precursor cell proliferation|negative regulation of Notch signaling pathway|phagocytosis|positive regulation of angiogenesis|positive regulation of phagocytosis|positive regulation of transcription from RNA polymerase II promoter nucleoplasm C2H2 zinc finger domain binding|chromatin binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding haematopoietic_and_lymphoid_tissue(13)|lung(1)|skin(1) 15 GBM - Glioblastoma multiforme(114;0.173) CCCGCTGCCTCCCCCGCTCCC 0.672 0.50 6 6 TNK2 10188 broad.mit.edu 37 3 195595228 195595229 + Frame_Shift_Ins INS - G G MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr3:195595228_195595229insG uc003fvu.1 - 12 2438_2439 c.1895_1896insC c.(1894-1896)CCGfs p.P632fs TNK2_uc003fvq.1_Frame_Shift_Ins_p.P39fs|TNK2_uc003fvr.1_Frame_Shift_Ins_p.P157fs|TNK2_uc003fvs.1_Frame_Shift_Ins_p.P664fs|TNK2_uc003fvt.1_Frame_Shift_Ins_p.P710fs|TNK2_uc010hzw.1_RNA|TNK2_uc003fvv.1_3'UTR NM_005781 NP_005772 Q07912 ACK1_HUMAN tyrosine kinase, non-receptor, 2 isoform 1 632 Required for interaction with SRC.|Required for interaction with NEDD4 (By similarity).|Pro-rich. Missing (in Ref. 4; AAH08884). positive regulation of peptidyl-tyrosine phosphorylation|protein ubiquitination|small GTPase mediated signal transduction adherens junction|cytoplasmic vesicle membrane|endosome|nucleus ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1) 10 all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206) Lung NSC(153;0.191) Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05) GBM - Glioblastoma multiforme(46;0.000757) Adenosine triphosphate(DB00171) CATAGGCGGGCGGGGGGGGCAG 0.728 0.64 16 28 GRK4 2868 broad.mit.edu 37 4 3015469 3015470 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr4:3015469_3015470insA uc003ggn.1 + 8 1110_1111 c.655_656insA c.(655-657)CAAfs p.Q219fs GRK4_uc003ggo.1_Frame_Shift_Ins_p.Q219fs|GRK4_uc003ggp.1_Frame_Shift_Ins_p.Q187fs|GRK4_uc003ggq.1_Frame_Shift_Ins_p.Q187fs NM_182982 NP_892027 P32298 GRK4_HUMAN G protein-coupled receptor kinase 4 isoform 219 Protein kinase. cell cortex ATP binding|G-protein coupled receptor kinase activity|signal transducer activity lung(1) 1 UCEC - Uterine corpus endometrioid carcinoma (64;0.168) 0.000 0.51 249 260 RBPJ 3516 broad.mit.edu 37 4 26417097 26417098 + Frame_Shift_Ins INS - T T MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr4:26417097_26417098insT uc003grx.1 + 5 431_432 c.195_196insT c.(193-198)AGGTTTfs p.R65fs RBPJ_uc003gry.1_Frame_Shift_Ins_p.R50fs|RBPJ_uc003grz.1_Frame_Shift_Ins_p.R65fs|RBPJ_uc011bxt.1_Frame_Shift_Ins_p.R65fs|RBPJ_uc003gsa.1_Frame_Shift_Ins_p.R51fs|RBPJ_uc003gsb.1_Frame_Shift_Ins_p.R52fs|RBPJ_uc003gsc.1_Frame_Shift_Ins_p.R51fs NM_005349 NP_005340 Q06330 SUH_HUMAN recombining binding protein suppressor of 65_66 DNA recombination|negative regulation of transcription, DNA-dependent|positive regulation of transcription of Notch receptor target cytoplasm|nucleolus|nucleoplasm DNA binding|protein binding|recombinase activity|sequence-specific DNA binding transcription factor activity ovary(1)|lung(1)|central_nervous_system(1) 3 Breast(46;0.0503) TATTCTTCAGGTTTTTTTGCCC 0.332 0.19 30 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.54 6 7 ALPK1 80216 broad.mit.edu 37 4 113356325 113356326 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr4:113356325_113356326insA uc003iap.3 + 12 3335_3336 c.3056_3057insA c.(3055-3057)TCAfs p.S1019fs ALPK1_uc003ian.3_Frame_Shift_Ins_p.S1019fs|ALPK1_uc011cfx.1_Frame_Shift_Ins_p.S941fs|ALPK1_uc003iao.3_RNA|ALPK1_uc010imo.2_Frame_Shift_Ins_p.S847fs NM_025144 NP_079420 Q96QP1 ALPK1_HUMAN alpha-kinase 1 1019 Alpha-type protein kinase. ATP binding|protein serine/threonine kinase activity ovary(5) 5 Ovarian(17;0.0446)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.00325) TTAAAATATTCAAAAAAATCTG 0.356 0.17 39 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 69 103 DCLK2 166614 broad.mit.edu 37 4 151023860 151023860 + Frame_Shift_Del DEL A - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr4:151023860delA uc003ilm.3 + 2 752 c.652delA c.(652-654)AAAfs p.K218fs DCLK2_uc003iln.3_Frame_Shift_Del_p.K218fs|DCLK2_uc003ilo.3_Frame_Shift_Del_p.K218fs|DCLK2_uc003ilp.3_RNA NM_001040260 NP_001035350 Q8N568 DCLK2_HUMAN doublecortin-like kinase 2 isoform a 218 Doublecortin 2. intracellular signal transduction cytoplasm|cytoskeleton ATP binding|protein serine/threonine kinase activity ovary(3) 3 all_hematologic(180;0.151) CCTTCTGAATAAAAAGACTGC 0.418 0.36 42 24 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.76 20 64 PIK3R1 5295 broad.mit.edu 37 5 67522740 67522741 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr5:67522740_67522741insA uc003jva.2 + 2 797_798 c.237_238insA c.(235-240)AGGAAAfs p.R79fs PIK3R1_uc003jvb.2_Frame_Shift_Ins_p.R79fs NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 79_80 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) ATATTGGAAGGAAAAAAATCTC 0.490 0.43 35 26 PIK3R1 5295 broad.mit.edu 37 5 67588948 67588950 + In_Frame_Del DEL CTT - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr5:67588948_67588950delCTT uc003jva.2 + 9 1599_1601 c.1039_1041delCTT c.(1039-1041)CTTdel p.L347del PIK3R1_uc003jvb.2_In_Frame_Del_p.L347del|PIK3R1_uc003jvc.2_In_Frame_Del_p.L47del|PIK3R1_uc003jvd.2_In_Frame_Del_p.L77del|PIK3R1_uc003jve.2_In_Frame_Del_p.L26del|PIK3R1_uc011crb.1_In_Frame_Del_p.L17del NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 347 SH2 1. epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.?(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) GAATGAAAAACTTCGAGATACAG 0.335 0.46 64 55 APC 324 broad.mit.edu 37 5 112176063 112176064 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr5:112176063_112176064insA uc010jby.2 + 16 5152_5153 c.4772_4773insA c.(4771-4773)GCAfs p.A1591fs APC_uc011cvt.1_Frame_Shift_Ins_p.A1573fs|APC_uc003kpz.3_Frame_Shift_Ins_p.A1591fs|APC_uc003kpy.3_Frame_Shift_Ins_p.A1591fs|APC_uc010jbz.2_Frame_Shift_Ins_p.A1308fs|APC_uc010jca.2_Frame_Shift_Ins_p.A891fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1591 Ser-rich. A -> G (in Ref. 1; AAA60353/AAA60354). canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.P1594fs*38(2)|p.K1192fs*3(1)|p.?(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) TCACGTAAAGCAAAAAAGCCAG 0.401 0.44 23 18 PGGT1B 5229 broad.mit.edu 37 5 114557642 114557643 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr5:114557642_114557643insA uc003kqw.3 - 7 742_743 c.721_722insT c.(721-723)TCAfs p.S241fs PGGT1B_uc003kqx.3_Frame_Shift_Ins_p.S118fs|PGGT1B_uc010jch.2_Intron NM_005023 NP_005014 P53609 PGTB1_HUMAN geranylgeranyltransferase type 1 beta 241 protein geranylgeranylation CAAX-protein geranylgeranyltransferase complex CAAX-protein geranylgeranyltransferase activity 0 all_cancers(142;0.000523)|all_epithelial(76;6.45e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195) Epithelial(69;2.95e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.98e-08)|all cancers(49;3.1e-06) Pravastatin(DB00175) TTCTTTTTCTGAAAAAACTTCT 0.351 0.39 79 51 CSNK1G3 1456 broad.mit.edu 37 5 122881495 122881495 + Frame_Shift_Del DEL A - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr5:122881495delA uc003ktm.2 + 2 857 c.138delA c.(136-138)GGAfs p.G46fs CSNK1G3_uc003ktl.2_Frame_Shift_Del_p.G46fs|CSNK1G3_uc003ktn.2_Frame_Shift_Del_p.G46fs|CSNK1G3_uc003kto.2_Frame_Shift_Del_p.G46fs|CSNK1G3_uc011cwr.1_Intron|CSNK1G3_uc011cws.1_Intron|CSNK1G3_uc010jda.2_Frame_Shift_Del_p.G46fs NM_004384 NP_004375 Q9Y6M4 KC1G3_HUMAN casein kinase 1, gamma 3 isoform 1 46 Protein kinase. Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity 0 all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245) KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229) OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176) TTAGAGTTGGAAAAAAAATTG 0.363 0.34 53 27 ACSL6 23305 broad.mit.edu 37 5 131298340 131298340 + Frame_Shift_Del DEL T - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr5:131298340delT uc010jdo.1 - 18 1753 c.1670delA c.(1669-1671)AAGfs p.K557fs ACSL6_uc003kvv.1_RNA|ACSL6_uc003kvx.1_Frame_Shift_Del_p.K582fs|ACSL6_uc003kvy.1_Frame_Shift_Del_p.K582fs|ACSL6_uc003kwb.2_Frame_Shift_Del_p.K547fs|ACSL6_uc003kvz.1_Frame_Shift_Del_p.K482fs|ACSL6_uc003kwa.1_Frame_Shift_Del_p.K568fs|ACSL6_uc003kvw.1_Frame_Shift_Del_p.K203fs|ACSL6_uc010jdn.1_Frame_Shift_Del_p.K572fs NM_015256 NP_056071 Q9UKU0 ACSL6_HUMAN acyl-CoA synthetase long-chain family member 6 557 Cytoplasmic (Potential). fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane|plasma membrane ATP binding|long-chain fatty acid-CoA ligase activity upper_aerodigestive_tract(1)|ovary(1)|skin(1) 3 all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) AAATATATGCTTTTTCCGATC 0.438 0.46 110 92 CSF1R 1436 broad.mit.edu 37 5 149441304 149441304 + Frame_Shift_Del DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr5:149441304delG uc003lrl.2 - 11 1930 c.1735delC c.(1735-1737)CGGfs p.R579fs CSF1R_uc011dcd.1_Frame_Shift_Del_p.R431fs|CSF1R_uc010jhc.2_RNA|CSF1R_uc003lrm.2_Frame_Shift_Del_p.R579fs NM_005211 NP_005202 P07333 CSF1R_HUMAN colony stimulating factor 1 receptor precursor 579 Cytoplasmic (Potential). cell proliferation|multicellular organismal development|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane|receptor complex ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity haematopoietic_and_lymphoid_tissue(38)|lung(6)|central_nervous_system(3)|liver(3)|breast(2)|endometrium(1)|ovary(1) 54 KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147) Imatinib(DB00619)|Sunitinib(DB01268) AGGTTGTTCCGGGGGAACTCC 0.567 0.60 4 6 BAT3 7917 broad.mit.edu 37 6 31612922 31612923 + Frame_Shift_Ins INS - G G MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr6:31612922_31612923insG uc003nvg.3 - 10 1501_1502 c.1187_1188insC c.(1186-1188)CCAfs p.P396fs BAT3_uc003nvf.3_Frame_Shift_Ins_p.P390fs|BAT3_uc003nvh.3_Frame_Shift_Ins_p.P390fs|BAT3_uc003nvi.3_Frame_Shift_Ins_p.P390fs|BAT3_uc011dnw.1_Frame_Shift_Ins_p.P390fs|BAT3_uc011dnx.1_Frame_Shift_Ins_p.P390fs|BAT3_uc003nvj.1_Frame_Shift_Ins_p.P390fs NM_004639 NP_004630 P46379 BAG6_HUMAN HLA-B associated transcript-3 isoform a 396 Pro-rich.|4 X 29 AA approximate repeats. apoptosis in response to endoplasmic reticulum stress|brain development|cell differentiation|chromatin modification|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|embryo development|internal peptidyl-lysine acetylation|kidney development|lung development|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|protein stabilization|spermatogenesis|synaptonemal complex assembly|tail-anchored membrane protein insertion into ER membrane|transport|ubiquitin-dependent protein catabolic process BAT3 complex|nucleus polyubiquitin binding|proteasome binding|ribosome binding 0 CATTGGGAGTTGGGGGGGGCCG 0.579 0.36 58 33 STK38 11329 broad.mit.edu 37 6 36465583 36465583 + Frame_Shift_Del DEL A - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr6:36465583delA uc003omg.2 - 11 1734 c.1146delT c.(1144-1146)TTTfs p.F382fs STK38_uc003omh.2_Frame_Shift_Del_p.F382fs|STK38_uc003omi.2_Frame_Shift_Del_p.F382fs NM_007271 NP_009202 Q15208 STK38_HUMAN serine/threonine kinase 38 382 Protein kinase. intracellular protein kinase cascade|negative regulation of MAP kinase activity cytoplasm|MLL5-L complex ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1) 6 CAACGCCTTCAAAAAAAGAGT 0.368 0.47 56 50 RUNX2 860 broad.mit.edu 37 6 45514583 45514583 + Frame_Shift_Del DEL T - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr6:45514583delT uc011dvx.1 + 9 1317 c.1107delT c.(1105-1107)CCTfs p.P369fs RUNX2_uc011dvy.1_Frame_Shift_Del_p.P347fs|RUNX2_uc003oxt.2_Frame_Shift_Del_p.P355fs NM_001024630 NP_001019801 Q13950 RUNX2_HUMAN runt-related transcription factor 2 isoform a 369 Interaction with MYST3 (By similarity).|Pro/Ser/Thr-rich. negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent nucleus ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity ovary(2)|skin(1) 3 AACTGGGCCCTTTTTCAGACC 0.413 0.48 44 41 TNFAIP3 7128 broad.mit.edu 37 6 138199945 138199945 + Frame_Shift_Del DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr6:138199945delG uc003qhr.2 + 7 1429 c.1363delG c.(1363-1365)GGGfs p.G455fs TNFAIP3_uc003qhs.2_Frame_Shift_Del_p.G455fs NM_006290 NP_006281 P21580 TNAP3_HUMAN tumor necrosis factor, alpha-induced protein 3 455 Interaction with NAF1 (By similarity). anti-apoptosis|apoptosis|B-1 B cell homeostasis|negative regulation of B cell activation|negative regulation of bone resorption|negative regulation of CD40 signaling pathway|negative regulation of endothelial cell apoptosis|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of inflammatory response|negative regulation of interleukin-2 production|negative regulation of interleukin-6 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of osteoclast proliferation|negative regulation of protein ubiquitination|negative regulation of smooth muscle cell proliferation|negative regulation of toll-like receptor 2 signaling pathway|negative regulation of toll-like receptor 3 signaling pathway|negative regulation of tumor necrosis factor production|negative regulation of type I interferon production|positive regulation of protein catabolic process|protein K48-linked ubiquitination|protein K63-linked deubiquitination|protein oligomerization|regulation of defense response to virus by host|regulation of germinal center formation|regulation of vascular wound healing|tolerance induction to lipopolysaccharide centrosome|cytosol|nucleus caspase inhibitor activity|DNA binding|protease binding|protein self-association|ubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-protein ligase activity|ubiquitin-specific protease activity|zinc ion binding p.0?(22)|p.P450fs*21(1) haematopoietic_and_lymphoid_tissue(133)|lung(3)|ovary(1) 137 Breast(32;0.135)|Colorectal(23;0.24) GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468) GGAGTCCACTGGGGGGCCTCA 0.657 0.42 37 27 MAP3K4 4216 broad.mit.edu 37 6 161469775 161469776 + Frame_Shift_Ins INS - A A rs80180935 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr6:161469775_161469776insA uc003qtn.2 + 3 613_614 c.471_472insA c.(469-474)CATAAAfs p.H157fs MAP3K4_uc010kkc.1_Frame_Shift_Ins_p.R157fs|MAP3K4_uc003qto.2_Frame_Shift_Ins_p.H157fs|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_5'UTR NM_005922 NP_005913 Q9Y6R4 M3K4_HUMAN mitogen-activated protein kinase kinase kinase 4 157_158 activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity perinuclear region of cytoplasm ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding ovary(3)|lung(3)|skin(2)|stomach(1) 9 Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771) OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05) AGCGTGATCGTAAAAAAAATGT 0.406 0.38 58 36 RPS6KA2 6196 broad.mit.edu 37 6 166944721 166944721 + Frame_Shift_Del DEL T - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr6:166944721delT uc003qvb.1 - 3 516 c.297delA c.(295-297)AAAfs p.K99fs RPS6KA2_uc011ego.1_Frame_Shift_Del_p.K10fs|RPS6KA2_uc010kkl.1_Frame_Shift_Del_p.K10fs|RPS6KA2_uc003qvc.1_Frame_Shift_Del_p.K107fs|RPS6KA2_uc003qvd.1_Frame_Shift_Del_p.K124fs NM_021135 NP_066958 Q15349 KS6A2_HUMAN ribosomal protein S6 kinase, 90kDa, polypeptide 99 Protein kinase 1. axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|magnesium ion binding|protein serine/threonine kinase activity ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1) 8 Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105) OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05) AGCTCTTACCTTTTAGGGTGG 0.473 0.39 33 21 PMS2 5395 broad.mit.edu 37 7 6027001 6027001 + Frame_Shift_Del DEL T - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr7:6027001delT uc003spl.2 - 11 1482 c.1395delA c.(1393-1395)AAAfs p.K465fs PMS2_uc003spj.2_Frame_Shift_Del_p.K359fs|PMS2_uc003spk.2_Frame_Shift_Del_p.K330fs|PMS2_uc011jwl.1_Frame_Shift_Del_p.K330fs|PMS2_uc010ktg.2_Frame_Shift_Del_p.K154fs|PMS2_uc010kte.2_Intron|PMS2_uc010ktf.1_Frame_Shift_Del_p.K465fs NM_000535 NP_000526 P54278 PMS2_HUMAN PMS2 postmeiotic segregation increased 2 isoform 465 mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes MutLalpha complex ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding lung(1)|central_nervous_system(1) 2 Ovarian(82;0.0694) UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15) TCAGGACGCCTTTGTCAGAGA 0.567 0.45 192 157 EPHB4 2050 broad.mit.edu 37 7 100403122 100403122 + Splice_Site DEL C - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr7:100403122delC uc003uwn.1 - 15 3169 c.2678_splice c.e15+1 p.G893_splice EPHB4_uc003uwm.1_Splice_Site_p.G800_splice|EPHB4_uc010lhj.1_Splice_Site_p.G893_splice NM_004444 NP_004435 P54760 EPHB4_HUMAN EPH receptor B4 precursor cell proliferation|organ morphogenesis|regulation of angiogenesis cell surface|integral to plasma membrane ATP binding|ephrin receptor activity lung(4)|stomach(3)|skin(3)|central_nervous_system(2)|ovary(2)|breast(1) 15 Lung NSC(181;0.041)|all_lung(186;0.0581) GCAGTCCTCACCCGCCATTCT 0.657 0.68 14 30 TRIM24 8805 broad.mit.edu 37 7 138145354 138145354 + Frame_Shift_Del DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr7:138145354delG uc003vuc.2 + 1 276 c.61delG c.(61-63)GGGfs p.G21fs TRIM24_uc003vub.2_Frame_Shift_Del_p.G21fs NM_015905 NP_056989 O15164 TIF1A_HUMAN transcriptional intermediary factor 1 alpha 21 cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter cytoplasm chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1) 8 0.000 0.33 411 207 KIAA1549 57670 broad.mit.edu 37 7 138602055 138602056 + Frame_Shift_Ins INS - G G rs61746877 by1000genomes MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr7:138602055_138602056insG uc011kql.1 - 2 2365_2366 c.2316_2317insC c.(2314-2319)CCCGGCfs p.P772fs KIAA1549_uc003vuk.3_Frame_Shift_Ins_p.P722fs|KIAA1549_uc011kqj.1_Frame_Shift_Ins_p.P772fs NM_020910 NP_065961 Q9HCM3 K1549_HUMAN hypothetical protein LOC57670 isoform 1 772_773 integral to membrane KIAA1549/BRAF(229) central_nervous_system(229)|pancreas(1) 230 GACTCAGAGCCGGGGGGCACCA 0.460 0.34 44 23 NOS3 4846 broad.mit.edu 37 7 150698397 150698398 + Frame_Shift_Ins INS - G G MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr7:150698397_150698398insG uc003wif.2 + 11 1608_1609 c.1312_1313insG c.(1312-1314)AGGfs p.R438fs NOS3_uc011kuy.1_Frame_Shift_Ins_p.R232fs|NOS3_uc011kuz.1_Frame_Shift_Ins_p.R438fs|NOS3_uc011kva.1_Frame_Shift_Ins_p.R438fs|NOS3_uc011kvb.1_Frame_Shift_Ins_p.R438fs NM_000603 NP_000594 P29474 NOS3_HUMAN nitric oxide synthase 3 isoform 1 438 Interaction with NOSIP. anti-apoptosis|arginine catabolic process|blood vessel remodeling|endothelial cell migration|mitochondrion organization|negative regulation of muscle hyperplasia|negative regulation of platelet activation|nitric oxide biosynthetic process|platelet activation|positive regulation of angiogenesis|positive regulation of guanylate cyclase activity|positive regulation of vasodilation|regulation of blood vessel size|regulation of nitric-oxide synthase activity|regulation of systemic arterial blood pressure by endothelin|response to fluid shear stress|response to heat|smooth muscle hyperplasia caveola|cytoskeleton|cytosol|Golgi membrane actin monomer binding|arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding central_nervous_system(5)|large_intestine(2)|skin(1) 8 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) L-Arginine(DB00125)|L-Citrulline(DB00155)|Rosuvastatin(DB01098)|Tetrahydrobiopterin(DB00360) GCAGAAGGCCAGGGGGGGCTGC 0.614 0.68 12 25 PAXIP1 22976 broad.mit.edu 37 7 154760669 154760670 + In_Frame_Ins INS - TGC TGC MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr7:154760669_154760670insTGC uc003wlp.2 - 7 1284_1285 c.1241_1242insGCA c.(1240-1242)CAC>CAGCAC p.413_414insQ PAXIP1_uc003wlq.1_In_Frame_Ins_p.379_380insQ|PAXIP1_uc011kvs.1_In_Frame_Ins_p.377_378insQ|PAXIP1_uc003wlr.1_In_Frame_Ins_p.322_323insQ NM_007349 NP_031375 Q6ZW49 PAXI1_HUMAN PAX interacting protein 1 413_414 Gln-rich. DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent histone methyltransferase complex|nuclear matrix lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_neural(206;0.119) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.0296) UCEC - Uterine corpus endometrioid carcinoma (81;0.178) GTAAAACCGGGtgctgctgctg 0.366 0.29 75 30 ADAM28 10863 broad.mit.edu 37 8 24167472 24167473 + Frame_Shift_Ins INS - AA AA MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr8:24167472_24167473insAA uc003xdy.2 + 3 299_300 c.216_217insAA c.(214-219)TTGAAAfs p.L72fs ADAM28_uc003xdx.2_Frame_Shift_Ins_p.L72fs|ADAM28_uc011kzz.1_5'UTR|ADAM28_uc011laa.1_RNA NM_014265 NP_055080 Q9UKQ2 ADA28_HUMAN ADAM metallopeptidase domain 28 isoform 1 72_73 proteolysis|spermatogenesis extracellular region|integral to membrane|plasma membrane metalloendopeptidase activity|zinc ion binding skin(3)|lung(1)|central_nervous_system(1) 5 Prostate(55;0.0959) Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175) TGCTTTATTTGAAAAAAAACAA 0.332 0.48 22 20 ADAM28 10863 broad.mit.edu 37 8 24167707 24167709 + In_Frame_Del DEL TAT - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr8:24167707_24167709delTAT uc003xdy.2 + 4 342_344 c.259_261delTAT c.(259-261)TATdel p.Y88del ADAM28_uc003xdx.2_In_Frame_Del_p.Y88del|ADAM28_uc011kzz.1_5'UTR|ADAM28_uc011laa.1_RNA NM_014265 NP_055080 Q9UKQ2 ADA28_HUMAN ADAM metallopeptidase domain 28 isoform 1 88 proteolysis|spermatogenesis extracellular region|integral to membrane|plasma membrane metalloendopeptidase activity|zinc ion binding skin(3)|lung(1)|central_nervous_system(1) 5 Prostate(55;0.0959) Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175) CACGGAAACATATTATAATTCCA 0.404 0.61 62 95 ARFGEF1 10565 broad.mit.edu 37 8 68140283 68140284 + Frame_Shift_Ins INS - T T MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr8:68140283_68140284insT uc003xxo.1 - 25 3895_3896 c.3505_3506insA c.(3505-3507)ATAfs p.I1169fs ARFGEF1_uc003xxl.1_Frame_Shift_Ins_p.I623fs|ARFGEF1_uc003xxn.1_Frame_Shift_Ins_p.I152fs NM_006421 NP_006412 Q9Y6D6 BIG1_HUMAN brefeldin A-inhibited guanine 1169 exocytosis|regulation of ARF protein signal transduction cytoplasm ARF guanyl-nucleotide exchange factor activity|myosin binding ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1) 8 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206) TATTTCTACTATTTTTTGTAGA 0.327 0.44 68 54 RGS22 26166 broad.mit.edu 37 8 100975124 100975124 + Frame_Shift_Del DEL T - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr8:100975124delT uc003yjb.1 - 25 3893 c.3698delA c.(3697-3699)AAGfs p.K1233fs RGS22_uc003yja.1_Frame_Shift_Del_p.K1052fs|RGS22_uc003yjc.1_Frame_Shift_Del_p.K1221fs NM_015668 NP_056483 Q8NE09 RGS22_HUMAN regulator of G-protein signaling 22 1233 K -> KK (in Ref. 2; CAB55986). negative regulation of signal transduction cytoplasm|plasma membrane GTPase activator activity|signal transducer activity ovary(3)|skin(2)|breast(1)|central_nervous_system(1) 7 Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169) 0.000 0.47 70 63 COL14A1 7373 broad.mit.edu 37 8 121379470 121379471 + Frame_Shift_Ins INS - C C MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr8:121379470_121379471insC uc003yox.2 + 46 5403_5404 c.5138_5139insC c.(5137-5139)GGCfs p.G1713fs COL14A1_uc003yoz.2_Frame_Shift_Ins_p.G678fs NM_021110 NP_066933 Q05707 COEA1_HUMAN collagen, type XIV, alpha 1 precursor 1713 Triple-helical region 2 (COL1). cell-cell adhesion|collagen fibril organization collagen type XIV|extracellular space collagen binding|extracellular matrix structural constituent|protein binding, bridging ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1) 12 Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503) GGTCCAAGAGGCCCCCCTGGAC 0.371 0.31 29 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 45 ENHO 375704 broad.mit.edu 37 9 34521668 34521669 + Frame_Shift_Ins INS - C C MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr9:34521668_34521669insC uc003zun.1 - 2 449_450 c.25_26insG c.(25-27)GCCfs p.A9fs ENHO_uc003zuo.2_RNA NM_198573 NP_940975 Q6UWT2 ENHO_HUMAN adropin precursor 9 extracellular region 0 0.000 0.50 305 310 DAPK1 1612 broad.mit.edu 37 9 90296460 90296460 + Frame_Shift_Del DEL T - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr9:90296460delT uc004apc.2 + 20 2281 c.2143delT c.(2143-2145)TTTfs p.F715fs DAPK1_uc004apd.2_Frame_Shift_Del_p.F715fs|DAPK1_uc011ltg.1_Frame_Shift_Del_p.F715fs|DAPK1_uc011lth.1_Frame_Shift_Del_p.F452fs|DAPK1_uc004apf.1_Frame_Shift_Del_p.F269fs NM_004938 NP_004929 P53355 DAPK1_HUMAN death-associated protein kinase 1 715 apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade actin cytoskeleton|cytoplasm ATP binding|calmodulin binding|protein serine/threonine kinase activity ovary(1)|breast(1) 2 GCTGAGGAGCTTTTTCAGAAG 0.552 0.40 78 51 DAPK1 1612 broad.mit.edu 37 9 90321802 90321802 + Frame_Shift_Del DEL G - - rs56169226 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr9:90321802delG uc004apc.2 + 26 3954 c.3816delG c.(3814-3816)ATGfs p.M1272fs DAPK1_uc004apd.2_Frame_Shift_Del_p.M1272fs|DAPK1_uc011ltg.1_Frame_Shift_Del_p.M1206fs|DAPK1_uc011lth.1_Frame_Shift_Del_p.M1009fs|DAPK1_uc004apg.2_Frame_Shift_Del_p.M249fs NM_004938 NP_004929 P53355 DAPK1_HUMAN death-associated protein kinase 1 1272 apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade actin cytoskeleton|cytoplasm ATP binding|calmodulin binding|protein serine/threonine kinase activity ovary(1)|breast(1) 2 CCAACACCATGGGGGGGTACA 0.582 0.40 15 10 FOXE1 2304 broad.mit.edu 37 9 100616762 100616763 + Frame_Shift_Ins INS - CC CC MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr9:100616762_100616763insCC uc004axu.2 + 1 1226_1227 c.566_567insCC c.(565-567)CGCfs p.R189fs NM_004473 NP_004464 O00358 FOXE1_HUMAN forkhead box E1 189 Pro-rich.|Ala-rich. cell migration|embryonic organ morphogenesis|hair follicle morphogenesis|hard palate development|lens morphogenesis in camera-type eye|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|peripheral nervous system development|pharynx development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|soft palate development|thymus development|thyroid gland development|thyroid hormone generation transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding 0 Acute lymphoblastic leukemia(62;0.158) 0.000 0.41 24 17 SMC2 10592 broad.mit.edu 37 9 106862449 106862450 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr9:106862449_106862450insA uc004bbv.2 + 6 844_845 c.556_557insA c.(556-558)GAAfs p.E186fs SMC2_uc004bbu.1_Frame_Shift_Ins_p.E186fs|SMC2_uc004bbw.2_Frame_Shift_Ins_p.E186fs|SMC2_uc011lvl.1_Frame_Shift_Ins_p.E186fs|SMC2_uc010mtg.1_Frame_Shift_Ins_p.E41fs|SMC2_uc010mth.1_Frame_Shift_Ins_p.E136fs|SMC2_uc004bbx.2_Frame_Shift_Ins_p.E186fs NM_001042551 NP_001036016 O95347 SMC2_HUMAN structural maintenance of chromosomes 2 186 Potential. cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism condensin complex|cytoplasm|nuclear chromosome ATP binding|protein heterodimerization activity p.E186K(1) ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1) 9 GAAAACTATAGAAAAAAAGGAG 0.297 0.54 12 14 SMC2 10592 broad.mit.edu 37 9 106864417 106864418 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr9:106864417_106864418insA uc004bbv.2 + 8 1101_1102 c.813_814insA c.(811-816)GATAAAfs p.D271fs SMC2_uc004bbu.1_Frame_Shift_Ins_p.D271fs|SMC2_uc004bbw.2_Frame_Shift_Ins_p.D271fs|SMC2_uc011lvl.1_Frame_Shift_Ins_p.D271fs|SMC2_uc010mtg.1_Frame_Shift_Ins_p.D126fs|SMC2_uc010mth.1_Frame_Shift_Ins_p.D221fs|SMC2_uc004bbx.2_Frame_Shift_Ins_p.D271fs NM_001042551 NP_001036016 O95347 SMC2_HUMAN structural maintenance of chromosomes 2 271_272 Potential. cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism condensin complex|cytoplasm|nuclear chromosome ATP binding|protein heterodimerization activity ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1) 9 CTGAGAATGATAAAAAAATAAA 0.297 0.38 13 8 CUBN 8029 broad.mit.edu 37 10 17113553 17113554 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr10:17113553_17113554insA uc001ioo.2 - 19 2548_2549 c.2496_2497insT c.(2494-2499)TTTCCTfs p.F832fs NM_001081 NP_001072 O60494 CUBN_HUMAN cubilin precursor 832_833 CUB 4. cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1) 19 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) TACACGTTAGGAAAAAAAGGCG 0.416 0.30 76 32 PTEN 5728 broad.mit.edu 37 10 89720811 89720812 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr10:89720811_89720812insA uc001kfb.2 + 9 1993_1994 c.962_963insA c.(961-963)ACAfs p.T321fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 321 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.T321fs*23(9)|p.T321fs*3(7)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.N323fs*2(2)|p.T319_K332del(1)|p.T321fs*22(1)|p.G165_*404del(1)|p.G165_K342del(1)|p.L316fs*1(1)|p.W274_F341del(1)|p.V317_K322del(1)|p.T321fs*4(1)|p.T321fs*6(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) CTTACTTTAACAAAAAATGATC 0.327 0.39 56 36 TNKS2 80351 broad.mit.edu 37 10 93601945 93601946 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr10:93601945_93601946insA uc001khp.2 + 16 2153_2154 c.1856_1857insA c.(1855-1857)ACAfs p.T619fs NM_025235 NP_079511 Q9H2K2 TNKS2_HUMAN tankyrase, TRF1-interacting ankyrin-related 619 ANK 12. positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm NAD+ ADP-ribosyltransferase activity|protein binding kidney(3)|skin(3)|ovary(1)|lung(1) 8 Colorectal(252;0.162) GCAGACCCTACAAAAAAAAACA 0.391 0.50 8 8 PIPSL 266971 broad.mit.edu 37 10 95719926 95719927 + Frame_Shift_Ins INS - T T MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr10:95719926_95719927insT uc009xuj.2 - 1 1746_1747 c.1227_1228insA c.(1225-1230)AAACTTfs p.K409fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCAGACCGAAGTTTTTTGGAAG 0.505 0.47 87 77 NLRP6 171389 broad.mit.edu 37 11 280595 280595 + Frame_Shift_Del DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr11:280595delG uc010qvs.1 + 4 861 c.861delG c.(859-861)CTGfs p.L287fs NLRP6_uc010qvt.1_Frame_Shift_Del_p.L287fs NM_138329 NP_612202 P59044 NALP6_HUMAN NLR family, pyrin domain containing 6 287 NACHT. cytoplasm ATP binding upper_aerodigestive_tract(1)|skin(1) 2 all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122) 0.000 0.42 231 167 STK33 65975 broad.mit.edu 37 11 8496261 8496262 + Frame_Shift_Ins INS - T T MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr11:8496261_8496262insT uc001mgi.1 - 1 1110_1111 c.191_192insA c.(190-192)AATfs p.N64fs STK33_uc001mgj.1_Frame_Shift_Ins_p.N64fs|STK33_uc001mgk.1_Frame_Shift_Ins_p.N64fs|STK33_uc010rbn.1_Frame_Shift_Ins_p.N23fs|STK33_uc001mgl.3_Intron|STK33_uc009yfp.2_Intron NM_030906 NP_112168 Q9BYT3 STK33_HUMAN serine/threonine kinase 33 64 Golgi apparatus|nucleus|perinuclear region of cytoplasm ATP binding|protein serine/threonine kinase activity ovary(2)|lung(2)|pancreas(1)|central_nervous_system(1)|skin(1) 7 Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239) CTCTGTTGATATTTTTTTCTTT 0.376 0.44 51 40 FANCF 2188 broad.mit.edu 37 11 22647278 22647278 + Frame_Shift_Del DEL C - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr11:22647278delC uc001mql.1 - 1 110 c.79delG c.(79-81)GACfs p.D27fs NM_022725 NP_073562 Q9NPI8 FANCF_HUMAN Fanconi anemia, complementation group F 27 DNA repair nucleoplasm protein binding skin(1) 1 GTGGCGGGGTCCCAGGTGCTG 0.652 0.46 26 22 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.85 2 11 ANO1 55107 broad.mit.edu 37 11 70011585 70011585 + Frame_Shift_Del DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr11:70011585delG uc001opj.2 + 20 2265 c.1960delG c.(1960-1962)GGGfs p.G654fs ANO1_uc001opl.1_RNA|ANO1_uc010rqk.1_Frame_Shift_Del_p.G363fs NM_018043 NP_060513 Q5XXA6 ANO1_HUMAN anoctamin 1, calcium activated chloride channel 654 Extracellular (Potential). multicellular organismal development chloride channel complex|cytoplasm|plasma membrane intracellular calcium activated chloride channel activity ovary(1)|pancreas(1) 2 0.000 0.42 926 672 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 351 64 SIK3 23387 broad.mit.edu 37 11 116747030 116747031 + Frame_Shift_Ins INS - G G MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr11:116747030_116747031insG uc001ppy.2 - 8 895_896 c.859_860insC c.(859-861)CTGfs p.L287fs SIK3_uc001ppz.2_Frame_Shift_Ins_p.L186fs|SIK3_uc001pqa.2_Frame_Shift_Ins_p.L287fs NM_025164 NP_079440 Q9Y2K2 SIK3_HUMAN serine/threonine-protein kinase QSK 287 UBA. cytoplasm ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1) 12 ATCCTCATTCAGGGGGTCCACC 0.465 0.41 176 120 WNK1 65125 broad.mit.edu 37 12 989023 989023 + Frame_Shift_Del DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr12:989023delG uc001qio.3 + 11 3165 c.2658delG c.(2656-2658)CCGfs p.P886fs WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron NM_018979 NP_061852 Q9H4A3 WNK1_HUMAN WNK lysine deficient protein kinase 1 886 intracellular protein kinase cascade|ion transport|neuron development cytoplasm ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1) 23 all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632) Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197) CTGCGATCCCGGGGGTATCAA 0.552 0.50 137 135 WNK1 65125 broad.mit.edu 37 12 1005704 1005704 + Frame_Shift_Del DEL T - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr12:1005704delT uc001qio.3 + 24 6558 c.6051delT c.(6049-6051)GCTfs p.A2017fs WNK1_uc001qip.3_Frame_Shift_Del_p.A1769fs|WNK1_uc001qir.3_Frame_Shift_Del_p.A1190fs NM_018979 NP_061852 Q9H4A3 WNK1_HUMAN WNK lysine deficient protein kinase 1 2017 intracellular protein kinase cascade|ion transport|neuron development cytoplasm ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1) 23 all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632) Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197) CGGAGGCCGCTTTTTTAAGTA 0.498 0.47 45 40 PIK3C2G 5288 broad.mit.edu 37 12 18435392 18435392 + Frame_Shift_Del DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr12:18435392delG uc001rdt.2 + 2 493 c.377delG c.(376-378)TGGfs p.W126fs PIK3C2G_uc010sia.1_RNA|PIK3C2G_uc010sib.1_Frame_Shift_Del_p.W126fs|PIK3C2G_uc010sic.1_5'UTR NM_004570 NP_004561 O75747 P3C2G_HUMAN phosphoinositide-3-kinase, class 2 gamma 126 cell communication|phosphatidylinositol-mediated signaling membrane|phosphatidylinositol 3-kinase complex 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2) 21 Hepatocellular(102;0.194) GAATGCTCCTGGGGAAGCCCC 0.398 0.56 30 38 ACVR1B 91 broad.mit.edu 37 12 52345606 52345607 + Frame_Shift_Ins INS - G G MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr12:52345606_52345607insG uc001rzn.2 + 1 121_122 c.79_80insG c.(79-81)CGGfs p.R27fs ACVR1B_uc001rzl.2_Frame_Shift_Ins_p.R27fs|ACVR1B_uc001rzm.2_Frame_Shift_Ins_p.R27fs|ACVR1B_uc010snn.1_Frame_Shift_Ins_p.R27fs NM_004302 NP_004293 P36896 ACV1B_HUMAN activin A receptor, type IB isoform a precursor 27 Extracellular (Potential). G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|peptidyl-threonine phosphorylation|positive regulation of activin receptor signaling pathway|positive regulation of erythrocyte differentiation|protein autophosphorylation|transmembrane receptor protein serine/threonine kinase signaling pathway cell surface activin receptor activity, type I|ATP binding|metal ion binding|SMAD binding|transforming growth factor beta receptor activity|ubiquitin protein ligase binding pancreas(4)|breast(2)|ovary(1)|lung(1)|kidney(1) 9 BRCA - Breast invasive adenocarcinoma(357;0.104) Adenosine triphosphate(DB00171) 0.000 0.38 181 109 APAF1 317 broad.mit.edu 37 12 99071206 99071207 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr12:99071206_99071207insA uc001tfz.2 + 13 2374_2375 c.1797_1798insA c.(1795-1800)AACAAAfs p.N599fs APAF1_uc001tfy.2_Frame_Shift_Ins_p.N588fs|APAF1_uc001tga.2_Frame_Shift_Ins_p.N588fs|APAF1_uc001tgb.2_Frame_Shift_Ins_p.N599fs|APAF1_uc001tgc.2_Intron|APAF1_uc009zto.2_Frame_Shift_Ins_p.N8fs NM_181861 NP_863651 O14727 APAF_HUMAN apoptotic peptidase activating factor 1 isoform 599_600 activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development cytosol|Golgi apparatus|nucleus ATP binding|caspase activator activity|protein binding ovary(2)|lung(1) 3 Adenosine triphosphate(DB00171) TATTTAGAAACAAAAAAAACAT 0.347 0.42 51 37 TAOK3 51347 broad.mit.edu 37 12 118599599 118599600 + Frame_Shift_Ins INS - T T MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr12:118599599_118599600insT uc001twx.2 - 18 2427_2428 c.2132_2133insA c.(2131-2133)AACfs p.N711fs TAOK3_uc001twv.2_Frame_Shift_Ins_p.N251fs|TAOK3_uc001tww.2_Frame_Shift_Ins_p.N541fs|TAOK3_uc001twy.3_Frame_Shift_Ins_p.N711fs NM_016281 NP_057365 Q9H2K8 TAOK3_HUMAN TAO kinase 3 711 MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation mitochondrion|plasma membrane ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity lung(5)|central_nervous_system(1) 6 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) TTACCTTTAAGTTTTTTGGCTG 0.337 0.42 203 150 XPO4 64328 broad.mit.edu 37 13 21371001 21371002 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr13:21371001_21371002insA uc001unq.3 - 17 2553_2554 c.2517_2518insT c.(2515-2520)ATTGGAfs p.I839fs NM_022459 NP_071904 Q9C0E2 XPO4_HUMAN exportin 4 839_840 protein transport cytoplasm|nucleus protein binding large_intestine(1)|ovary(1)|kidney(1) 3 all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244) all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548) TCCATCAATCCAATGCAATTGG 0.406 0.51 72 74 SACS 26278 broad.mit.edu 37 13 23915644 23915644 + Frame_Shift_Del DEL A - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr13:23915644delA uc001uon.2 - 10 2960 c.2371delT c.(2371-2373)TCAfs p.S791fs SACS_uc001uoo.2_Frame_Shift_Del_p.S644fs|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Frame_Shift_Del_p.S644fs NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 791 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) AAATCCTCTGAAAAATGTATA 0.363 0.46 49 42 LNX2 222484 broad.mit.edu 37 13 28124520 28124521 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr13:28124520_28124521insA uc001url.3 - 9 2195_2196 c.1886_1887insT c.(1885-1887)TTCfs p.F629fs NM_153371 NP_699202 Q8N448 LNX2_HUMAN ligand of numb-protein X 2 629 PDZ 4. zinc ion binding ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1) 6 Lung SC(185;0.0156) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248) TAGTTTTAATGAAAAAAGGCTG 0.371 0.41 103 72 FLT1 2321 broad.mit.edu 37 13 28964076 28964077 + Frame_Shift_Ins INS - T T MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr13:28964076_28964077insT uc001usb.3 - 13 2110_2111 c.1825_1826insA c.(1825-1827)ATGfs p.M609fs FLT1_uc010aar.1_Frame_Shift_Ins_p.M609fs|FLT1_uc001usc.3_Frame_Shift_Ins_p.M609fs|FLT1_uc010aas.1_RNA|FLT1_uc010aat.1_Frame_Shift_Ins_p.M92fs NM_002019 NP_002010 P17948 VGFR1_HUMAN fms-related tyrosine kinase 1 isoform 1 609 Ig-like C2-type 6.|Extracellular (Potential). cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway extracellular space|Golgi apparatus|integral to plasma membrane|nucleus ATP binding|growth factor binding|vascular endothelial growth factor receptor activity lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1) 24 Acute lymphoblastic leukemia(6;0.04) Lung SC(185;0.0262)|Breast(139;0.188) Colorectal(13;0.000674) all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207) Sunitinib(DB01268) AGTGATGGCCATTTTTTGCTTG 0.411 0.43 207 157 ERCC5 2073 broad.mit.edu 37 13 103498619 103498619 + Frame_Shift_Del DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr13:103498619delG uc001vpw.2 + 1 446 c.3delG c.(1-3)ATGfs p.M1fs ERCC5_uc001vpu.1_Intron|ERCC5_uc010tjb.1_Frame_Shift_Del_p.M1fs NM_000123 NP_000114 P28715 ERCC5_HUMAN XPG-complementing protein 1 N-domain. negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection nucleoplasm bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding ovary(4)|lung(1)|central_nervous_system(1)|skin(1) 7 all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211) GCCGCCTCATGGGGGTCCAGG 0.642 0.30 21 9 IRS2 8660 broad.mit.edu 37 13 110435128 110435129 + Frame_Shift_Ins INS - G G MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr13:110435128_110435129insG uc001vqv.2 - 1 3786_3787 c.3272_3273insC c.(3271-3273)CCGfs p.P1091fs NM_003749 NP_003740 Q9Y4H2 IRS2_HUMAN insulin receptor substrate 2 1091 fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus cytosol|plasma membrane insulin receptor binding|signal transducer activity large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|skin(1)|ovary(1)|kidney(1) 8 all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155) Breast(118;0.159) all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147) 0.000 0.18 780 175 AKAP6 9472 broad.mit.edu 37 14 33201693 33201693 + Frame_Shift_Del DEL A - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr14:33201693delA uc001wrq.2 + 10 3204 c.3034delA c.(3034-3036)AAAfs p.K1012fs AKAP6_uc010aml.2_Frame_Shift_Del_p.K1009fs NM_004274 NP_004265 Q13023 AKAP6_HUMAN A-kinase anchor protein 6 1012 protein targeting calcium channel complex|nuclear membrane|sarcoplasmic reticulum protein kinase A binding|receptor binding breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1) 21 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) GBM - Glioblastoma multiforme(265;0.019) CAGACACCTGAAAAAGACGGA 0.363 0.51 33 35 SIX4 51804 broad.mit.edu 37 14 61180412 61180412 + Frame_Shift_Del DEL C - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr14:61180412delC uc001xfc.2 - 3 2059 c.2059delG c.(2059-2061)GAAfs p.E687fs NM_017420 NP_059116 Q9UIU6 SIX4_HUMAN sine oculis homeobox homolog 4 687 nucleus breast(3)|ovary(1) 4 OV - Ovarian serous cystadenocarcinoma(108;0.0275) GGAACTATTTCCCCAAGGGCA 0.473 0.41 190 132 PAK6 56924 broad.mit.edu 37 15 40564617 40564618 + Frame_Shift_Ins INS - C C MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr15:40564617_40564618insC uc010bbl.2 + 6 1491_1492 c.1051_1052insC c.(1051-1053)TCCfs p.S351fs PAK6_uc010bbm.2_Frame_Shift_Ins_p.S351fs|PAK6_uc001zky.3_Frame_Shift_Ins_p.S351fs|PAK6_uc010bbn.2_Frame_Shift_Ins_p.S351fs|PAK6_uc001zlb.2_Frame_Shift_Ins_p.S351fs NM_001128628 NP_001122100 Q9NQU5 PAK6_HUMAN p21-activated kinase 6 351 Linker. ATP binding|protein binding|protein serine/threonine kinase activity lung(5)|large_intestine(1)|ovary(1)|skin(1) 8 all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544) CCCAGCGGGATCCCCCCGCACC 0.673 0.38 93 56 UNC13C 440279 broad.mit.edu 37 15 54792362 54792362 + Frame_Shift_Del DEL A - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr15:54792362delA uc002ack.2 + 19 5146 c.5146delA c.(5146-5148)AAAfs p.K1716fs NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 1716 MHD1. exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) GGGAAGAGACAAAAAAGATGG 0.348 0.43 54 40 PML 5371 broad.mit.edu 37 15 74336979 74336979 + Frame_Shift_Del DEL C - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr15:74336979delC uc002awv.2 + 9 2419 c.2279delC c.(2278-2280)TCCfs p.S760fs PML_uc002awu.2_Frame_Shift_Del_p.S712fs|PML_uc010ule.1_Frame_Shift_Del_p.S321fs NM_033238 NP_150241 P29590 PML_HUMAN promyelocytic leukemia protein isoform 1 760 cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding central_nervous_system(2)|kidney(2)|breast(1) 5 CTCGAGGTCTCCCCGGGCCCC 0.677 0.33 20 10 RASGRF1 5923 broad.mit.edu 37 15 79310182 79310182 + Frame_Shift_Del DEL G - - rs139535493 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr15:79310182delG uc002beq.2 - 12 2048 c.1673delC c.(1672-1674)CCGfs p.P558fs RASGRF1_uc002bep.2_Frame_Shift_Del_p.P558fs|RASGRF1_uc010blm.1_Frame_Shift_Del_p.P480fs|RASGRF1_uc002ber.3_Frame_Shift_Del_p.P558fs|RASGRF1_uc010unh.1_5'UTR NM_002891 NP_002882 Q13972 RGRF1_HUMAN Ras protein-specific guanine 558 PH 2. activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission cytosol|growth cone|plasma membrane|synaptosome Rho guanyl-nucleotide exchange factor activity p.P558P(1) skin(4)|ovary(1)|central_nervous_system(1) 6 TGTAAAGGGCGGGGAATCCTT 0.507 0.24 22 7 BLM 641 broad.mit.edu 37 15 91310207 91310208 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr15:91310207_91310208insA uc002bpr.2 + 10 2358_2359 c.2261_2262insA c.(2260-2262)TCAfs p.S754fs BLM_uc010uqh.1_Frame_Shift_Ins_p.S754fs|BLM_uc010uqi.1_Frame_Shift_Ins_p.S379fs|BLM_uc010bnx.2_Frame_Shift_Ins_p.S754fs|BLM_uc002bps.1_Frame_Shift_Ins_p.S316fs NM_000057 NP_000048 P54132 BLM_HUMAN Bloom syndrome protein 754 Helicase ATP-binding. double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray cytoplasm|lateral element|nuclear matrix|nucleolus|PML body ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding ovary(3)|skin(2)|breast(1) 6 Lung NSC(78;0.0875)|all_lung(78;0.109) Lung(145;0.189) CTCCAGTTATCAAAAAAAGACC 0.267 0.46 39 33 TAOK2 9344 broad.mit.edu 37 16 30002685 30002685 + Frame_Shift_Del DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr16:30002685delG uc002dvc.1 + 19 3729 c.2946delG c.(2944-2946)CTGfs p.L982fs uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron NM_004783 NP_004774 Q9UL54 TAOK2_HUMAN TAO kinase 2 isoform 1 881 Glu-rich. actin cytoskeleton organization|activation of MAPKK activity|apoptosis|cell migration|focal adhesion assembly|positive regulation of JNK cascade|protein targeting to membrane|regulation of cell growth|regulation of cell shape|response to stress cytoplasmic vesicle membrane|cytoskeleton|dendrite|integral to membrane|nucleolus ATP binding|protein serine/threonine kinase activity ovary(1) 1 CAAACTGGCTGGGGCCCCCCA 0.721 0.70 3 7 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.23 53 16 RBL2 5934 broad.mit.edu 37 16 53476579 53476580 + Frame_Shift_Ins INS - T T MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr16:53476579_53476580insT uc002ehi.3 + 3 499_500 c.381_382insT c.(379-384)GAATTTfs p.E127fs RBL2_uc010vgv.1_Frame_Shift_Ins_p.E53fs NM_005611 NP_005602 Q08999 RBL2_HUMAN retinoblastoma-like 2 (p130) 127_128 cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleolus DNA binding|protein binding ovary(2)|lung(2)|upper_aerodigestive_tract(1) 5 GCTTAATCGAATTTTTTAATAA 0.312 0.39 20 13 CHD3 1107 broad.mit.edu 37 17 7797756 7797756 + Frame_Shift_Del DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr17:7797756delG uc002gje.2 + 8 1249 c.1099delG c.(1099-1101)GGGfs p.G367fs CHD3_uc002gjd.2_Frame_Shift_Del_p.G426fs|CHD3_uc002gjf.2_Frame_Shift_Del_p.G367fs|CHD3_uc002gjg.1_Frame_Shift_Del_p.G195fs NM_001005273 NP_001005273 Q12873 CHD3_HUMAN chromodomain helicase DNA binding protein 3 367 chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent microtubule organizing center|NuRD complex ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|zinc ion binding breast(1) 1 Prostate(122;0.202) TGCAGTGGCCGGGGAGGAGGA 0.438 0.45 17 14 PER1 5187 broad.mit.edu 37 17 8050888 8050889 + Frame_Shift_Ins INS - G G MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr17:8050888_8050889insG uc002gkd.2 - 12 1634_1635 c.1396_1397insC c.(1396-1398)CTGfs p.L466fs PER1_uc010vuq.1_RNA|PER1_uc010vur.1_Frame_Shift_Ins_p.L450fs NM_002616 NP_002607 O15534 PER1_HUMAN period 1 466 circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus signal transducer activity lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1) 9 GTCCTCATTCAGGGGGGCCCTG 0.658 0.35 115 62 TAOK1 57551 broad.mit.edu 37 17 27778628 27778630 + In_Frame_Del DEL AAG - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr17:27778628_27778630delAAG uc002hdz.1 + 2 256_258 c.62_64delAAG c.(61-66)AAAGAA>AAA p.E22del TAOK1_uc010wbe.1_In_Frame_Del_p.E22del|TAOK1_uc010wbf.1_In_Frame_Del_p.E22del NM_020791 NP_065842 Q7L7X3 TAOK1_HUMAN TAO kinase 1 22 mitotic prometaphase cytosol|intracellular membrane-bounded organelle ATP binding|protein serine/threonine kinase activity upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1) 4 Colorectal(6;0.198) 0.000 0.37 259 150 ACACA 31 broad.mit.edu 37 17 35580492 35580493 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr17:35580492_35580493insA uc002hnm.2 - 28 3584_3585 c.3393_3394insT c.(3391-3396)TTTGATfs p.F1131fs ACACA_uc002hnk.2_Frame_Shift_Ins_p.F1053fs|ACACA_uc002hnl.2_Frame_Shift_Ins_p.F1073fs|ACACA_uc002hnn.2_Frame_Shift_Ins_p.F1131fs|ACACA_uc002hno.2_Frame_Shift_Ins_p.F1168fs|ACACA_uc010cuz.2_Frame_Shift_Ins_p.F1131fs NM_198836 NP_942133 Q13085 ACACA_HUMAN acetyl-Coenzyme A carboxylase alpha isoform 2 1131_1132 acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process cytosol acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding large_intestine(1)|ovary(1) 2 Breast(25;0.00157)|Ovarian(249;0.15) Biotin(DB00121) GGTAGGACATCAAAAATAGATG 0.381 0.45 71 57 COL1A1 1277 broad.mit.edu 37 17 48275532 48275532 + Frame_Shift_Del DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr17:48275532delG uc002iqm.2 - 7 704 c.578delC c.(577-579)CCTfs p.P193fs NM_000088 NP_000079 P02452 CO1A1_HUMAN alpha 1 type I collagen preproprotein 193 Triple-helical region. axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception collagen type I|extracellular space|plasma membrane identical protein binding|platelet-derived growth factor binding COL1A1/PDGFB(372) soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1) 382 Collagenase(DB00048)|Palifermin(DB00039) 0.000 0.38 630 393 AXIN2 8313 broad.mit.edu 37 17 63533517 63533517 + Frame_Shift_Del DEL C - - rs145717795 byFrequency MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr17:63533517delC uc002jfi.2 - 6 1926 c.1637delG c.(1636-1638)GGCfs p.G546fs AXIN2_uc002jfh.2_Frame_Shift_Del_p.G546fs NM_004655 NP_004646 Q9Y2T1 AXIN2_HUMAN axin 2 546 cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding central_nervous_system(1)|skin(1) 2 ATACTCGCTGCCCCCAGGGCA 0.612 0.41 113 79 SEPT9 10801 broad.mit.edu 37 17 75488715 75488717 + In_Frame_Del DEL CTG - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr17:75488715_75488717delCTG uc002jts.3 + 9 1519_1521 c.1393_1395delCTG c.(1393-1395)CTGdel p.L466del SEPT9_uc010wtk.1_In_Frame_Del_p.L447del|SEPT9_uc002jtt.3_In_Frame_Del_p.L302del|SEPT9_uc002jtu.3_In_Frame_Del_p.L448del|SEPT9_uc002jtv.2_In_Frame_Del_p.L459del|SEPT9_uc002jtw.2_In_Frame_Del_p.L302del|SEPT9_uc010wtl.1_In_Frame_Del_p.L242del|SEPT9_uc002jty.3_In_Frame_Del_p.L215del|SEPT9_uc010wtm.1_In_Frame_Del_p.L215del|SEPT9_uc010wtn.1_In_Frame_Del_p.L215del|SEPT9_uc010dhd.2_In_Frame_Del_p.L354del NM_001113491 NP_001106963 Q9UHD8 SEPT9_HUMAN septin 9 isoform a 466 cell cycle|cell division|protein heterooligomerization microtubule|perinuclear region of cytoplasm|stress fiber GTP binding|GTPase activity|protein binding|protein binding breast(2)|ovary(1) 3 BRCA - Breast invasive adenocarcinoma(99;0.153) CACCGCAGACCTGCTGTCCAACG 0.576 0.48 59 54 TCF3 6929 broad.mit.edu 37 19 1620978 1620979 + Frame_Shift_Ins INS - G G MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr19:1620978_1620979insG uc002ltr.2 - 13 1148_1149 c.1081_1082insC c.(1081-1083)CAGfs p.Q361fs TCF3_uc002lto.2_Frame_Shift_Ins_p.Q123fs|TCF3_uc002ltt.3_Frame_Shift_Ins_p.Q361fs|TCF3_uc002ltq.2_Frame_Shift_Ins_p.Q310fs|TCF3_uc002lts.1_Frame_Shift_Ins_p.Q277fs|TCF3_uc010dso.1_5'Flank NM_003200 NP_003191 P15923 TFE2_HUMAN transcription factor 3 isoform E12 361 B cell lineage commitment|B cell lineage commitment|G1 phase of mitotic cell cycle|immunoglobulin V(D)J recombination|muscle cell differentiation|positive regulation of B cell proliferation|positive regulation of cell cycle|positive regulation of muscle cell differentiation|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter cytoplasm|nucleus|protein complex|transcription factor complex bHLH transcription factor binding|DNA binding|E-box binding|identical protein binding|mitogen-activated protein kinase kinase kinase binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|vitamin D response element binding lung(2)|breast(2)|ovary(1)|large_intestine(1)|skin(1) 7 Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.21 327 87 PIP5K1C 23396 broad.mit.edu 37 19 3661060 3661060 + Frame_Shift_Del DEL G - - rs116791909 byFrequency;by1000genomes MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr19:3661060delG uc002lyj.1 - 5 429 c.372delC c.(370-372)CCCfs p.P124fs PIP5K1C_uc010xhq.1_Frame_Shift_Del_p.P124fs|PIP5K1C_uc010xhr.1_Frame_Shift_Del_p.P124fs NM_012398 NP_036530 O60331 PI51C_HUMAN phosphatidylinositol-4-phosphate 5-kinase, type 124 PIPK. axon guidance cytosol|plasma membrane 1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding stomach(2)|skin(2) 4 Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183) AGTGGTGGGCGGGGGTGAGGT 0.617 0.36 101 58 MAP2K7 5609 broad.mit.edu 37 19 7976402 7976402 + Frame_Shift_Del DEL C - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr19:7976402delC uc002mit.2 + 9 1083 c.1018delC c.(1018-1020)CCCfs p.P340fs MAP2K7_uc002miv.2_Frame_Shift_Del_p.P347fs|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_Frame_Shift_Del_p.P347fs|MAP2K7_uc010dvv.2_Frame_Shift_Del_p.P215fs NM_145185 NP_660186 O14733 MP2K7_HUMAN mitogen-activated protein kinase kinase 7 340 Protein kinase. activation of JUN kinase activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleus ATP binding|JUN kinase kinase activity|magnesium ion binding|protein binding|protein kinase binding|protein phosphatase binding|protein serine/threonine kinase activity|protein tyrosine kinase activity large_intestine(7)|central_nervous_system(2)|ovary(1)|lung(1) 11 Etoposide(DB00773) 0.000 0.42 605 430 PRKACA 5566 broad.mit.edu 37 19 14208263 14208264 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr19:14208263_14208264insA uc002myc.2 - 8 874_875 c.674_675insT c.(673-675)CTGfs p.L225fs PRKACA_uc002myb.2_Frame_Shift_Ins_p.L217fs|PRKACA_uc010xnm.1_Frame_Shift_Ins_p.L167fs|PRKACA_uc002myd.2_3'UTR NM_002730 NP_002721 P17612 KAPCA_HUMAN cAMP-dependent protein kinase catalytic subunit 225 Protein kinase. activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|G2/M transition of mitotic cell cycle|gluconeogenesis|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|regulation of insulin secretion|transmembrane transport|triglyceride catabolic process|water transport cAMP-dependent protein kinase complex|centrosome|cytosol|nucleoplasm|plasma membrane ATP binding|cAMP-dependent protein kinase activity|cAMP-dependent protein kinase inhibitor activity|protein kinase binding lung(1) 1 TAAGAACCCCCAGGGCCCACCA 0.624 0.60 24 36 PIK3R2 5296 broad.mit.edu 37 19 18277046 18277047 + Frame_Shift_Del DEL AA - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr19:18277046_18277047delAA uc002nia.1 + 12 2005_2006 c.1493_1494delAA c.(1492-1494)CAAfs p.Q498fs PIK3R2_uc002nib.1_RNA|PIK3R2_uc010ebi.1_RNA NM_005027 NP_005018 O00459 P85B_HUMAN phosphoinositide-3-kinase, regulatory subunit 2 498 fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|negative regulation of anti-apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|T cell costimulation|T cell receptor signaling pathway phosphatidylinositol 3-kinase complex GTPase activator activity|phosphatidylinositol 3-kinase regulator activity|protein binding lung(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1) 6 GGCCAGACTCAAGAGAAATGCA 0.574 0.30 38 16 PSENEN 55851 broad.mit.edu 37 19 36237319 36237319 + Splice_Site DEL G - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr19:36237319delG uc002obi.1 + 3 266 c.62_splice c.e3-1 p.G21_splice TMEM149_uc010eej.2_5'Flank|U2AF1L4_uc002obh.1_5'Flank|U2AF1L4_uc002obe.2_5'Flank|U2AF1L4_uc002obf.2_5'Flank|U2AF1L4_uc002obg.2_5'Flank|PSENEN_uc002obj.1_Splice_Site_p.G21_splice|PSENEN_uc002obk.1_Splice_Site|LIN37_uc002obm.2_5'Flank NM_172341 NP_758844 Q9NZ42 PEN2_HUMAN presenilin enhancer 2 amyloid precursor protein catabolic process|apoptosis|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing endoplasmic reticulum membrane|Golgi cisterna membrane|integral to plasma membrane aspartic-type endopeptidase activity|protein binding ovary(2) 2 all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) TTTCTCCCTAGGGGGGTTTGC 0.463 0.38 60 36 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.56 34 44 NR1H2 7376 broad.mit.edu 37 19 50881825 50881826 + In_Frame_Ins INS - CAA CAA rs55817866 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr19:50881825_50881826insCAA uc010enw.2 + 7 798_799 c.522_523insCAA c.(520-525)insCAA p.176_177insQ NR1H2_uc002prv.3_RNA|NR1H2_uc002prz.3_In_Frame_Ins_p.175_176insQ|NR1H2_uc002psa.3_In_Frame_Ins_p.78_79insQ NM_007121 NP_009052 P55055 NR1H2_HUMAN nuclear receptor subfamily 1, group H, member 2 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment_176 negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of pinocytosis|negative regulation of transcription, DNA-dependent|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor cytoplasm|nucleoplasm sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding 0 all_neural(266;0.057) OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186) TTCGGAAACAGCAGCAGGAGTC 0.639 0.49 65 62 ZNF331 55422 broad.mit.edu 37 19 54079989 54079990 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr19:54079989_54079990insA uc002qbx.1 + 7 1609_1610 c.175_176insA c.(175-177)GAAfs p.E59fs ZNF331_uc002qby.1_Frame_Shift_Ins_p.E59fs|ZNF331_uc002qbz.1_Frame_Shift_Ins_p.E59fs|ZNF331_uc002qca.1_Frame_Shift_Ins_p.E59fs|ZNF331_uc010eqr.1_Frame_Shift_Ins_p.E59fs|ZNF331_uc002qcb.1_Frame_Shift_Ins_p.E59fs|ZNF331_uc002qcc.1_Frame_Shift_Ins_p.E59fs|ZNF331_uc002qcd.1_Frame_Shift_Ins_p.E59fs NM_018555 NP_061025 Q9NQX6 ZN331_HUMAN zinc finger protein 331 59 KRAB. E -> K (in Ref. 3; AAH09433). regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding skin(3)|upper_aerodigestive_tract(1)|ovary(1)|lung(1) 6 GBM - Glioblastoma multiforme(134;0.00555) TTTACCTACAGAAAAAAACATT 0.366 0.38 30 18 PRKCG 5582 broad.mit.edu 37 19 54403949 54403949 + Frame_Shift_Del DEL C - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr19:54403949delC uc002qcq.1 + 14 1803 c.1521delC c.(1519-1521)TTCfs p.F507fs PRKCG_uc010yeg.1_Frame_Shift_Del_p.F507fs|PRKCG_uc010yeh.1_Frame_Shift_Del_p.F394fs NM_002739 NP_002730 P05129 KPCG_HUMAN protein kinase C, gamma 507 Protein kinase. activation of phospholipase C activity|cell death|intracellular signal transduction|negative regulation of protein catabolic process|negative regulation of protein ubiquitination|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of mismatch repair|synaptic transmission cytosol ATP binding|protein kinase C activity|zinc ion binding lung(4)|ovary(2)|pancreas(2)|large_intestine(1) 9 all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218) GBM - Glioblastoma multiforme(134;0.0521) AGAACGTCTTCCCCGGGACGA 0.577 0.39 57 37 NCOA3 8202 broad.mit.edu 37 20 46262816 46262816 + Frame_Shift_Del DEL C - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr20:46262816delC uc002xtk.2 + 10 1194 c.989delC c.(988-990)ACCfs p.T330fs NCOA3_uc010ght.1_Frame_Shift_Del_p.T340fs|NCOA3_uc002xtl.2_Frame_Shift_Del_p.T330fs|NCOA3_uc002xtm.2_Frame_Shift_Del_p.T330fs|NCOA3_uc002xtn.2_Frame_Shift_Del_p.T330fs|NCOA3_uc010zyc.1_Frame_Shift_Del_p.T125fs NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 330 androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 CATGCAGAAACCCCAGTATAT 0.418 0.34 57 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.41 298 209 COL18A1 80781 broad.mit.edu 37 21 46925149 46925150 + Frame_Shift_Ins INS - GGCCCCCCCC GGCCCCCCCC MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr21:46925149_46925150insGGCCCCCCCC uc011afs.1 + 35 4227_4228 c.4206_4207insGGCCCCCCCC c.(4204-4209)CCAGGCfs p.P1402fs COL18A1_uc002zhg.2_Frame_Shift_Ins_p.P987fs|COL18A1_uc002zhi.2_Frame_Shift_Ins_p.P1167fs|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1405_1406 Triple-helical region 9 (COL9). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.19 521 125 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.82 8 37 SMARCB1 6598 broad.mit.edu 37 22 24134056 24134057 + Frame_Shift_Ins INS - A A MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr22:24134056_24134057insA uc002zyb.2 + 2 414_415 c.207_208insA c.(205-210)GGTAAAfs p.G69fs SMARCB1_uc002zyg.2_Frame_Shift_Ins_p.G69fs|SMARCB1_uc011ajb.1_Splice_Site_p.D69_splice|SMARCB1_uc002zya.2_Frame_Shift_Ins_p.G69fs|SMARCB1_uc002zyc.2_Splice_Site_p.D69_splice|SMARCB1_uc002zyd.2_Splice_Site_p.D69_splice|SMARCB1_uc002zye.1_Frame_Shift_Ins_p.G32fs|SMARCB1_uc002zyf.1_Splice_Site|SMARCB1_uc010gue.1_Splice_Site NM_003073 NP_003064 Q12824 SNF5_HUMAN SWI/SNF related, matrix associated, actin 69_70 cell cycle|chromatin remodeling|DNA integration|interspecies interaction between organisms|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|retroviral genome replication|transcription, DNA-dependent nBAF complex|npBAF complex|nucleolus|nucleoplasm|SWI/SNF complex p53 binding p.?(2) soft_tissue(193)|central_nervous_system(172)|haematopoietic_and_lymphoid_tissue(23)|meninges(5)|skin(5)|bone(4)|ovary(2)|endometrium(1)|lung(1)|pancreas(1) 407 Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05) CGTCACATGGTAAAAAAACAAA 0.441 0.44 27 21 MN1 4330 broad.mit.edu 37 22 28196403 28196403 + Frame_Shift_Del DEL C - - MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr22:28196403delC uc003adj.2 - 1 1084 c.129delG c.(127-129)GGGfs p.G43fs NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 43 binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 0.000 0.50 389 383 TIMP3 7078 broad.mit.edu 37 22 33255323 33255324 + Frame_Shift_Ins INS - C C MFE319_ENDOMETRIUM NA MFE319_ENDOMETRIUM NA g.chr22:33255323_33255324insC uc003anb.2 + 5 1781_1782 c.595_596insC c.(595-597)GCCfs p.A199fs SYN3_uc003amx.2_Intron|SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron NM_000362 NP_000353 P35625 TIMP3_HUMAN tissue inhibitor of metalloproteinase 3 199 negative regulation of membrane protein ectodomain proteolysis|visual perception metal ion binding|metalloendopeptidase inhibitor activity|protein binding lung(1) 1 CCGAGGATGGGCCCCCCCGGAT 0.604 0.33 54 27 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MG63_BONE NA MG63_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 57 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MG63_BONE NA MG63_BONE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.25 38 13 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MG63_BONE NA MG63_BONE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.15 121 21 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MG63_BONE NA MG63_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 75 104 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MG63_BONE NA MG63_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.49 41 40 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 MG63_BONE NA MG63_BONE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.68 8 17 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 MG63_BONE NA MG63_BONE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.36 28 16 COL14A1 7373 broad.mit.edu 37 8 121379429 121379430 + Frame_Shift_Ins INS - T T MG63_BONE NA MG63_BONE NA g.chr8:121379429_121379430insT uc003yox.2 + 46 5362_5363 c.5097_5098insT c.(5095-5100)GGAGAAfs p.G1699fs COL14A1_uc003yoz.2_Frame_Shift_Ins_p.G664fs NM_021110 NP_066933 Q05707 COEA1_HUMAN collagen, type XIV, alpha 1 precursor 1699_1700 Triple-helical region 2 (COL1). cell-cell adhesion|collagen fibril organization collagen type XIV|extracellular space collagen binding|extracellular matrix structural constituent|protein binding, bridging ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1) 12 Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503) GTATCAAAGGAGAAAAAGGAAA 0.361 0.25 52 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MG63_BONE NA MG63_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 858 324 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency MG63_BONE NA MG63_BONE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.45 82 66 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 MG63_BONE NA MG63_BONE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.46 22 19 SRP14 6727 broad.mit.edu 37 15 40328597 40328605 + In_Frame_Del DEL TGCTGCTGC - - MG63_BONE NA MG63_BONE NA g.chr15:40328597_40328605delTGCTGCTGC uc001zkq.2 - 5 412_420 c.340_348delGCAGCAGCA c.(340-348)GCAGCAGCAdel p.AAA114del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 114_116 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgcggcaggtgctgctgctgctgctgct 0.239 0.52 47 51 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MG63_BONE NA MG63_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 48 242 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MG63_BONE NA MG63_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 5 41 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MG63_BONE NA MG63_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 102 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.30 76 33 HEPH 9843 broad.mit.edu 37 X 65393494 65393495 + Frame_Shift_Ins INS - C C MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:65393494_65393495insC uc011moz.1 + 4 545_546 c.485_486insC c.(484-486)GGCfs p.G162fs HEPH_uc004dwn.2_Frame_Shift_Ins_p.G162fs|HEPH_uc004dwo.2_5'UTR|HEPH_uc010nkr.2_Frame_Shift_Ins_p.G162fs|HEPH_uc011mpa.1_Frame_Shift_Ins_p.G162fs NM_138737 NP_620074 Q9BQS7 HEPH_HUMAN hephaestin isoform a 159 Extracellular (Potential).|Plastocyanin-like 1. cellular iron ion homeostasis|copper ion transport|transmembrane transport integral to membrane|plasma membrane copper ion binding|oxidoreductase activity lung(5)|ovary(4) 9 CCCCCGGGGGGCAGCCATATCT 0.535 0.10 95 11 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 4 77 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.48 122 114 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.51 47 48 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.87 4 27 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825380 + In_Frame_Del DEL TGCTGC - - rs11277537 MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825380delTGCTGC uc001pfw.1 - 2 3100_3105 c.1815_1820delGCAGCA c.(1813-1821)CAGCAGCAA>CAA p.605_607QQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 605_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgct 0.117 0.16 130 25 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 103 819 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 2 33 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 4 95 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.14 114 18 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.20 84 21 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 88 101 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 70 34 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.89 3 25 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 371 93 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.54 6 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 32 20 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.25 52 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 72 468 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 93 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 38 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.35 17 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 94 139 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 19 54 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.11 70 9 STK19 8859 broad.mit.edu 37 6 31939829 31939830 + Frame_Shift_Ins INS - A A MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:31939829_31939830insA uc003nyv.2 + 1 184_185 c.56_57insA c.(55-57)GCAfs p.A19fs DOM3Z_uc003nyo.1_5'UTR|DOM3Z_uc003nyp.1_5'UTR|DOM3Z_uc003nyq.1_5'UTR|DOM3Z_uc003nyr.1_5'UTR|DOM3Z_uc003nys.1_5'Flank|DOM3Z_uc010jtl.1_5'UTR|STK19_uc003nyt.2_5'UTR|DOM3Z_uc003nyu.1_5'UTR|STK19_uc011dow.1_Frame_Shift_Ins_p.A19fs|STK19_uc011dox.1_5'UTR|STK19_uc003nyw.2_Frame_Shift_Ins_p.A19fs|STK19_uc010jtn.1_5'Flank NM_032454 NP_115830 P49842 STK19_HUMAN serine/threonine kinase 19 isoform 2 19 nucleus ATP binding|protein binding|protein serine/threonine kinase activity skin(4) 4 CAGTGGCGGGCAAACCCCTCCC 0.634 0.23 24 7 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.30 21 9 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.36 7 4 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 44 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 784 397 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.46 7 6 ETV6 2120 broad.mit.edu 37 12 12038881 12038893 + Frame_Shift_Del DEL GAGAAAATGTCCA - - MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:12038881_12038893delGAGAAAATGTCCA uc001qzz.2 + 7 1448_1460 c.1174_1186delGAGAAAATGTCCA c.(1174-1188)GAGAAAATGTCCAGAfs p.E392fs ETV6_uc001raa.1_Intron NM_001987 NP_001978 P41212 ETV6_HUMAN ets variant 6 392_396 ETS. cytoplasm|nucleolus protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity ETV6/NTRK3(234)|ETV6/JAK2(11) soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1) 250 all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36) CATGACCTATGAGAAAATGTCCAGAGCCCTGCG 0.432 0.74 6 17 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.28 28 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.42 107 79 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 104 306 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 8 111 BTK 695 broad.mit.edu 37 X 100608923 100608924 + Frame_Shift_Ins INS - G G rs104894770;rs128621204 MHHES1_BONE NA MHHES1_BONE NA g.chrX:100608923_100608924insG uc004ehg.2 - 17 1877_1878 c.1684_1685insC c.(1684-1686)CGGfs p.R562fs BTK_uc004ehf.2_Frame_Shift_Ins_p.R62fs|BTK_uc010nnh.2_Intron|BTK_uc010nni.2_Intron|BTK_uc004ehe.2_RNA|BTK_uc010nnj.2_RNA|BTK_uc010nnk.2_RNA|BTK_uc010nnl.2_Frame_Shift_Ins_p.R38fs|BTK_uc010nnm.2_Frame_Shift_Ins_p.R132fs|BTK_uc010nnn.2_Frame_Shift_Ins_p.R386fs|BTK_uc010nno.2_Frame_Shift_Ins_p.R596fs|BTK_uc004ehh.1_RNA NM_000061 NP_000052 Q06187 BTK_HUMAN Bruton agammaglobulinemia tyrosine kinase 562 Protein kinase. R -> W (in XLA). calcium-mediated signaling|induction of apoptosis by extracellular signals|mesoderm development cytosol|membrane raft|nucleus|plasma membrane ATP binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol-3,4,5-trisphosphate binding lung(3)|central_nervous_system(2)|ovary(1) 6 TGGGGACCACCGGACTGGAAAT 0.446 0.12 50 7 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MHHES1_BONE NA MHHES1_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 3 51 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MHHES1_BONE NA MHHES1_BONE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.32 21 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MHHES1_BONE NA MHHES1_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 111 163 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MHHES1_BONE NA MHHES1_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 23 47 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes MHHES1_BONE NA MHHES1_BONE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.67 5 10 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 MHHES1_BONE NA MHHES1_BONE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.30 35 15 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - MHHES1_BONE NA MHHES1_BONE NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.41 117 82 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MHHES1_BONE NA MHHES1_BONE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 2 18 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G MHHES1_BONE NA MHHES1_BONE NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.14 310 51 MAMDC4 158056 broad.mit.edu 37 9 139751886 139751887 + Frame_Shift_Ins INS - G G rs139519920 by1000genomes MHHES1_BONE NA MHHES1_BONE NA g.chr9:139751886_139751887insG uc004cjs.2 + 18 2224_2225 c.2174_2175insG c.(2173-2175)CCGfs p.P725fs MAMDC4_uc011mej.1_Frame_Shift_Ins_p.P62fs NM_206920 NP_996803 Q6UXC1 AEGP_HUMAN apical early endosomal glycoprotein precursor 804 MAM 4.|Extracellular (Potential). protein transport integral to membrane breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1) 7 all_cancers(76;0.0763)|all_epithelial(76;0.198) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171) GCCGTGCGGCCGGGCCCCTGCT 0.688 0.21 53 14 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 MHHES1_BONE NA MHHES1_BONE NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.39 11 7 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency MHHES1_BONE NA MHHES1_BONE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.38 117 71 TP53 7157 broad.mit.edu 37 17 7578204 7578206 + In_Frame_Del DEL ACT - - MHHES1_BONE NA MHHES1_BONE NA g.chr17:7578204_7578206delACT uc002gim.2 - 6 837_839 c.643_645delAGT c.(643-645)AGTdel p.S215del TP53_uc002gig.1_In_Frame_Del_p.S215del|TP53_uc002gih.2_In_Frame_Del_p.S215del|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_In_Frame_Del_p.S83del|TP53_uc010cng.1_In_Frame_Del_p.S83del|TP53_uc002gii.1_In_Frame_Del_p.S83del|TP53_uc010cnh.1_In_Frame_Del_p.S215del|TP53_uc010cni.1_In_Frame_Del_p.S215del|TP53_uc002gij.2_In_Frame_Del_p.S215del|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_In_Frame_Del_p.S122del|TP53_uc002gio.2_In_Frame_Del_p.S83del|TP53_uc010vug.1_In_Frame_Del_p.S176del NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 215 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). S -> R (in sporadic cancers; somatic mutation).|S -> C (in sporadic cancers; somatic mutation).|S -> K (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|S -> N (in sporadic cancers; somatic mutation).|S -> T (in sporadic cancers; somatic mutation).|S -> G (in sporadic cancers; somatic mutation).|S -> I (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.S215R(16)|p.S215I(15)|p.0?(7)|p.S215G(6)|p.S215N(6)|p.S215C(5)|p.S215fs*32(4)|p.S215T(3)|p.S215S(2)|p.H214fs*5(2)|p.K164_P219del(1)|p.V216fs*6(1)|p.V216fs*32(1)|p.V216fs*33(1)|p.H214fs*7(1)|p.S215fs*27(1)|p.S215del(1)|p.S215fs*29(1)|p.D208_V216delDRNTFRHSV(1)|p.H214_S215insX(1)|p.T211_S215delTFRHS(1)|p.D208fs*1(1)|p.S215fs*31(1)|p.S215_V216insX(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.S215_V218>R(1)|p.R213fs*32(1)|p.R209fs*6(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GCACCACCACACTATGTCGAAAA 0.532 0.89 12 100 FFAR2 2867 broad.mit.edu 37 19 35940696 35940697 + Frame_Shift_Ins INS - G G MHHES1_BONE NA MHHES1_BONE NA g.chr19:35940696_35940697insG uc002nzg.2 + 2 160_161 c.80_81insG c.(79-81)CTGfs p.L27fs FFAR2_uc010eea.2_Frame_Shift_Ins_p.L27fs NM_005306 NP_005297 O15552 FFAR2_HUMAN free fatty acid receptor 2 27 Helical; Name=1; (Potential). integral to plasma membrane G-protein coupled receptor activity|lipid binding central_nervous_system(1) 1 all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0724) GCCAACCTCCTGGCCCTGCGGG 0.629 0.15 39 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MHHES1_BONE NA MHHES1_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 42 178 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MHHES1_BONE NA MHHES1_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 70 324 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MHHES1_BONE NA MHHES1_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 6 78 MN1 4330 broad.mit.edu 37 22 28194771 28194772 + Frame_Shift_Ins INS - C C MHHES1_BONE NA MHHES1_BONE NA g.chr22:28194771_28194772insC uc003adj.2 - 1 2715_2716 c.1760_1761insG c.(1759-1761)GGCfs p.G587fs NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 587 binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 GCACCAGGCCGCCCTGGCCCAC 0.723 0.15 40 7 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 25 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.35 13 7 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 30 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 87 139 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.76 6 19 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 16 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.42 21 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 807 90 NR4A3 8013 broad.mit.edu 37 9 102590615 102590616 + In_Frame_Ins INS - CAC CAC MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr9:102590615_102590616insCAC uc004baf.1 + 3 1020_1021 c.291_292insCAC c.(289-294)insCAC p.108_109insH NR4A3_uc004bae.2_In_Frame_Ins_p.108_109insH|NR4A3_uc004bag.1_In_Frame_Ins_p.108_109insH|NR4A3_uc004bai.2_In_Frame_Ins_p.119_120insH NM_006981 NP_008912 Q92570 NR4A3_HUMAN nuclear receptor subfamily 4, group A, member 3 108_109 regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor steroid hormone receptor activity|thyroid hormone receptor activity|zinc ion binding EWSR1/NR4A3(140)|TAF15/NR4A3(33) bone(173) 173 Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189) accatcaccatcaccaccacca 0.485 0.26 40 14 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.45 6 5 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 641 253 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 62 668 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 1.00 0 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 33 81 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.48 372 344 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MHHNB11_AUTONOMIC_GANGLIA NA MHHNB11_AUTONOMIC_GANGLIA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 79 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 4 36 EPHA10 284656 broad.mit.edu 37 1 38186060 38186060 + Frame_Shift_Del DEL C - - MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:38186060delC uc009vvi.2 - 13 2461 c.2375delG c.(2374-2376)GGCfs p.G792fs EPHA10_uc001cbt.2_RNA|EPHA10_uc009vvh.1_RNA|EPHA10_uc001cbu.2_RNA|EPHA10_uc001cbv.1_RNA NM_001099439 NP_001092909 Q5JZY3 EPHAA_HUMAN EPH receptor A10 isofom 3 792 Cytoplasmic (Potential).|Protein kinase. extracellular region|integral to membrane|integral to plasma membrane ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity breast(4)|stomach(3)|lung(1) 8 Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197) Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) 0.000 0.27 637 234 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 503 101 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.40 6 4 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.26 61 21 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 113 129 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.46 106 91 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 1 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.61 32 50 PSKH2 85481 broad.mit.edu 37 8 87076575 87076575 + Frame_Shift_Del DEL C - - MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:87076575delC uc011lfy.1 - 2 471 c.471delG c.(469-471)GAGfs p.E157fs NM_033126 NP_149117 Q96QS6 KPSH2_HUMAN protein serine kinase H2 157 Protein kinase. ATP binding|protein serine/threonine kinase activity stomach(2)|lung(2)|ovary(1) 5 STAD - Stomach adenocarcinoma(118;0.129) CGGCATCCCGCTCTGTAAAGG 0.478 0.35 176 94 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 270 122 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.50 6 6 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.38 8 5 MGA 23269 broad.mit.edu 37 15 42003014 42003015 + Frame_Shift_Ins INS - C C MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:42003014_42003015insC uc001zog.1 + 8 2642_2643 c.2551_2552insC c.(2551-2553)TCTfs p.S851fs MGA_uc010ucy.1_Frame_Shift_Ins_p.S851fs|MGA_uc010ucz.1_Frame_Shift_Ins_p.S851fs NM_001080541 NP_001074010 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 2 851 MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) TGCTCCCACATCTCCTGTGGTG 0.401 0.65 167 312 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 54 536 TRIM37 4591 broad.mit.edu 37 17 57141768 57141769 + Splice_Site INS - A A rs147621691 MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:57141768_57141769insA uc002iwy.3 - 10 1254 c.810_splice c.e10-1 p.S270_splice TRIM37_uc002iwz.3_Splice_Site_p.S270_splice|TRIM37_uc002ixa.3_Splice_Site_p.S148_splice|TRIM37_uc010woc.1_Splice_Site_p.S236_splice NM_001005207 NP_001005207 O94972 TRI37_HUMAN tripartite motif-containing 37 protein perinuclear region of cytoplasm|peroxisome ligase activity|protein binding|zinc ion binding lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1) 7 Medulloblastoma(34;0.0922)|all_neural(34;0.101) ACTAATTCACTAAAAAAAAAAA 0.272 0.24 32 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.57 15 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 180 797 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.99 1 80 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 46 ST6GALNAC5 81849 broad.mit.edu 37 1 77334276 77334277 + In_Frame_Ins INS - GCA GCA rs113832855 MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:77334276_77334277insGCA uc001dhi.2 + 2 285_286 c.110_111insGCA c.(109-111)CCG>CCGCAG p.49_50insQ ST6GALNAC5_uc010ori.1_In_Frame_Ins_p.49_50insQ|ST6GALNAC5_uc009wbw.2_RNA NM_030965 NP_112227 Q9BVH7 SIA7E_HUMAN sialyltransferase 7E 49_50 Lumenal (Potential). protein glycosylation integral to Golgi membrane sialyltransferase activity pancreas(1)|skin(1) 2 GAGCGGCCCCCgcagcagcagc 0.579 0.30 19 8 NPR1 4881 broad.mit.edu 37 1 153653143 153653144 + Frame_Shift_Ins INS - G G MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:153653143_153653144insG uc001fcs.3 + 2 1309_1310 c.888_889insG c.(886-891)GATGGGfs p.D296fs NPR1_uc010pdz.1_Frame_Shift_Ins_p.D42fs NM_000906 NP_000897 P16066 ANPRA_HUMAN natriuretic peptide receptor 1 precursor 296_297 Extracellular (Potential). body fluid secretion|intracellular signal transduction|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation ATP binding|GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity ovary(3)|lung(2)|stomach(1)|breast(1) 7 all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Nesiritide(DB04899)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)|Nitroprusside(DB00325) AGAGAGGGGATGGGCAGGATGT 0.594 0.41 167 117 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 110 165 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.77 11 36 PHIP 55023 broad.mit.edu 37 6 79671443 79671443 + Frame_Shift_Del DEL C - - MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:79671443delC uc003pir.2 - 31 3846 c.3620delG c.(3619-3621)AGTfs p.S1207fs PHIP_uc003piq.2_Frame_Shift_Del_p.S231fs|PHIP_uc011dyp.1_Frame_Shift_Del_p.S1206fs|PHIP_uc003pio.3_Frame_Shift_Del_p.S93fs NM_017934 NP_060404 Q8WWQ0 PHIP_HUMAN pleckstrin homology domain interacting protein 1207 Bromo 1. insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis nucleus insulin receptor binding large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1) 6 all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219) BRCA - Breast invasive adenocarcinoma(397;0.231) TTTAATTGTACTTAGATCCGT 0.398 0.41 23 16 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.14 570 94 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 1 10 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.10 233 25 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.88 4 29 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.41 79 55 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.60 8 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 763 417 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.10 121 14 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 1 20 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.22 25 7 FFAR2 2867 broad.mit.edu 37 19 35940696 35940697 + Frame_Shift_Ins INS - G G MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:35940696_35940697insG uc002nzg.2 + 2 160_161 c.80_81insG c.(79-81)CTGfs p.L27fs FFAR2_uc010eea.2_Frame_Shift_Ins_p.L27fs NM_005306 NP_005297 O15552 FFAR2_HUMAN free fatty acid receptor 2 27 Helical; Name=1; (Potential). integral to plasma membrane G-protein coupled receptor activity|lipid binding central_nervous_system(1) 1 all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0724) GCCAACCTCCTGGCCCTGCGGG 0.629 0.21 30 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.79 38 145 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 54 434 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 8 95 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MKN45_STOMACH NA MKN45_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 51 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MKN45_STOMACH NA MKN45_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.32 375 174 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes MKN45_STOMACH NA MKN45_STOMACH NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.44 18 14 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MKN45_STOMACH NA MKN45_STOMACH NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.53 20 23 HTT 3064 broad.mit.edu 37 4 3076604 3076606 + In_Frame_Del DEL CAG - - rs10618869 MKN45_STOMACH NA MKN45_STOMACH NA g.chr4:3076604_3076606delCAG uc011bvq.1 + 2 203_205 c.58_60delCAG c.(58-60)CAGdel p.Q40del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagc 0.335 0.24 44 14 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MKN45_STOMACH NA MKN45_STOMACH NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.45 12 10 CCNA2 890 broad.mit.edu 37 4 122743803 122743804 + Splice_Site INS - A A MKN45_STOMACH NA MKN45_STOMACH NA g.chr4:122743803_122743804insA uc003iec.3 - 2 519 c.214_splice c.e2-1 p.V72_splice NM_001237 NP_001228 P20248 CCNA2_HUMAN cyclin A cell division|mitosis|mitotic cell cycle G2/M transition DNA damage checkpoint|Ras protein signal transduction|regulation of cyclin-dependent protein kinase activity cytoplasm|nucleoplasm protein kinase binding ovary(1) 1 GGGTGCAACCTAAAAAAAAATT 0.406 0.33 203 102 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MKN45_STOMACH NA MKN45_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.71 124 308 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 MKN45_STOMACH NA MKN45_STOMACH NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.40 347 231 PKHD1 5314 broad.mit.edu 37 6 51890253 51890253 + Frame_Shift_Del DEL A - - MKN45_STOMACH NA MKN45_STOMACH NA g.chr6:51890253delA uc003pah.1 - 32 4631 c.4355delT c.(4354-4356)TTGfs p.L1452fs PKHD1_uc003pai.2_Frame_Shift_Del_p.L1452fs NM_138694 NP_619639 P08F94 PKHD1_HUMAN fibrocystin isoform 1 1452 IPT/TIG 9.|Extracellular (Potential). cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body protein binding|receptor activity lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1) 44 Lung NSC(77;0.0605) AGCTCCAGGCAAGGGGTCACC 0.527 0.41 45 31 MAP3K4 4216 broad.mit.edu 37 6 161470484 161470487 + Frame_Shift_Del DEL TGTT - - MKN45_STOMACH NA MKN45_STOMACH NA g.chr6:161470484_161470487delTGTT uc003qtn.2 + 3 1322_1325 c.1180_1183delTGTT c.(1180-1185)TGTTTGfs p.C394fs MAP3K4_uc010kkc.1_Frame_Shift_Del_p.C394fs|MAP3K4_uc003qto.2_Frame_Shift_Del_p.C394fs|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_5'UTR NM_005922 NP_005913 Q9Y6R4 M3K4_HUMAN mitogen-activated protein kinase kinase kinase 4 394_395 activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity perinuclear region of cytoplasm ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding ovary(3)|lung(3)|skin(2)|stomach(1) 9 Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771) OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05) GCAGGCACTCTGTTTGTGGTTAAA 0.407 0.97 3 84 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MKN45_STOMACH NA MKN45_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.83 2 10 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MKN45_STOMACH NA MKN45_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.20 41 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MKN45_STOMACH NA MKN45_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 43 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 MKN45_STOMACH NA MKN45_STOMACH NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.43 12 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MKN45_STOMACH NA MKN45_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.49 291 278 CDH1 999 broad.mit.edu 37 16 68844235 68844252 + Splice_Site DEL GCTCTTCCAGGTATATCC - - MKN45_STOMACH NA MKN45_STOMACH NA g.chr16:68844235_68844252delGCTCTTCCAGGTATATCC uc002ewg.1 + 6 956 c.832_splice c.e6+1 p.G278_splice CDH1_uc010vlj.1_Splice_Site|CDH1_uc010cfg.1_Splice_Site_p.G278_splice NM_004360 NP_004351 P12830 CADH1_HUMAN cadherin 1, type 1 preproprotein adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm cell adhesion molecule binding|gamma-catenin binding p.G274_P277del(2)|p.?(2) breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1) 243 all_neural(199;0.0189)|Ovarian(137;0.0563) Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261) CATGGAAGGTGCTCTTCCAGGTATATCCACTAATGAGA 0.445 0.95 2 39 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MKN45_STOMACH NA MKN45_STOMACH NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.98 1 46 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MKN45_STOMACH NA MKN45_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.42 103 76 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 MKN45_STOMACH NA MKN45_STOMACH NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.22 196 54 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MKN45_STOMACH NA MKN45_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 190 1676 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MKN45_STOMACH NA MKN45_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 77 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MKN74_STOMACH NA MKN74_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 3 42 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MKN74_STOMACH NA MKN74_STOMACH NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.14 84 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MKN74_STOMACH NA MKN74_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 66 91 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 MKN74_STOMACH NA MKN74_STOMACH NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.78 50 174 RASA1 5921 broad.mit.edu 37 5 86672788 86672789 + Frame_Shift_Ins INS - T T MKN74_STOMACH NA MKN74_STOMACH NA g.chr5:86672788_86672789insT uc003kiw.2 + 17 2393_2394 c.2275_2276insT c.(2275-2277)ATTfs p.I759fs RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_Frame_Shift_Ins_p.I582fs|RASA1_uc011ctv.1_Frame_Shift_Ins_p.I592fs|RASA1_uc011ctw.1_Frame_Shift_Ins_p.I593fs|RASA1_uc010jaw.2_Frame_Shift_Ins_p.I581fs NM_002890 NP_002881 P20936 RASA1_HUMAN RAS p21 protein activator 1 isoform 1 759 Ras-GAP. cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis cytosol|intrinsic to internal side of plasma membrane glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding upper_aerodigestive_tract(3)|ovary(1)|lung(1) 5 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) CCTACTGAGGATTTTTCTTCAC 0.391 0.90 15 133 ATXN1 6310 broad.mit.edu 37 6 16327907 16327909 + In_Frame_Del DEL TGA - - rs59310777 by1000genomes MKN74_STOMACH NA MKN74_STOMACH NA g.chr6:16327907_16327909delTGA uc003nbt.2 - 8 1604_1606 c.633_635delTCA c.(631-636)CATCAG>CAG p.H211del ATXN1_uc010jpi.2_In_Frame_Del_p.H211del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 211 Poly-Gln. H -> HQ (in Ref. 1; CAA55793). cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgctgatgctgatgct 0.384 0.73 3 8 MET 4233 broad.mit.edu 37 7 116371887 116371887 + Frame_Shift_Del DEL G - - MKN74_STOMACH NA MKN74_STOMACH NA g.chr7:116371887delG uc003vij.2 + 3 1553 c.1366delG c.(1366-1368)GGGfs p.G456fs MET_uc010lkh.2_Frame_Shift_Del_p.G456fs|MET_uc011knc.1_Frame_Shift_Del_p.G456fs|MET_uc011knd.1_Frame_Shift_Del_p.G456fs|MET_uc011kne.1_Frame_Shift_Del_p.G456fs|MET_uc011knf.1_Frame_Shift_Del_p.G456fs|MET_uc011kng.1_Frame_Shift_Del_p.G456fs|MET_uc011knh.1_Frame_Shift_Del_p.G456fs|MET_uc011kni.1_Frame_Shift_Del_p.G456fs|MET_uc011knj.1_Frame_Shift_Del_p.G26fs|MET_uc010lkg.2_Frame_Shift_Del_p.G456fs|MET_uc011kna.1_Frame_Shift_Del_p.G456fs|MET_uc011knb.1_Frame_Shift_Del_p.G456fs NM_000245 NP_000236 P08581 MET_HUMAN met proto-oncogene isoform b precursor 456 Extracellular (Potential).|Sema. axon guidance|cell proliferation basal plasma membrane|integral to plasma membrane ATP binding|hepatocyte growth factor receptor activity|protein binding upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1) 159 all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125) Ovarian(593;0.133) GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512) AGCTAATCTTGGGACATCAGA 0.423 0.41 44 30 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MKN74_STOMACH NA MKN74_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 41 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 MKN74_STOMACH NA MKN74_STOMACH NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.45 6 5 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MKN74_STOMACH NA MKN74_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 363 116 RB1 5925 broad.mit.edu 37 13 49051540 49051543 + Splice_Site DEL AGTA - - MKN74_STOMACH NA MKN74_STOMACH NA g.chr13:49051540_49051543delAGTA uc001vcb.2 + 26 2879 c.2713_splice c.e26+1 p.T905_splice NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.?(7) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) GGCAGAAATGAGTAAGTACTTTTT 0.309 0.43 56 42 NEK3 4752 broad.mit.edu 37 13 52725278 52725279 + Splice_Site INS - A A MKN74_STOMACH NA MKN74_STOMACH NA g.chr13:52725278_52725279insA uc001vgi.2 - 7 783 c.548_splice c.e7+1 p.S183_splice NEK3_uc001vgg.2_Splice_Site_p.S177_splice|NEK3_uc001vgh.2_Splice_Site_p.S204_splice|NEK3_uc010tgx.1_Splice_Site|NEK3_uc010tgy.1_Splice_Site_p.S183_splice NM_152720 NP_689933 P51956 NEK3_HUMAN NIMA-related kinase 3 isoform a cell division|mitosis nucleus ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173) GBM - Glioblastoma multiforme(99;2.81e-08) ATGCAGCACTCACCTTTTATTG 0.421 0.44 53 41 THAP11 57215 broad.mit.edu 37 16 67876823 67876824 + In_Frame_Ins INS - CAG CAG rs28647874;rs34213159 byFrequency MKN74_STOMACH NA MKN74_STOMACH NA g.chr16:67876823_67876824insCAG uc002euo.2 + 1 611_612 c.366_367insCAG c.(364-369)insCAG p.132_133insQ CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 132_133 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) agcagcagcaacagcagcagca 0.302 0.23 27 8 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MKN74_STOMACH NA MKN74_STOMACH NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 9 71 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT MKN74_STOMACH NA MKN74_STOMACH NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.10 570 63 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MKN74_STOMACH NA MKN74_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.40 29 19 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 MKN74_STOMACH NA MKN74_STOMACH NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 92 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MKN74_STOMACH NA MKN74_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 84 346 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MKN74_STOMACH NA MKN74_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.99 1 98 HUWE1 10075 broad.mit.edu 37 X 53587160 53587160 + Frame_Shift_Del DEL A - - MKN7_STOMACH NA MKN7_STOMACH NA g.chrX:53587160delA uc004dsp.2 - 56 8127 c.7725delT c.(7723-7725)CTTfs p.L2575fs HUWE1_uc004dsn.2_Frame_Shift_Del_p.L1399fs|uc004dss.2_5'Flank|MIRLET7F2_hsa-let-7f-2|MI0000068_5'Flank NM_031407 NP_113584 Q7Z6Z7 HUWE1_HUMAN HECT, UBA and WWE domain containing 1 2575 base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process cytoplasm|nucleus DNA binding|protein binding|ubiquitin-protein ligase activity ovary(8)|large_intestine(4)|breast(4)|kidney(1) 17 0.000 0.51 199 205 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MKN7_STOMACH NA MKN7_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 3 35 CELF3 11189 broad.mit.edu 37 1 151678707 151678708 + In_Frame_Ins INS - TGC TGC MKN7_STOMACH NA MKN7_STOMACH NA g.chr1:151678707_151678708insTGC uc001eys.1 - 10 1912_1913 c.1118_1119insGCA c.(1117-1119)CAA>CAGCAA p.373_373Q>QQ CELF3_uc010pdh.1_In_Frame_Ins_p.159_159Q>QQ|CELF3_uc001eyr.2_In_Frame_Ins_p.372_372Q>QQ|CELF3_uc009wmy.2_In_Frame_Ins_p.323_323Q>QQ|CELF3_uc009wmx.1_In_Frame_Ins_p.372_372Q>QQ NM_007185 NP_009116 Q5SZQ8 CELF3_HUMAN trinucleotide repeat containing 4 373 Gln-rich. nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome cytoplasm|nucleus mRNA binding|nucleotide binding ovary(1)|central_nervous_system(1) 2 CACCTTCTCTTtgctgctgctg 0.530 0.60 10 15 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MKN7_STOMACH NA MKN7_STOMACH NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.40 15 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MKN7_STOMACH NA MKN7_STOMACH NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.73 3 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MKN7_STOMACH NA MKN7_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.48 94 87 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MKN7_STOMACH NA MKN7_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.41 34 24 HOXA13 3209 broad.mit.edu 37 7 27239525 27239526 + In_Frame_Ins INS - GCCCCC GCCCCC MKN7_STOMACH NA MKN7_STOMACH NA g.chr7:27239525_27239526insGCCCCC uc003szb.1 - 1 200_201 c.171_172insGGGGGC c.(169-174)insGGGGGC p.57_58insGG uc003szc.1_5'Flank NM_000522 NP_000513 P31271 HXA13_HUMAN homeobox A13 57_58 skeletal system development nucleus sequence-specific DNA binding breast(1) 1 0.000 0.19 664 160 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MKN7_STOMACH NA MKN7_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.90 2 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MKN7_STOMACH NA MKN7_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 32 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MKN7_STOMACH NA MKN7_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.57 144 189 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MKN7_STOMACH NA MKN7_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 546 180 BIRC2 329 broad.mit.edu 37 11 102220640 102220640 + Frame_Shift_Del DEL A - - MKN7_STOMACH NA MKN7_STOMACH NA g.chr11:102220640delA uc001pgy.2 + 2 1454 c.55delA c.(55-57)AAGfs p.K19fs BIRC2_uc010ruq.1_Intron|BIRC2_uc010rur.1_Frame_Shift_Del_p.K19fs NM_001166 NP_001157 Q13490 BIRC2_HUMAN baculoviral IAP repeat-containing protein 2 19 cell surface receptor linked signaling pathway|cellular component disassembly involved in apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteasomal ubiquitin-dependent protein catabolic process|protein polyubiquitination CD40 receptor complex|cytosol|internal side of plasma membrane protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding ovary(1)|lung(1)|breast(1) 3 all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227) Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093) Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151) BRCA - Breast invasive adenocarcinoma(274;0.0144) TCAAAACATTAAGAGTATAAT 0.378 0.70 77 182 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes MKN7_STOMACH NA MKN7_STOMACH NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.17 59 12 MYH8 4626 broad.mit.edu 37 17 10314206 10314206 + Frame_Shift_Del DEL A - - MKN7_STOMACH NA MKN7_STOMACH NA g.chr17:10314206delA uc002gmm.2 - 15 1570 c.1475delT c.(1474-1476)TTCfs p.F492fs uc002gml.1_Intron NM_002472 NP_002463 P13535 MYH8_HUMAN myosin, heavy chain 8, skeletal muscle, 492 Myosin head-like. muscle filament sliding cytosol|muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle skin(6)|ovary(3)|breast(2) 11 GTGGTGGTTGAAAAACTGTTG 0.443 0.93 8 108 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MKN7_STOMACH NA MKN7_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 16 55 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MKN7_STOMACH NA MKN7_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 83 303 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MKN7_STOMACH NA MKN7_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 78 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ML1_THYROID NA ML1_THYROID NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 9 114 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376116 + In_Frame_Del DEL TGCTGC - - rs143860374;rs62265537 ML1_THYROID NA ML1_THYROID NA g.chr3:113376111_113376116delTGCTGC uc003eam.2 - 7 4824_4829 c.4413_4418delGCAGCA c.(4411-4419)CAGCAGCAA>CAA p.1471_1473QQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1415_1417QQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1471_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgct 0.359 0.38 10 6 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 ML1_THYROID NA ML1_THYROID NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.17 59 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ML1_THYROID NA ML1_THYROID NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 104 149 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 ML1_THYROID NA ML1_THYROID NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 58 101 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 ML1_THYROID NA ML1_THYROID NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 31 PSIP1 11168 broad.mit.edu 37 9 15474026 15474030 + Frame_Shift_Del DEL TCTCC - - ML1_THYROID NA ML1_THYROID NA g.chr9:15474026_15474030delTCTCC uc003zlv.3 - 9 1165_1169 c.835_839delGGAGA c.(835-840)GGAGATfs p.G279fs PSIP1_uc003zlw.3_Frame_Shift_Del_p.G279fs|PSIP1_uc003zlz.3_Frame_Shift_Del_p.G279fs|PSIP1_uc003zma.3_Frame_Shift_Del_p.G270fs|PSIP1_uc003zly.2_Frame_Shift_Del_p.G279fs NM_033222 NP_150091 O75475 PSIP1_HUMAN PC4 and SFRS1 interacting protein 1 isoform 2 279_280 initiation of viral infection|interspecies interaction between organisms|nuclear mRNA 5'-splice site recognition|provirus integration|regulation of transcription, DNA-dependent|response to heat|response to oxidative stress|transcription, DNA-dependent cytosol|nuclear heterochromatin|nuclear periphery|nucleoplasm|nucleoplasm|transcriptionally active chromatin activating transcription factor binding|chromatin binding|DNA secondary structure binding|RNA polymerase II transcription coactivator activity breast(1) 1 GBM - Glioblastoma multiforme(50;2.38e-06) TTCTTGATCATCTCCTTCTTCTTCA 0.273 0.63 77 129 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 ML1_THYROID NA ML1_THYROID NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 265 105 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C ML1_THYROID NA ML1_THYROID NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 15 131 TP53 7157 broad.mit.edu 37 17 7579547 7579547 + Frame_Shift_Del DEL G - - ML1_THYROID NA ML1_THYROID NA g.chr17:7579547delG uc002gim.2 - 4 334 c.140delC c.(139-141)CCGfs p.P47fs TP53_uc002gig.1_Frame_Shift_Del_p.P47fs|TP53_uc002gih.2_Frame_Shift_Del_p.P47fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.P47fs|TP53_uc010cni.1_Frame_Shift_Del_p.P47fs|TP53_uc002gij.2_Frame_Shift_Del_p.P47fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.P8fs|TP53_uc010cnk.1_Frame_Shift_Del_p.P62fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 47 Interaction with HRMT1L2. P -> L (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.P47fs*4(2)|p.P47L(2)|p.P47fs*76(2)|p.D48fs*55(1)|p.P47P(1)|p.P13fs*18(1)|p.S46_D49delSPDD(1)|p.S33fs*23(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.95 48 1010 PRKAR1A 5573 broad.mit.edu 37 17 66524034 66524038 + Frame_Shift_Del DEL TATTT - - ML1_THYROID NA ML1_THYROID NA g.chr17:66524034_66524038delTATTT uc002jhg.2 + 8 942_946 c.762_766delTATTT c.(760-768)TCTATTTTAfs p.S254fs PRKAR1A_uc002jhh.2_Frame_Shift_Del_p.S254fs|PRKAR1A_uc002jhi.2_Frame_Shift_Del_p.S254fs|PRKAR1A_uc002jhj.2_Frame_Shift_Del_p.S254fs|PRKAR1A_uc002jhk.2_Frame_Shift_Del_p.S130fs|PRKAR1A_uc002jhl.2_Frame_Shift_Del_p.S254fs|PRKAR1A_uc002jhm.2_Frame_Shift_Del_p.S254fs NM_212471 NP_997636 P10644 KAP0_HUMAN cAMP-dependent protein kinase, regulatory 254_256 cAMP 2. activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter|transmembrane transport|water transport cAMP-dependent protein kinase complex|cytosol cAMP binding|cAMP-dependent protein kinase regulator activity|protein binding adrenal_gland(4)|lung(3)|thyroid(2)|soft_tissue(2)|breast(1) 12 Breast(10;1.64e-13) GTAAAGTCTCTATTTTAGGTGAGTT 0.351 0.87 11 76 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 ML1_THYROID NA ML1_THYROID NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.72 26 66 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ML1_THYROID NA ML1_THYROID NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 165 618 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ML1_THYROID NA ML1_THYROID NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 6 147 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes ML1_THYROID NA ML1_THYROID NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.17 238 49 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.40 55 36 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.99 1 72 THBS3 7059 broad.mit.edu 37 1 155170259 155170263 + Frame_Shift_Del DEL TTGTC - - MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:155170259_155170263delTTGTC uc001fix.2 - 14 1710_1714 c.1687_1691delGACAA c.(1687-1692)GACAACfs p.D563fs RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Frame_Shift_Del_p.D554fs|THBS3_uc001fiz.2_Frame_Shift_Del_p.D526fs|THBS3_uc001fiy.2_Frame_Shift_Del_p.D92fs|THBS3_uc010pfu.1_Frame_Shift_Del_p.D443fs|THBS3_uc010pfv.1_Intron|THBS3_uc001fja.2_RNA NM_007112 NP_009043 P49746 TSP3_HUMAN thrombospondin 3 precursor 563_564 TSP type-3 4. cell-matrix adhesion extracellular region|perinuclear region of cytoplasm calcium ion binding|heparin binding|structural molecule activity breast(3)|ovary(2) 5 all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) ATCCACGTCGTTGTCACAGGCATCT 0.546 0.10 624 73 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.38 15 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 90 159 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.76 12 39 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 3 21 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 43 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.33 74 37 SLC3A2 6520 broad.mit.edu 37 11 62638220 62638221 + Frame_Shift_Ins INS - G G MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638220_62638221insG uc001nwd.2 + 2 340_341 c.116_117insG c.(115-117)TTGfs p.L39fs SLC3A2_uc001nwb.2_Frame_Shift_Ins_p.L39fs|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c 39 blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.21 42 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 663 373 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.70 19 44 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.33 10 5 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.59 44 63 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 213 586 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 5 57 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 3 28 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.46 84 71 HOXD13 3239 broad.mit.edu 37 2 176957786 176957797 + In_Frame_Del DEL GGCGGCGGCGGC - - rs3832095 MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:176957786_176957797delGGCGGCGGCGGC uc002ukf.1 + 1 255_266 c.168_179delGGCGGCGGCGGC c.(166-180)CGGGCGGCGGCGGCG>CGG p.AAAA65del NM_000523 NP_000514 P35453 HXD13_HUMAN homeobox D13 65_68 Poly-Ala. skeletal system development|transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding lung(1) 1 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0526)|READ - Rectum adenocarcinoma(9;0.0678) 0.000 0.24 370 120 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.36 7 4 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.45 6 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 59 82 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 16 30 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.28 194 77 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.35 17 9 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.14 580 91 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 375 168 CBL 867 broad.mit.edu 37 11 119149006 119149019 + Splice_Site DEL AGGTACGGATCTAA - - MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:119149006_119149019delAGGTACGGATCTAA uc001pwe.2 + 8 1365 c.1227_splice c.e8+1 p.Q409_splice NM_005188 NP_005179 P22681 CBL_HUMAN Cas-Br-M (murine) ecotropic retroviral epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis cytosol|nucleus calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding p.E366_Q409del(13)|p.?(3)|p.G397_I429del(1)|p.E366_K477del(1) haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1) 149 Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784) ACATCCTGGCAGGTACGGATCTAAACAGCGACTT 0.407 0.35 22 12 PIK3C2G 5288 broad.mit.edu 37 12 18443818 18443827 + Frame_Shift_Del DEL TTAATTTCAA - - MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:18443818_18443827delTTAATTTCAA uc001rdt.2 + 4 907_916 c.791_800delTTAATTTCAA c.(790-801)GTTAATTTCAATfs p.V264fs PIK3C2G_uc010sia.1_RNA|PIK3C2G_uc010sib.1_Frame_Shift_Del_p.V264fs|PIK3C2G_uc010sic.1_Frame_Shift_Del_p.V42fs NM_004570 NP_004561 O75747 P3C2G_HUMAN phosphoinositide-3-kinase, class 2 gamma 264_267 cell communication|phosphatidylinositol-mediated signaling membrane|phosphatidylinositol 3-kinase complex 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2) 21 Hepatocellular(102;0.194) GCAGCTGATGTTAATTTCAATTCTGGGAAG 0.338 0.41 20 14 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.84 4 21 MYH8 4626 broad.mit.edu 37 17 10314206 10314206 + Frame_Shift_Del DEL A - - MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:10314206delA uc002gmm.2 - 15 1570 c.1475delT c.(1474-1476)TTCfs p.F492fs uc002gml.1_Intron NM_002472 NP_002463 P13535 MYH8_HUMAN myosin, heavy chain 8, skeletal muscle, 492 Myosin head-like. muscle filament sliding cytosol|muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle skin(6)|ovary(3)|breast(2) 11 GTGGTGGTTGAAAAACTGTTG 0.443 0.48 37 34 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.10 551 63 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 29 81 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 48 610 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 69 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 52 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.54 205 243 IRS1 3667 broad.mit.edu 37 2 227660807 227660808 + In_Frame_Ins INS - GCT GCT MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:227660807_227660808insGCT uc002voh.3 - 1 2699_2700 c.2647_2648insAGC c.(2647-2649)CCC>CAGCCC p.882_883insQ NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 882_883 fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) GTGCAGCAAGGgctgctgctgc 0.554 0.58 8 11 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.21 27 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.37 17 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 64 113 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.62 168 269 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.74 40 115 MSH5 4439 broad.mit.edu 37 6 31727933 31727934 + Frame_Shift_Ins INS - G G rs28405564 MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:31727933_31727934insG uc003nwv.1 + 19 1831_1832 c.1752_1753insG c.(1750-1755)AAAGGGfs p.K584fs MSH5_uc003nwt.1_Frame_Shift_Ins_p.K601fs|MSH5_uc003nwu.1_Frame_Shift_Ins_p.K584fs|MSH5_uc003nww.1_Frame_Shift_Ins_p.K584fs|MSH5_uc003nwx.1_Frame_Shift_Ins_p.K601fs|MSH5_uc011dof.1_Frame_Shift_Ins_p.K283fs|MSH5_uc003nwy.1_Frame_Shift_Ins_p.K258fs|MSH5_uc003nwz.3_RNA|C6orf26_uc003nxa.3_5'Flank NM_172166 NP_751898 O43196 MSH5_HUMAN mutS homolog 5 isoform c 584_585 chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination synaptonemal complex ATP binding|DNA-dependent ATPase activity|mismatched DNA binding ovary(2)|breast(1) 3 GTGGGGACAAAGGGAGGGTCAA 0.574 0.10 104 11 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.10 199 23 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.89 5 42 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.19 132 31 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 803 415 ATN1 1822 broad.mit.edu 37 12 7045885 7045886 + In_Frame_Ins INS - CAG CAG MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:7045885_7045886insCAG uc001qrw.1 + 5 1692_1693 c.1455_1456insCAG c.(1453-1458)insCAG p.502_503insQ ATN1_uc001qrx.1_In_Frame_Ins_p.502_503insQ|ATN1_uc001qry.1_In_Frame_Ins_p.486_487insQ NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502_503 cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 ACCACcagcaacagcaacagca 0.441 0.53 44 49 NCOR2 9612 broad.mit.edu 37 12 124887059 124887067 + In_Frame_Del DEL GCTGCTGCT - - rs67031864 MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:124887059_124887067delGCTGCTGCT uc010tba.1 - 14 1640_1648 c.1523_1531delAGCAGCAGC c.(1522-1533)CAGCAGCAGCCC>CCC p.QQQ508del NCOR2_uc010tay.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010taz.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010tbb.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010tbc.1_In_Frame_Del_p.QQQ507del|NCOR2_uc001ugj.1_In_Frame_Del_p.QQQ508del NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 508_510 Poly-Gln. cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) CGGGGCATGGgctgctgctgctgctgctg 0.316 0.18 41 9 CREBBP 1387 broad.mit.edu 37 16 3778410 3778415 + In_Frame_Del DEL TGCTGT - - MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:3778410_3778415delTGCTGT uc002cvv.2 - 31 6837_6842 c.6633_6638delACAGCA c.(6631-6639)CAACAGCAG>CAG p.2211_2213QQQ>Q CREBBP_uc002cvw.2_In_Frame_Del_p.2173_2175QQQ>Q NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 2211_2213 Poly-Gln. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) Ttgctgctgctgctgttgctgctgtt 0.437 0.91 29 304 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 9 137 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.15 668 116 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 89 289 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 149 1035 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 11 79 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 5 37 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.59 7 10 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.47 10 9 BMP2K 55589 broad.mit.edu 37 4 79792137 79792145 + In_Frame_Del DEL CAGCAGCAG - - rs17855588 MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:79792137_79792145delCAGCAGCAG uc003hlk.2 + 11 1598_1606 c.1432_1440delCAGCAGCAG c.(1432-1440)CAGCAGCAGdel p.QQQ484del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQ484del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 484_486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 gcaacagcaacagcagcagcagcagcagc 0.177 0.33 138 68 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 126 158 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.29 41 17 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.81 22 94 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.55 38 46 C6orf97 80129 broad.mit.edu 37 6 151907077 151907077 + Frame_Shift_Del DEL G - - MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:151907077delG uc003qol.2 + 7 1235 c.1146delG c.(1144-1146)AAGfs p.K382fs NM_025059 NP_079335 Q8IYT3 CF097_HUMAN hypothetical protein LOC80129 382 Potential. 0 Ovarian(120;0.126) BRCA - Breast invasive adenocarcinoma(37;0.111) OV - Ovarian serous cystadenocarcinoma(155;1.48e-10) AGTTGGGAAAGGAGTCTGGGT 0.483 0.49 29 28 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 749 418 PLEKHA5 54477 broad.mit.edu 37 12 19427887 19427888 + Frame_Shift_Ins INS - G G MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:19427887_19427888insG uc001reb.2 + 10 1351_1352 c.1265_1266insG c.(1264-1266)AAGfs p.K422fs PLEKHA5_uc010sie.1_Frame_Shift_Ins_p.K428fs|PLEKHA5_uc001rea.2_Frame_Shift_Ins_p.K422fs|PLEKHA5_uc009zin.2_Frame_Shift_Ins_p.K180fs|PLEKHA5_uc010sif.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc010sig.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc010sih.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc001rec.1_Frame_Shift_Ins_p.K110fs NM_019012 NP_061885 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A 422 1-phosphatidylinositol binding|protein binding ovary(1)|kidney(1)|skin(1) 3 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) AAAATCCAGAAGGGGAGGGGTC 0.470 0.18 59 13 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.67 5 10 FFAR2 2867 broad.mit.edu 37 19 35940696 35940697 + Frame_Shift_Ins INS - G G MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:35940696_35940697insG uc002nzg.2 + 2 160_161 c.80_81insG c.(79-81)CTGfs p.L27fs FFAR2_uc010eea.2_Frame_Shift_Ins_p.L27fs NM_005306 NP_005297 O15552 FFAR2_HUMAN free fatty acid receptor 2 27 Helical; Name=1; (Potential). integral to plasma membrane G-protein coupled receptor activity|lipid binding central_nervous_system(1) 1 all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0724) GCCAACCTCCTGGCCCTGCGGG 0.629 0.15 61 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.47 151 135 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 28 303 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 10 196 TNRC6B 23112 broad.mit.edu 37 22 40696458 40696458 + Splice_Site DEL G - - MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:40696458delG uc011aor.1 + 13 3920 c.3709_splice c.e13-1 p.V1237_splice TNRC6B_uc003aym.2_Splice_Site_p.V433_splice|TNRC6B_uc003ayn.3_Splice_Site_p.V1127_splice|TNRC6B_uc003ayo.2_Splice_Site_p.V984_splice NM_001162501 NP_001155973 Q9UPQ9 TNR6B_HUMAN trinucleotide repeat containing 6B isoform 1 gene silencing by RNA|regulation of translation cytoplasmic mRNA processing body nucleotide binding|RNA binding 0 TTTTTGGCTAGGTTTCTGCCT 0.373 0.52 46 49 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 96 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.61 7 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 68 109 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.32 61 29 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 12 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.17 48 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 11 RRP12 23223 broad.mit.edu 37 10 99139529 99139530 + Splice_Site INS - GCA GCA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:99139529_99139530insGCA uc001knf.2 - 14 1673 c.1534_splice c.e14-1 p.C512_splice RRP12_uc009xvm.2_Splice_Site_p.C230_splice|RRP12_uc010qou.1_Splice_Site_p.C451_splice|RRP12_uc009xvn.2_Splice_Site_p.C412_splice NM_015179 NP_055994 Q5JTH9 RRP12_HUMAN ribosomal RNA processing 12 homolog isoform 1 integral to membrane|nuclear membrane|nucleolus protein binding ovary(2)|central_nervous_system(1) 3 Colorectal(252;0.162) Epithelial(162;2.72e-09)|all cancers(201;1.76e-07) 0.000 0.80 2 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 341 168 DRD2 1813 broad.mit.edu 37 11 113283333 113283339 + Frame_Shift_Del DEL CCTACGG - - rs138873192 byFrequency MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:113283333_113283339delCCTACGG uc001pnz.2 - 6 1398_1404 c.1077_1083delCCGTAGG c.(1075-1083)AGCCGTAGGfs p.S359fs DRD2_uc010rwv.1_Frame_Shift_Del_p.S358fs|DRD2_uc001poa.3_Frame_Shift_Del_p.S359fs|DRD2_uc001pob.3_Frame_Shift_Del_p.S330fs NM_000795 NP_000786 P14416 DRD2_HUMAN dopamine receptor D2 isoform long 359_361 Cytoplasmic (By similarity).|Interaction with PPP1R9B (By similarity). activation of phospholipase C activity by dopamine receptor signaling pathway|adenohypophysis development|adult walking behavior|arachidonic acid secretion|axonogenesis|behavioral response to cocaine|behavioral response to ethanol|branching morphogenesis of a nerve|cerebral cortex GABAergic interneuron migration|circadian regulation of gene expression|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|intracellular protein kinase cascade|negative regulation of blood pressure|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of dopamine receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|negative regulation of synaptic transmission, glutamatergic|neurological system process involved in regulation of systemic arterial blood pressure|peristalsis|phosphatidylinositol metabolic process|positive regulation of dopamine uptake|positive regulation of growth hormone secretion|positive regulation of neuroblast proliferation|prepulse inhibition|protein localization|regulation of heart rate|regulation of long-term neuronal synaptic plasticity|regulation of potassium ion transport|regulation of sodium ion transport|regulation of synaptic transmission, GABAergic|release of sequestered calcium ion into cytosol|response to amphetamine|response to drug|response to histamine|response to morphine|sensory perception of smell|synapse assembly|temperature homeostasis|visual learning integral to plasma membrane dopamine D2 receptor activity|dopamine receptor activity, coupled via Gi/Go|drug binding|potassium channel regulator activity|protein binding pancreas(1)|skin(1) 2 all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494) BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216) Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Carphenazine(DB01038)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Domperidone(DB01184)|Droperidol(DB00450)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Mesoridazine(DB00933)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Sulpiride(DB00391)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Ziprasidone(DB00246)|Zuclopenthixol(DB01624) GGGAGAGCTTCCTACGGCTCATGGTCT 0.560 0.38 104 65 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 6 55 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 143 553 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 54 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 40 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.43 28 21 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.32 199 92 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.55 21 26 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.32 111 52 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.50 6 6 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 15 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 10 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.33 407 205 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 854 291 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.65 17 32 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.17 95 20 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.50 79 80 LMTK3 114783 broad.mit.edu 37 19 49001791 49001792 + Frame_Shift_Ins INS - G G MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:49001791_49001792insG uc002pjk.2 - 12 2621_2622 c.2621_2622insC c.(2620-2622)CCGfs p.P874fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) CCCGGGGCCCCGGGAGTGGGAG 0.718 0.11 93 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 85 277 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 6 119 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 3 49 ABL2 27 broad.mit.edu 37 1 179084039 179084039 + Frame_Shift_Del DEL G - - MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:179084039delG uc001gmj.3 - 9 1822 c.1535delC c.(1534-1536)CCTfs p.P512fs ABL2_uc010pnf.1_Frame_Shift_Del_p.P512fs|ABL2_uc010png.1_Frame_Shift_Del_p.P491fs|ABL2_uc010pnh.1_Frame_Shift_Del_p.P491fs|ABL2_uc009wxe.2_Frame_Shift_Del_p.P491fs|ABL2_uc001gmg.3_Frame_Shift_Del_p.P497fs|ABL2_uc001gmi.3_Frame_Shift_Del_p.P497fs|ABL2_uc001gmh.3_Frame_Shift_Del_p.P476fs|ABL2_uc010pne.1_Frame_Shift_Del_p.P476fs NM_007314 NP_009298 P42684 ABL2_HUMAN arg tyrosine kinase isoform b 512 Protein kinase. axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction cytoskeleton|cytosol ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(8)|breast(3)|ovary(2)|central_nervous_system(1) 14 Adenosine triphosphate(DB00171)|Dasatinib(DB01254) ATAAACCTTAGGGGGGCATCC 0.388 0.26 90 32 BCL11A 53335 broad.mit.edu 37 2 60689254 60689254 + Frame_Shift_Del DEL G - - MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:60689254delG uc002sae.1 - 4 1021 c.793delC c.(793-795)CTGfs p.L265fs BCL11A_uc002sab.2_Frame_Shift_Del_p.L265fs|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Frame_Shift_Del_p.L231fs|BCL11A_uc002sad.1_Frame_Shift_Del_p.L113fs|BCL11A_uc002saf.1_Frame_Shift_Del_p.L231fs NM_022893 NP_075044 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A isoform 1 265 Pro-rich. negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|cytoplasm|nucleus|nucleus nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding central_nervous_system(6)|breast(3)|ovary(2)|skin(2) 13 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) 0.000 0.36 788 441 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.15 46 8 PLK4 10733 broad.mit.edu 37 4 128811106 128811106 + Frame_Shift_Del DEL A - - MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:128811106delA uc003ifo.2 + 7 1790 c.1545delA c.(1543-1545)TCAfs p.S515fs PLK4_uc011cgs.1_Frame_Shift_Del_p.S483fs|PLK4_uc011cgt.1_Frame_Shift_Del_p.S474fs NM_014264 NP_055079 O00444 PLK4_HUMAN polo-like kinase 4 515 G2/M transition of mitotic cell cycle|positive regulation of centriole replication|trophoblast giant cell differentiation centriole|cleavage furrow|cytosol|nucleolus ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity 0 AGGACACATCAAAAAATGCCT 0.383 0.11 98 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.44 79 63 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 28 59 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.33 30 15 WRN 7486 broad.mit.edu 37 8 30945345 30945345 + Frame_Shift_Del DEL A - - MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:30945345delA uc003xio.3 + 12 2273 c.1485delA c.(1483-1485)TTAfs p.L495fs WRN_uc011lbe.1_Frame_Shift_Del_p.L23fs|WRN_uc010lvk.2_5'UTR NM_000553 NP_000544 Q14191 WRN_HUMAN Werner syndrome protein 495 base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance centrosome|nucleolus|nucleoplasm 3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1) 7 Breast(100;0.195) KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192) 0.000 0.10 620 72 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.18 969 206 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 272 83 IRAK3 11213 broad.mit.edu 37 12 66641939 66641940 + Frame_Shift_Ins INS - A A MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:66641939_66641940insA uc001sth.2 + 12 1881_1882 c.1779_1780insA c.(1777-1782)TACAAAfs p.Y593fs IRAK3_uc010ssy.1_Frame_Shift_Ins_p.Y532fs NM_007199 NP_009130 Q9Y616 IRAK3_HUMAN interleukin-1 receptor-associated kinase 3 593_594 interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|negative regulation of innate immune response|negative regulation of interleukin-12 production|negative regulation of interleukin-6 production|negative regulation of macrophage cytokine production|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein catabolic process|negative regulation of protein complex disassembly|negative regulation of toll-like receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of macrophage tolerance induction|positive regulation of NF-kappaB transcription factor activity|response to exogenous dsRNA|response to lipopolysaccharide|response to peptidoglycan cytoplasm|nucleus ATP binding|magnesium ion binding|protein heterodimerization activity|protein homodimerization activity|protein serine/threonine kinase activity lung(3)|ovary(2)|breast(2)|central_nervous_system(1) 8 GBM - Glioblastoma multiforme(28;0.0203) ATGAACAGTACAAAAAAGAATA 0.421 0.23 105 31 C14orf43 91748 broad.mit.edu 37 14 74205925 74205926 + In_Frame_Ins INS - CTG CTG MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:74205925_74205926insCTG uc001xot.2 - 2 1569_1570 c.786_787insCAG c.(784-789)insCAG p.262_263insQ C14orf43_uc001xou.2_In_Frame_Ins_p.262_263insQ|C14orf43_uc010tud.1_In_Frame_Ins_p.262_263insQ|C14orf43_uc010arw.2_RNA NM_194278 NP_919254 Q6PJG2 CN043_HUMAN hypothetical protein LOC91748 262_263 Pro-rich.|Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding ovary(4)|central_nervous_system(1) 5 BRCA - Breast invasive adenocarcinoma(234;0.00358)|KIRC - Kidney renal clear cell carcinoma(182;0.0878)|OV - Ovarian serous cystadenocarcinoma(108;0.115) GGTAGGgctgcctgctgctgct 0.465 0.32 17 8 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 71 856 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 16 44 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.23 103 31 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 229 626 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 97 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.22 54 15 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 6 88 SPEN 23013 broad.mit.edu 37 1 16258889 16258889 + Frame_Shift_Del DEL A - - MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:16258889delA uc001axk.1 + 11 6358 c.6154delA c.(6154-6156)AAAfs p.K2052fs SPEN_uc010obp.1_Frame_Shift_Del_p.K2011fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2052 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) TGGCACAGACAAAAACCCCCC 0.502 0.13 239 37 DENND4B 9909 broad.mit.edu 37 1 153907278 153907279 + In_Frame_Ins INS - CTG CTG rs141373027 by1000genomes MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:153907278_153907279insCTG uc001fdd.1 - 18 3131_3132 c.2730_2731insCAG c.(2728-2733)insCAG p.910_911insQ uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910_911 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) GACACctgctcctgctgctgct 0.455 0.16 41 8 FMN2 56776 broad.mit.edu 37 1 240256066 240256067 + In_Frame_Ins INS - CAG CAG MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:240256066_240256067insCAG uc010pyd.1 + 1 882_883 c.657_658insCAG c.(655-660)insCAG p.225_226insQ FMN2_uc010pye.1_In_Frame_Ins_p.225_226insQ NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 225_226 Potential.|Gln-rich. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) agctccagcaacagcagcagca 0.465 0.20 56 14 IRS1 3667 broad.mit.edu 37 2 227661396 227661398 + In_Frame_Del DEL TGC - - MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:227661396_227661398delTGC uc002voh.3 - 1 2109_2111 c.2057_2059delGCA c.(2056-2061)AGCAAC>AAC p.S686del NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 686 Poly-Ser. fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) GGGACGGCGTtgctgctgctgct 0.547 0.31 122 55 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.32 25 12 TNK2 10188 broad.mit.edu 37 3 195597045 195597046 + Frame_Shift_Ins INS - G G MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:195597045_195597046insG uc003fvu.1 - 11 2025_2026 c.1482_1483insC c.(1480-1485)CCCGACfs p.P494fs TNK2_uc003fvq.1_5'Flank|TNK2_uc003fvr.1_Frame_Shift_Ins_p.P4fs|TNK2_uc003fvs.1_Frame_Shift_Ins_p.P526fs|TNK2_uc003fvt.1_Frame_Shift_Ins_p.P557fs|TNK2_uc010hzw.1_RNA|TNK2_uc003fvv.1_Frame_Shift_Ins_p.P324fs NM_005781 NP_005772 Q07912 ACK1_HUMAN tyrosine kinase, non-receptor, 2 isoform 1 494_495 Missing (in Ref. 4; AAH08884). positive regulation of peptidyl-tyrosine phosphorylation|protein ubiquitination|small GTPase mediated signal transduction adherens junction|cytoplasmic vesicle membrane|endosome|nucleus ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1) 10 all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206) Lung NSC(153;0.191) Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05) GBM - Glioblastoma multiforme(46;0.000757) Adenosine triphosphate(DB00171) CTCAGGAGGTCGGGGGGGTCCA 0.619 0.38 87 53 N4BP2 55728 broad.mit.edu 37 4 40144449 40144449 + Frame_Shift_Del DEL A - - MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:40144449delA uc003guy.3 + 15 5280 c.4942delA c.(4942-4944)AAAfs p.K1648fs N4BP2_uc010ifq.2_Frame_Shift_Del_p.K1568fs|N4BP2_uc010ifr.2_Frame_Shift_Del_p.K1551fs NM_018177 NP_060647 Q86UW6 N4BP2_HUMAN Nedd4 binding protein 2 1648 cytoplasm ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding lung(3)|breast(2)|kidney(2)|ovary(1) 8 TCGGATAGGGAAAAAAAATGT 0.398 0.14 169 27 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 83 146 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 32 62 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.33 115 56 FBN2 2201 broad.mit.edu 37 5 127704879 127704880 + Frame_Shift_Ins INS - T T MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:127704879_127704880insT uc003kuu.2 - 16 2682_2683 c.2243_2244insA c.(2242-2244)AATfs p.N748fs FBN2_uc003kuv.2_Frame_Shift_Ins_p.N715fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 748 TB 3. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) GACTACCTGAATTTTTTGCAGG 0.455 0.23 96 28 NOTCH4 4855 broad.mit.edu 37 6 32165215 32165216 + Frame_Shift_Ins INS - G G MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32165215_32165216insG uc003obb.2 - 27 5051_5052 c.4912_4913insC c.(4912-4914)CTGfs p.L1638fs GPSM3_uc003oaz.2_5'Flank|NOTCH4_uc011dpt.1_Frame_Shift_Ins_p.L47fs|NOTCH4_uc003oba.2_Frame_Shift_Ins_p.L298fs|NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc011dpw.1_Frame_Shift_Ins_p.L47fs NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 1638 Cytoplasmic (Potential).|ANK 1. cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 AGCCAGGTGCAGGGGGGTCTCC 0.693 0.17 52 11 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 2 24 MLL3 58508 broad.mit.edu 37 7 152012386 152012386 + Frame_Shift_Del DEL T - - MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:152012386delT uc003wla.2 - 4 646 c.427delA c.(427-429)AGTfs p.S143fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 143 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) CCTAAGGAACTTTTTTCCCCA 0.378 0.19 316 74 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.90 1 9 WHSC1L1 54904 broad.mit.edu 37 8 38205092 38205092 + Frame_Shift_Del DEL T - - MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:38205092delT uc003xli.2 - 2 1116 c.598delA c.(598-600)AGCfs p.S200fs WHSC1L1_uc011lbm.1_Frame_Shift_Del_p.S200fs|WHSC1L1_uc010lwe.2_Frame_Shift_Del_p.S200fs|WHSC1L1_uc003xlj.2_Frame_Shift_Del_p.S200fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 200 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TGCTTGTTGCTTTTTTTCCTC 0.378 0.14 383 64 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 26 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.57 253 330 MASTL 84930 broad.mit.edu 37 10 27459056 27459056 + Frame_Shift_Del DEL A - - MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:27459056delA uc001itm.2 + 8 1807 c.1168delA c.(1168-1170)AAAfs p.K390fs MASTL_uc001itl.2_Frame_Shift_Del_p.K390fs|MASTL_uc009xkw.1_Frame_Shift_Del_p.K390fs|MASTL_uc009xkx.1_RNA NM_032844 NP_116233 Q96GX5 GWL_HUMAN microtubule associated serine/threonine 390 Protein kinase. cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus centrosome|cleavage furrow|nucleus ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity p.C392fs*17(1) stomach(1)|ovary(1)|lung(1) 3 AAACCTTGCTAAAAAATGCTT 0.418 0.12 77 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 406 156 HSP90B1 7184 broad.mit.edu 37 12 104327763 104327764 + Frame_Shift_Del DEL CA - - MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:104327763_104327764delCA uc001tkb.1 + 5 546_547 c.441_442delCA c.(439-444)GTCACAfs p.V147fs HSP90B1_uc010swg.1_Intron|HSP90B1_uc009zui.1_Frame_Shift_Del_p.V147fs NM_003299 NP_003290 P14625 ENPL_HUMAN heat shock protein 90kDa beta, member 1 147_148 actin rod assembly|anti-apoptosis|cellular response to ATP|ER-associated protein catabolic process|protein folding|protein transport|regulation of phosphoprotein phosphatase activity|response to hypoxia|sequestering of calcium ion cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|melanosome|microsome|midbody|perinuclear region of cytoplasm ATP binding|calcium ion binding|low-density lipoprotein particle receptor binding|protein phosphatase binding|RNA binding|unfolded protein binding|virion binding ovary(2)|skin(1) 3 Rifabutin(DB00615) TGCTGCATGTCACAGACACCGG 0.381 0.15 82 15 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.34 75 38 HSP90AB4P 664618 broad.mit.edu 37 15 58983757 58983759 + In_Frame_Del DEL TAA - - MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:58983757_58983759delTAA uc002afh.1 - 3 1061_1063 c.1061_1063delTTA c.(1060-1065)ATTAAC>AAC p.I354del ADAM10_uc002afd.1_Intron|ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron|ADAM10_uc002afg.2_Intron NR_002927 RecName: Full=Putative heat shock protein HSP 90-beta 4; 0 TGTCGCCAGTTAATAGAGTCCTC 0.463 0.42 38 27 CREBBP 1387 broad.mit.edu 37 16 3779072 3779072 + Frame_Shift_Del DEL C - - MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:3779072delC uc002cvv.2 - 31 6180 c.5976delG c.(5974-5976)GGGfs p.G1992fs CREBBP_uc002cvw.2_Frame_Shift_Del_p.G1954fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1992 cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) CCATCTGGCTCCCCGGGGTCC 0.697 0.18 45 10 CSF3 1440 broad.mit.edu 37 17 38171995 38171995 + Frame_Shift_Del DEL C - - MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:38171995delC uc002htp.2 + 2 132 c.92delC c.(91-93)ACCfs p.T31fs CSF3_uc002hto.2_Frame_Shift_Del_p.T31fs|CSF3_uc002htq.2_Frame_Shift_Del_p.T27fs|CSF3_uc010wep.1_Frame_Shift_Del_p.T27fs NM_000759 NP_000750 P09919 CSF3_HUMAN colony stimulating factor 3 isoform a precursor 31 cytokine-mediated signaling pathway|granulocyte differentiation|immune response|positive regulation of cell proliferation extracellular space cytokine activity|enzyme binding|granulocyte colony-stimulating factor receptor binding|growth factor activity ovary(1) 1 Colorectal(19;0.000442) Myeloproliferative disorder(1115;0.0255) Filgrastim(DB00099)|Pegfilgrastim(DB00019) 0.000 0.16 1068 200 SMAD4 4089 broad.mit.edu 37 18 48584514 48584514 + Frame_Shift_Del DEL G - - MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr18:48584514delG uc010xdp.1 + 6 1225 c.687delG c.(685-687)CTGfs p.L229fs SMAD4_uc010xdo.1_RNA|SMAD4_uc002lfb.3_Frame_Shift_Del_p.L74fs NM_005359 NP_005350 Q13485 SMAD4_HUMAN mothers against decapentaplegic homolog 4 229 BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway activin responsive factor complex|centrosome|cytosol I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity p.0?(35)|p.?(2) pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1) 369 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155) 0.000 0.14 646 109 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.75 27 79 RBL1 5933 broad.mit.edu 37 20 35696591 35696592 + Splice_Site INS - A A MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:35696591_35696592insA uc002xgi.2 - 3 370 c.291_splice c.e3-1 p.S97_splice RBL1_uc010zvt.1_Splice_Site|RBL1_uc002xgj.1_Splice_Site_p.S97_splice|RBL1_uc010gfv.1_Splice_Site NM_002895 NP_002886 P28749 RBL1_HUMAN retinoblastoma-like protein 1 isoform a cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent transcription factor binding lung(5)|skin(3)|ovary(2) 10 Myeloproliferative disorder(115;0.00878) TGTATTAAACTAAAAAAAAAAA 0.272 0.23 36 11 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.19 122 28 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 80 263 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 7 99 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 39 TTN 7273 broad.mit.edu 37 2 179424125 179424127 + In_Frame_Del DEL CTT - - MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179424125_179424127delCTT uc010zfg.1 - 275 79252_79254 c.79028_79030delAAG c.(79027-79032)GAAGGA>GGA p.E26343del uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.E20038del|TTN_uc010zfi.1_In_Frame_Del_p.E19971del|TTN_uc010zfj.1_In_Frame_Del_p.E19846del NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 27270 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TAGATAGCTCCTTCTTGTAAATT 0.394 0.47 135 122 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.23 37 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 61 112 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 33 56 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 280 133 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.59 24 35 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 52 199 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 77 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 33 TTN 7273 broad.mit.edu 37 2 179424125 179424127 + In_Frame_Del DEL CTT - - MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179424125_179424127delCTT uc010zfg.1 - 275 79252_79254 c.79028_79030delAAG c.(79027-79032)GAAGGA>GGA p.E26343del uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.E20038del|TTN_uc010zfi.1_In_Frame_Del_p.E19971del|TTN_uc010zfj.1_In_Frame_Del_p.E19846del NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 27270 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TAGATAGCTCCTTCTTGTAAATT 0.394 0.43 119 89 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.14 50 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 135 167 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 15 42 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.82 2 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 5 52 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.80 2 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 733 313 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.48 26 24 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.27 32 12 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 91 69 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 128 454 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 36 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MORCPR_LUNG NA MORCPR_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.04 -1 25 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MORCPR_LUNG NA MORCPR_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.49 19 18 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MORCPR_LUNG NA MORCPR_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.28 102 39 FGF2 2247 broad.mit.edu 37 4 123748258 123748259 + Frame_Shift_Ins INS - G G MORCPR_LUNG NA MORCPR_LUNG NA g.chr4:123748258_123748259insG uc003iev.1 + 1 396_397 c.328_329insG c.(328-330)CGGfs p.R110fs NM_002006 NP_001997 P09038 FGF2_HUMAN fibroblast growth factor 2 110 activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing extracellular space fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity ovary(1)|lung(1)|central_nervous_system(1) 3 Pentosan Polysulfate(DB00686) 0.000 0.13 61 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MORCPR_LUNG NA MORCPR_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 75 94 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MORCPR_LUNG NA MORCPR_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 27 44 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 MORCPR_LUNG NA MORCPR_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.54 75 89 APC 324 broad.mit.edu 37 5 112177642 112177643 + In_Frame_Ins INS - GCT GCT MORCPR_LUNG NA MORCPR_LUNG NA g.chr5:112177642_112177643insGCT uc010jby.2 + 16 6731_6732 c.6351_6352insGCT c.(6349-6354)insGCT p.2122_2123insA APC_uc011cvt.1_In_Frame_Ins_p.2104_2105insA|APC_uc003kpz.3_In_Frame_Ins_p.2122_2123insA|APC_uc003kpy.3_In_Frame_Ins_p.2122_2123insA|APC_uc010jbz.2_In_Frame_Ins_p.1839_1840insA|APC_uc010jca.2_In_Frame_Ins_p.1422_1423insA NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 2122_2123 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.A2122_C2123insA(1)|p.?(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GTTTACATCAAGCTGCTGCTGC 0.406 0.73 51 137 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MORCPR_LUNG NA MORCPR_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.62 8 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MORCPR_LUNG NA MORCPR_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 31 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MORCPR_LUNG NA MORCPR_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 203 80 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 MORCPR_LUNG NA MORCPR_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.70 3 7 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes MORCPR_LUNG NA MORCPR_LUNG NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.10 146 17 CDH3 1001 broad.mit.edu 37 16 68679613 68679614 + Frame_Shift_Ins INS - A A MORCPR_LUNG NA MORCPR_LUNG NA g.chr16:68679613_68679614insA uc002ewf.2 + 2 1252_1253 c.120_121insA c.(118-123)GCGGGAfs p.A40fs CDH3_uc010vli.1_Intron NM_001793 NP_001784 P22223 CADH3_HUMAN cadherin 3, type 1 preproprotein 40_41 adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception integral to membrane calcium ion binding p.?(1) ovary(3)|breast(1)|skin(1) 5 Ovarian(137;0.0564) OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384) 0.000 0.92 1 11 TP53 7157 broad.mit.edu 37 17 7578475 7578475 + Frame_Shift_Del DEL G - - MORCPR_LUNG NA MORCPR_LUNG NA g.chr17:7578475delG uc002gim.2 - 5 649 c.455delC c.(454-456)CCGfs p.P152fs TP53_uc002gig.1_Frame_Shift_Del_p.P152fs|TP53_uc002gih.2_Frame_Shift_Del_p.P152fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.P20fs|TP53_uc010cng.1_Frame_Shift_Del_p.P20fs|TP53_uc002gii.1_Frame_Shift_Del_p.P20fs|TP53_uc010cnh.1_Frame_Shift_Del_p.P152fs|TP53_uc010cni.1_Frame_Shift_Del_p.P152fs|TP53_uc002gij.2_Frame_Shift_Del_p.P152fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.P59fs|TP53_uc002gio.2_Frame_Shift_Del_p.P20fs|TP53_uc010vug.1_Frame_Shift_Del_p.P113fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 152 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). P -> R (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|P -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> A (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.P152L(57)|p.P152S(21)|p.P152fs*18(17)|p.P152T(7)|p.0?(7)|p.P152fs*29(5)|p.P152P(5)|p.P152Q(4)|p.P153fs*28(4)|p.P152fs*14(4)|p.P152fs*28(3)|p.P152R(3)|p.T150fs*16(3)|p.P152A(2)|p.P153fs*16(1)|p.P151_V173del23(1)|p.P152_P153del(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.D148fs*23(1)|p.P152del(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.Q144_G154del11(1)|p.P152_P153insXXX(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGTGCCGGGCGGGGGTGTGGA 0.612 0.89 7 58 MYH1 4619 broad.mit.edu 37 17 10399832 10399832 + Frame_Shift_Del DEL C - - MORCPR_LUNG NA MORCPR_LUNG NA g.chr17:10399832delC uc002gmo.2 - 34 4785 c.4691delG c.(4690-4692)CGCfs p.R1564fs uc002gml.1_Intron NM_005963 NP_005954 P12882 MYH1_HUMAN myosin, heavy chain 1, skeletal muscle, adult 1564 Potential. muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1) 21 AAGCTGGATGCGCAGGATCTT 0.393 0.14 133 22 KEAP1 9817 broad.mit.edu 37 19 10599924 10599924 + Frame_Shift_Del DEL T - - MORCPR_LUNG NA MORCPR_LUNG NA g.chr19:10599924delT uc002moq.1 - 5 1808 c.1652delA c.(1651-1653)AAGfs p.K551fs KEAP1_uc002mop.1_Intron|KEAP1_uc002mor.1_Frame_Shift_Del_p.K551fs NM_012289 NP_036421 Q14145 KEAP1_HUMAN kelch-like ECH-associated protein 1 551 Kelch 5. regulation of transcription, DNA-dependent|transcription, DNA-dependent centrosome|midbody|nucleus protein binding lung(12)|breast(3)|ovary(1)|pancreas(1) 17 OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05) 0.000 0.97 5 182 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MORCPR_LUNG NA MORCPR_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 16 53 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MORCPR_LUNG NA MORCPR_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 150 397 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MORCPR_LUNG NA MORCPR_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 60 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MPP89_PLEURA NA MPP89_PLEURA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.85 5 29 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A MPP89_PLEURA NA MPP89_PLEURA NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.14 48 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MPP89_PLEURA NA MPP89_PLEURA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 80 102 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MPP89_PLEURA NA MPP89_PLEURA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.76 14 45 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - MPP89_PLEURA NA MPP89_PLEURA NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.35 11 6 UBR5 51366 broad.mit.edu 37 8 103277384 103277384 + Frame_Shift_Del DEL A - - MPP89_PLEURA NA MPP89_PLEURA NA g.chr8:103277384delA uc003ykr.1 - 53 7578 c.7545delT c.(7543-7545)ACTfs p.T2515fs UBR5_uc003yks.1_Frame_Shift_Del_p.T2514fs|UBR5_uc003ykq.2_Frame_Shift_Del_p.T26fs NM_015902 NP_056986 O95071 UBR5_HUMAN ubiquitin protein ligase E3 component n-recognin 2515 HECT. cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus nucleus|soluble fraction protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1) 28 all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05) OV - Ovarian serous cystadenocarcinoma(57;0.000442) CAGGCCTTGGAGTATAAAATC 0.373 0.23 166 49 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MPP89_PLEURA NA MPP89_PLEURA NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 28 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MPP89_PLEURA NA MPP89_PLEURA NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.14 44 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MPP89_PLEURA NA MPP89_PLEURA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 228 90 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes MPP89_PLEURA NA MPP89_PLEURA NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.14 42 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MPP89_PLEURA NA MPP89_PLEURA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 19 187 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MPP89_PLEURA NA MPP89_PLEURA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 24 70 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MPP89_PLEURA NA MPP89_PLEURA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 49 248 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MPP89_PLEURA NA MPP89_PLEURA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 5 57 NF2 4771 broad.mit.edu 37 22 30074194 30074203 + Frame_Shift_Del DEL CCAATTCCAG - - rs147506929 MPP89_PLEURA NA MPP89_PLEURA NA g.chr22:30074194_30074203delCCAATTCCAG uc003age.3 + 14 1899_1908 c.1456_1465delCCAATTCCAG c.(1456-1467)CCAATTCCAGCAfs p.P486fs NF2_uc003afy.3_Frame_Shift_Del_p.P486fs|NF2_uc003afz.3_Frame_Shift_Del_p.P403fs|NF2_uc003agf.3_Frame_Shift_Del_p.P486fs|NF2_uc003agb.3_Frame_Shift_Del_p.P409fs|NF2_uc003agc.3_Frame_Shift_Del_p.P448fs|NF2_uc003agd.3_RNA|NF2_uc003agg.3_Frame_Shift_Del_p.P486fs|NF2_uc003aga.3_Frame_Shift_Del_p.P444fs|NF2_uc003agh.3_Frame_Shift_Del_p.P445fs|NF2_uc003agi.3_Frame_Shift_Del_p.P403fs|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Frame_Shift_Del_p.P448fs|NF2_uc010gvp.2_Frame_Shift_Del_p.P150fs|NF2_uc011akq.1_Frame_Shift_Del_p.P112fs NM_000268 NP_000259 P35240 MERL_HUMAN neurofibromin 2 isoform 1 486_489 actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane cytoskeletal protein binding|protein binding p.I487fs*28(1)|p.P486fs*26(1)|p.P483fs*17(1)|p.?(1)|p.I487V(1) meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1) 728 GCCCATGAACCCAATTCCAGCACCGTTGCC 0.481 0.93 3 43 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 33 HOXD11 3237 broad.mit.edu 37 2 176972405 176972410 + In_Frame_Del DEL GCGGCG - - MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr2:176972405_176972410delGCGGCG uc002uki.2 + 1 322_327 c.322_327delGCGGCG c.(322-327)GCGGCGdel p.AA118del HOXD11_uc010fqx.2_Intron NM_021192 NP_067015 P31277 HXD11_HUMAN homeobox D11 118_119 Poly-Ala. nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678) 0.000 0.37 47 28 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.38 18 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 71 86 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 26 47 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.54 83 99 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.17 52 11 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 21 NLRP6 171389 broad.mit.edu 37 11 284578 284579 + Frame_Shift_Ins INS - C C rs149974030 MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr11:284578_284579insC uc010qvs.1 + 7 2476_2477 c.2476_2477insC c.(2476-2478)GCCfs p.A826fs NLRP6_uc010qvt.1_Frame_Shift_Ins_p.A825fs NM_138329 NP_612202 P59044 NALP6_HUMAN NLR family, pyrin domain containing 6 826 LRR 4. cytoplasm ATP binding upper_aerodigestive_tract(1)|skin(1) 2 all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122) 0.000 0.31 495 224 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 201 82 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 18 241 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.60 25 37 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.33 77 38 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 52 320 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MSTO211H_PLEURA NA MSTO211H_PLEURA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 44 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.19 294 70 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.39 17 11 PHOX2B 8929 broad.mit.edu 37 4 41748011 41748028 + In_Frame_Del DEL GCCGCCGCCGCTGCCGCG - - rs17882335 MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:41748011_41748028delGCCGCCGCCGCTGCCGCG uc003gwf.3 - 3 1101_1118 c.741_758delCGCGGCAGCGGCGGCGGC c.(739-759)GCCGCGGCAGCGGCGGCGGCG>GCG p.247_253AAAAAAA>A NM_003924 NP_003915 Q99453 PHX2B_HUMAN paired-like homeobox 2b 247_253 Poly-Ala. positive regulation of transcription from RNA polymerase II promoter nuclear chromatin RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity p.A241fs*64(1) autonomic_ganglia(7)|lung(2)|ovary(2)|central_nervous_system(1) 12 0.000 0.33 8 4 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.15 46 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 62 115 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 51 25 IKZF1 10320 broad.mit.edu 37 7 50444469 50444470 + Frame_Shift_Ins INS - GGGGCTCC GGGGCTCC MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:50444469_50444470insGGGGCTCC uc003tow.3 + 5 567_568 c.399_400insGGGGCTCC c.(397-402)ATGGTTfs p.M133fs IKZF1_uc003tox.3_Frame_Shift_Ins_p.M133fs|IKZF1_uc003toy.3_Frame_Shift_Ins_p.M133fs|IKZF1_uc011kck.1_Intron|IKZF1_uc003toz.3_Frame_Shift_Ins_p.M103fs|IKZF1_uc010kyx.2_Intron NM_006060 NP_006051 Q13422 IKZF1_HUMAN zinc finger protein, subfamily 1A, 1 (Ikaros) 133_134 C2H2-type 1. cell cycle|chromatin modification|mesoderm development cytoplasm|nucleus zinc ion binding p.?(74) haematopoietic_and_lymphoid_tissue(147)|lung(1) 148 Glioma(55;0.08)|all_neural(89;0.245) Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07) ATGTGCTCATGGTTCACAAAAG 0.505 0.42 7 5 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.18 701 149 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 2 19 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 20 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.30 779 340 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 364 179 SLC7A5 8140 broad.mit.edu 37 16 87902684 87902685 + Frame_Shift_Ins INS - CC CC rs17853938 byFrequency;by1000genomes MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:87902684_87902685insCC uc002fkm.2 - 1 416_417 c.344_345insGG c.(343-345)GGCfs p.G115fs NM_003486 NP_003477 Q01650 LAT1_HUMAN solute carrier family 7 (cationic amino acid 115 blood coagulation|cell differentiation|cellular amino acid metabolic process|ion transport|leukocyte migration|nervous system development apical plasma membrane|cytosol|integral to membrane neutral amino acid transmembrane transporter activity|peptide antigen binding 0 BRCA - Breast invasive adenocarcinoma(80;0.049) 0.000 0.14 1925 322 NOTCH3 4854 broad.mit.edu 37 19 15311682 15311684 + In_Frame_Del DEL CGG - - MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:15311682_15311684delCGG uc002nan.2 - 1 109_111 c.33_35delCCG c.(31-36)CGCCGT>CGT p.11_12RR>R NOTCH3_uc002nao.1_In_Frame_Del_p.11_12RR>R NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 11_12 Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.16 52 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 25 99 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 125 552 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 82 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 3 33 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 82 83 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 22 40 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 18 CUBN 8029 broad.mit.edu 37 10 16960687 16960693 + Frame_Shift_Del DEL TAACCTC - - MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:16960687_16960693delTAACCTC uc001ioo.2 - 45 6980_6986 c.6928_6934delGAGGTTA c.(6928-6936)GAGGTTATGfs p.E2310fs NM_001081 NP_001072 O60494 CUBN_HUMAN cubilin precursor 2310_2312 CUB 16. cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1) 19 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) CTCAAATACATAACCTCTCCTGAGGAC 0.391 0.35 82 44 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.59 9 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 238 66 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.85 8 45 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.67 14 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 46 335 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 68 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.88 2 15 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.48 169 155 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 68 76 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 45 76 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane "calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle" ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.34 42 22 STK33 65975 broad.mit.edu 37 11 8476297 8476302 + In_Frame_Del DEL GTTTAA - - NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:8476297_8476302delGTTTAA uc001mgi.1 - 6 1694_1699 c.775_780delTTAAAC c.(775-780)TTAAACdel p.LN259del STK33_uc001mgj.1_In_Frame_Del_p.LN259del|STK33_uc001mgk.1_In_Frame_Del_p.LN259del|STK33_uc010rbn.1_In_Frame_Del_p.LN218del|STK33_uc001mgl.3_In_Frame_Del_p.LN72del|STK33_uc009yfp.2_Intron NM_030906 NP_112168 Q9BYT3 STK33_HUMAN serine/threonine kinase 33 259_260 Protein kinase. Golgi apparatus|nucleus|perinuclear region of cytoplasm ATP binding|protein serine/threonine kinase activity ovary(2)|lung(2)|pancreas(1)|central_nervous_system(1)|skin(1) 7 Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239) TTACCTTTATGTTTAAGTTTATTTCA 0.301 0.43 26 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 197 43 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.73 4 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 50 508 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 12 34 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 "B melanoma antigen family, member 2 precursor" 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.32 75 36 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 132 501 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.93 5 65 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.93 4 53 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. "regulation of transcription, DNA-dependent" membrane|nucleus "calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity" skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.36 0.36 16 9 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN "phosphoinositide-3-kinase, regulatory subunit 4" fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.15 123 22 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.27 65 24 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.48 125 116 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 33 53 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 429 70 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). "histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent" NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.42 15 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 5 39 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.5 27 27 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 "B melanoma antigen family, member 2 precursor" 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 110 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 84 439 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.98 2 92 FAM123B 139285 broad.mit.edu 37 X 63412648 63412648 + Frame_Shift_Del DEL A - - NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:63412648delA uc004dvo.2 - 2 792 c.519delT c.(517-519)TTTfs p.F173fs NM_152424 NP_689637 Q5JTC6 F123B_HUMAN family with sequence similarity 123B 173 Wnt receptor signaling pathway cytoplasm|nucleus|plasma membrane p.0?(40)|p.F173fs*36(2) kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1) 112 GGATACTGCTAAAAAAGCCTT 0.562 0.20 48 12 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 36 MPL 4352 broad.mit.edu 37 1 43818248 43818248 + Frame_Shift_Del DEL C - - NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:43818248delC uc001ciw.2 + 12 1758 c.1713delC c.(1711-1713)CTCfs p.L571fs MPL_uc009vwr.2_Frame_Shift_Del_p.L564fs NM_005373 NP_005364 P40238 TPOR_HUMAN myeloproliferative leukemia virus oncogene 571 Cytoplasmic (Potential). cell proliferation|platelet activation integral to plasma membrane cytokine receptor activity haematopoietic_and_lymphoid_tissue(361)|upper_aerodigestive_tract(1)|pancreas(1) 363 all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0505) TTGAAATCCTCCCCAAGTCCT 0.567 0.48 132 120 PKDCC 91461 broad.mit.edu 37 2 42282438 42282438 + Frame_Shift_Del DEL G - - NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:42282438delG uc002rsg.2 + 5 1306 c.1127delG c.(1126-1128)TGGfs p.W376fs NM_138370 NP_612379 Q504Y2 PKDCC_HUMAN protein kinase-like protein SgK493 376 Protein kinase. cell differentiation|embryonic digestive tract development|lung alveolus development|negative regulation of Golgi to plasma membrane protein transport|ossification|palate development|positive regulation of bone mineralization|positive regulation of chondrocyte differentiation|protein transport Golgi apparatus ATP binding|protein kinase activity breast(1) 1 0.000 0.42 267 195 EIF2AK3 9451 broad.mit.edu 37 2 88882965 88882966 + Frame_Shift_Ins INS - T T NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:88882965_88882966insT uc002stc.3 - 10 1947_1948 c.1745_1746insA c.(1744-1746)AACfs p.N582fs NM_004836 NP_004827 Q9NZJ5 E2AK3_HUMAN eukaryotic translation initiation factor 2-alpha 582 Cytoplasmic (Potential). activation of caspase activity|bone mineralization|calcium-mediated signaling|chondrocyte development|endocrine pancreas development|endoplasmic reticulum organization|endoplasmic reticulum unfolded protein response|ER overload response|insulin secretion|insulin-like growth factor receptor signaling pathway|negative regulation of myelination|negative regulation of translational initiation in response to stress|protein autophosphorylation|protein homooligomerization endoplasmic reticulum membrane|integral to membrane ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|identical protein binding ovary(3) 3 TATATCCAGAGTTTTTTATGTC 0.327 0.15 94 17 ROBO2 6092 broad.mit.edu 37 3 77526677 77526678 + Frame_Shift_Ins INS - A A NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:77526677_77526678insA uc003dpy.3 + 3 1144_1145 c.501_502insA c.(499-504)TGGAAAfs p.W167fs ROBO2_uc003dpz.2_Frame_Shift_Ins_p.W167fs|ROBO2_uc011bgj.1_RNA|ROBO2_uc011bgk.1_Frame_Shift_Ins_p.W167fs NM_002942 NP_002933 Q9HCK4 ROBO2_HUMAN roundabout, axon guidance receptor, homolog 2 167_168 Ig-like C2-type 2.|Extracellular (Potential). apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development axolemma|cell surface|integral to membrane axon guidance receptor activity|identical protein binding lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1) 11 Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103) CCATCTACTGGAAAAAAGACAA 0.450 0.47 44 39 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.33 12 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 89 98 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.36 48 27 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.37 138 82 PMS2 5395 broad.mit.edu 37 7 6027157 6027157 + Frame_Shift_Del DEL T - - NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:6027157delT uc003spl.2 - 11 1326 c.1239delA c.(1237-1239)AAAfs p.K413fs PMS2_uc003spj.2_Frame_Shift_Del_p.K307fs|PMS2_uc003spk.2_Frame_Shift_Del_p.K278fs|PMS2_uc011jwl.1_Frame_Shift_Del_p.K278fs|PMS2_uc010ktg.2_Frame_Shift_Del_p.K102fs|PMS2_uc010kte.2_Intron|PMS2_uc010ktf.1_Frame_Shift_Del_p.K413fs NM_000535 NP_000526 P54278 PMS2_HUMAN PMS2 postmeiotic segregation increased 2 isoform 413 mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes MutLalpha complex ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding lung(1)|central_nervous_system(1) 2 Ovarian(82;0.0694) UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15) TGGACACGTCTTTTTTTTCTT 0.458 0.10 257 27 ITGB8 3696 broad.mit.edu 37 7 20371450 20371450 + Frame_Shift_Del DEL T - - NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:20371450delT uc003suu.2 + 1 726 c.21delT c.(19-21)GCTfs p.A7fs ITGB8_uc011jyh.1_Intron|ITGB8_uc003sut.2_Frame_Shift_Del_p.A7fs NM_002214 NP_002205 P26012 ITB8_HUMAN integrin, beta 8 precursor 7 cell-matrix adhesion|integrin-mediated signaling pathway|placenta blood vessel development integrin complex protein binding|receptor activity skin(3) 3 CGGCCCTGGCTTTTTTTACCG 0.562 0.21 41 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 239 40 GUCY1A2 2977 broad.mit.edu 37 11 106810792 106810792 + Frame_Shift_Del DEL A - - NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:106810792delA uc001pjg.1 - 4 990 c.600delT c.(598-600)TTTfs p.F200fs GUCY1A2_uc010rvo.1_Frame_Shift_Del_p.F200fs|GUCY1A2_uc009yxn.1_Frame_Shift_Del_p.F200fs NM_000855 NP_000846 P33402 GCYA2_HUMAN guanylate cyclase 1, soluble, alpha 2 200 intracellular signal transduction|platelet activation cytoplasm GTP binding|guanylate cyclase activity|heme binding large_intestine(3)|lung(2)|pancreas(2)|ovary(1) 8 all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068) BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476) CAAAGCCGTTAAAAAAGTCCT 0.403 0.50 79 79 WNT1 7471 broad.mit.edu 37 12 49374348 49374348 + Frame_Shift_Del DEL G - - NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:49374348delG uc001rsu.2 + 3 698 c.500delG c.(499-501)TGGfs p.W167fs NM_005430 NP_005421 P04628 WNT1_HUMAN wingless-type MMTV integration site family, 167 brain segmentation|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|central nervous system morphogenesis|cerebellum formation|dermatome development|diencephalon development|embryonic axis specification|forebrain anterior/posterior pattern formation|fourth ventricle development|hemopoietic stem cell proliferation|hepatocyte differentiation|inner ear morphogenesis|mesoderm morphogenesis|midbrain development|midbrain-hindbrain boundary maturation during brain development|negative regulation of cell-cell adhesion|negative regulation of cell-substrate adhesion|negative regulation of DNA damage checkpoint|negative regulation of fat cell differentiation|neuron fate determination|positive regulation of fibroblast proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of lamellipodium assembly|positive regulation of Notch signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to wounding|signal transduction in response to DNA damage|Spemann organizer formation|T cell differentiation in thymus|Wnt receptor signaling pathway, calcium modulating pathway early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix cytokine activity|frizzled-2 binding|transcription regulatory region DNA binding kidney(1) 1 BRCA - Breast invasive adenocarcinoma(357;0.244) gACTGGCACTGGGGGGGCTGC 0.552 0.31 11 5 DCLK1 9201 broad.mit.edu 37 13 36382429 36382430 + Frame_Shift_Ins INS - A A NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:36382429_36382430insA uc001uvf.2 - 14 2027_2028 c.1794_1795insT c.(1792-1797)TTTGATfs p.F598fs DCLK1_uc001uve.3_Frame_Shift_Ins_p.F291fs|DCLK1_uc010teh.1_Frame_Shift_Ins_p.F291fs|DCLK1_uc010abk.2_Frame_Shift_Ins_p.F118fs NM_004734 NP_004725 O15075 DCLK1_HUMAN doublecortin-like kinase 1 598_599 Protein kinase. cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus integral to plasma membrane ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity stomach(6)|ovary(2)|skin(1) 9 Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638) AAAATCTGATCAAAAAGCACCT 0.436 0.15 56 10 CATSPERB 79820 broad.mit.edu 37 14 92058236 92058236 + Frame_Shift_Del DEL T - - NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:92058236delT uc001xzs.1 - 23 2960 c.2820delA c.(2818-2820)AAAfs p.K940fs CATSPERB_uc010aub.1_Frame_Shift_Del_p.K462fs NM_024764 NP_079040 Q9H7T0 CTSRB_HUMAN cation channel, sperm-associated, beta 940 cell differentiation|multicellular organismal development|spermatogenesis integral to membrane breast(2)|skin(2)|ovary(1) 5 all_cancers(154;0.0663)|all_epithelial(191;0.236) ATGATCTTACTTTTTCCCTGC 0.348 0.14 140 23 TP53BP1 7158 broad.mit.edu 37 15 43713332 43713333 + Frame_Shift_Del DEL CA - - NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:43713332_43713333delCA uc001zrs.2 - 20 4273_4274 c.4125_4126delTG c.(4123-4128)TGTGAGfs p.C1375fs TP53BP1_uc010udp.1_Frame_Shift_Del_p.C1375fs|TP53BP1_uc001zrq.3_Frame_Shift_Del_p.C1380fs|TP53BP1_uc001zrr.3_Frame_Shift_Del_p.C1380fs|TP53BP1_uc010udq.1_Frame_Shift_Del_p.C1380fs NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 1375_1376 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) CCATCCTCCTCACACACTGGCG 0.559 0.39 11 7 CSPG4 1464 broad.mit.edu 37 15 75970186 75970186 + Frame_Shift_Del DEL G - - NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:75970186delG uc002baw.2 - 9 5085 c.4992delC c.(4990-4992)CCCfs p.P1664fs NM_001897 NP_001888 Q6UVK1 CSPG4_HUMAN chondroitin sulfate proteoglycan 4 precursor 1664 Extracellular (Potential).|Cysteine-containing.|Neurite growth inhibition (By similarity).|CSPG 11. angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane protein kinase binding|signal transducer activity ovary(2)|pancreas(1) 3 0.000 0.19 736 178 FURIN 5045 broad.mit.edu 37 15 91424957 91424957 + Frame_Shift_Del DEL G - - rs35641241 byFrequency NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:91424957delG uc002bpu.1 + 16 2450 c.2234delG c.(2233-2235)CGGfs p.R745fs FES_uc010uqj.1_5'Flank|FES_uc010uqk.1_5'Flank|FES_uc002bpw.2_5'Flank|FES_uc002bpv.2_5'Flank NM_002569 NP_002560 P09958 FURIN_HUMAN furin preproprotein 745 cell proliferation|negative regulation of low-density lipoprotein particle receptor catabolic process|negative regulation of transforming growth factor-beta1 production|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|Notch signaling pathway|peptide biosynthetic process|peptidyl-glutamic acid carboxylation|post-translational protein modification|secretion by cell|signal peptide processing|transforming growth factor beta receptor signaling pathway|viral assembly, maturation, egress, and release cell surface|Golgi lumen|Golgi membrane|integral to membrane|membrane raft|plasma membrane|trans-Golgi network|trans-Golgi network transport vesicle metal ion binding|nerve growth factor binding|peptide binding|protease binding|serine-type endopeptidase activity|serine-type endopeptidase inhibitor activity central_nervous_system(4)|lung(2)|breast(1) 7 Lung NSC(78;0.0771)|all_lung(78;0.137) Lung(145;0.189) TTTAGTTTTCGGGGGGTGAAG 0.622 0.14 203 33 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.17 101 20 BCAR1 9564 broad.mit.edu 37 16 75268944 75268944 + Frame_Shift_Del DEL C - - NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:75268944delC uc002fdv.2 - 5 1976 c.1853delG c.(1852-1854)GGTfs p.G618fs BCAR1_uc002fdt.2_Frame_Shift_Del_p.G71fs|BCAR1_uc002fdu.2_Frame_Shift_Del_p.G408fs|BCAR1_uc010cgu.2_Frame_Shift_Del_p.G607fs|BCAR1_uc010vna.1_Frame_Shift_Del_p.G616fs|BCAR1_uc010vnb.1_Frame_Shift_Del_p.G664fs|BCAR1_uc002fdw.2_Frame_Shift_Del_p.G618fs|BCAR1_uc010vnc.1_Frame_Shift_Del_p.G470fs|BCAR1_uc010vnd.1_Frame_Shift_Del_p.G636fs|BCAR1_uc002fdx.2_Frame_Shift_Del_p.G636fs NM_014567 NP_055382 P56945 BCAR1_HUMAN breast cancer anti-estrogen resistance 1 618 actin filament organization|B cell receptor signaling pathway|blood coagulation|cell adhesion|cell division|cell migration|cell proliferation|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|integrin-mediated signaling pathway|nerve growth factor receptor signaling pathway|platelet-derived growth factor receptor signaling pathway|positive regulation of cell migration|regulation of apoptosis|regulation of cell growth|T cell receptor signaling pathway cytosol|focal adhesion|membrane fraction|ruffle protein kinase binding|protein phosphatase binding|SH3 domain binding|signal transducer activity central_nervous_system(5)|breast(2)|prostate(1) 8 BRCA - Breast invasive adenocarcinoma(221;0.169) 0.000 0.10 747 85 MYH8 4626 broad.mit.edu 37 17 10301935 10301936 + Frame_Shift_Del DEL GC - - rs142232788 byFrequency;by1000genomes NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:10301935_10301936delGC uc002gmm.2 - 30 4098_4099 c.4003_4004delGC c.(4003-4005)GCCfs p.A1335fs uc002gml.1_Intron NM_002472 NP_002463 P13535 MYH8_HUMAN myosin, heavy chain 8, skeletal muscle, 1335 Potential. muscle filament sliding cytosol|muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle skin(6)|ovary(3)|breast(2) 11 GGACTGCAGGGCGTGTGCCAGG 0.530 0.36 34 19 MAST1 22983 broad.mit.edu 37 19 12985060 12985060 + Frame_Shift_Del DEL G - - NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:12985060delG uc002mvm.2 + 26 4217 c.4089delG c.(4087-4089)CCGfs p.P1363fs NM_014975 NP_055790 Q9Y2H9 MAST1_HUMAN microtubule associated serine/threonine kinase 1363 cytoskeleton organization|intracellular protein kinase cascade cytoplasm|cytoskeleton|plasma membrane ATP binding|magnesium ion binding|protein serine/threonine kinase activity ovary(3)|lung(2)|large_intestine(1)|skin(1) 7 0.000 0.10 669 73 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.46 20 17 COL18A1 80781 broad.mit.edu 37 21 46917559 46917559 + Frame_Shift_Del DEL C - - NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46917559delC uc011afs.1 + 31 3933 c.3912delC c.(3910-3912)GGCfs p.G1304fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.G889fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.G1069fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1304 Triple-helical region 7 (COL7). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.12 689 98 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 32 394 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 72 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.86 5 31 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.32 359 169 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 0.92 1 11 CCDC50 152137 broad.mit.edu 37 3 191098658 191098659 + Frame_Shift_Ins INS - A A NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr3:191098658_191098659insA uc003fsw.2 + 8 1241_1242 c.651_652insA c.(649-654)TACAAAfs p.Y217fs CCDC50_uc003fsv.2_Frame_Shift_Ins_p.Y393fs NM_174908 NP_777568 Q8IVM0 CCD50_HUMAN Ymer protein short isoform 217_218 Lys-rich. cytoplasm protein binding 0 all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221) LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06) GBM - Glioblastoma multiforme(46;0.000136) AGAAAGCTTACAAAAAAGCCAA 0.366 0.15 41 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.35 32 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.51 82 84 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 29 74 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.32 240 112 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.40 9 6 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 1 14 VPS13B 157680 broad.mit.edu 37 8 100847893 100847909 + Frame_Shift_Del DEL TGAGAGTTGAACCTCTA - - rs143728471 NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr8:100847893_100847909delTGAGAGTTGAACCTCTA uc003yiv.2 + 54 10055_10071 c.9944_9960delTGAGAGTTGAACCTCTA c.(9943-9960)TTGAGAGTTGAACCTCTAfs p.L3315fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.L3290fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 3315_3320 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) AGCCTACTTTTGAGAGTTGAACCTCTAGATGAAGTAA 0.438 0.17 50 10 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.64 275 480 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 176 77 MLL2 8085 broad.mit.edu 37 12 49426754 49426759 + In_Frame_Del DEL GTTGCT - - NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr12:49426754_49426759delGTTGCT uc001rta.3 - 39 11729_11734 c.11729_11734delAGCAAC c.(11728-11736)CAGCAACTT>CTT p.QQ3910del NM_003482 NP_003473 O14686 MLL2_HUMAN myeloid/lymphoid or mixed-lineage leukemia 2 3910_3911 Potential.|Gln-rich. chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent histone methyltransferase complex histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2) 41 tgctgctgaagttgctgttgctgttg 0.199 0.40 36 24 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.20 40 10 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.80 2 8 ADAMTSL3 57188 broad.mit.edu 37 15 84561502 84561505 + Frame_Shift_Del DEL TGTG - - NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr15:84561502_84561505delTGTG uc002bjz.3 + 13 1553_1556 c.1329_1332delTGTG c.(1327-1332)TTTGTGfs p.F443fs ADAMTSL3_uc010bmt.1_Frame_Shift_Del_p.F443fs|ADAMTSL3_uc010bmu.1_Frame_Shift_Del_p.F443fs NM_207517 NP_997400 P82987 ATL3_HUMAN ADAMTS-like 3 precursor 443_444 TSP type-1 2. proteinaceous extracellular matrix metallopeptidase activity|zinc ion binding ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1) 27 BRCA - Breast invasive adenocarcinoma(143;0.211) GACGGAGCTTTGTGTGTGTAGAGG 0.422 0.64 5 9 THAP11 57215 broad.mit.edu 37 16 67876821 67876823 + In_Frame_Del DEL CAA - - rs34138555;rs28647874 byFrequency NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr16:67876821_67876823delCAA uc002euo.2 + 1 609_611 c.364_366delCAA c.(364-366)CAAdel p.Q132del CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 132 Gln-rich. Missing (in Ref. 2; AAH12182). regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) gcagcagcagcaacagcagcagc 0.305 0.20 79 20 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 21 248 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.44 28 22 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.21 71 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 147 477 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NB1_AUTONOMIC_GANGLIA NA NB1_AUTONOMIC_GANGLIA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 80 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 26 RBM15 64783 broad.mit.edu 37 1 110882115 110882123 + In_Frame_Del DEL CGGGTTACT - - NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:110882115_110882123delCGGGTTACT uc001dzl.1 + 1 171_179 c.88_96delCGGGTTACT c.(88-96)CGGGTTACTdel p.RVT30del RBM15_uc001dzm.1_In_Frame_Del_p.RVT30del|uc001dzj.2_5'Flank NM_022768 NP_073605 Q96T37 RBM15_HUMAN RNA binding motif protein 15 30_32 interspecies interaction between organisms nucleus nucleotide binding|protein binding|RNA binding ovary(3) 3 all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634) BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135) CGCGGGGCGGCGGGTTACTCAGCTCCGCG 0.656 0.62 6 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.40 12 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 55 60 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.23 41 12 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.28 18 7 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 111 12 PCDH15 65217 broad.mit.edu 37 10 55663057 55663058 + Frame_Shift_Ins INS - TAGAA TAGAA NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:55663057_55663058insTAGAA uc001jju.1 - 26 3841_3842 c.3446_3447insTTCTA c.(3445-3447)TACfs p.Y1149fs PCDH15_uc010qhq.1_Frame_Shift_Ins_p.Y1154fs|PCDH15_uc010qhr.1_Frame_Shift_Ins_p.Y1149fs|PCDH15_uc010qhs.1_Frame_Shift_Ins_p.Y1161fs|PCDH15_uc010qht.1_Frame_Shift_Ins_p.Y1156fs|PCDH15_uc010qhu.1_Frame_Shift_Ins_p.Y1149fs|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Frame_Shift_Ins_p.Y1149fs|PCDH15_uc010qhw.1_Frame_Shift_Ins_p.Y1112fs|PCDH15_uc010qhx.1_Frame_Shift_Ins_p.Y1078fs|PCDH15_uc010qhy.1_Frame_Shift_Ins_p.Y1154fs|PCDH15_uc010qhz.1_Frame_Shift_Ins_p.Y1149fs|PCDH15_uc010qia.1_Frame_Shift_Ins_p.Y1127fs|PCDH15_uc010qib.1_Frame_Shift_Ins_p.Y1127fs NM_033056 NP_149045 Q96QU1 PCD15_HUMAN protocadherin 15 isoform CD1-4 precursor 1149 Cadherin 11.|Extracellular (Potential). equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse calcium ion binding pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2) 13 Melanoma(3;0.117)|Lung SC(717;0.238) CACCTCCGATGTAGAATTTTTT 0.361 0.26 73 26 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 298 70 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 11 86 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.31 64 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 50 316 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 2 21 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.46 119 103 PBRM1 55193 broad.mit.edu 37 3 52620499 52620501 + In_Frame_Del DEL TCA - - NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr3:52620499_52620501delTCA uc003des.2 - 20 3339_3341 c.3327_3329delTGA c.(3325-3330)GATGAG>GAG p.D1109del PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_In_Frame_Del_p.D1109del|PBRM1_uc003der.2_In_Frame_Del_p.D1077del|PBRM1_uc003det.2_In_Frame_Del_p.D1124del|PBRM1_uc003deu.2_In_Frame_Del_p.D1124del|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_In_Frame_Del_p.D1109del|PBRM1_uc010hmk.1_In_Frame_Del_p.D1084del|PBRM1_uc003dey.2_In_Frame_Del_p.D1084del|PBRM1_uc003dez.1_In_Frame_Del_p.D1108del|PBRM1_uc003dfb.1_In_Frame_Del_p.D1021del|PBRM1_uc003dfa.1_In_Frame_Del_p.D455del NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 1109 chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.12 786 109 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.36 9 5 ALPK1 80216 broad.mit.edu 37 4 113360940 113360941 + Frame_Shift_Del DEL AG - - NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr4:113360940_113360941delAG uc003iap.3 + 14 3729_3730 c.3450_3451delAG c.(3448-3453)ACAGAAfs p.T1150fs ALPK1_uc003ian.3_Frame_Shift_Del_p.T1150fs|ALPK1_uc011cfx.1_Frame_Shift_Del_p.T1072fs|ALPK1_uc003iao.3_RNA|ALPK1_uc010imo.2_Frame_Shift_Del_p.T978fs NM_025144 NP_079420 Q96QP1 ALPK1_HUMAN alpha-kinase 1 1150_1151 Alpha-type protein kinase. ATP binding|protein serine/threonine kinase activity ovary(5) 5 Ovarian(17;0.0446)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.00325) TGGTGAAAACAGAATACAAAGC 0.366 0.79 4 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.24 68 22 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.50 19 19 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 1 12 NCOA4 8031 broad.mit.edu 37 10 51584882 51584883 + Frame_Shift_Ins INS - T T NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr10:51584882_51584883insT uc001jis.3 + 8 1184_1185 c.981_982insT c.(979-984)AAGTTTfs p.K327fs PARG_uc001jih.2_Intron|uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|NCOA4_uc009xon.2_Frame_Shift_Ins_p.K343fs|NCOA4_uc010qhd.1_Frame_Shift_Ins_p.K343fs|NCOA4_uc010qhe.1_Frame_Shift_Ins_p.K227fs|NCOA4_uc010qhf.1_Frame_Shift_Ins_p.K161fs|NCOA4_uc001jit.2_Frame_Shift_Ins_p.K327fs|NCOA4_uc009xoo.2_Frame_Shift_Ins_p.K327fs NM_001145263 NP_001138735 Q13772 NCOA4_HUMAN nuclear receptor coactivator 4 isoform 3 327_328 androgen receptor signaling pathway|male gonad development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus androgen receptor binding|transcription coactivator activity central_nervous_system(1)|kidney(1) 2 CCAGTGAGAAGTTTAAGCTCTT 0.470 0.41 66 46 MYST4 23522 broad.mit.edu 37 10 76788645 76788647 + In_Frame_Del DEL GAG - - NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr10:76788645_76788647delGAG uc001jwn.1 + 18 4556_4558 c.4063_4065delGAG c.(4063-4065)GAGdel p.E1368del MYST4_uc001jwo.1_In_Frame_Del_p.E1076del|MYST4_uc001jwp.1_In_Frame_Del_p.E1185del NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1368 Poly-Glu. histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) ggaagaggaagaggaggaggagg 0.241 0.46 25 21 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 136 36 RIPK3 11035 broad.mit.edu 37 14 24807186 24807186 + Frame_Shift_Del DEL A - - NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr14:24807186delA uc001wpb.2 - 6 935 c.725delT c.(724-726)TTGfs p.L242fs ADCY4_uc001wox.2_5'Flank|ADCY4_uc001woy.2_5'Flank|RIPK3_uc001wpa.2_Frame_Shift_Del_p.L42fs|RIPK3_uc010alq.2_RNA|RIPK3_uc010toi.1_Frame_Shift_Del_p.L21fs NM_006871 NP_006862 Q9Y572 RIPK3_HUMAN receptor-interacting serine-threonine kinase 3 242 Protein kinase. apoptosis|induction of apoptosis by extracellular signals cytoplasm ATP binding|protein binding|transcription coactivator activity central_nervous_system(2)|ovary(1)|lung(1) 4 GBM - Glioblastoma multiforme(265;0.0181) CAGCTCAGCCAATGAAGGCCG 0.592 0.30 121 53 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.40 9 6 CDH1 999 broad.mit.edu 37 16 68849545 68849562 + In_Frame_Del DEL CCCCCATCTTTGTGCCTC - - NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr16:68849545_68849562delCCCCCATCTTTGTGCCTC uc002ewg.1 + 10 1572_1589 c.1448_1465delCCCCCATCTTTGTGCCTC c.(1447-1467)GCCCCCATCTTTGTGCCTCCT>GCT p.PIFVPP484del CDH1_uc010vlj.1_RNA|CDH1_uc010cfg.1_In_Frame_Del_p.PIFVPP423del NM_004360 NP_004351 P12830 CADH1_HUMAN cadherin 1, type 1 preproprotein 484_489 Extracellular (Potential).|Cadherin 4. adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm cell adhesion molecule binding|gamma-catenin binding breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1) 243 all_neural(199;0.0189)|Ovarian(137;0.0563) Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261) GTGAATGAAGCCCCCATCTTTGTGCCTCCTGAAAAGAG 0.509 0.63 34 58 NCOA6 23054 broad.mit.edu 37 20 33345717 33345718 + In_Frame_Ins INS - TGC TGC NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr20:33345717_33345718insTGC uc002xav.2 - 8 3404_3405 c.833_834insGCA c.(832-834)CAA>CAGCAA p.278_278Q>QQ NCOA6_uc002xaw.2_In_Frame_Ins_p.278_278Q>QQ|NCOA6_uc010gew.1_In_Frame_Ins_p.235_235Q>QQ NM_014071 NP_054790 Q14686 NCOA6_HUMAN nuclear receptor coactivator 6 278 TBP/GTF2A-binding region.|NCOA1-binding region.|Gln-rich.|CREBBP-binding region. brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter transcription factor complex chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding ovary(3)|breast(3)|central_nervous_system(1) 7 gctgttgctgttgttgctgctg 0.317 0.25 50 17 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.19 134 32 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 98 406 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCCSTCK140_STOMACH NA NCCSTCK140_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 78 RPS6KA3 6197 broad.mit.edu 37 X 20173536 20173536 + Frame_Shift_Del DEL T - - NCIH1048_LUNG NA NCIH1048_LUNG NA g.chrX:20173536delT uc004czu.2 - 22 2203 c.2203delA c.(2203-2205)ATCfs p.I735fs RPS6KA3_uc011mjk.1_Frame_Shift_Del_p.I705fs|RPS6KA3_uc004czv.2_Frame_Shift_Del_p.I722fs|RPS6KA3_uc011mjl.1_Frame_Shift_Del_p.I706fs|RPS6KA3_uc011mjm.1_Frame_Shift_Del_p.I707fs NM_004586 NP_004577 P51812 KS6A3_HUMAN ribosomal protein S6 kinase, 90kDa, polypeptide 735 axon guidance|central nervous system development|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|skeletal system development|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|caspase inhibitor activity|magnesium ion binding|protein serine/threonine kinase activity central_nervous_system(4)|stomach(1)|ovary(1)|lung(1)|breast(1) 8 GTTGAGGTGATTTTTTTAATA 0.473 0.50 23 23 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 NCIH1048_LUNG NA NCIH1048_LUNG NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.22 62 17 TAF1 6872 broad.mit.edu 37 X 70602999 70603000 + Frame_Shift_Ins INS - A A NCIH1048_LUNG NA NCIH1048_LUNG NA g.chrX:70602999_70603000insA uc004dzu.3 + 12 1980_1981 c.1929_1930insA c.(1927-1932)ATCAAAfs p.I643fs BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Frame_Shift_Ins_p.I664fs NM_138923 NP_620278 P21675 TAF1_HUMAN TBP-associated factor 1 isoform 2 643_644 G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction MLL1 complex|transcription factor TFIID complex ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1) 17 Renal(35;0.156) all_lung(315;0.000321) TAAAGCACATCAAAAAAAAGGC 0.312 0.11 65 8 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1048_LUNG NA NCIH1048_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 9 90 ARID1A 8289 broad.mit.edu 37 1 27023145 27023146 + Frame_Shift_Del DEL GC - - NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr1:27023145_27023146delGC uc001bmv.1 + 1 624_625 c.251_252delGC c.(250-252)GGCfs p.G84fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.G84fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.G84fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 84 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.24 600 192 NRAS 4893 broad.mit.edu 37 1 115258722 115258723 + Frame_Shift_Del DEL TG - - NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr1:115258722_115258723delTG uc009wgu.2 - 2 313_314 c.59_60delCA c.(58-60)ACAfs p.T20fs NM_002524 NP_002515 P01111 RASN_HUMAN neuroblastoma RAS viral (v-ras) oncogene homolog 20 activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction Golgi membrane|plasma membrane GTP binding|GTPase activity p.T20T(1) haematopoietic_and_lymphoid_tissue(1008)|skin(956)|thyroid(334)|large_intestine(62)|NS(60)|soft_tissue(32)|lung(31)|upper_aerodigestive_tract(25)|urinary_tract(12)|liver(10)|adrenal_gland(9)|autonomic_ganglia(8)|testis(8)|central_nervous_system(8)|prostate(8)|breast(7)|biliary_tract(6)|ovary(6)|stomach(5)|pancreas(5)|endometrium(2)|kidney(2)|cervix(2)|eye(1) 2607 all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211) all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05) Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133) TTAGCTGGATTGTCAGTGCGCT 0.500 0.38 52 32 PDE4DIP 9659 broad.mit.edu 37 1 144912160 144912160 + Frame_Shift_Del DEL G - - NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr1:144912160delG uc001elw.3 - 15 2406 c.2115delC c.(2113-2115)CCCfs p.P705fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.P771fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.P705fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.P705fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.P868fs|PDE4DIP_uc001eme.1_Frame_Shift_Del_p.P234fs|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.P490fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 705 cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) GACAGCCAGTGGGGGTAACTT 0.413 0.12 275 37 FMN2 56776 broad.mit.edu 37 1 240256066 240256067 + In_Frame_Ins INS - CAG CAG NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr1:240256066_240256067insCAG uc010pyd.1 + 1 882_883 c.657_658insCAG c.(655-660)insCAG p.225_226insQ FMN2_uc010pye.1_In_Frame_Ins_p.225_226insQ NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 225_226 Potential.|Gln-rich. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) agctccagcaacagcagcagca 0.465 0.11 108 14 TTN 7273 broad.mit.edu 37 2 179445078 179445078 + Frame_Shift_Del DEL T - - NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr2:179445078delT uc010zfg.1 - 266 59548 c.59324delA c.(59323-59325)AAGfs p.K19775fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.K13470fs|TTN_uc010zfi.1_Frame_Shift_Del_p.K13403fs|TTN_uc010zfj.1_Frame_Shift_Del_p.K13278fs|uc002umv.1_3'UTR NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 20702 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GGTATATTCCTTTTTACCACA 0.299 0.51 76 78 ROBO1 6091 broad.mit.edu 37 3 78710235 78710235 + Frame_Shift_Del DEL A - - NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr3:78710235delA uc003dqe.2 - 16 2473 c.2265delT c.(2263-2265)TTTfs p.F755fs ROBO1_uc003dqb.2_Frame_Shift_Del_p.F716fs|ROBO1_uc003dqc.2_Frame_Shift_Del_p.F719fs|ROBO1_uc003dqd.2_Frame_Shift_Del_p.F719fs|ROBO1_uc010hoh.2_5'UTR|ROBO1_uc011bgl.1_Frame_Shift_Del_p.F327fs|ROBO1_uc003dqf.1_Frame_Shift_Del_p.F434fs NM_002941 NP_002932 Q9Y6N7 ROBO1_HUMAN roundabout 1 isoform a 755 Extracellular (Potential).|Fibronectin type-III 2. activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway cell surface|cytoplasm|integral to plasma membrane axon guidance receptor activity|identical protein binding|LRR domain binding large_intestine(2) 2 Lung SC(41;0.0257)|Lung NSC(201;0.0439) LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274) GAAATTCATTAAAAAAAGGGC 0.398 0.42 52 37 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 71 60 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 18 29 HIPK2 28996 broad.mit.edu 37 7 139315954 139315954 + Frame_Shift_Del DEL A - - NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr7:139315954delA uc003vvf.3 - 4 1478 c.1304delT c.(1303-1305)TTCfs p.F435fs HIPK2_uc003vvd.3_Frame_Shift_Del_p.F435fs NM_022740 NP_073577 Q9H2X6 HIPK2_HUMAN homeodomain interacting protein kinase 2 isoform 435 Protein kinase.|Interaction with DAXX. apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction centrosome|nuclear membrane|PML body ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding ovary(3)|central_nervous_system(3)|skin(1) 7 Melanoma(164;0.205) GTCACGGTTGAAAAACCTAGT 0.483 0.35 11 6 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 25 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.33 421 207 PSIP1 11168 broad.mit.edu 37 9 15486068 15486069 + Splice_Site INS - A A NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr9:15486068_15486069insA uc003zlv.3 - 6 724 c.394_splice c.e6-1 p.D132_splice PSIP1_uc003zlw.3_Splice_Site_p.D132_splice|PSIP1_uc003zlz.3_Splice_Site_p.D132_splice|PSIP1_uc003zma.3_Splice_Site_p.D132_splice|PSIP1_uc003zly.2_Splice_Site_p.D132_splice NM_033222 NP_150091 O75475 PSIP1_HUMAN PC4 and SFRS1 interacting protein 1 isoform 2 initiation of viral infection|interspecies interaction between organisms|nuclear mRNA 5'-splice site recognition|provirus integration|regulation of transcription, DNA-dependent|response to heat|response to oxidative stress|transcription, DNA-dependent cytosol|nuclear heterochromatin|nuclear periphery|nucleoplasm|nucleoplasm|transcriptionally active chromatin activating transcription factor binding|chromatin binding|DNA secondary structure binding|RNA polymerase II transcription coactivator activity breast(1) 1 GBM - Glioblastoma multiforme(50;2.38e-06) AGTCACATCCTAAAAAAGAAAA 0.356 0.37 47 28 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 255 37 ZNF384 171017 broad.mit.edu 37 12 6777070 6777075 + In_Frame_Del DEL TGCTGC - - rs151322806;rs111332695;rs78573212;rs1052680 NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr12:6777070_6777075delTGCTGC uc010sfh.1 - 11 1747_1752 c.1539_1544delGCAGCA c.(1537-1545)CAGCAGCAA>CAA p.513_515QQQ>Q ZNF384_uc001qpz.2_In_Frame_Del_p.452_454QQQ>Q|ZNF384_uc001qqa.2_In_Frame_Del_p.452_454QQQ>Q|ZNF384_uc001qqb.2_In_Frame_Del_p.436_438QQQ>Q|ZNF384_uc001qqc.2_In_Frame_Del_p.452_454QQQ>Q|ZNF384_uc001qqd.2_In_Frame_Del_p.397_399QQQ>Q|ZNF384_uc001qqe.2_In_Frame_Del_p.436_438QQQ>Q NM_001135734 NP_001129206 Q8TF68 ZN384_HUMAN nuclear matrix transcription factor 4 isoform d 513_515 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding EWSR1/ZNF384(4) haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1) 8 TGGTGgctgttgctgctgctgctgct 0.335 0.20 93 23 PIP4K2C 79837 broad.mit.edu 37 12 57989687 57989688 + Frame_Shift_Ins INS - C C NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr12:57989687_57989688insC uc001sou.2 + 4 517_518 c.386_387insC c.(385-387)AACfs p.N129fs PIP4K2C_uc001sot.2_Frame_Shift_Ins_p.N129fs|PIP4K2C_uc010srs.1_Frame_Shift_Ins_p.N111fs|PIP4K2C_uc010srt.1_Intron NM_001146258 NP_001139730 Q8TBX8 PI42C_HUMAN phosphatidylinositol-5-phosphate 4-kinase, type 129 PIPK. cytoplasm|membrane 1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|identical protein binding central_nervous_system(2)|lung(1) 3 Melanoma(17;0.122) CTTACCCGAAACCCCCCCAGCG 0.495 0.39 57 37 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.12 87 12 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.38 10 6 Unknown 0 broad.mit.edu 37 15 20663144 20663144 + Frame_Shift_Del DEL G - - NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr15:20663144delG uc001ytg.2 - 9 1177 c.468delC c.(466-468)CCCfs p.P156fs uc010tyx.1_RNA|uc001yth.3_Frame_Shift_Del_p.P156fs|uc010tyy.1_Frame_Shift_Del_p.P156fs|uc010tyz.1_Frame_Shift_Del_p.P4fs RecName: Full=Putative HERC2-like protein 3; CGGGATGCTCGGGGGGAAACA 0.453 0.32 21 10 CREBBP 1387 broad.mit.edu 37 16 3781324 3781326 + In_Frame_Del DEL AGG - - NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr16:3781324_3781326delAGG uc002cvv.2 - 30 5243_5245 c.5039_5041delCCT c.(5038-5043)TCCTTG>TTG p.S1680del CREBBP_uc002cvw.2_In_Frame_Del_p.S1642del NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1680 Interaction with TRERF1. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) GAGCGGCGCAAGGAGGAGAACTC 0.645 0.77 3 10 TP53 7157 broad.mit.edu 37 17 7579547 7579547 + Frame_Shift_Del DEL G - - NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr17:7579547delG uc002gim.2 - 4 334 c.140delC c.(139-141)CCGfs p.P47fs TP53_uc002gig.1_Frame_Shift_Del_p.P47fs|TP53_uc002gih.2_Frame_Shift_Del_p.P47fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.P47fs|TP53_uc010cni.1_Frame_Shift_Del_p.P47fs|TP53_uc002gij.2_Frame_Shift_Del_p.P47fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.P8fs|TP53_uc010cnk.1_Frame_Shift_Del_p.P62fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 47 Interaction with HRMT1L2. P -> L (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.P47fs*4(2)|p.P47L(2)|p.P47fs*76(2)|p.D48fs*55(1)|p.P47P(1)|p.P13fs*18(1)|p.S46_D49delSPDD(1)|p.S33fs*23(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.50 1222 1243 TOP2A 7153 broad.mit.edu 37 17 38546327 38546328 + Frame_Shift_Del DEL GA - - NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr17:38546327_38546328delGA uc002huq.2 - 34 4482_4483 c.4356_4357delTC c.(4354-4359)TCTCAAfs p.S1452fs NM_001067 NP_001058 P11388 TOP2A_HUMAN DNA topoisomerase II, alpha isozyme 1452_1453 apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1) 7 Breast(137;0.00328) STAD - Stomach adenocarcinoma(5;0.00183) Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385) TCAGGCTTTTGAGAGACACCAG 0.446 0.39 101 64 ALPK2 115701 broad.mit.edu 37 18 56246941 56246941 + Frame_Shift_Del DEL A - - NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr18:56246941delA uc002lhj.3 - 4 1281 c.1067delT c.(1066-1068)TTAfs p.L356fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 356 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 GCTTTCTAATAAAAAAACATG 0.478 0.49 64 62 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 11 27 BCL3 602 broad.mit.edu 37 19 45262726 45262726 + Frame_Shift_Del DEL C - - NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr19:45262726delC uc010xxe.1 + 9 1289 c.1219delC c.(1219-1221)CCCfs p.P407fs NM_005178 NP_005169 P20749 BCL3_HUMAN B-cell CLL/lymphoma 3 407 Pro/Ser-rich. DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|I-kappaB kinase/NF-kappaB cascade|maintenance of protein location in nucleus|negative regulation of apoptosis|negative regulation of interleukin-8 biosynthetic process|negative regulation of transcription, DNA-dependent|positive regulation of translation|protein import into nucleus, translocation|regulation of DNA binding|regulation of NF-kappaB import into nucleus|response to UV-C|response to virus Bcl3-Bcl10 complex|Bcl3/NF-kappaB2 complex|nucleus|perinuclear region of cytoplasm protein binding, bridging|transcription factor binding ovary(1)|lung(1) 2 Lung NSC(12;0.000698)|all_lung(12;0.002) Ovarian(192;0.0728) CTCCCAGTCTCCCCCCAGGGA 0.498 0.39 163 106 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.24 74 24 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 97 331 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1048_LUNG NA NCIH1048_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 7 88 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1092_LUNG NA NCIH1092_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 8 70 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 57 79 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.77 6 20 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.35 13 7 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.44 10 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 285 31 LRP1 4035 broad.mit.edu 37 12 57581135 57581135 + Frame_Shift_Del DEL C - - NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr12:57581135delC uc001snd.2 + 42 7393 c.6927delC c.(6925-6927)CGCfs p.R2309fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 2309 LDL-receptor class B 22.|Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CCATCACGCGCCACACAGTGG 0.607 0.52 127 137 ABCC4 10257 broad.mit.edu 37 13 95696565 95696565 + Frame_Shift_Del DEL T - - NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr13:95696565delT uc001vmd.3 - 28 3703 c.3584delA c.(3583-3585)AATfs p.N1195fs ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_Frame_Shift_Del_p.N1148fs NM_005845 NP_005836 O15439 MRP4_HUMAN ATP-binding cassette, sub-family C, member 4 1195 ABC transporter 2. platelet activation|platelet degranulation integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane 15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity central_nervous_system(3)|skin(1) 4 all_neural(89;0.0878)|Medulloblastoma(90;0.163) Cefazolin(DB01327) CAATATCTGATTTTTCCTGAG 0.408 0.13 187 27 HIF1A 3091 broad.mit.edu 37 14 62207796 62207796 + Frame_Shift_Del DEL T - - NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr14:62207796delT uc001xfq.2 + 12 2387 c.1983delT c.(1981-1983)GATfs p.D661fs HIF1A_uc001xfr.2_Frame_Shift_Del_p.D661fs|HIF1A_uc001xfs.2_Frame_Shift_Del_p.D662fs NM_001530 NP_001521 Q16665 HIF1A_HUMAN hypoxia-inducible factor 1, alpha subunit 661 ID. cellular response to hypoxia|collagen metabolic process|connective tissue replacement involved in inflammatory response wound healing|elastin metabolic process|epithelial to mesenchymal transition|oxygen homeostasis|positive regulation of chemokine production|positive regulation of epithelial cell migration|positive regulation of hormone biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|regulation of transforming growth factor-beta2 production cytoplasm|nucleolus|transcription factor complex histone acetyltransferase binding|Hsp90 protein binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding kidney(3)|lung(1) 4 OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189) CATATAGAGATACTCAAAGTC 0.408 0.56 59 75 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 55 494 TSSK6 83983 broad.mit.edu 37 19 19625495 19625495 + Frame_Shift_Del DEL G - - NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr19:19625495delG uc002nmr.2 - 1 975 c.742delC c.(742-744)CTGfs p.L248fs TSSK6_uc002nmq.2_RNA|NDUFA13_uc002nms.2_5'Flank|NDUFA13_uc010xqx.1_5'Flank|NDUFA13_uc010xqy.1_5'Flank NM_032037 NP_114426 Q9BXA6 TSSK6_HUMAN testis-specific serine kinase 6 248 Protein kinase. multicellular organismal development|sperm chromatin condensation ATP binding|magnesium ion binding|protein serine/threonine kinase activity stomach(1) 1 0.000 0.14 901 152 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.79 3 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 162 747 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1092_LUNG NA NCIH1092_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 6 74 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1105_LUNG NA NCIH1105_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.86 4 24 CTNNA2 1496 broad.mit.edu 37 2 79971632 79971632 + Frame_Shift_Del DEL G - - NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr2:79971632delG uc010ysh.1 + 2 227 c.222delG c.(220-222)AAGfs p.K74fs CTNNA2_uc010yse.1_Frame_Shift_Del_p.K74fs|CTNNA2_uc010ysf.1_Frame_Shift_Del_p.K74fs|CTNNA2_uc010ysg.1_Frame_Shift_Del_p.K74fs NM_004389 NP_004380 P26232 CTNA2_HUMAN catenin, alpha 2 isoform 1 74 axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity actin cytoskeleton|axon|cytosol cadherin binding|structural constituent of cytoskeleton pancreas(4)|lung(3)|breast(1)|skin(1) 9 TCCTGGAAAAGGGTGAACAGA 0.458 0.31 94 42 LRP1B 53353 broad.mit.edu 37 2 141607758 141607758 + Frame_Shift_Del DEL C - - NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr2:141607758delC uc002tvj.1 - 29 5824 c.4852delG c.(4852-4854)GAAfs p.E1618fs LRP1B_uc010fnl.1_Frame_Shift_Del_p.E800fs NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 1618 Extracellular (Potential).|LDL-receptor class B 14. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) TATAAACGTTCCTCAGATGCA 0.368 0.59 97 142 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.14 240 40 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.54 11 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 48 83 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 22 62 BAI3 577 broad.mit.edu 37 6 69666019 69666019 + Frame_Shift_Del DEL A - - NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr6:69666019delA uc003pev.3 + 7 1747 c.1299delA c.(1297-1299)GGAfs p.G433fs BAI3_uc010kak.2_Frame_Shift_Del_p.G433fs NM_001704 NP_001695 O60242 BAI3_HUMAN brain-specific angiogenesis inhibitor 3 433 TSP type-1 3.|Extracellular (Potential). negative regulation of angiogenesis|neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1) 50 all_lung(197;0.212) CTGCCCATGGAGGCTCCGAAT 0.557 0.48 119 112 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 17 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 111 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 255 125 RB1 5925 broad.mit.edu 37 13 48878088 48878089 + Frame_Shift_Ins INS - C C NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr13:48878088_48878089insC uc001vcb.2 + 1 206_207 c.40_41insC c.(40-42)GCCfs p.A14fs RB1_uc010acs.1_RNA|uc001vca.2_5'Flank NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 14 Poly-Ala. androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.0?(13)|p.A14A(1)|p.?(1) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) 0.000 0.96 15 328 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.59 7 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 9 134 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.11 555 69 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.48 37 34 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 61 304 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1105_LUNG NA NCIH1105_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 74 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 5 59 ZAK 51776 broad.mit.edu 37 2 174131008 174131008 + Frame_Shift_Del DEL A - - NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr2:174131008delA uc002uhz.2 + 20 2133 c.1933delA c.(1933-1935)AAAfs p.K645fs uc002uib.2_Intron NM_016653 NP_057737 Q9NYL2 MLTK_HUMAN MLK-related kinase isoform 1 645 activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation cytoplasm|nucleus ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding lung(3)|stomach(1)|ovary(1)|skin(1) 6 OV - Ovarian serous cystadenocarcinoma(117;0.176) TGGACTGACCAAAAACTTCTC 0.507 0.40 96 63 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.62 10 16 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.49 41 39 HTT 3064 broad.mit.edu 37 4 3076604 3076606 + In_Frame_Del DEL CAG - - rs10618869 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr4:3076604_3076606delCAG uc011bvq.1 + 2 203_205 c.58_60delCAG c.(58-60)CAGdel p.Q40del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagc 0.335 0.25 57 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.72 96 241 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 35 101 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.18 212 47 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 33 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.13 440 67 SMARCA2 6595 broad.mit.edu 37 9 2039779 2039780 + In_Frame_Ins INS - CAG CAG rs62639301 byFrequency NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr9:2039779_2039780insCAG uc003zhc.2 + 4 768_769 c.669_670insCAG c.(667-672)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) agcagcaacagcagcagcagca 0.272 0.14 95 16 TLR4 7099 broad.mit.edu 37 9 120476775 120476775 + Frame_Shift_Del DEL G - - NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr9:120476775delG uc004bjz.2 + 3 2660 c.2369delG c.(2368-2370)AGCfs p.S790fs TLR4_uc004bka.2_Frame_Shift_Del_p.S750fs|TLR4_uc004bkb.2_Frame_Shift_Del_p.S590fs NM_138554 NP_612564 O00206 TLR4_HUMAN toll-like receptor 4 precursor 790 Cytoplasmic (Potential).|TIR. activation of MAPK activity|cellular response to mechanical stimulus|detection of fungus|detection of lipopolysaccharide|I-kappaB phosphorylation|innate immune response|intestinal epithelial structure maintenance|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of interleukin-23 production|negative regulation of interleukin-6 production|negative regulation of osteoclast differentiation|negative regulation of tumor necrosis factor production|positive regulation of chemokine production|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interferon-gamma production|positive regulation of interleukin-1 production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 biosynthetic process|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of platelet activation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor biosynthetic process|positive regulation of tumor necrosis factor production|T-helper 1 type immune response|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway external side of plasma membrane|integral to plasma membrane|lipopolysaccharide receptor complex|perinuclear region of cytoplasm lipopolysaccharide receptor activity|transmembrane receptor activity lung(10)|ovary(4)|breast(1)|skin(1) 16 CGCCTTCTCAGCAGGAACACT 0.547 0.95 2 40 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.88 2 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.49 471 455 CDKN1B 1027 broad.mit.edu 37 12 12870905 12870906 + Frame_Shift_Ins INS - T T NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr12:12870905_12870906insT uc001rat.2 + 1 604_605 c.132_133insT c.(130-135)GACTTGfs p.D44fs NM_004064 NP_004055 P46527 CDN1B_HUMAN cyclin-dependent kinase inhibitor 1B 44_45 autophagic cell death|cell cycle arrest|cellular response to lithium ion|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of transcription, DNA-dependent|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process|S phase of mitotic cell cycle cytosol|endosome|nucleoplasm cyclin-dependent protein kinase inhibitor activity|protein phosphatase binding|transforming growth factor beta receptor, cytoplasmic mediator activity ovary(1)|lung(1) 2 Prostate(47;0.0322)|all_epithelial(100;0.159) BRCA - Breast invasive adenocarcinoma(232;0.0336) TAACCCGGGACTTGGAGAAGCA 0.594 0.85 28 164 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.75 3 9 CDX2 1045 broad.mit.edu 37 13 28537278 28537278 + Frame_Shift_Del DEL C - - rs142861632 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr13:28537278delC uc001urv.2 - 3 1090 c.916delG c.(916-918)GTGfs p.V306fs NM_001265 NP_001256 Q99626 CDX2_HUMAN caudal type homeobox 2 306 organ morphogenesis|transcription from RNA polymerase II promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity lung(1) 1 all_cancers(110;0.191)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155) Lung SC(185;0.0156) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199) GGGTTTAGCACCCCCCCAGTT 0.627 0.30 43 18 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.44 31 24 SMAD4 4089 broad.mit.edu 37 18 48573523 48573524 + Frame_Shift_Ins INS - A A NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr18:48573523_48573524insA uc010xdp.1 + 2 645_646 c.107_108insA c.(106-108)GCAfs p.A36fs SMAD4_uc010xdo.1_RNA NM_005359 NP_005350 Q13485 SMAD4_HUMAN mothers against decapentaplegic homolog 4 36 MH1. BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway activin responsive factor complex|centrosome|cytosol I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity p.0?(35)|p.?(5) pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1) 369 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155) GAAACATTTGCAAAAAGAGCAA 0.356 0.39 189 121 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.84 26 139 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 86 318 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1155_LUNG NA NCIH1155_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 6 67 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1184_LUNG NA NCIH1184_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 15 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1184_LUNG NA NCIH1184_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 9 4 PARP9 83666 broad.mit.edu 37 3 122274139 122274139 + Frame_Shift_Del DEL C - - NCIH1184_LUNG NA NCIH1184_LUNG NA g.chr3:122274139delC uc010hri.2 - 4 1129 c.984delG c.(982-984)TGGfs p.W328fs PARP9_uc003eff.3_Frame_Shift_Del_p.W293fs|PARP9_uc011bjs.1_Frame_Shift_Del_p.W293fs|PARP9_uc003efg.2_Intron|PARP9_uc003efi.2_Frame_Shift_Del_p.W293fs|PARP9_uc003efh.2_Frame_Shift_Del_p.W328fs|PARP9_uc003efj.2_Frame_Shift_Del_p.W293fs NM_001146102 NP_001139574 Q8IXQ6 PARP9_HUMAN poly (ADP-ribose) polymerase family, member 9 328 Macro 2. cell migration cytosol|nucleus NAD+ ADP-ribosyltransferase activity|protein binding ovary(1)|pancreas(1)|prostate(1)|skin(1) 4 GBM - Glioblastoma multiforme(114;0.0519) TTACCGTCTGCCATTCAATGT 0.443 0.35 30 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1184_LUNG NA NCIH1184_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.51 45 47 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1184_LUNG NA NCIH1184_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 17 38 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH1184_LUNG NA NCIH1184_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.90 2 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1184_LUNG NA NCIH1184_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 112 48 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes NCIH1184_LUNG NA NCIH1184_LUNG NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.46 21 18 AATK 9625 broad.mit.edu 37 17 79096509 79096511 + In_Frame_Del DEL CTC - - NCIH1184_LUNG NA NCIH1184_LUNG NA g.chr17:79096509_79096511delCTC uc010dia.2 - 11 1305_1307 c.1225_1227delGAG c.(1225-1227)GAGdel p.E409del AATK_uc010dhz.2_5'Flank NM_001080395 NP_001073864 Q6ZMQ8 LMTK1_HUMAN apoptosis-associated tyrosine kinase 409 integral to membrane|mitochondrion|perinuclear region of cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1) 9 all_neural(118;0.101) BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524) GCCGTTCAAACTCCTCCTCTGCT 0.517 0.67 11 22 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH1184_LUNG NA NCIH1184_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.24 48 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1184_LUNG NA NCIH1184_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 98 316 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1184_LUNG NA NCIH1184_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 1 27 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1299_LUNG NA NCIH1299_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 29 COL3A1 1281 broad.mit.edu 37 2 189854864 189854864 + Frame_Shift_Del DEL C - - NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr2:189854864delC uc002uqj.1 + 9 850 c.733delC c.(733-735)CCTfs p.P245fs COL3A1_uc010frw.1_5'Flank NM_000090 NP_000081 P02461 CO3A1_HUMAN collagen type III alpha 1 preproprotein 245 Triple-helical region. axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway collagen type III|extracellular space extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding central_nervous_system(7)|ovary(4)|large_intestine(2) 13 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141) Collagenase(DB00048)|Palifermin(DB00039) GCGAGGATTGCCTGGACCTCC 0.378 0.49 37 36 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.35 33 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.67 47 94 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.53 20 23 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 53 CD44 960 broad.mit.edu 37 11 35236423 35236424 + Frame_Shift_Ins INS - T T rs140969647 byFrequency NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr11:35236423_35236424insT uc001mvu.2 + 15 2269_2270 c.1835_1836insT c.(1834-1836)AGTfs p.S612fs CD44_uc001mvv.2_Frame_Shift_Ins_p.S569fs|CD44_uc001mvw.2_Frame_Shift_Ins_p.S363fs|CD44_uc001mvx.2_Frame_Shift_Ins_p.S231fs|CD44_uc001mvy.2_Intron|CD44_uc001mwc.3_Frame_Shift_Ins_p.S299fs|CD44_uc010rer.1_Intron|CD44_uc009ykh.2_RNA NM_000610 NP_000601 P16070 CD44_HUMAN CD44 antigen isoform 1 precursor 612 Extracellular (Potential).|Stem. cell-cell adhesion|cell-matrix adhesion|interferon-gamma-mediated signaling pathway|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation cell surface|Golgi apparatus|integral to plasma membrane collagen binding|hyaluronic acid binding|receptor activity pancreas(1) 1 all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112) all_hematologic(20;0.107) STAD - Stomach adenocarcinoma(6;0.00731) Hyaluronidase(DB00070) TTCCACCCCAGTGGGGGGTCCC 0.426 0.42 42 31 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 522 232 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.14 56 9 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 4 56 CLTC 1213 broad.mit.edu 37 17 57768031 57768033 + In_Frame_Del DEL AAG - - NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr17:57768031_57768033delAAG uc002ixq.1 + 31 5305_5307 c.4862_4864delAAG c.(4861-4866)AAAGAA>AAA p.E1624del CLTC_uc002ixp.2_In_Frame_Del_p.E1624del|CLTC_uc002ixr.1_In_Frame_Del_p.E1628del NM_004859 NP_004850 Q00610 CLH1_HUMAN clathrin heavy chain 1 1624 Heavy chain arm.|Proximal segment.|Trimerization (By similarity). axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle protein binding|structural molecule activity CLTC/ALK(44)|CLTC/TFE3(2) haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1) 48 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) TCACTGAGAAAAGAAGAAGAACA 0.335 0.60 6 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 62 200 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 80 511 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1299_LUNG NA NCIH1299_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 106 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1339_LUNG NA NCIH1339_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.60 30 45 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 898 303 TTN 7273 broad.mit.edu 37 2 179599088 179599089 + Frame_Shift_Ins INS - C C NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr2:179599088_179599089insC uc010zfg.1 - 49 11954_11955 c.11730_11731insG c.(11728-11733)GGCAAGfs p.G3910fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Ins_p.G571fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 4837_4838 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CAGCCACACTTGCCGACTTCAT 0.386 0.46 149 127 MAPKAPK3 7867 broad.mit.edu 37 3 50685471 50685471 + Frame_Shift_Del DEL C - - NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr3:50685471delC uc003day.1 + 13 1739 c.1143delC c.(1141-1143)AACfs p.N381fs MAPKAPK3_uc003daz.1_Frame_Shift_Del_p.N381fs|MAPKAPK3_uc003dba.1_Frame_Shift_Del_p.N381fs|MAPKAPK3_uc010hlr.1_Frame_Shift_Del_p.N381fs NM_004635 NP_004626 Q16644 MAPK3_HUMAN mitogen-activated protein kinase-activated 381 activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|MAP kinase kinase activity|protein serine/threonine kinase activity ovary(1)|central_nervous_system(1) 2 BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.0188)|Kidney(197;0.0223) GCTGCAACAACCAGTAGCTCA 0.562 0.49 35 33 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.35 31 17 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 50 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.67 70 143 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.77 20 67 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.18 47 10 TNRC18 84629 broad.mit.edu 37 7 5352791 5352799 + In_Frame_Del DEL GCTGCTGCT - - NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr7:5352791_5352799delGCTGCTGCT uc003soi.3 - 27 8072_8080 c.7723_7731delAGCAGCAGC c.(7723-7731)AGCAGCAGCdel p.SSS2575del NM_001080495 NP_001073964 O15417 TNC18_HUMAN trinucleotide repeat containing 18 2575_2577 Ser-rich. DNA binding 0 Ovarian(82;0.142) UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15) TCTCCGAgccgctgctgctgctgctgctg 0.498 0.41 19 13 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.77 3 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 29 MLLT3 4300 broad.mit.edu 37 9 20414278 20414286 + In_Frame_Del DEL CTGCTGCTG - - NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr9:20414278_20414286delCTGCTGCTG uc003zoe.2 - 5 817_825 c.558_566delCAGCAGCAG c.(556-567)AGCAGCAGCAGT>AGT p.186_189SSSS>S MLLT3_uc011lne.1_In_Frame_Del_p.154_157SSSS>S|MLLT3_uc011lnf.1_In_Frame_Del_p.183_186SSSS>S|MLLT3_uc003zof.2_5'UTR NM_004529 NP_004520 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia 186_189 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding lung(2)|ovary(1) 3 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) ACTGGTActactgctgctgctgctgctgc 0.177 0.34 341 178 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 384 209 C15orf2 23742 broad.mit.edu 37 15 24922362 24922363 + Frame_Shift_Ins INS - T T NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr15:24922362_24922363insT uc001ywo.2 + 1 1822_1823 c.1348_1349insT c.(1348-1350)ATGfs p.M450fs NM_018958 NP_061831 Q9NZP6 CO002_HUMAN hypothetical protein LOC23742 450 Pro-rich. cell differentiation|multicellular organismal development|spermatogenesis ovary(2)|large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1) 8 all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086) all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229) CACACCAAAAATGGATGAGAAA 0.510 0.95 4 82 THAP11 57215 broad.mit.edu 37 16 67876788 67876796 + In_Frame_Del DEL CAGCAGCAA - - NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr16:67876788_67876796delCAGCAGCAA uc002euo.2 + 1 576_584 c.331_339delCAGCAGCAA c.(331-339)CAGCAGCAAdel p.QQQ129del CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 129_131 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) acagcagcagcagcagcaacagcagcaac 0.316 0.44 69 55 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 18 235 TP53 7157 broad.mit.edu 37 17 7579582 7579583 + Frame_Shift_Ins INS - A A rs121912661 NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr17:7579582_7579583insA uc002gim.2 - 4 298_299 c.104_105insT c.(103-105)TTGfs p.L35fs TP53_uc002gig.1_Frame_Shift_Ins_p.L35fs|TP53_uc002gih.2_Frame_Shift_Ins_p.L35fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Ins_p.L35fs|TP53_uc010cni.1_Frame_Shift_Ins_p.L35fs|TP53_uc002gij.2_Frame_Shift_Ins_p.L35fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_5'UTR|TP53_uc010cnk.1_Frame_Shift_Ins_p.L50fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 35 Transcription activation (acidic).|Interaction with HRMT1L2. L -> F (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.L35F(3)|p.L35fs*9(2)|p.L35fs*8(1)|p.?(1)|p.S33fs*23(1)|p.P13fs*18(1)|p.S33fs*6(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) CTTGGGACGGCAAGGGGGACTG 0.391 0.55 5 6 MYH4 4622 broad.mit.edu 37 17 10359164 10359165 + Frame_Shift_Ins INS - T T NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr17:10359164_10359165insT uc002gmn.2 - 18 2133_2134 c.2022_2023insA c.(2020-2025)GTGCGGfs p.V674fs uc002gml.1_Intron NM_017533 NP_060003 Q9Y623 MYH4_HUMAN myosin, heavy polypeptide 4, skeletal muscle 674_675 Myosin head-like.|Actin-binding (By similarity). muscle filament sliding muscle myosin complex|myosin filament|sarcomere actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle ovary(10)|skin(2)|central_nervous_system(1) 13 ATGATGCACCGCACAAAGTGGG 0.431 0.37 142 84 SMARCA4 6597 broad.mit.edu 37 19 11094995 11094995 + Frame_Shift_Del DEL C - - NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr19:11094995delC uc002mqf.3 + 2 452 c.168delC c.(166-168)ATCfs p.I56fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.I56fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.I56fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.I56fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.I56fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.I56fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.I56fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.I56fs|SMARCA4_uc002mqe.2_Frame_Shift_Del_p.I56fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 56 Necessary for interaction with SS18L1/CREST (By similarity). chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) 0.000 0.95 54 1112 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.53 105 118 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.49 37 35 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 40 230 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 86 EP300 2033 broad.mit.edu 37 22 41566508 41566512 + Frame_Shift_Del DEL GACTG - - NCIH1339_LUNG NA NCIH1339_LUNG NA g.chr22:41566508_41566512delGACTG uc003azl.3 + 27 4780_4784 c.4385_4389delGACTG c.(4384-4389)CGACTGfs p.R1462fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1462_1463 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 AAGCCCAAGCGACTGCAGGAATGGT 0.473 0.41 175 120 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 NCIH1355_LUNG NA NCIH1355_LUNG NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.33 90 45 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1355_LUNG NA NCIH1355_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 28 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1355_LUNG NA NCIH1355_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.14 131 22 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH1355_LUNG NA NCIH1355_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.44 51 40 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1355_LUNG NA NCIH1355_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.26 154 55 NKD2 85409 broad.mit.edu 37 5 1033515 1033515 + Frame_Shift_Del DEL C - - NCIH1355_LUNG NA NCIH1355_LUNG NA g.chr5:1033515delC uc003jbt.1 + 5 236 c.231delC c.(229-231)GGCfs p.G77fs NKD2_uc010itf.1_Frame_Shift_Del_p.G77fs NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 77 Targeting to the basolateral cell membrane. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.27 849 310 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1355_LUNG NA NCIH1355_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.55 45 56 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1355_LUNG NA NCIH1355_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 212 61 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1355_LUNG NA NCIH1355_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 18 178 STK11 6794 broad.mit.edu 37 19 1207054 1207054 + Frame_Shift_Del DEL A - - NCIH1355_LUNG NA NCIH1355_LUNG NA g.chr19:1207054delA uc002lrl.1 + 1 1257 c.142delA c.(142-144)AAGfs p.K48fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 48 anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.?(3)|p.K48fs*3(2)|p.A43_L50del(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.88 177 1355 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1355_LUNG NA NCIH1355_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.44 55 44 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH1355_LUNG NA NCIH1355_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 165 31 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1355_LUNG NA NCIH1355_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 112 545 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1373_LUNG NA NCIH1373_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.99 1 87 DENND4B 9909 broad.mit.edu 37 1 153907278 153907279 + In_Frame_Ins INS - CTG CTG rs141373027 by1000genomes NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr1:153907278_153907279insCTG uc001fdd.1 - 18 3131_3132 c.2730_2731insCAG c.(2728-2733)insCAG p.910_911insQ uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910_911 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) GACACctgctcctgctgctgct 0.455 0.29 75 31 ULK4 54986 broad.mit.edu 37 3 41756973 41756973 + Frame_Shift_Del DEL A - - NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr3:41756973delA uc003ckv.3 - 24 2744 c.2543delT c.(2542-2544)CTGfs p.L848fs NM_017886 NP_060356 Q96C45 ULK4_HUMAN unc-51-like kinase 4 848 HEAT 1. ATP binding|protein serine/threonine kinase activity 0 KIRC - Kidney renal clear cell carcinoma(284;0.214) TACAGGCATCAGGGGGAGACA 0.433 0.38 10 6 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.13 348 54 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.27 74 28 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 148 223 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 42 110 ATXN1 6310 broad.mit.edu 37 6 16327901 16327909 + In_Frame_Del DEL TGCTGCTGA - - rs66949327;rs3817753;rs59310777 by1000genomes NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr6:16327901_16327909delTGCTGCTGA uc003nbt.2 - 8 1604_1612 c.633_641delTCAGCAGCA c.(631-642)CATCAGCAGCAG>CAG p.HQQ211del ATXN1_uc010jpi.2_In_Frame_Del_p.HQQ211del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 211_213 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgctgctgctgatgctgatgct 0.388 0.58 20 28 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.46 7 6 COL14A1 7373 broad.mit.edu 37 8 121326250 121326250 + Frame_Shift_Del DEL C - - NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr8:121326250delC uc003yox.2 + 38 4800 c.4535delC c.(4534-4536)TCCfs p.S1512fs COL14A1_uc003yoz.2_Frame_Shift_Del_p.S477fs NM_021110 NP_066933 Q05707 COEA1_HUMAN collagen, type XIV, alpha 1 precursor 1512 Triple-helical region 1 (COL2). cell-cell adhesion|collagen fibril organization collagen type XIV|extracellular space collagen binding|extracellular matrix structural constituent|protein binding, bridging ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1) 12 Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503) AGTGGTCTGTCCATTCAAGGA 0.483 0.54 115 136 PAPPA 5069 broad.mit.edu 37 9 118949932 118949932 + Frame_Shift_Del DEL C - - NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr9:118949932delC uc004bjn.2 + 2 1296 c.915delC c.(913-915)AGCfs p.S305fs PAPPA_uc011lxp.1_Frame_Shift_Del_p.S98fs|PAPPA_uc011lxq.1_Frame_Shift_Del_p.S98fs NM_002581 NP_002572 Q13219 PAPP1_HUMAN pregnancy-associated plasma protein A 305 Metalloprotease. cell differentiation|female pregnancy cytoplasm|extracellular region|membrane metalloendopeptidase activity|zinc ion binding ovary(4)|skin(4)|pancreas(1) 9 ATGGCAGCAGCCCCAAAGTGG 0.567 0.53 23 26 ATN1 1822 broad.mit.edu 37 12 7045892 7045897 + In_Frame_Del DEL CAGCAG - - rs66756893;rs67074116;rs145352906 byFrequency NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr12:7045892_7045897delCAGCAG uc001qrw.1 + 5 1699_1704 c.1462_1467delCAGCAG c.(1462-1467)CAGCAGdel p.QQ500del ATN1_uc001qrx.1_In_Frame_Del_p.QQ500del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 500_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagc 0.456 0.26 67 24 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.25 99 33 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 10 154 MYH8 4626 broad.mit.edu 37 17 10322332 10322332 + Frame_Shift_Del DEL C - - NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr17:10322332delC uc002gmm.2 - 4 321 c.226delG c.(226-228)GAAfs p.E76fs uc002gml.1_Intron NM_002472 NP_002463 P13535 MYH8_HUMAN myosin, heavy chain 8, skeletal muscle, 76 Myosin head-like. muscle filament sliding cytosol|muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle skin(6)|ovary(3)|breast(2) 11 ACTTGGTCTTCCCTGACAGTT 0.333 0.95 7 130 RPTOR 57521 broad.mit.edu 37 17 78931459 78931476 + In_Frame_Del DEL GGCCTCCTCATGAGCTCA - - NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr17:78931459_78931476delGGCCTCCTCATGAGCTCA uc002jyt.1 + 29 4211_4228 c.3406_3423delGGCCTCCTCATGAGCTCA c.(3406-3423)GGCCTCCTCATGAGCTCAdel p.GLLMSS1136del RPTOR_uc010wug.1_In_Frame_Del_p.GLLMSS978del|RPTOR_uc002jyu.1_In_Frame_Del_p.GLLMSS29del NM_020761 NP_065812 Q8N122 RPTOR_HUMAN raptor isoform 1 1136_1141 WD 3. cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade cytosol|lysosome|TORC1 complex protein complex binding lung(4)|urinary_tract(1)|ovary(1) 6 GCAGGAGACCGGCCTCCTCATGAGCTCAGGAGACGTGC 0.633 0.13 283 44 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 49 166 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 200 774 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 3 51 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 NCIH1373_LUNG NA NCIH1373_LUNG NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.52 163 180 ABL2 27 broad.mit.edu 37 1 179077136 179077137 + Frame_Shift_Ins INS - T T NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr1:179077136_179077137insT uc001gmj.3 - 12 3552_3553 c.3265_3266insA c.(3265-3267)CTGfs p.L1089fs ABL2_uc010pnf.1_Frame_Shift_Ins_p.L986fs|ABL2_uc010png.1_Frame_Shift_Ins_p.L965fs|ABL2_uc010pnh.1_Frame_Shift_Ins_p.L1068fs|ABL2_uc001gmg.3_Frame_Shift_Ins_p.L971fs|ABL2_uc001gmi.3_Frame_Shift_Ins_p.L1074fs|ABL2_uc001gmh.3_Frame_Shift_Ins_p.L1053fs|ABL2_uc010pne.1_Frame_Shift_Ins_p.L950fs NM_007314 NP_009298 P42684 ABL2_HUMAN arg tyrosine kinase isoform b 1089 F-actin-binding (By similarity). axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction cytoskeleton|cytosol ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(8)|breast(3)|ovary(2)|central_nervous_system(1) 14 Adenosine triphosphate(DB00171)|Dasatinib(DB01254) ACATTCCAGCAGGGCCTCTTTG 0.530 0.42 30 22 MSH2 4436 broad.mit.edu 37 2 47641559 47641564 + Splice_Site DEL TAAAAA - - rs11309117;rs71886715 NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr2:47641559_47641564delTAAAAA uc002rvy.1 + 5 1010 c.942_splice c.e5+2 p.Q314_splice MSH2_uc010yoh.1_Splice_Site_p.Q248_splice|MSH2_uc002rvz.2_Splice_Site_p.Q314_splice|MSH2_uc010fbg.2_Intron NM_000251 NP_000242 P43246 MSH2_HUMAN mutS homolog 2 B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes MutSalpha complex|MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding p.?(1) large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1) 55 all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) CTTTTTCAGGTaaaaaaaaaaaaaaa 0.291 0.31 9 4 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.31 9 4 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.35 30 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.85 4 23 PAXIP1 22976 broad.mit.edu 37 7 154760540 154760541 + In_Frame_Ins INS - TGC TGC NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr7:154760540_154760541insTGC uc003wlp.2 - 7 1413_1414 c.1370_1371insGCA c.(1369-1371)CAA>CAGCAA p.457_457Q>QQ PAXIP1_uc003wlq.1_In_Frame_Ins_p.423_423Q>QQ|PAXIP1_uc011kvs.1_In_Frame_Ins_p.421_421Q>QQ|PAXIP1_uc003wlr.1_In_Frame_Ins_p.366_366Q>QQ NM_007349 NP_031375 Q6ZW49 PAXI1_HUMAN PAX interacting protein 1 457 Gln-rich. DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent histone methyltransferase complex|nuclear matrix p.F457C(1) lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_neural(206;0.119) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.0296) UCEC - Uterine corpus endometrioid carcinoma (81;0.178) 0.000 0.23 373 111 PRKDC 5591 broad.mit.edu 37 8 48691217 48691217 + Frame_Shift_Del DEL C - - NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr8:48691217delC uc003xqi.2 - 84 11713 c.11656delG c.(11656-11658)GCCfs p.A3886fs PRKDC_uc003xqj.2_Frame_Shift_Del_p.A3855fs|PRKDC_uc011ldh.1_Intron NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic 3886 PI3K/PI4K. cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) CTCACGAAGGCCCGCCTACAA 0.557 0.55 14 17 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.33 8 4 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 1.00 0 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 61 30 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 48 524 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.36 9 5 KEAP1 9817 broad.mit.edu 37 19 10602688 10602689 + Frame_Shift_Ins INS - A A NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr19:10602688_10602689insA uc002moq.1 - 3 1045_1046 c.889_890insT c.(889-891)TGCfs p.C297fs KEAP1_uc002mop.1_Frame_Shift_Ins_p.C15fs|KEAP1_uc002mor.1_Frame_Shift_Ins_p.C297fs NM_012289 NP_036421 Q14145 KEAP1_HUMAN kelch-like ECH-associated protein 1 297 regulation of transcription, DNA-dependent|transcription, DNA-dependent centrosome|midbody|nucleus protein binding lung(12)|breast(3)|ovary(1)|pancreas(1) 17 OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05) 0.000 0.69 197 429 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 13 36 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1385_LUNG NA NCIH1385_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 66 152 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 34 SOS1 6654 broad.mit.edu 37 2 39222519 39222520 + Frame_Shift_Ins INS - T T NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr2:39222519_39222520insT uc002rrk.3 - 20 3131_3132 c.3090_3091insA c.(3088-3093)AAATATfs p.K1030fs SOS1_uc002rrj.3_Frame_Shift_Ins_p.K644fs NM_005633 NP_005624 Q07889 SOS1_HUMAN son of sevenless homolog 1 1030_1031 apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction cytosol DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity ovary(4)|breast(3)|lung(2)|central_nervous_system(1) 10 all_hematologic(82;0.21) GGATAGCTATATTTTTTTGGCT 0.391 0.18 443 99 CTNNA2 1496 broad.mit.edu 37 2 80101382 80101382 + Frame_Shift_Del DEL A - - NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr2:80101382delA uc010ysh.1 + 5 771 c.766delA c.(766-768)AATfs p.N256fs CTNNA2_uc010yse.1_Frame_Shift_Del_p.N256fs|CTNNA2_uc010ysf.1_Frame_Shift_Del_p.N256fs|CTNNA2_uc010ysg.1_Frame_Shift_Del_p.N256fs NM_004389 NP_004380 P26232 CTNA2_HUMAN catenin, alpha 2 isoform 1 256 axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity actin cytoskeleton|axon|cytosol cadherin binding|structural constituent of cytoskeleton pancreas(4)|lung(3)|breast(1)|skin(1) 9 CGGCATCTCCAATGCTGCTCA 0.582 0.74 59 171 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.72 5 13 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.68 6 13 HTT 3064 broad.mit.edu 37 4 3076604 3076606 + In_Frame_Del DEL CAG - - rs10618869 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr4:3076604_3076606delCAG uc011bvq.1 + 2 203_205 c.58_60delCAG c.(58-60)CAGdel p.Q40del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagc 0.335 0.23 88 27 HTT 3064 broad.mit.edu 37 4 3076672 3076673 + In_Frame_Ins INS - CCGCCGCCG CCGCCGCCG rs76533208 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr4:3076672_3076673insCCGCCGCCG uc011bvq.1 + 2 271_272 c.126_127insCCGCCGCCG c.(124-129)insCCGCCGCCG p.51_52insPPP NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 49_50 establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) aacagccgccaccgccgccgcc 0.084 0.28 75 29 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.50 17 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 95 176 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.32 84 39 STK32A 202374 broad.mit.edu 37 5 146763030 146763031 + Frame_Shift_Del DEL CT - - NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr5:146763030_146763031delCT uc010jgn.1 + 12 1339_1340 c.1059_1060delCT c.(1057-1062)GACTCTfs p.D353fs STK32A_uc011dbw.1_Frame_Shift_Del_p.D353fs NM_001112724 NP_001106195 Q8WU08 ST32A_HUMAN serine/threonine kinase 32A isoform 1 353_354 ATP binding|metal ion binding|protein serine/threonine kinase activity lung(2)|skin(1) 3 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) AGCACCTTGACTCTGTCCAGAA 0.401 0.66 56 107 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.35 55 30 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.21 76 20 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 27 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 45 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.54 6 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.50 399 407 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.33 16 8 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.12 213 30 STK11 6794 broad.mit.edu 37 19 1207077 1207077 + Frame_Shift_Del DEL G - - NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr19:1207077delG uc002lrl.1 + 1 1280 c.165delG c.(163-165)CTGfs p.L55fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 55 ATP (By similarity).|Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.E57fs*7(4)|p.?(3)|p.G56fs*107(1)|p.G52_P179del(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.96 7 170 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.85 38 215 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 9 46 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1395_LUNG NA NCIH1395_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 7 113 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1435_LUNG NA NCIH1435_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 5 38 SRPK3 26576 broad.mit.edu 37 X 153049488 153049488 + Frame_Shift_Del DEL G - - NCIH1435_LUNG NA NCIH1435_LUNG NA g.chrX:153049488delG uc004fil.2 + 10 999 c.967delG c.(967-969)GGGfs p.G323fs SRPK3_uc004fik.2_Frame_Shift_Del_p.G389fs|SRPK3_uc010nul.2_Intron|SRPK3_uc004fin.2_Frame_Shift_Del_p.G322fs|SRPK3_uc004fim.2_Intron NM_014370 NP_055185 Q9UPE1 SRPK3_HUMAN serine arginine rich protein-specific kinase 3 323 Protein kinase. cell differentiation|muscle organ development|muscle tissue development ATP binding|protein serine/threonine kinase activity pancreas(2)|lung(1) 3 all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05) 0.000 0.36 722 407 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 303 93 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.35 15 8 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.28 163 64 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 30 53 APC 324 broad.mit.edu 37 5 112174762 112174762 + Frame_Shift_Del DEL G - - rs143927847 byFrequency;by1000genomes NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr5:112174762delG uc010jby.2 + 16 3851 c.3471delG c.(3469-3471)GAGfs p.E1157fs APC_uc011cvt.1_Frame_Shift_Del_p.E1139fs|APC_uc003kpz.3_Frame_Shift_Del_p.E1157fs|APC_uc003kpy.3_Frame_Shift_Del_p.E1157fs|APC_uc010jbz.2_Frame_Shift_Del_p.E874fs|APC_uc010jca.2_Frame_Shift_Del_p.E457fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1157 Ser-rich.|Responsible for down-regulation through a process mediated by direct ubiquitination. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.?(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) AAGAAGAAGAGAGACCAACAA 0.343 0.72 17 44 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.32 17 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 30 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.12 292 39 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 152 69 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 10 163 ZNF521 25925 broad.mit.edu 37 18 22806112 22806113 + Frame_Shift_Ins INS - A A NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr18:22806112_22806113insA uc002kvk.2 - 4 2016_2017 c.1769_1770insT c.(1768-1770)TTGfs p.L590fs ZNF521_uc010xbe.1_RNA|ZNF521_uc010dly.2_Frame_Shift_Ins_p.L590fs|ZNF521_uc002kvl.2_Frame_Shift_Ins_p.L370fs NM_015461 NP_056276 Q96K83 ZN521_HUMAN zinc finger protein 521 590 cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein domain specific binding|zinc ion binding ovary(4)|large_intestine(2)|lung(1) 7 all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991) AATTCAGGGCCAAGGGAATGTT 0.411 0.92 5 57 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.20 353 90 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.68 29 63 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 89 451 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1435_LUNG NA NCIH1435_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 15 105 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1437_LUNG NA NCIH1437_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 23 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH1437_LUNG NA NCIH1437_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 318 70 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1437_LUNG NA NCIH1437_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.23 144 42 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1437_LUNG NA NCIH1437_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 59 33 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1437_LUNG NA NCIH1437_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 19 51 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH1437_LUNG NA NCIH1437_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 308 36 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH1437_LUNG NA NCIH1437_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.94 1 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1437_LUNG NA NCIH1437_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 297 100 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1437_LUNG NA NCIH1437_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.67 10 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1437_LUNG NA NCIH1437_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 119 325 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1437_LUNG NA NCIH1437_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 36 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH146_LUNG NA NCIH146_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 75 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes NCIH146_LUNG NA NCIH146_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.47 18 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH146_LUNG NA NCIH146_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 115 171 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH146_LUNG NA NCIH146_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 28 43 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC NCIH146_LUNG NA NCIH146_LUNG NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.13 103 16 EPO 2056 broad.mit.edu 37 7 100320315 100320316 + Frame_Shift_Ins INS - G G NCIH146_LUNG NA NCIH146_LUNG NA g.chr7:100320315_100320316insG uc003uwi.2 + 4 456_457 c.275_276insG c.(274-276)CAGfs p.Q92fs EPO_uc011kkc.1_Frame_Shift_Ins_p.Q92fs NM_000799 NP_000790 P01588 EPO_HUMAN erythropoietin precursor 92 blood circulation|cellular hyperosmotic response|erythrocyte maturation|negative regulation of apoptosis|negative regulation of ion transmembrane transporter activity|negative regulation of sodium ion transport|positive regulation of cell proliferation|positive regulation of DNA replication|positive regulation of Ras protein signal transduction|positive regulation of transcription, DNA-dependent|positive regulation of tyrosine phosphorylation of Stat5 protein|signal transduction extracellular space erythropoietin receptor binding|eukaryotic cell surface binding|hormone activity central_nervous_system(2) 2 Lung NSC(181;0.041)|all_lung(186;0.0581) Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016) GAAGTCTGGCAGGGCCTGGCCC 0.658 0.11 55 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH146_LUNG NA NCIH146_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 22 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH146_LUNG NA NCIH146_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.57 6 8 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 NCIH146_LUNG NA NCIH146_LUNG NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.85 5 29 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH146_LUNG NA NCIH146_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.57 21 28 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH146_LUNG NA NCIH146_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 15 223 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH146_LUNG NA NCIH146_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 54 221 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH146_LUNG NA NCIH146_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 112 373 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH146_LUNG NA NCIH146_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 101 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1563_LUNG NA NCIH1563_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 60 RHOB 388 broad.mit.edu 37 2 20647283 20647284 + Frame_Shift_Ins INS - T T NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr2:20647283_20647284insT uc002rdv.2 + 1 449_450 c.57_58insT c.(55-60)ACGTGCfs p.T19fs NM_004040 NP_004031 P62745 RHOB_HUMAN ras homolog gene family, member B precursor 19_20 angiogenesis|axon guidance|cell adhesion|endosome to lysosome transport|negative regulation of cell cycle|platelet activation|positive regulation of angiogenesis|protein transport|regulation of small GTPase mediated signal transduction|Rho protein signal transduction|transformed cell apoptosis cytosol|late endosome membrane|nucleus|plasma membrane GTP binding|GTPase activity|protein binding ovary(1)|lung(1) 2 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) all_epithelial(98;4.19e-09)|Lung NSC(108;0.00452)|Ovarian(717;0.0164) OV - Ovarian serous cystadenocarcinoma(76;1.14e-22)|Epithelial(75;7.84e-19) GTGGCAAGACGTGCCTGCTGAT 0.663 0.40 6 4 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.43 20 15 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 88 24 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.43 26 20 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 127 211 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.80 12 48 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.73 3 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 1 9 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.46 29 25 ARFGEF1 10565 broad.mit.edu 37 8 68165829 68165830 + Frame_Shift_Del DEL TA - - NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr8:68165829_68165830delTA uc003xxo.1 - 18 2944_2945 c.2554_2555delTA c.(2554-2556)TACfs p.Y852fs ARFGEF1_uc003xxl.1_Frame_Shift_Del_p.Y306fs NM_006421 NP_006412 Q9Y6D6 BIG1_HUMAN brefeldin A-inhibited guanine 852 exocytosis|regulation of ARF protein signal transduction cytoplasm ARF guanyl-nucleotide exchange factor activity|myosin binding ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1) 8 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206) CATCTTAATGTATTGTTCCTTT 0.277 0.70 60 141 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 1080 389 GPR183 1880 broad.mit.edu 37 13 99947941 99947942 + Frame_Shift_Ins INS - A A NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr13:99947941_99947942insA uc001vog.2 - 2 632_633 c.458_459insT c.(457-459)ATAfs p.I153fs UBAC2_uc001voa.3_Intron|UBAC2_uc010tiu.1_Intron|UBAC2_uc001vob.3_Intron|UBAC2_uc010tiv.1_Intron|UBAC2_uc001vod.2_Intron|UBAC2_uc001voc.2_Intron|UBAC2_uc010tiw.1_Intron NM_004951 NP_004942 P32249 GP183_HUMAN EBV-induced G protein-coupled receptor 2 153 Helical; Name=4; (Potential). humoral immune response|mature B cell differentiation involved in immune response integral to plasma membrane purinergic nucleotide receptor activity, G-protein coupled 0 TCCAGACAAATATGCACACGCC 0.441 0.23 495 148 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 14 143 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 66 223 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 129 389 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1563_LUNG NA NCIH1563_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 8 179 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1568_LUNG NA NCIH1568_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 5 111 GPR119 139760 broad.mit.edu 37 X 129518594 129518595 + Frame_Shift_Ins INS - G G NCIH1568_LUNG NA NCIH1568_LUNG NA g.chrX:129518594_129518595insG uc011muv.1 - 1 827_828 c.827_828insC c.(826-828)CCAfs p.P276fs NM_178471 NP_848566 Q8TDV5 GP119_HUMAN G protein-coupled receptor 119 276 Helical; Name=7; (Potential). integral to membrane|plasma membrane lipid binding ovary(2) 2 CATAGATGAGTGGGTTGAGCAG 0.574 0.89 13 105 F8 2157 broad.mit.edu 37 X 154159089 154159089 + Frame_Shift_Del DEL A - - NCIH1568_LUNG NA NCIH1568_LUNG NA g.chrX:154159089delA uc004fmt.2 - 14 3147 c.2976delT c.(2974-2976)TTTfs p.F992fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 992 B. acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) TTTTCCCTTTAAATAACCTAC 0.323 0.95 5 98 ZNF642 339559 broad.mit.edu 37 1 40960968 40960969 + Frame_Shift_Ins INS - T T NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr1:40960968_40960969insT uc001cfo.2 + 6 1112_1113 c.818_819insT c.(817-819)TGTfs p.C273fs ZNF642_uc009vwb.2_Frame_Shift_Ins_p.C273fs|ZNF642_uc010ojk.1_Frame_Shift_Ins_p.C274fs NM_198494 NP_940896 Q49AA0 ZN642_HUMAN zinc finger protein 642 273 C2H2-type 1. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding 0 Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;8.81e-19) ACCTATGAATGTAATATATGTG 0.332 0.61 11 17 VRK2 7444 broad.mit.edu 37 2 58373508 58373509 + Frame_Shift_Ins INS - A A rs139700760 NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr2:58373508_58373509insA uc002rzo.2 + 15 1826_1827 c.1081_1082insA c.(1081-1083)GAAfs p.E361fs VRK2_uc010fcb.2_Frame_Shift_Ins_p.E361fs|VRK2_uc002rzs.2_Frame_Shift_Ins_p.E361fs|VRK2_uc002rzr.2_Frame_Shift_Ins_p.E361fs|VRK2_uc010fcc.2_Frame_Shift_Ins_p.E243fs|VRK2_uc002rzv.2_Frame_Shift_Ins_p.E361fs|VRK2_uc010fcd.2_Frame_Shift_Ins_p.E338fs|VRK2_uc002rzp.2_Frame_Shift_Ins_p.E361fs|VRK2_uc010ypg.1_Frame_Shift_Ins_p.E361fs|VRK2_uc002rzq.2_Frame_Shift_Ins_p.E361fs|VRK2_uc002rzu.2_Frame_Shift_Ins_p.E361fs|VRK2_uc002rzt.2_Frame_Shift_Ins_p.E243fs NM_001130482 NP_001123954 Q86Y07 VRK2_HUMAN vaccinia related kinase 2 isoform 2 361 integral to membrane ATP binding|protein binding|protein serine/threonine kinase activity ovary(1) 1 TAGGTTAATCGAAAAAAAAGTC 0.386 0.18 32 7 NFE2L2 4780 broad.mit.edu 37 2 178098808 178098816 + In_Frame_Del DEL CTCTTCATC - - NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr2:178098808_178098816delCTCTTCATC uc002ulh.3 - 2 784_792 c.229_237delGATGAAGAG c.(229-237)GATGAAGAGdel p.DEE77del NFE2L2_uc002ulg.3_In_Frame_Del_p.DEE61del|NFE2L2_uc010zfa.1_In_Frame_Del_p.DEE61del|NFE2L2_uc002uli.3_In_Frame_Del_p.DEE61del|NFE2L2_uc010fra.2_In_Frame_Del_p.DEE61del|NFE2L2_uc010frb.2_In_Frame_Del_p.DEE61del NM_006164 NP_006155 Q16236 NF2L2_HUMAN nuclear factor erythroid 2-like 2 isoform 1 77_79 transcription from RNA polymerase II promoter centrosome|cytosol|nucleus|plasma membrane protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity central_nervous_system(1) 1 Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935) 0.000 0.42 502 365 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.26 23 8 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.19 35 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 112 159 ADAM29 11086 broad.mit.edu 37 4 175898930 175898983 + In_Frame_Del DEL CCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAA - - rs111721161;rs139608576;rs149749808;rs146283611;rs139492823 byFrequency;byFrequency;byFrequency NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr4:175898930_175898983delCCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAA uc003iuc.2 + 5 2924_2977 c.2254_2307delCCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAA c.(2254-2307)CCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAAdel p.PQVMPSQSQPPVTPSQSQ752del ADAM29_uc003iud.2_In_Frame_Del_p.PQVMPSQSQPPVTPSQSQ752del|ADAM29_uc010irr.2_In_Frame_Del_p.PQVMPSQSQPPVTPSQSQ752del|ADAM29_uc011cki.1_In_Frame_Del_p.PQVMPSQSQPPVTPSQSQ752del NM_014269 NP_055084 Q9UKF5 ADA29_HUMAN ADAM metallopeptidase domain 29 preproprotein 752_769 Cytoplasmic (Potential).|4.|9 X 9 AA approximate repeats. QPRVM -> HPQLT (in Ref. 1; AAF03777). proteolysis|spermatogenesis integral to plasma membrane metalloendopeptidase activity|zinc ion binding skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1) 16 Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164) all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286) CCAGAGTCATCCTCAGGTGATGCCTTCCCAGAGTCAACCTCCTGTGACACCCTCCCAGAGTCAACCTCGGGTGA 0.559 0.19 307 74 CDH10 1008 broad.mit.edu 37 5 24535224 24535224 + Frame_Shift_Del DEL G - - NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr5:24535224delG uc003jgr.1 - 5 1143 c.811delC c.(811-813)CAGfs p.Q271fs CDH10_uc011cnu.1_RNA NM_006727 NP_006718 Q9Y6N8 CAD10_HUMAN cadherin 10, type 2 preproprotein 271 Cadherin 3.|Extracellular (Potential). adherens junction organization|cell junction assembly|homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding ovary(6)|pancreas(4)|breast(2) 12 STAD - Stomach adenocarcinoma(35;0.0556) TGCTTACTCTGGGGGAAACGT 0.418 0.37 22 13 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 13 36 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.80 2 8 PHIP 55023 broad.mit.edu 37 6 79752650 79752651 + Frame_Shift_Ins INS - T T NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr6:79752650_79752651insT uc003pir.2 - 7 735_736 c.509_510insA c.(508-510)TATfs p.Y170fs PHIP_uc011dyp.1_Frame_Shift_Ins_p.Y170fs NM_017934 NP_060404 Q8WWQ0 PHIP_HUMAN pleckstrin homology domain interacting protein 170 insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis nucleus insulin receptor binding large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1) 6 all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219) BRCA - Breast invasive adenocarcinoma(397;0.231) TCATGTGCTGATACACTGCAGT 0.376 0.19 168 40 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.34 249 129 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 19 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.14 57 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 772 294 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.80 17 68 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.79 44 164 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1568_LUNG NA NCIH1568_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 82 869 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1573_LUNG NA NCIH1573_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 39 ZFYVE9 9372 broad.mit.edu 37 1 52759261 52759261 + Frame_Shift_Del DEL G - - NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr1:52759261delG uc001cto.2 + 11 3334 c.3162delG c.(3160-3162)TTGfs p.L1054fs ZFYVE9_uc001ctp.2_Frame_Shift_Del_p.L995fs NM_004799 NP_004790 O95405 ZFYV9_HUMAN zinc finger, FYVE domain containing 9 isoform 3 1054 endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway early endosome membrane metal ion binding|protein binding|receptor activity|serine-type peptidase activity ovary(2)|lung(2)|central_nervous_system(2)|skin(2) 8 CACCTTACTTGTTTGGGATTC 0.423 0.41 126 89 ECM1 1893 broad.mit.edu 37 1 150485236 150485236 + Frame_Shift_Del DEL C - - NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr1:150485236delC uc001eus.2 + 9 1539 c.1340delC c.(1339-1341)GCCfs p.A447fs ECM1_uc001eut.2_Frame_Shift_Del_p.A322fs|ECM1_uc001euu.2_Frame_Shift_Del_p.A476fs|ECM1_uc001euv.2_Frame_Shift_Del_p.A474fs|ECM1_uc009wlu.2_Frame_Shift_Del_p.A207fs NM_004425 NP_004416 Q16610 ECM1_HUMAN extracellular matrix protein 1 isoform 1 447 angiogenesis|biomineral tissue development|negative regulation of bone mineralization|negative regulation of peptidase activity|ossification|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of I-kappaB kinase/NF-kappaB cascade proteinaceous extracellular matrix laminin binding|protease binding|protein C-terminus binding|signal transducer activity ovary(2)|central_nervous_system(1) 3 all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171) UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206) AACATGACTGCCCGCTGCTGT 0.557 0.48 47 43 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.20 41 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.32 88 42 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.79 6 22 PCDH15 65217 broad.mit.edu 37 10 55913017 55913017 + Frame_Shift_Del DEL C - - NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr10:55913017delC uc001jju.1 - 14 2022 c.1627delG c.(1627-1629)GAGfs p.E543fs PCDH15_uc010qhq.1_Frame_Shift_Del_p.E548fs|PCDH15_uc010qhr.1_Frame_Shift_Del_p.E543fs|PCDH15_uc010qhs.1_Frame_Shift_Del_p.E555fs|PCDH15_uc010qht.1_Frame_Shift_Del_p.E550fs|PCDH15_uc010qhu.1_Frame_Shift_Del_p.E543fs|PCDH15_uc001jjv.1_Frame_Shift_Del_p.E521fs|PCDH15_uc010qhv.1_Frame_Shift_Del_p.E543fs|PCDH15_uc010qhw.1_Frame_Shift_Del_p.E506fs|PCDH15_uc010qhx.1_Frame_Shift_Del_p.E543fs|PCDH15_uc010qhy.1_Frame_Shift_Del_p.E548fs|PCDH15_uc010qhz.1_Frame_Shift_Del_p.E543fs|PCDH15_uc010qia.1_Frame_Shift_Del_p.E521fs|PCDH15_uc010qib.1_Frame_Shift_Del_p.E521fs|PCDH15_uc001jjw.2_Frame_Shift_Del_p.E543fs NM_033056 NP_149045 Q96QU1 PCD15_HUMAN protocadherin 15 isoform CD1-4 precursor 543 Cadherin 5.|Extracellular (Potential). equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse calcium ion binding pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2) 13 Melanoma(3;0.117)|Lung SC(717;0.238) TATGTGATCTCCCCATTTGAC 0.458 0.47 102 89 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 91 12 MLL 4297 broad.mit.edu 37 11 118366492 118366493 + Frame_Shift_Ins INS - C C rs140150911 by1000genomes NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr11:118366492_118366493insC uc001pta.2 + 19 5455_5456 c.5432_5433insC c.(5431-5433)AACfs p.N1811fs MLL_uc001ptb.2_Frame_Shift_Ins_p.N1814fs NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 1811 apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) CGAGAGGAAAACAGCCACACTG 0.450 0.13 105 16 GRIN2B 2904 broad.mit.edu 37 12 13722807 13722807 + Frame_Shift_Del DEL C - - NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr12:13722807delC uc001rbt.2 - 11 2495 c.2316delG c.(2314-2316)TGGfs p.W772fs NM_000834 NP_000825 Q13224 NMDE2_HUMAN N-methyl-D-aspartate receptor subunit 2B 772 Extracellular (Potential). response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding central_nervous_system(4)|ovary(3)|skin(3)|lung(2) 12 Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043) CCTGGCGCTTCCACCCAGAAT 0.522 0.49 61 59 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 24 148 BRIP1 83990 broad.mit.edu 37 17 59763496 59763496 + Frame_Shift_Del DEL T - - NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr17:59763496delT uc002izk.1 - 19 2747 c.2606delA c.(2605-2607)CAGfs p.Q869fs BRIP1_uc002izl.1_Frame_Shift_Del_p.Q250fs NM_032043 NP_114432 Q9BX63 FANCJ_HUMAN BRCA1 interacting protein C-terminal helicase 1 869 DNA damage checkpoint|double-strand break repair|regulation of transcription from RNA polymerase II promoter cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding ovary(1) 1 TGAATGGTGCTGAATCTGCTG 0.343 0.56 58 75 LAMA1 284217 broad.mit.edu 37 18 7014041 7014041 + Frame_Shift_Del DEL A - - NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr18:7014041delA uc002knm.2 - 23 3230 c.3136delT c.(3136-3138)TGCfs p.C1046fs LAMA1_uc010wzj.1_Frame_Shift_Del_p.C522fs NM_005559 NP_005550 P25391 LAMA1_HUMAN laminin, alpha 1 precursor 1046 Laminin EGF-like 12. axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development extracellular space|laminin-1 complex|laminin-3 complex extracellular matrix structural constituent|receptor binding ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1) 21 Colorectal(10;0.172) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) ACGAGACTGCAATTGCAGGCC 0.478 0.56 47 59 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 93 315 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes NCIH1573_LUNG NA NCIH1573_LUNG NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.17 75 15 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1581_LUNG NA NCIH1581_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.65 18 34 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1581_LUNG NA NCIH1581_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 39 44 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1581_LUNG NA NCIH1581_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.84 6 32 APC 324 broad.mit.edu 37 5 112174604 112174605 + Frame_Shift_Ins INS - G G NCIH1581_LUNG NA NCIH1581_LUNG NA g.chr5:112174604_112174605insG uc010jby.2 + 16 3693_3694 c.3313_3314insG c.(3313-3315)CGGfs p.R1105fs APC_uc011cvt.1_Frame_Shift_Ins_p.R1087fs|APC_uc003kpz.3_Frame_Shift_Ins_p.R1105fs|APC_uc003kpy.3_Frame_Shift_Ins_p.R1105fs|APC_uc010jbz.2_Frame_Shift_Ins_p.R822fs|APC_uc010jca.2_Frame_Shift_Ins_p.R405fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1105 Ser-rich.|Responsible for down-regulation through a process mediated by direct ubiquitination. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.?(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) ATACAGGTCACGGGGAGCCAAT 0.396 0.89 5 40 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH1581_LUNG NA NCIH1581_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.39 14 9 TFR2 7036 broad.mit.edu 37 7 100224483 100224484 + Frame_Shift_Ins INS - C C NCIH1581_LUNG NA NCIH1581_LUNG NA g.chr7:100224483_100224484insC uc003uvv.1 - 17 2079_2080 c.2038_2039insG c.(2038-2040)GACfs p.D680fs TFR2_uc010lhc.1_Frame_Shift_Ins_p.D221fs|TFR2_uc003uvu.1_Frame_Shift_Ins_p.D509fs NM_003227 NP_003218 Q9UP52 TFR2_HUMAN transferrin receptor 2 680 Extracellular (Potential). cellular iron ion homeostasis|iron ion transport|proteolysis cytoplasm|integral to plasma membrane peptidase activity|transferrin receptor activity ovary(1)|pancreas(1) 2 Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439) CCGGATGTAGTCCCCCCGCGCC 0.698 0.35 83 45 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1581_LUNG NA NCIH1581_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 35 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH1581_LUNG NA NCIH1581_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.65 227 423 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1581_LUNG NA NCIH1581_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 218 86 ATXN2 6311 broad.mit.edu 37 12 112036783 112036791 + In_Frame_Del DEL TGCTGCTGC - - NCIH1581_LUNG NA NCIH1581_LUNG NA g.chr12:112036783_112036791delTGCTGCTGC uc001tsj.2 - 1 690_698 c.528_536delGCAGCAGCA c.(526-537)CAGCAGCAGCAA>CAA p.176_179QQQQ>Q ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_RNA|ATXN2_uc001tsm.1_5'Flank NM_002973 NP_002964 Q99700 ATX2_HUMAN ataxin 2 176_179 Poly-Gln. cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network protein C-terminus binding|RNA binding ovary(1)|breast(1) 2 ctgctgctgttgctgctgctgctgctgct 0.517 0.33 8 4 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1581_LUNG NA NCIH1581_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 26 198 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1581_LUNG NA NCIH1581_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 79 345 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1581_LUNG NA NCIH1581_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 2 30 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1618_LUNG NA NCIH1618_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 2 108 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1618_LUNG NA NCIH1618_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.30 16 7 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1618_LUNG NA NCIH1618_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 76 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1618_LUNG NA NCIH1618_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 162 191 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1618_LUNG NA NCIH1618_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.54 28 33 ATXN1 6310 broad.mit.edu 37 6 16327865 16327867 + In_Frame_Del DEL TGC - - NCIH1618_LUNG NA NCIH1618_LUNG NA g.chr6:16327865_16327867delTGC uc003nbt.2 - 8 1646_1648 c.675_677delGCA c.(673-678)CAGCAC>CAC p.Q225del ATXN1_uc010jpi.2_In_Frame_Del_p.Q225del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCTGCTGAGGtgctgctgctgct 0.369 0.12 64 9 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1618_LUNG NA NCIH1618_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 19 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1618_LUNG NA NCIH1618_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 4 95 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 NCIH1618_LUNG NA NCIH1618_LUNG NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.62 12 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1618_LUNG NA NCIH1618_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 540 205 ULK3 25989 broad.mit.edu 37 15 75131050 75131050 + Frame_Shift_Del DEL C - - NCIH1618_LUNG NA NCIH1618_LUNG NA g.chr15:75131050delC uc010bkf.1 - 10 1142 c.1036delG c.(1036-1038)GCCfs p.A346fs ULK3_uc010ulp.1_Frame_Shift_Del_p.A256fs|ULK3_uc010ulq.1_Frame_Shift_Del_p.A357fs|ULK3_uc010ulr.1_Frame_Shift_Del_p.A229fs|ULK3_uc002ayv.2_Frame_Shift_Del_p.A346fs|ULK3_uc010uls.1_Frame_Shift_Del_p.A229fs NM_001099436 NP_001092906 Q6PHR2 ULK3_HUMAN unc-51-like kinase 3 346 MIT 1. cytoplasm ATP binding|protein serine/threonine kinase activity breast(2) 2 GAGACGATGGCCTTGAGCTCC 0.647 0.91 11 114 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1618_LUNG NA NCIH1618_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.78 59 214 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1618_LUNG NA NCIH1618_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 40 482 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1618_LUNG NA NCIH1618_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 8 156 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1623_LUNG NA NCIH1623_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.83 3 15 DENND4B 9909 broad.mit.edu 37 1 153907279 153907281 + In_Frame_Del DEL CTG - - NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr1:153907279_153907281delCTG uc001fdd.1 - 18 3129_3131 c.2728_2730delCAG c.(2728-2730)CAGdel p.Q910del uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) ACACctgctcctgctgctgctgc 0.463 0.10 70 8 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.23 24 7 KDR 3791 broad.mit.edu 37 4 55984857 55984857 + Frame_Shift_Del DEL G - - NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr4:55984857delG uc003has.2 - 3 574 c.272delC c.(271-273)CCAfs p.P91fs KDR_uc003hat.1_Frame_Shift_Del_p.P91fs|KDR_uc011bzx.1_Frame_Shift_Del_p.P91fs NM_002253 NP_002244 P35968 VGFR2_HUMAN kinase insert domain receptor precursor 91 Ig-like C2-type 1.|Extracellular (Potential). angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape integral to plasma membrane ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1) 33 all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101) Epithelial(7;0.189) Sorafenib(DB00398)|Sunitinib(DB01268) GATCACTTTTGGAATTGTGAG 0.483 0.53 101 114 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.45 12 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 60 61 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 31 54 RASA1 5921 broad.mit.edu 37 5 86564405 86564405 + Frame_Shift_Del DEL C - - NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr5:86564405delC uc003kiw.2 + 1 255 c.137delC c.(136-138)GCCfs p.A46fs RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_5'Flank|RASA1_uc011ctv.1_5'Flank|RASA1_uc011ctw.1_5'Flank|RASA1_uc010jaw.2_5'Flank|RASA1_uc011ctu.1_Frame_Shift_Del_p.A46fs NM_002890 NP_002881 P20936 RASA1_HUMAN RAS p21 protein activator 1 isoform 1 46 cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis cytosol|intrinsic to internal side of plasma membrane glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding upper_aerodigestive_tract(3)|ovary(1)|lung(1) 5 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) 0.000 0.33 282 137 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.33 8 4 HOXA13 3209 broad.mit.edu 37 7 27239298 27239299 + In_Frame_Ins INS - GCG GCG NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr7:27239298_27239299insGCG uc003szb.1 - 1 427_428 c.398_399insCGC c.(397-399)GCG>GCCGCG p.133_133A>AA uc003szc.1_5'Flank NM_000522 NP_000513 P31271 HXA13_HUMAN homeobox A13 133 Poly-Ala. skeletal system development nucleus sequence-specific DNA binding breast(1) 1 0.000 0.12 415 56 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 284 110 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.72 19 49 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 81 395 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1623_LUNG NA NCIH1623_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 83 FAM48B1 100130302 broad.mit.edu 37 X 24382374 24382394 + In_Frame_Del DEL TGCTGCTGCTGCTGCTGCTGC - - rs10560780 NCIH1648_LUNG NA NCIH1648_LUNG NA g.chrX:24382374_24382394delTGCTGCTGCTGCTGCTGCTGC uc011mjx.1 + 1 1497_1517 c.1497_1517delTGCTGCTGCTGCTGCTGCTGC c.(1495-1518)ATTGCTGCTGCTGCTGCTGCTGCT>ATT p.AAAAAAA507del NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 ctgctgctattgctgctgctgctgctgctgctgctgctgct 0.186 0.30 16 7 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1648_LUNG NA NCIH1648_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 6 79 CELF3 11189 broad.mit.edu 37 1 151678722 151678723 + In_Frame_Ins INS - TGC TGC NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr1:151678722_151678723insTGC uc001eys.1 - 10 1897_1898 c.1103_1104insGCA c.(1102-1104)CAA>CAGCAA p.368_368Q>QQ CELF3_uc010pdh.1_In_Frame_Ins_p.154_154Q>QQ|CELF3_uc001eyr.2_In_Frame_Ins_p.367_367Q>QQ|CELF3_uc009wmy.2_In_Frame_Ins_p.318_318Q>QQ|CELF3_uc009wmx.1_In_Frame_Ins_p.367_367Q>QQ NM_007185 NP_009116 Q5SZQ8 CELF3_HUMAN trinucleotide repeat containing 4 368 Gln-rich. nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome cytoplasm|nucleus mRNA binding|nucleotide binding ovary(1)|central_nervous_system(1) 2 gctgctgctgttgctgctgctg 0.505 0.56 27 34 FAM171B 165215 broad.mit.edu 37 2 187559029 187559030 + In_Frame_Ins INS - CAGCAG CAGCAG NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr2:187559029_187559030insCAGCAG uc002ups.2 + 1 241_242 c.129_130insCAGCAG c.(127-132)insCAGCAG p.55_56insQQ FAM171B_uc002upr.1_In_Frame_Ins_p.55_56insQQ NM_177454 NP_803237 Q6P995 F171B_HUMAN KIAA1946 55_56 Extracellular (Potential).|Gln-rich. integral to membrane DNA binding ovary(6)|breast(3)|central_nervous_system(1) 10 GCCTCATCcaacagcagcagca 0.520 0.50 5 5 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.29 52 21 BMP2K 55589 broad.mit.edu 37 4 79792082 79792083 + In_Frame_Ins INS - CAG CAG rs5859654;rs35071794 NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr4:79792082_79792083insCAG uc003hlk.2 + 11 1543_1544 c.1377_1378insCAG c.(1375-1380)insCAG p.486_487insQ BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Ins_p.486_487insQ|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486_487 Gln/His-rich. nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 GTCATCCTCACcagcagcagca 0.262 0.26 135 48 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 137 169 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 29 58 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.40 9 6 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.83 4 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 5 107 ATN1 1822 broad.mit.edu 37 12 7045892 7045909 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr12:7045892_7045909delCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1716 c.1462_1479delCAGCAGCAGCAGCAGCAG c.(1462-1479)CAGCAGCAGCAGCAGCAGdel p.QQQQQQ494del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQ494del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 494_499 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagc 0.472 0.25 65 22 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.18 128 28 AKAP6 9472 broad.mit.edu 37 14 33014828 33014828 + Frame_Shift_Del DEL G - - NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr14:33014828delG uc001wrq.2 + 4 1139 c.969delG c.(967-969)CTGfs p.L323fs AKAP6_uc010aml.2_Frame_Shift_Del_p.L320fs NM_004274 NP_004265 Q13023 AKAP6_HUMAN A-kinase anchor protein 6 323 protein targeting calcium channel complex|nuclear membrane|sarcoplasmic reticulum protein kinase A binding|receptor binding breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1) 21 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) GBM - Glioblastoma multiforme(265;0.019) GCTTAACACTGGGGGTGTCAT 0.488 0.39 373 243 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.12 112 15 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 13 174 CHERP 10523 broad.mit.edu 37 19 16640581 16640589 + In_Frame_Del DEL TGCTGCTGC - - NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr19:16640581_16640589delTGCTGCTGC uc002nei.1 - 8 1073_1081 c.999_1007delGCAGCAGCA c.(997-1008)CAGCAGCAGCAA>CAA p.333_336QQQQ>Q MED26_uc002nee.2_Intron NM_006387 NP_006378 Q8IWX8 CHERP_HUMAN calcium homeostasis endoplasmic reticulum 333_336 Gln-rich. cellular calcium ion homeostasis|negative regulation of cell proliferation|nervous system development|RNA processing endoplasmic reticulum|perinuclear region of cytoplasm RNA binding ovary(2) 2 ctgctgctgttgctgctgctgctgctgct 0.555 0.69 4 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.78 44 157 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.15 77 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 105 604 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1648_LUNG NA NCIH1648_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 6 49 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1650_LUNG NA NCIH1650_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.81 12 52 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 341 103 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.60 10 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 116 132 NKD2 85409 broad.mit.edu 37 5 1038446 1038447 + In_Frame_Ins INS - CAC CAC rs3840989 NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr5:1038446_1038447insCAC uc003jbt.1 + 10 1319_1320 c.1314_1315insCAC c.(1312-1317)insCAC p.447_448insH NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 447_448 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.12 315 45 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 29 74 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.73 3 8 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.31 22 10 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.22 266 74 EGFR 1956 broad.mit.edu 37 7 55242465 55242479 + In_Frame_Del DEL GGAATTAAGAGAAGC - - rs121913421;rs121913426;rs121913425;rs121913435;rs121913436;rs121913441;rs121913229 NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr7:55242465_55242479delGGAATTAAGAGAAGC uc003tqk.2 + 19 2481_2495 c.2235_2249delGGAATTAAGAGAAGC c.(2233-2250)AAGGAATTAAGAGAAGCA>AAA p.ELREA746del EGFR_uc010kzg.1_In_Frame_Del_p.ELREA701del|EGFR_uc011kco.1_In_Frame_Del_p.ELREA693del NM_005228 NP_005219 P00533 EGFR_HUMAN epidermal growth factor receptor isoform a 746_750 Cytoplasmic (Potential).|Protein kinase. Missing (found in a lung cancer sample). activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity p.E746_A750del(1613)|p.L747_P753>S(110)|p.L747_A750>P(74)|p.E746_S752>V(67)|p.L747_T751del(62)|p.E746_T751>A(30)|p.L747_S752del(28)|p.L747_T751>P(20)|p.E746_T751del(18)|p.L747_E749del(18)|p.K745_E749del(14)|p.E746_E749del(12)|p.E746_S752del(10)|p.L747_T751>S(7)|p.L747_P753>Q(7)|p.E746_P753>VS(6)|p.E746_A750>IP(5)|p.L747_T751>Q(5)|p.E746_T751>I(5)|p.E746_T751>V(5)|p.E746_S752>A(5)|p.E746_T751>IP(5)|p.E746_A750>QP(4)|p.E746V(4)|p.E746_S752>D(4)|p.K745_A750del(4)|p.L747S(3)|p.L747_S752>Q(3)|p.A750P(3)|p.E746_T751>VA(3)|p.E746_T751>VP(3)|p.E746_A750>RP(2)|p.E746_A750>S(2)|p.E746_S752>T(2)|p.A750_E758>P(2)|p.E746_T751>Q(2)|p.E746_T751>S(2)|p.E746_A750>DP(2)|p.E746_T751>L(2)|p.E746K(2)|p.E746_P753del(2)|p.E746_S752>I(2)|p.K745_E746insVPVAIK(2)|p.E746_A750>AP(2)|p.L747_K754>ST(1)|p.E746_A750>A(1)|p.E746_T751>P(1)|p.E746del(1)|p.A750_K754del(1)|p.L747_S752>QH(1)|p.L747P(1)|p.E746_A750>VP(1)|p.L747_K754>N(1)|p.L747_R748>FP(1)|p.K745_L747del(1)|p.L747_T751>A(1)|p.E746_P753>LS(1)|p.E746_P753>VQ(1)|p.E746_T751>LS(1)|p.A750_E758del(1)|p.E746_R748del(1)|p.I744_A750>VK(1)|p.E746I(1)|p.L747_K754del(1)|p.R748I(1)|p.E746_A750>KP(1)|p.E746_A750>EP(1) lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1) 9571 all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318) GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607) Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072) TCGCTATCAAGGAATTAAGAGAAGCAACATCTCCG 0.479 0.43 102 77 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.85 2 11 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.50 6 6 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 4 82 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 920 100 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.27 51 19 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 551 212 NCOR2 9612 broad.mit.edu 37 12 124887059 124887061 + In_Frame_Del DEL GCT - - rs67031864 NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr12:124887059_124887061delGCT uc010tba.1 - 14 1646_1648 c.1529_1531delAGC c.(1528-1533)CAGCCC>CCC p.Q510del NCOR2_uc010tay.1_In_Frame_Del_p.Q510del|NCOR2_uc010taz.1_In_Frame_Del_p.Q510del|NCOR2_uc010tbb.1_In_Frame_Del_p.Q510del|NCOR2_uc010tbc.1_In_Frame_Del_p.Q509del|NCOR2_uc001ugj.1_In_Frame_Del_p.Q510del NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 510 Poly-Gln. cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) CGGGGCATGGgctgctgctgctg 0.305 0.44 24 19 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.67 4 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 51 158 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 34 486 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1650_LUNG NA NCIH1650_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 10 134 SHROOM4 57477 broad.mit.edu 37 X 50350728 50350729 + In_Frame_Ins INS - TCC TCC rs143151534 NCIH1651_LUNG NA NCIH1651_LUNG NA g.chrX:50350728_50350729insTCC uc004dpe.2 - 6 3439_3440 c.3413_3414insGGA c.(3412-3414)GAA>GAGGAA p.1138_1138E>EE SHROOM4_uc004dpd.3_RNA NM_020717 NP_065768 Q9ULL8 SHRM4_HUMAN shroom family member 4 1138 Glu-rich. actin filament organization|brain development|cell morphogenesis|cognition apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus actin filament binding upper_aerodigestive_tract(1) 1 Ovarian(276;0.236) cttcttcttcttcctcctcctc 0.223 0.50 9 9 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1651_LUNG NA NCIH1651_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 63 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.15 1767 306 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.19 98 23 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.26 351 126 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 269 224 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 97 47 NUP153 9972 broad.mit.edu 37 6 17633077 17633078 + Splice_Site INS - AA AA rs36027788;rs147103527 NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr6:17633077_17633078insAA uc003ncd.1 - 17 2665 c.2465_splice c.e17-1 p.G822_splice NUP153_uc011dje.1_Splice_Site_p.G853_splice|NUP153_uc010jpl.1_Splice_Site_p.G780_splice NM_005124 NP_005115 P49790 NU153_HUMAN nucleoporin 153kDa carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm DNA binding|protein binding|transporter activity|zinc ion binding lung(4)|ovary(2)|breast(2)|skin(1) 9 Breast(50;0.0259)|Ovarian(93;0.0584) all_hematologic(90;0.125) all cancers(50;0.0981)|Epithelial(50;0.112) CTGAACTTCCTAAAAAAAAAAA 0.406 0.11 100 12 DAXX 1616 broad.mit.edu 37 6 33289506 33289507 + Frame_Shift_Ins INS - G G NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr6:33289506_33289507insG uc003oec.2 - 2 400_401 c.196_197insC c.(196-198)CTGfs p.L66fs DAXX_uc011drd.1_Intron|DAXX_uc011dre.1_Frame_Shift_Ins_p.L78fs|DAXX_uc003oed.2_Frame_Shift_Ins_p.L66fs|DAXX_uc010juw.2_5'UTR NM_001350 NP_001341 Q9UER7 DAXX_HUMAN death-domain associated protein isoform a 66 Necessary for interaction with USP7. activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent chromosome, centromeric region|cytosol|nucleolus|PML body androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding pancreas(18)|ovary(2)|skin(2)|prostate(1) 23 CTCTTCGAACAGCTTCTCATTC 0.475 0.45 113 91 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 2 37 IRS2 8660 broad.mit.edu 37 13 110437788 110437789 + Frame_Shift_Ins INS - G G NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr13:110437788_110437789insG uc001vqv.2 - 1 1126_1127 c.612_613insC c.(610-615)CCCAAGfs p.P204fs NM_003749 NP_003740 Q9Y4H2 IRS2_HUMAN insulin receptor substrate 2 204_205 IRS-type PTB. fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus cytosol|plasma membrane insulin receptor binding|signal transducer activity large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|skin(1)|ovary(1)|kidney(1) 8 all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155) Breast(118;0.159) all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147) 0.000 0.33 727 352 SMG1 23049 broad.mit.edu 37 16 18827626 18827645 + Frame_Shift_Del DEL TAGCCATAGCTTTCAAGAGA - - NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr16:18827626_18827645delTAGCCATAGCTTTCAAGAGA uc002dfm.2 - 58 10644_10663 c.10281_10300delTCTCTTGAAAGCTATGGCTA c.(10279-10302)CATCTCTTGAAAGCTATGGCTAAGfs p.H3427fs SMG1_uc010bwb.2_Frame_Shift_Del_p.H3287fs|SMG1_uc010bwa.2_Frame_Shift_Del_p.H2158fs NM_015092 NP_055907 Q96Q15 SMG1_HUMAN PI-3-kinase-related kinase SMG-1 3427_3434 DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation cytoplasm|nucleus ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1) 16 AGTCTTACCTTAGCCATAGCTTTCAAGAGATGTTTGACAT 0.350 0.10 953 103 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 8 59 NF1 4763 broad.mit.edu 37 17 29556992 29556992 + Frame_Shift_Del DEL G - - NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr17:29556992delG uc002hgg.2 + 22 3323 c.2990delG c.(2989-2991)AGGfs p.R997fs NF1_uc002hgh.2_Frame_Shift_Del_p.R997fs|NF1_uc010csn.1_Frame_Shift_Del_p.R857fs|NF1_uc002hgi.1_Frame_Shift_Del_p.R30fs NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 997 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2)|p.R997fs*16(1)|p.R997K(1) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) AATCTGGTCAGGTAAGCATTC 0.353 0.23 794 243 SMURF2 64750 broad.mit.edu 37 17 62589571 62589571 + Frame_Shift_Del DEL G - - NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr17:62589571delG uc002jep.1 - 4 709 c.321delC c.(319-321)CTCfs p.L107fs SMURF2_uc002jeq.1_5'UTR|SMURF2_uc002jer.1_5'UTR NM_022739 NP_073576 Q9HAU4 SMUF2_HUMAN SMAD specific E3 ubiquitin protein ligase 2 107 BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex identical protein binding|SMAD binding|ubiquitin-protein ligase activity skin(3)|lung(1) 4 Breast(5;1.32e-14) BRCA - Breast invasive adenocarcinoma(8;9.88e-12) CAGTGTCTTTGAGGCGGTTGA 0.308 0.47 312 280 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 48 326 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes NCIH1651_LUNG NA NCIH1651_LUNG NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.18 208 46 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1666_LUNG NA NCIH1666_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 9 231 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.26 1810 636 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.28 71 27 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.51 76 80 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 214 149 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 112 201 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.83 2 10 TRIM52 84851 broad.mit.edu 37 5 180687429 180687431 + In_Frame_Del DEL TCT - - rs139642393;rs3073543;rs78075294 NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr5:180687429_180687431delTCT uc003mnp.2 - 1 689_691 c.384_386delAGA c.(382-387)GAAGAG>GAG p.128_129EE>E uc003mnq.2_5'Flank NM_032765 NP_116154 Q96A61 TRI52_HUMAN tripartite motif-containing 52 128_129 Glu-rich. intracellular zinc ion binding 0 all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654) all_cancers(40;0.0106)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0588)|all_lung(500;0.149) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) all cancers(165;0.232) CTGATCTTCCTCTTCTTCTTCTT 0.453 0.69 4 9 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.60 198 299 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.19 980 236 CLK2P 1197 broad.mit.edu 37 7 23625392 23625392 + Frame_Shift_Del DEL G - - NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr7:23625392delG uc003swk.2 - 1 755 c.105delC c.(103-105)CCCfs p.P35fs NR_002711 SubName: Full=cDNA FLJ61616, highly similar to Dual specificity protein kinase CLK2 (EC 2.7.12.1); SubName: Full=CDC-like kinase 2, isoform CRA_c; SubName: Full=Putative uncharacterized protein CLK2; 0 CTTGGTGGATGGGGTAGGGCA 0.512 0.25 308 104 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 3 23 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 31 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 264 42 GRIN2B 2904 broad.mit.edu 37 12 13717082 13717084 + In_Frame_Del DEL GGA - - NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr12:13717082_13717084delGGA uc001rbt.2 - 13 3267_3269 c.3088_3090delTCC c.(3088-3090)TCCdel p.S1030del NM_000834 NP_000825 Q13224 NMDE2_HUMAN N-methyl-D-aspartate receptor subunit 2B 1030 Cytoplasmic (Potential). response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding central_nervous_system(4)|ovary(3)|skin(3)|lung(2) 12 Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043) GGCTGTGCTTGGAGGAGGGGAGG 0.586 0.81 29 126 Unknown 0 broad.mit.edu 37 12 63359550 63359552 + In_Frame_Del DEL CTG - - NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr12:63359550_63359552delCTG uc001srn.1 + 1 451_453 c.446_448delCTG c.(445-450)ACTGCT>ACT p.A159del SubName: Full=Putative uncharacterized protein RPL14P1; ACTAAGGGTActgctgctgctgc 0.374 0.38 8 5 STK11 6794 broad.mit.edu 37 19 1220579 1220579 + Splice_Site DEL G - - NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr19:1220579delG uc002lrl.1 + 5 1713 c.598_splice c.e5-1 p.A200_splice NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.?(4) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.41 165 113 STK11 6794 broad.mit.edu 37 19 1220684 1220685 + Frame_Shift_Ins INS - A A NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr19:1220684_1220685insA uc002lrl.1 + 5 1817_1818 c.702_703insA c.(700-705)TTCAAGfs p.F234fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 234_235 Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.?(2) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.45 260 209 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.32 78 37 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 157 390 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1666_LUNG NA NCIH1666_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 13 297 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1693_LUNG NA NCIH1693_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 24 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH1693_LUNG NA NCIH1693_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.27 287 105 AFF1 4299 broad.mit.edu 37 4 88035749 88035777 + Frame_Shift_Del DEL AAAGAGGAGCTGTCAGAAGTCTCCGGCAC - - rs116537098 by1000genomes NCIH1693_LUNG NA NCIH1693_LUNG NA g.chr4:88035749_88035777delAAAGAGGAGCTGTCAGAAGTCTCCGGCAC uc003hqj.3 + 11 2150_2178 c.1743_1771delAAAGAGGAGCTGTCAGAAGTCTCCGGCAC c.(1741-1773)GGAAAGAGGAGCTGTCAGAAGTCTCCGGCACAGfs p.G581fs AFF1_uc011ccz.1_Frame_Shift_Del_p.G588fs|AFF1_uc003hqk.3_Frame_Shift_Del_p.G581fs|AFF1_uc011cda.1_Frame_Shift_Del_p.G219fs NM_005935 NP_005926 P51825 AFF1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 581_591 nucleus sequence-specific DNA binding transcription factor activity breast(1) 1 Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114) OV - Ovarian serous cystadenocarcinoma(123;0.000233) 0.000 0.40 102 68 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1693_LUNG NA NCIH1693_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 71 86 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1693_LUNG NA NCIH1693_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 34 78 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH1693_LUNG NA NCIH1693_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.17 40 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1693_LUNG NA NCIH1693_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 22 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1693_LUNG NA NCIH1693_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 556 81 ABCA3 21 broad.mit.edu 37 16 2327918 2327918 + Frame_Shift_Del DEL A - - NCIH1693_LUNG NA NCIH1693_LUNG NA g.chr16:2327918delA uc002cpy.1 - 31 5583 c.4871delT c.(4870-4872)CTGfs p.L1624fs ABCA3_uc010bsk.1_Frame_Shift_Del_p.L1566fs NM_001089 NP_001080 Q99758 ABCA3_HUMAN ATP-binding cassette, sub-family A member 3 1624 response to drug integral to membrane|lamellar body|membrane fraction|plasma membrane ATP binding|ATPase activity, coupled to transmembrane movement of substances breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1) 16 Ovarian(90;0.17) GAACTCCTCCAGCGCCTCCTG 0.672 0.98 1 59 SMARCA4 6597 broad.mit.edu 37 19 11138497 11138513 + Frame_Shift_Del DEL CTTGATAGAATTCTTCC - - NCIH1693_LUNG NA NCIH1693_LUNG NA g.chr19:11138497_11138513delCTTGATAGAATTCTTCC uc002mqf.3 + 24 3537_3553 c.3253_3269delCTTGATAGAATTCTTCC c.(3253-3270)CTTGATAGAATTCTTCCCfs p.L1085fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.L1085fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.L1085fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.L1085fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.L1085fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.L1085fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.L1085fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.L1085fs|SMARCA4_uc010dxt.1_Frame_Shift_Del_p.L305fs|SMARCA4_uc002mqh.3_Frame_Shift_Del_p.L208fs|SMARCA4_uc002mqi.1_Frame_Shift_Del_p.L288fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 1085_1090 Helicase C-terminal. chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.L1085fs*32(2)|p.?(2) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) ATTTGAGCTTCTTGATAGAATTCTTCCCAAACTCCGA 0.512 0.68 25 53 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH1693_LUNG NA NCIH1693_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 194 25 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1693_LUNG NA NCIH1693_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 113 639 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1693_LUNG NA NCIH1693_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 4 121 MN1 4330 broad.mit.edu 37 22 28194769 28194769 + Frame_Shift_Del DEL C - - NCIH1693_LUNG NA NCIH1693_LUNG NA g.chr22:28194769delC uc003adj.2 - 1 2718 c.1763delG c.(1762-1764)GGCfs p.G588fs NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 588 binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 ATGCACCAGGCCGCCCTGGCC 0.716 1.00 0 15 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1694_LUNG NA NCIH1694_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 5 57 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.41 301 205 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.33 27 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 113 157 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 9 27 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.98 4 165 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 17 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.82 3 14 MOS 4342 broad.mit.edu 37 8 57026407 57026408 + In_Frame_Ins INS - CGG CGG NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr8:57026407_57026408insCGG uc011leb.1 - 1 134_135 c.134_135insCCG c.(133-135)CGG>CGCCGG p.45_45R>RR NM_005372 NP_005363 P00540 MOS_HUMAN v-mos Moloney murine sarcoma viral oncogene 45 ATP binding|protein binding|protein serine/threonine kinase activity lung(2)|ovary(1)|central_nervous_system(1) 4 Epithelial(17;0.00117)|all cancers(17;0.00879) 0.000 0.29 305 122 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 54 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 343 109 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.57 60 80 ZNF790 388536 broad.mit.edu 37 19 37310183 37310184 + Frame_Shift_Del DEL GA - - NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr19:37310183_37310184delGA uc002oew.2 - 5 1181_1182 c.1062_1063delTC c.(1060-1065)ACTCAGfs p.T354fs uc002oev.1_Intron NM_206894 NP_996777 Q6PG37 ZN790_HUMAN zinc finger protein 790 354_355 C2H2-type 6. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding upper_aerodigestive_tract(1)|skin(1) 2 Esophageal squamous(110;0.183) COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065) CTCTGATGCTGAGTTAGGTGTG 0.386 0.67 5 10 LMTK3 114783 broad.mit.edu 37 19 49001791 49001792 + Frame_Shift_Ins INS - G G NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr19:49001791_49001792insG uc002pjk.2 - 12 2621_2622 c.2621_2622insC c.(2620-2622)CCGfs p.P874fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) CCCGGGGCCCCGGGAGTGGGAG 0.718 0.10 123 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1694_LUNG NA NCIH1694_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 250 604 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1703_LUNG NA NCIH1703_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 48 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.15 896 156 MAP4K3 8491 broad.mit.edu 37 2 39505602 39505602 + Frame_Shift_Del DEL T - - NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr2:39505602delT uc002rro.2 - 24 1831 c.1740delA c.(1738-1740)GAAfs p.E580fs MAP4K3_uc002rrp.2_Frame_Shift_Del_p.E559fs|MAP4K3_uc010yns.1_Frame_Shift_Del_p.E133fs NM_003618 NP_003609 Q8IVH8 M4K3_HUMAN mitogen-activated protein kinase kinase kinase 580 CNH. JNK cascade ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity ovary(3)|lung(3)|stomach(1)|pancreas(1) 8 all_hematologic(82;0.211) AAATCCCTTCTTCGGCACCAA 0.244 0.28 142 56 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.33 12 6 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.23 197 60 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 80 112 PKHD1 5314 broad.mit.edu 37 6 51893090 51893090 + Frame_Shift_Del DEL C - - NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr6:51893090delC uc003pah.1 - 30 3700 c.3424delG c.(3424-3426)GAAfs p.E1142fs PKHD1_uc003pai.2_Frame_Shift_Del_p.E1142fs NM_138694 NP_619639 P08F94 PKHD1_HUMAN fibrocystin isoform 1 1142 Extracellular (Potential).|IPT/TIG 6; atypical. cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body protein binding|receptor activity lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1) 44 Lung NSC(77;0.0605) ACGTGGACTTCCACATCCAAA 0.567 0.35 24 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.86 3 19 GLYAT 10249 broad.mit.edu 37 11 58477306 58477307 + Frame_Shift_Ins INS - T T NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr11:58477306_58477307insT uc001nnb.2 - 6 978_979 c.823_824insA c.(823-825)ATGfs p.M275fs NM_201648 NP_964011 Q6IB77 GLYAT_HUMAN glycine-N-acyltransferase isoform a 275 acyl-CoA metabolic process|response to toxin|xenobiotic metabolic process mitochondrial matrix glycine N-acyltransferase activity|glycine N-benzoyltransferase activity 0 Breast(21;0.0044)|all_epithelial(135;0.0157) Glycine(DB00145) TGTGTAACTCATTTTTTGCATA 0.455 0.43 155 117 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 324 48 LRRK2 120892 broad.mit.edu 37 12 40626083 40626083 + Frame_Shift_Del DEL G - - NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr12:40626083delG uc001rmg.3 + 3 366 c.245delG c.(244-246)TGGfs p.W82fs NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 82 activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) CAGGTGGGTTGGTCACTTCTG 0.378 0.41 102 71 MKRN3 7681 broad.mit.edu 37 15 23811565 23811565 + Frame_Shift_Del DEL C - - NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr15:23811565delC uc001ywh.3 + 1 1112 c.636delC c.(634-636)TACfs p.Y212fs MKRN3_uc001ywi.2_Intron|MKRN3_uc010ayi.1_Frame_Shift_Del_p.Y212fs NM_005664 NP_005655 Q13064 MKRN3_HUMAN makorin ring finger protein 3 212 ribonucleoprotein complex ligase activity|nucleic acid binding|zinc ion binding lung(6)|large_intestine(2)|ovary(2) 10 all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14) all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012) GGCAGCCCTACCGGGGCCGCT 0.587 0.45 34 28 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 23 224 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 13 37 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 90 331 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1703_LUNG NA NCIH1703_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 8 70 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 NCIH1734_LUNG NA NCIH1734_LUNG NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.36 28 16 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1734_LUNG NA NCIH1734_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.76 9 29 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.14 548 89 TTN 7273 broad.mit.edu 37 2 179546149 179546149 + Frame_Shift_Del DEL T - - NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr2:179546149delT uc010zfg.1 - 134 29693 c.29469delA c.(29467-29469)AAAfs p.K9823fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.K6484fs|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10750 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GCACTGGTACTTTTTCTTCAG 0.338 0.49 136 131 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.19 39 9 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.28 116 44 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 64 80 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.66 51 97 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.93 1 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 26 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.86 2 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 369 119 CYP1A1 1543 broad.mit.edu 37 15 75013576 75013577 + Frame_Shift_Ins INS - G G NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr15:75013576_75013577insG uc002ayp.3 - 5 1251_1252 c.1129_1130insC c.(1129-1131)CGAfs p.R377fs CYP1A1_uc010bjv.2_RNA|CYP1A1_uc010bjw.2_RNA|CYP1A1_uc010bju.2_Frame_Shift_Ins_p.R113fs|CYP1A1_uc010bjx.2_Frame_Shift_Ins_p.R113fs|CYP1A1_uc002ayq.3_Frame_Shift_Ins_p.R377fs|CYP1A1_uc010bjy.2_Frame_Shift_Ins_p.R377fs|CYP1A1_uc010bjz.1_Frame_Shift_Ins_p.R113fs NM_000499 NP_000490 P04798 CP1A1_HUMAN cytochrome P450, family 1, subfamily A, 377 cellular lipid metabolic process|drug metabolic process|xenobiotic metabolic process endoplasmic reticulum membrane|microsome aromatase activity|electron carrier activity|heme binding|oxygen binding|vitamin D 24-hydroxylase activity ovary(2)|breast(2)|pancreas(1) 5 Arsenic trioxide(DB01169)|Benzphetamine(DB00865)|Bleomycin(DB00290)|Chlorzoxazone(DB00356)|Dacarbazine(DB00851)|Dactinomycin(DB00970)|Esomeprazole(DB00736)|Estrone(DB00655)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Ginseng(DB01404)|Granisetron(DB00889)|Ketoconazole(DB01026)|Menadione(DB00170)|Picrotoxin(DB00466)|Primaquine(DB01087)|Quinidine(DB00908)|Quinine(DB00468)|Thiabendazole(DB00730) GGAAGAGTGTCGGAAGGTCTCC 0.569 0.29 29 12 NR2F2 7026 broad.mit.edu 37 15 96877541 96877542 + Frame_Shift_Ins INS - C C NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr15:96877541_96877542insC uc010uri.1 + 2 1903_1904 c.679_680insC c.(679-681)GCCfs p.A227fs NR2F2_uc002btp.2_Frame_Shift_Ins_p.A94fs|NR2F2_uc010urj.1_Frame_Shift_Ins_p.A74fs|NR2F2_uc010urk.1_Frame_Shift_Ins_p.A74fs NM_021005 NP_066285 P24468 COT2_HUMAN nuclear receptor subfamily 2, group F, member 2 227 Interaction with ZFPM2 (By similarity).|Ligand-binding (By similarity). lipid metabolic process|negative regulation of cyclin-dependent protein kinase activity|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment nucleus ligand-regulated transcription factor activity|protein homodimerization activity|retinoic acid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription corepressor activity|zinc ion binding ovary(2)|breast(1) 3 Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297) OV - Ovarian serous cystadenocarcinoma(32;0.0856) 0.000 0.53 9 10 STK11 6794 broad.mit.edu 37 19 1207063 1207064 + Frame_Shift_Ins INS - TC TC NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr19:1207063_1207064insTC uc002lrl.1 + 1 1266_1267 c.151_152insTC c.(151-153)ATGfs p.M51fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 51 Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.?(3)|p.L50_D53del(1)|p.M51fs*14(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.69 307 690 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.18 137 31 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 132 365 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1734_LUNG NA NCIH1734_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 2 27 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1755_LUNG NA NCIH1755_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.99 1 71 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.42 7 5 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 124 28 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.71 109 266 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 46 113 ARID1B 57492 broad.mit.edu 37 6 157099426 157099427 + In_Frame_Ins INS - CAGCAG CAGCAG rs78253128 NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr6:157099426_157099427insCAGCAG uc003qqn.2 + 1 341_342 c.189_190insCAGCAG c.(187-192)insCAGCAG p.73_74insQQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) agcagcagcaacagcagcagca 0.193 0.30 100 43 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 2 37 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.74 19 54 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 53 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.49 605 589 NCOR2 9612 broad.mit.edu 37 12 124887058 124887059 + In_Frame_Ins INS - GCTGCT GCTGCT rs35831183;rs67031864 NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr12:124887058_124887059insGCTGCT uc010tba.1 - 14 1648_1649 c.1531_1532insAGCAGC c.(1531-1533)CCC>CAGCAGCCC p.510_511insQQ NCOR2_uc010tay.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010taz.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbb.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbc.1_In_Frame_Ins_p.509_510insQQ|NCOR2_uc001ugj.1_In_Frame_Ins_p.510_511insQQ NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 510_511 cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) GCGGGGCATGGgctgctgctgc 0.312 0.18 77 17 STK11 6794 broad.mit.edu 37 19 1221314 1221314 + Frame_Shift_Del DEL C - - rs67873004 NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr19:1221314delC uc002lrl.1 + 6 1952 c.837delC c.(835-837)GGCfs p.G279fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 279 Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.P281fs*6(2)|p.?(2)|p.Y246fs*3(1)|p.G279F(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) GCGACTGTGGCCCCCCGCTCT 0.607 0.94 3 45 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 163 99 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.30 150 64 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 112 325 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1755_LUNG NA NCIH1755_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 4 123 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1781_LUNG NA NCIH1781_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 41 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1781_LUNG NA NCIH1781_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.15 138 24 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1781_LUNG NA NCIH1781_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 90 90 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1781_LUNG NA NCIH1781_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 20 36 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH1781_LUNG NA NCIH1781_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.33 10 5 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1781_LUNG NA NCIH1781_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 2 39 PTEN 5728 broad.mit.edu 37 10 89717710 89717714 + Frame_Shift_Del DEL GCCGT - - NCIH1781_LUNG NA NCIH1781_LUNG NA g.chr10:89717710_89717714delGCCGT uc001kfb.2 + 8 1766_1770 c.735_739delGCCGT c.(733-741)CAGCCGTTAfs p.Q245fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 245_247 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.Q245*(6)|p.P246L(6)|p.R55fs*1(4)|p.P246fs*10(3)|p.L247fs*10(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.L247fs*11(1)|p.L247fs*12(1)|p.G165_*404del(1)|p.L247fs*6(1)|p.?(1)|p.F243fs*9(1)|p.L247fs*8(1)|p.P246fs*11(1)|p.P246_L247insGP(1)|p.G165_K342del(1)|p.Q245fs*20(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) AGTTCCCTCAGCCGTTACCTGTGTG 0.410 1.00 0 135 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1781_LUNG NA NCIH1781_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 241 64 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1781_LUNG NA NCIH1781_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 8 95 ERBB2 2064 broad.mit.edu 37 17 37880997 37880998 + In_Frame_Ins INS - TGT TGT rs28933369;rs144434331 NCIH1781_LUNG NA NCIH1781_LUNG NA g.chr17:37880997_37880998insTGT uc002hso.2 + 20 2564_2565 c.2326_2327insTGT c.(2326-2328)GGT>GTGTGT p.776_776G>VC ERBB2_uc002hsm.2_In_Frame_Ins_p.746_746G>VC|ERBB2_uc010cwa.2_In_Frame_Ins_p.761_761G>VC|ERBB2_uc002hsp.2_In_Frame_Ins_p.579_579G>VC|ERBB2_uc010cwb.2_In_Frame_Ins_p.776_776G>VC|ERBB2_uc010wek.1_In_Frame_Ins_p.500_500G>VC NM_004448 NP_004439 P04626 ERBB2_HUMAN erbB-2 isoform a 776 Cytoplasmic (Potential).|Protein kinase. cell proliferation|heart development|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of cell adhesion|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|protein autophosphorylation|regulation of angiogenesis|regulation of microtubule-based process|regulation of transcription, DNA-dependent|transcription, DNA-dependent|wound healing integral to membrane|nucleus|perinuclear region of cytoplasm|receptor complex ATP binding|DNA binding|epidermal growth factor receptor activity|ErbB-3 class receptor binding|identical protein binding|protein C-terminus binding|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity p.A775_G776insYVMA(19)|p.G776>VC(8)|p.G776>LC(3)|p.G776V(2)|p.G776S(2) lung(73)|central_nervous_system(16)|ovary(16)|stomach(14)|breast(9)|upper_aerodigestive_tract(5)|large_intestine(3)|liver(3)|endometrium(2)|skin(1)|pancreas(1) 143 all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052) Ovarian(249;0.0547)|Colorectal(1115;0.234) UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171) UCEC - Uterine corpus endometrioid carcinoma (308;0.0767) Lapatinib(DB01259)|Letrozole(DB01006)|Trastuzumab(DB00072) CGTGATGGCTGGTGTGGGCTCC 0.579 1.00 0 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1781_LUNG NA NCIH1781_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 140 683 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1781_LUNG NA NCIH1781_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 57 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1792_LUNG NA NCIH1792_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 22 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1792_LUNG NA NCIH1792_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.30 19 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1792_LUNG NA NCIH1792_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 98 132 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1792_LUNG NA NCIH1792_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.53 28 31 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH1792_LUNG NA NCIH1792_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.15 61 11 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH1792_LUNG NA NCIH1792_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.53 14 16 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH1792_LUNG NA NCIH1792_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.11 205 26 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1792_LUNG NA NCIH1792_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 817 294 ERBB3 2065 broad.mit.edu 37 12 56478851 56478859 + In_Frame_Del DEL CGCGTGGTG - - rs146486757;rs984896 NCIH1792_LUNG NA NCIH1792_LUNG NA g.chr12:56478851_56478859delCGCGTGGTG uc001sjh.2 + 3 500_508 c.307_315delCGCGTGGTG c.(307-315)CGCGTGGTGdel p.RVV103del ERBB3_uc009zoj.2_RNA|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_In_Frame_Del_p.RVV44del|ERBB3_uc001sjg.2_In_Frame_Del_p.RVV103del NM_001982 NP_001973 P21860 ERBB3_HUMAN erbB-3 isoform 1 precursor 103_105 Extracellular (Potential). cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity p.V104M(1) lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1) 8 OV - Ovarian serous cystadenocarcinoma(18;0.112) GCCCAACCTCCGCGTGGTGCGAGGGACCC 0.522 0.53 64 72 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH1792_LUNG NA NCIH1792_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.11 165 20 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1792_LUNG NA NCIH1792_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.25 168 57 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1792_LUNG NA NCIH1792_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 78 439 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1792_LUNG NA NCIH1792_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 6 69 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1793_LUNG NA NCIH1793_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 10 92 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.32 44 21 AFF1 4299 broad.mit.edu 37 4 87968040 87968052 + Frame_Shift_Del DEL TCCACCACCAGTC - - rs139425059 byFrequency NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr4:87968040_87968052delTCCACCACCAGTC uc003hqj.3 + 3 739_751 c.332_344delTCCACCACCAGTC c.(331-345)GTCCACCACCAGTCCfs p.V111fs AFF1_uc011ccx.1_Frame_Shift_Del_p.V52fs|AFF1_uc003hqh.1_Frame_Shift_Del_p.V118fs|AFF1_uc011ccy.1_Frame_Shift_Del_p.V118fs|AFF1_uc011ccz.1_Frame_Shift_Del_p.V118fs|AFF1_uc003hqk.3_Frame_Shift_Del_p.V111fs|AFF1_uc011cda.1_Intron NM_005935 NP_005926 P51825 AFF1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 111_115 nucleus sequence-specific DNA binding transcription factor activity breast(1) 1 Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114) OV - Ovarian serous cystadenocarcinoma(123;0.000233) CACACTAGTGTCCACCACCAGTCCATTCACACT 0.498 0.36 288 165 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 194 173 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 61 103 DGKB 1607 broad.mit.edu 37 7 14613892 14613894 + In_Frame_Del DEL TCA - - NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr7:14613892_14613894delTCA uc003ssz.2 - 19 1903_1905 c.1716_1718delTGA c.(1714-1719)GATGAG>GAG p.D572del DGKB_uc011jxt.1_In_Frame_Del_p.D553del|DGKB_uc003sta.2_In_Frame_Del_p.D572del|DGKB_uc011jxu.1_In_Frame_Del_p.D571del NM_004080 NP_004071 Q9Y6T7 DGKB_HUMAN diacylglycerol kinase, beta isoform 1 572 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation cytoplasm|plasma membrane ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding lung(5)|ovary(4)|breast(2)|skin(1) 12 Phosphatidylserine(DB00144) GTCTCCTTTCTCATCTTTGTCAT 0.365 0.43 873 647 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 10 TRPM6 140803 broad.mit.edu 37 9 77343171 77343171 + Frame_Shift_Del DEL C - - NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr9:77343171delC uc004ajl.1 - 38 6157 c.5919delG c.(5917-5919)CGGfs p.R1973fs TRPM6_uc004ajk.1_Frame_Shift_Del_p.R1968fs|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Frame_Shift_Del_p.R924fs|TRPM6_uc010mpd.1_Frame_Shift_Del_p.R806fs|TRPM6_uc010mpe.1_Frame_Shift_Del_p.R520fs|TRPM6_uc004ajj.1_Frame_Shift_Del_p.R929fs NM_017662 NP_060132 Q9BX84 TRPM6_HUMAN transient receptor potential cation channel, 1973 Alpha-type protein kinase.|Cytoplasmic (Potential). response to toxin integral to membrane ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1) 8 GTTTGAGCTTCCGGCAGCAGG 0.413 0.98 11 474 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 322 62 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.62 5 8 MYH8 4626 broad.mit.edu 37 17 10314145 10314145 + Frame_Shift_Del DEL C - - rs139038037 NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr17:10314145delC uc002gmm.2 - 15 1631 c.1536delG c.(1534-1536)ACGfs p.T512fs uc002gml.1_Intron NM_002472 NP_002463 P13535 MYH8_HUMAN myosin, heavy chain 8, skeletal muscle, 512 Myosin head-like. muscle filament sliding cytosol|muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle skin(6)|ovary(3)|breast(2) 11 AGTCAATGAACGTCCACTCGA 0.483 0.27 341 128 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.59 34 49 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.64 10 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 58 336 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1793_LUNG NA NCIH1793_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 21 289 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1836_LUNG NA NCIH1836_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 46 F8 2157 broad.mit.edu 37 X 154156923 154156924 + Frame_Shift_Ins INS - G G NCIH1836_LUNG NA NCIH1836_LUNG NA g.chrX:154156923_154156924insG uc004fmt.2 - 14 5312_5313 c.5141_5142insC c.(5140-5142)ACAfs p.T1714fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1714 F5/8 type A 3.|Plastocyanin-like 5. T -> S (in HEMA; moderate). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AATAGTGTCGTGTTTTCTTTTG 0.396 0.14 49 8 ALK 238 broad.mit.edu 37 2 29416468 29416468 + Frame_Shift_Del DEL G - - NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr2:29416468delG uc002rmy.2 - 29 5392 c.4485delC c.(4483-4485)TCCfs p.S1495fs ALK_uc010ymo.1_Frame_Shift_Del_p.S427fs NM_004304 NP_004295 Q9UM73 ALK_HUMAN anaplastic lymphoma kinase precursor 1495 Cytoplasmic (Potential). protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2) haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1) 1218 Acute lymphoblastic leukemia(172;0.155) Adenosine triphosphate(DB00171) GCTTGTTTCTGGATCCGTGGA 0.537 0.34 21 11 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.54 16 19 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.39 14 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 112 152 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 15 35 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 61 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 791 420 PLEKHA5 54477 broad.mit.edu 37 12 19427887 19427888 + Frame_Shift_Ins INS - G G NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr12:19427887_19427888insG uc001reb.2 + 10 1351_1352 c.1265_1266insG c.(1264-1266)AAGfs p.K422fs PLEKHA5_uc010sie.1_Frame_Shift_Ins_p.K428fs|PLEKHA5_uc001rea.2_Frame_Shift_Ins_p.K422fs|PLEKHA5_uc009zin.2_Frame_Shift_Ins_p.K180fs|PLEKHA5_uc010sif.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc010sig.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc010sih.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc001rec.1_Frame_Shift_Ins_p.K110fs NM_019012 NP_061885 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A 422 1-phosphatidylinositol binding|protein binding ovary(1)|kidney(1)|skin(1) 3 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) AAAATCCAGAAGGGGAGGGGTC 0.470 0.13 96 14 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.16 70 13 MINK1 50488 broad.mit.edu 37 17 4794336 4794337 + Frame_Shift_Ins INS - A A NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr17:4794336_4794337insA uc010vsl.1 + 15 1853_1854 c.1657_1658insA c.(1657-1659)CAGfs p.Q553fs MINK1_uc010vsk.1_Frame_Shift_Ins_p.Q553fs|MINK1_uc010vsm.1_Frame_Shift_Ins_p.Q553fs|MINK1_uc010vsn.1_Frame_Shift_Ins_p.Q553fs|MINK1_uc010vso.1_Frame_Shift_Ins_p.Q498fs|MINK1_uc010vsp.1_Frame_Shift_Ins_p.Q43fs NM_153827 NP_722549 Q8N4C8 MINK1_HUMAN misshapen-like kinase 1 isoform 3 553 JNK cascade cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)|skin(1) 6 CCCCATCCCCCAGGCCTCCCCA 0.644 0.34 55 28 ALPK2 115701 broad.mit.edu 37 18 56149057 56149058 + Frame_Shift_Ins INS - G G NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr18:56149057_56149058insG uc002lhj.3 - 13 6724_6725 c.6510_6511insC c.(6508-6513)ACCTAAfs p.T2170fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 2170_2171 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 CAGGGACGTTAGGTTTTCTTTT 0.495 0.12 198 27 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.30 110 47 ID1 3397 broad.mit.edu 37 20 30193544 30193545 + Frame_Shift_Ins INS - G G rs11545371 NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr20:30193544_30193545insG uc002wwg.1 + 1 453_454 c.354_355insG c.(352-357)CCCGGGfs p.P118fs ID1_uc002wwh.1_Frame_Shift_Ins_p.P118fs|hsa-mir-3193|MI0014238_5'Flank NM_002165 NP_002156 P41134 ID1_HUMAN inhibitor of DNA binding 1 isoform a 118_119 angiogenesis|blood vessel endothelial cell migration|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by transcription factor localization|transforming growth factor beta receptor signaling pathway cytoplasm protein binding ovary(1) 1 all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198) Epithelial(4;1.99e-05)|all cancers(5;0.000169)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264) TTGGAACCCCCGGGGGCCGAGG 0.614 0.15 158 28 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.59 288 419 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1836_LUNG NA NCIH1836_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 106 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1838_LUNG NA NCIH1838_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.85 11 60 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.42 138 98 ACOXL 55289 broad.mit.edu 37 2 111525995 111525996 + Frame_Shift_Del DEL AG - - NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr2:111525995_111525996delAG uc002tgr.3 + 2 253_254 c.29_30delAG c.(28-30)AAGfs p.K10fs ACOXL_uc010fkc.2_Frame_Shift_Del_p.K10fs|ACOXL_uc010yxk.1_Frame_Shift_Del_p.K10fs NM_001105516 NP_001098986 Q9NUZ1 ACOXL_HUMAN acyl-Coenzyme A oxidase-like 2 10 fatty acid beta-oxidation peroxisome acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity 0 CAGAGAGTGAAGTTTGCCATGG 0.356 0.16 116 22 PHOX2B 8929 broad.mit.edu 37 4 41748014 41748028 + In_Frame_Del DEL GCCGCCGCTGCCGCG - - rs17882335 NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr4:41748014_41748028delGCCGCCGCTGCCGCG uc003gwf.3 - 3 1101_1115 c.741_755delCGCGGCAGCGGCGGC c.(739-756)GCCGCGGCAGCGGCGGCG>GCG p.247_252AAAAAA>A NM_003924 NP_003915 Q99453 PHX2B_HUMAN paired-like homeobox 2b 247_252 Poly-Ala. positive regulation of transcription from RNA polymerase II promoter nuclear chromatin RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity p.A241fs*64(1) autonomic_ganglia(7)|lung(2)|ovary(2)|central_nervous_system(1) 12 0.000 0.22 66 19 LPHN3 23284 broad.mit.edu 37 4 62845430 62845430 + Frame_Shift_Del DEL C - - NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr4:62845430delC uc010ihh.2 + 15 2924 c.2751delC c.(2749-2751)TGCfs p.C917fs LPHN3_uc003hcq.3_Frame_Shift_Del_p.C917fs|LPHN3_uc003hct.2_Frame_Shift_Del_p.C310fs NM_015236 NP_056051 Q9HAR2 LPHN3_HUMAN latrophilin 3 precursor 904 Helical; Name=2; (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity|sugar binding lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1) 18 0.000 0.98 13 573 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 212 271 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 18 49 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.25 24 8 GRM1 2911 broad.mit.edu 37 6 146755800 146755800 + Frame_Shift_Del DEL C - - NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr6:146755800delC uc010khw.1 + 9 3923 c.3453delC c.(3451-3453)TTCfs p.F1151fs GRM1_uc010khv.1_3'UTR|GRM1_uc003qll.2_3'UTR|GRM1_uc011edz.1_3'UTR|GRM1_uc011eea.1_3'UTR NM_000838 NP_000829 Q13255 GRM1_HUMAN glutamate receptor, metabotropic 1 isoform alpha 1151 Ser-rich.|Cytoplasmic (Potential). synaptic transmission integral to plasma membrane G-protein coupled receptor activity|glutamate receptor activity lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2) 19 Ovarian(120;0.0387) OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762) Acamprosate(DB00659)|L-Glutamic Acid(DB00142) 0.000 0.95 19 369 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 56 PTPRD 5789 broad.mit.edu 37 9 8340406 8340406 + Frame_Shift_Del DEL C - - NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr9:8340406delC uc003zkk.2 - 41 5901 c.5190delG c.(5188-5190)CGGfs p.R1730fs PTPRD_uc003zkp.2_Frame_Shift_Del_p.R1324fs|PTPRD_uc003zkq.2_Frame_Shift_Del_p.R1323fs|PTPRD_uc003zkr.2_Frame_Shift_Del_p.R1314fs|PTPRD_uc003zks.2_Frame_Shift_Del_p.R1323fs|PTPRD_uc003zkl.2_Frame_Shift_Del_p.R1721fs|PTPRD_uc003zkm.2_Frame_Shift_Del_p.R1717fs|PTPRD_uc003zkn.2_Frame_Shift_Del_p.R1319fs|PTPRD_uc003zko.2_Frame_Shift_Del_p.R1320fs NM_002839 NP_002830 P23468 PTPRD_HUMAN protein tyrosine phosphatase, receptor type, D 1730 Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2. transmembrane receptor protein tyrosine phosphatase signaling pathway integral to plasma membrane protein binding|transmembrane receptor protein tyrosine phosphatase activity lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1) 22 all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824) all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119) CCCAGAGCATCCGCCAGAAGT 0.478 0.98 1 42 MELK 9833 broad.mit.edu 37 9 36642994 36642994 + Frame_Shift_Del DEL T - - NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr9:36642994delT uc003zzn.2 + 11 973 c.835delT c.(835-837)TTTfs p.F279fs MELK_uc011lpm.1_Frame_Shift_Del_p.F148fs|MELK_uc011lpn.1_Frame_Shift_Del_p.F279fs|MELK_uc011lpo.1_Frame_Shift_Del_p.F85fs|MELK_uc010mll.2_Frame_Shift_Del_p.F247fs|MELK_uc011lpp.1_Frame_Shift_Del_p.F231fs|MELK_uc010mlm.2_Frame_Shift_Del_p.F208fs|MELK_uc011lpq.1_Frame_Shift_Del_p.F85fs|MELK_uc011lpr.1_Frame_Shift_Del_p.F208fs|MELK_uc011lps.1_Frame_Shift_Del_p.F199fs NM_014791 NP_055606 Q14680 MELK_HUMAN maternal embryonic leucine zipper kinase 279 cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1) 6 Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06) STAD - Stomach adenocarcinoma(86;0.228) TTTTTTGTAGTTTATTCACCT 0.269 1.00 0 37 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 448 146 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 23 227 NF1 4763 broad.mit.edu 37 17 29496977 29496978 + Frame_Shift_Ins INS - A A NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr17:29496977_29496978insA uc002hgg.2 + 5 881_882 c.548_549insA c.(547-549)ATCfs p.I183fs NF1_uc002hge.1_Frame_Shift_Ins_p.I183fs|NF1_uc002hgf.1_Frame_Shift_Ins_p.I183fs|NF1_uc002hgh.2_Frame_Shift_Ins_p.I183fs|NF1_uc010csn.1_Intron NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 183 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.E178_D186del(1) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) TTACAGTATATCAATGTGGATT 0.282 1.00 0 58 ZNF521 25925 broad.mit.edu 37 18 22805205 22805205 + Frame_Shift_Del DEL C - - NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr18:22805205delC uc002kvk.2 - 4 2924 c.2677delG c.(2677-2679)GCAfs p.A893fs ZNF521_uc010xbe.1_RNA|ZNF521_uc010dly.2_Frame_Shift_Del_p.A893fs|ZNF521_uc002kvl.2_Frame_Shift_Del_p.A673fs NM_015461 NP_056276 Q96K83 ZN521_HUMAN zinc finger protein 521 893 C2H2-type 21; degenerate. cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein domain specific binding|zinc ion binding ovary(4)|large_intestine(2)|lung(1) 7 all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991) GTGTAGGCTGCCCCACAAATG 0.517 0.54 86 99 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.82 5 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 137 438 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1838_LUNG NA NCIH1838_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 7 99 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1869_LUNG NA NCIH1869_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.35 26 14 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.44 14 11 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.27 40 15 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.32 15 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.40 9 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 69 112 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.89 16 131 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.83 3 15 POU3F2 5454 broad.mit.edu 37 6 99283172 99283173 + In_Frame_Ins INS - CAG CAG NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr6:99283172_99283173insCAG uc003ppe.2 + 1 593_594 c.423_424insCAG c.(421-426)insCAG p.149_150insQ NM_005604 NP_005595 P20265 PO3F2_HUMAN POU domain, class 3, transcription factor 2 149_150 positive regulation of cell proliferation identical protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197) BRCA - Breast invasive adenocarcinoma(108;0.0355) aacagcagcaacagcagcagca 0.465 0.29 82 33 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 1 10 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.53 7 8 TGFBR1 7046 broad.mit.edu 37 9 101867563 101867564 + Frame_Shift_Ins INS - T T NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr9:101867563_101867564insT uc004azc.2 + 1 152_153 c.76_77insT c.(76-78)GCGfs p.A26fs TGFBR1_uc004azd.2_Frame_Shift_Ins_p.A26fs NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.31 11 5 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 991 473 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.11 178 23 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.68 19 40 CREBBP 1387 broad.mit.edu 37 16 3900719 3900719 + Frame_Shift_Del DEL C - - NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr16:3900719delC uc002cvv.2 - 2 581 c.377delG c.(376-378)GGAfs p.G126fs CREBBP_uc002cvw.2_Frame_Shift_Del_p.G126fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 126 cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) 0.000 0.14 61 10 PNMT 5409 broad.mit.edu 37 17 37826206 37826206 + Frame_Shift_Del DEL A - - NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr17:37826206delA uc002hsi.1 + 3 635 c.413delA c.(412-414)GAAfs p.E138fs NM_002686 NP_002677 P11086 PNMT_HUMAN phenylethanolamine N-methyltransferase 138 catecholamine biosynthetic process|hormone biosynthetic process cytosol phenylethanolamine N-methyltransferase activity ovary(1) 1 all_cancers(6;6.59e-85)|all_epithelial(6;2.89e-103)|Breast(7;1.05e-86)|Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052) UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;3.87e-45)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171) CTGCACAGGGAATGCTGGCAG 0.652 0.16 104 20 SERPINB4 6318 broad.mit.edu 37 18 61306960 61306960 + Frame_Shift_Del DEL G - - NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr18:61306960delG uc002ljf.2 - 6 606 c.520delC c.(520-522)CTGfs p.L174fs SERPINB4_uc002lje.2_Frame_Shift_Del_p.L174fs|SERPINB4_uc002ljg.2_Intron NM_002974 NP_002965 P48594 SPB4_HUMAN serine (or cysteine) proteinase inhibitor, clade 174 immune response|regulation of proteolysis cytoplasm|extracellular region protein binding|serine-type endopeptidase inhibitor activity ovary(2)|lung(1) 3 ACAAGAACCAGTGTCGTATCA 0.348 0.29 29 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.95 2 42 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1869_LUNG NA NCIH1869_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.87 5 34 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1876_LUNG NA NCIH1876_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 3 23 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.65 6 11 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.61 9 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 43 71 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 29 54 DFNA5 1687 broad.mit.edu 37 7 24784238 24784238 + Frame_Shift_Del DEL C - - NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr7:24784238delC uc010kus.1 - 3 435 c.347delG c.(346-348)GGAfs p.G116fs DFNA5_uc003swz.2_5'UTR|DFNA5_uc003sxa.1_Frame_Shift_Del_p.G116fs|DFNA5_uc010kut.1_5'UTR|DFNA5_uc003sxb.2_Frame_Shift_Del_p.G116fs|DFNA5_uc003sxc.2_Frame_Shift_Del_p.G116fs NM_001127453 NP_001120925 O60443 DFNA5_HUMAN deafness, autosomal dominant 5 protein isoform 116 sensory perception of sound ovary(1) 1 CCTCAGGGTTCCAAATGAAGA 0.532 0.45 137 111 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.36 7 4 TMEM74 157753 broad.mit.edu 37 8 109796563 109796563 + Frame_Shift_Del DEL C - - NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr8:109796563delC uc003ymy.1 - 2 870 c.765delG c.(763-765)TGGfs p.W255fs TMEM74_uc003ymx.2_Intron NM_153015 NP_694560 Q96NL1 TMM74_HUMAN transmembrane protein 74 255 autophagy autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane ovary(1)|lung(1)|kidney(1)|skin(1) 4 OV - Ovarian serous cystadenocarcinoma(57;3.08e-10) GCTCCCCCTTCCACATGGACA 0.532 0.53 114 131 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 193 88 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.11 159 19 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 53 392 PRKCA 5578 broad.mit.edu 37 17 64731780 64731780 + Frame_Shift_Del DEL G - - NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr17:64731780delG uc002jfp.1 + 10 1274 c.1230delG c.(1228-1230)GTGfs p.V410fs PRKCA_uc002jfo.1_Frame_Shift_Del_p.V281fs NM_002737 NP_002728 P17252 KPCA_HUMAN protein kinase C, alpha 410 Protein kinase. activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1) 9 BRCA - Breast invasive adenocarcinoma(6;4.68e-09) Phosphatidylserine(DB00144)|Vitamin E(DB00163) TCCAGACAGTGGTAAGGACCC 0.552 1.00 0 41 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.67 13 26 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 115 656 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1876_LUNG NA NCIH1876_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 59 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1915_LUNG NA NCIH1915_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.86 6 37 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH1915_LUNG NA NCIH1915_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 14 10 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH1915_LUNG NA NCIH1915_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.27 174 65 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1915_LUNG NA NCIH1915_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 108 160 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH1915_LUNG NA NCIH1915_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 2 16 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH1915_LUNG NA NCIH1915_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.39 55 35 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1915_LUNG NA NCIH1915_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1915_LUNG NA NCIH1915_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 476 232 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes NCIH1915_LUNG NA NCIH1915_LUNG NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.71 7 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1915_LUNG NA NCIH1915_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 25 272 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1915_LUNG NA NCIH1915_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 110 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1930_LUNG NA NCIH1930_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.82 21 94 OBSCN 84033 broad.mit.edu 37 1 228563867 228563867 + Frame_Shift_Del DEL C - - NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr1:228563867delC uc009xez.1 + 99 22989 c.22945delC c.(22945-22947)CCCfs p.P7649fs OBSCN_uc001hsr.1_Frame_Shift_Del_p.P2278fs NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 7649 apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) 0.000 0.26 268 93 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 133 114 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 19 40 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.17 34 7 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.80 2 8 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.32 615 291 PAPPA 5069 broad.mit.edu 37 9 119124937 119124938 + Frame_Shift_Ins INS - A A NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr9:119124937_119124938insA uc004bjn.2 + 18 4795_4796 c.4414_4415insA c.(4414-4416)CAGfs p.Q1472fs PAPPA_uc011lxq.1_Frame_Shift_Ins_p.Q847fs NM_002581 NP_002572 Q13219 PAPP1_HUMAN pregnancy-associated plasma protein A 1472 Sushi 4. cell differentiation|female pregnancy cytoplasm|extracellular region|membrane metalloendopeptidase activity|zinc ion binding ovary(4)|skin(4)|pancreas(1) 9 CCATGTCTGCCAGGAGATGCAA 0.540 0.28 138 55 FADD 8772 broad.mit.edu 37 11 70049816 70049817 + Frame_Shift_Ins INS - G G NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr11:70049816_70049817insG uc001opm.2 + 1 548_549 c.251_252insG c.(250-252)GCGfs p.A84fs NM_003824 NP_003815 Q13158 FADD_HUMAN Fas-associated via death domain 84 activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction cytosol death receptor binding|identical protein binding ovary(1)|lung(1)|pancreas(1) 3 Esophageal squamous(2;1.19e-45) LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) 0.000 0.12 466 65 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 398 144 EP400 57634 broad.mit.edu 37 12 132547136 132547138 + In_Frame_Del DEL CAA - - rs60608267;rs111782215 byFrequency NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr12:132547136_132547138delCAA uc001ujn.2 + 46 8259_8261 c.8224_8226delCAA c.(8224-8226)CAAdel p.Q2748del EP400_uc001ujl.2_In_Frame_Del_p.Q2747del|EP400_uc001ujm.2_In_Frame_Del_p.Q2667del|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784 Poly-Gln.|Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) gcagcagcagcaacagcagcagc 0.325 0.12 56 8 MGA 23269 broad.mit.edu 37 15 41991322 41991322 + Frame_Shift_Del DEL G - - NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr15:41991322delG uc001zog.1 + 5 2244 c.2153delG c.(2152-2154)CGGfs p.R718fs MGA_uc010ucy.1_Frame_Shift_Del_p.R718fs|MGA_uc010ucz.1_Frame_Shift_Del_p.R718fs NM_001080541 NP_001074010 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 2 718 MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) AAGACTTTGCGGCACAAGCAG 0.289 0.55 39 47 MYH2 4620 broad.mit.edu 37 17 10451076 10451077 + Frame_Shift_Del DEL GC - - NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr17:10451076_10451077delGC uc010coi.2 - 3 289_290 c.161_162delGC c.(160-162)AGCfs p.S54fs uc002gml.1_Intron|MYH2_uc002gmp.3_Frame_Shift_Del_p.S54fs|MYH2_uc010coj.2_Frame_Shift_Del_p.S54fs NM_001100112 NP_001093582 Q9UKX2 MYH2_HUMAN myosin heavy chain IIa 54 Myosin head-like. muscle filament sliding muscle myosin complex|myosin filament|sarcomere actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1) 14 CTCCTTCTCTGCTCTGGATGGT 0.485 1.00 0 12 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.11 59 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 47 234 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1930_LUNG NA NCIH1930_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 94 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1944_LUNG NA NCIH1944_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.72 11 28 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 389 80 TTN 7273 broad.mit.edu 37 2 179395826 179395828 + In_Frame_Del DEL AGA - - NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr2:179395826_179395828delAGA uc010zfg.1 - 307 98034_98036 c.97810_97812delTCT c.(97810-97812)TCTdel p.S32604del uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.S26299del|TTN_uc010zfi.1_In_Frame_Del_p.S26232del|TTN_uc010zfj.1_In_Frame_Del_p.S26107del|TTN_uc002umq.2_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 33531 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GGTGGCGGGCAGAAGTACTTAGC 0.517 0.43 78 60 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 50 61 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.82 12 56 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.75 4 12 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.37 47 28 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 2 33 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 197 63 LRRK2 120892 broad.mit.edu 37 12 40714954 40714957 + Frame_Shift_Del DEL TTAC - - NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr12:40714954_40714957delTTAC uc001rmg.3 + 35 5255_5258 c.5134_5137delTTAC c.(5134-5139)TTACTTfs p.L1712fs LRRK2_uc009zjw.2_Frame_Shift_Del_p.L550fs|LRRK2_uc001rmi.2_Frame_Shift_Del_p.L545fs NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 1712_1713 activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) AATCAATCGATTACTTGAGATTTC 0.319 0.26 177 63 SOCS3 9021 broad.mit.edu 37 17 76354664 76354665 + Frame_Shift_Ins INS - C C NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr17:76354664_76354665insC uc002jvl.2 - 2 928_929 c.512_513insG c.(511-513)GGCfs p.G171fs NM_003955 NP_003946 O14543 SOCS3_HUMAN suppressor of cytokine signaling 3 171 anti-apoptosis|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|regulation of growth|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway cytosol protein kinase inhibitor activity ovary(1) 1 BRCA - Breast invasive adenocarcinoma(99;0.000688)|OV - Ovarian serous cystadenocarcinoma(97;0.0554) GGATCTTCTCGCCCCCGGAGTA 0.634 0.43 12 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.47 26 23 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 79 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 50 272 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1944_LUNG NA NCIH1944_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 5 38 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH1963_LUNG NA NCIH1963_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 52 MAGI1 9223 broad.mit.edu 37 3 65425586 65425591 + In_Frame_Del DEL TGCTGT - - rs62637700;rs139785185;rs35698502;rs79701778 byFrequency NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr3:65425586_65425591delTGCTGT uc003dmn.2 - 9 1759_1764 c.1233_1238delACAGCA c.(1231-1239)CAACAGCAG>CAG p.411_413QQQ>Q MAGI1_uc003dmm.2_In_Frame_Del_p.411_413QQQ>Q|MAGI1_uc003dmo.2_In_Frame_Del_p.411_413QQQ>Q|MAGI1_uc003dmp.2_In_Frame_Del_p.411_413QQQ>Q|MAGI1_uc010hny.2_In_Frame_Del_p.296_298QQQ>Q NM_001033057 NP_001028229 Q96QZ7 MAGI1_HUMAN membrane associated guanylate kinase, WW and PDZ 411_413 Poly-Gln. cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly tight junction ATP binding|protein C-terminus binding lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1) 6 Lung NSC(201;0.0016) BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133) ctgctgctgctgctgttgctgctgct 0.354 0.35 11 6 BMP2K 55589 broad.mit.edu 37 4 79792082 79792083 + In_Frame_Ins INS - CAG CAG rs5859654;rs35071794 NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr4:79792082_79792083insCAG uc003hlk.2 + 11 1543_1544 c.1377_1378insCAG c.(1375-1380)insCAG p.486_487insQ BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Ins_p.486_487insQ|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486_487 Gln/His-rich. nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 GTCATCCTCACcagcagcagca 0.262 0.14 75 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.42 98 71 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 15 35 ERBB2IP 55914 broad.mit.edu 37 5 65350015 65350017 + In_Frame_Del DEL ATA - - NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr5:65350015_65350017delATA uc003juk.1 + 21 3177_3179 c.2869_2871delATA c.(2869-2871)ATAdel p.I958del ERBB2IP_uc003jui.1_In_Frame_Del_p.I958del|ERBB2IP_uc003juj.1_In_Frame_Del_p.I958del|ERBB2IP_uc011cqx.1_In_Frame_Del_p.I958del|ERBB2IP_uc011cqy.1_In_Frame_Del_p.I958del|ERBB2IP_uc011cqz.1_Intron|ERBB2IP_uc010iwx.1_In_Frame_Del_p.I954del|ERBB2IP_uc003jul.1_In_Frame_Del_p.I954del NM_018695 NP_061165 Q96RT1 LAP2_HUMAN ERBB2 interacting protein isoform 2 958 basal protein localization|cell adhesion|cell cycle|cell growth|epidermal growth factor receptor signaling pathway|establishment or maintenance of epithelial cell apical/basal polarity|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization basement membrane|cytoplasm|hemidesmosome|nucleus ErbB-2 class receptor binding|integrin binding|structural constituent of cytoskeleton ovary(3)|lung(2)|central_nervous_system(2) 7 Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234) UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191) AGAGCCAAATATAATAAGAGGCC 0.389 0.43 78 58 FBN2 2201 broad.mit.edu 37 5 127627260 127627261 + Frame_Shift_Ins INS - T T rs34845843 byFrequency NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr5:127627260_127627261insT uc003kuu.2 - 49 6691_6692 c.6252_6253insA c.(6250-6255)CCCCCTfs p.P2084fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 2084_2085 EGF-like 35; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) ACAAAGCCAGGGGGGCAGAGGC 0.441 0.93 2 28 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.30 16 7 PTTG3P 26255 broad.mit.edu 37 8 67679936 67679936 + Frame_Shift_Del DEL T - - NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr8:67679936delT uc011leu.1 - 1 305 c.305delA c.(304-306)AACfs p.N102fs SGK3_uc003xwp.2_Intron|SGK3_uc003xwr.2_Intron NR_002734 RecName: Full=Securin-3; AltName: Full=Pituitary tumor transforming gene 3 protein; Short=hPTTG3; AltName: Full=rcPTTG1; 0 AGGAACAGAGTTTTTTGCTTT 0.418 0.41 40 28 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 19 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.67 7 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 266 124 MLL 4297 broad.mit.edu 37 11 118343686 118343689 + Frame_Shift_Del DEL GCAA - - NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr11:118343686_118343689delGCAA uc001pta.2 + 3 1835_1838 c.1812_1815delGCAA c.(1810-1815)ATGCAAfs p.M604fs MLL_uc001ptb.2_Frame_Shift_Del_p.M604fs|MLL_uc001psz.1_Frame_Shift_Del_p.M637fs|MLL_uc001ptd.1_Intron NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 604_605 apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) CTGCTCCTATGCAAGGGAAGCGAA 0.471 0.51 161 166 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.29 72 29 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 45 516 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.47 20 18 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 53 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 NCIH1963_LUNG NA NCIH1963_LUNG NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.16 65 12 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH196_LUNG NA NCIH196_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 5 38 TNFRSF4 7293 broad.mit.edu 37 1 1148411 1148411 + Frame_Shift_Del DEL C - - NCIH196_LUNG NA NCIH196_LUNG NA g.chr1:1148411delC uc001ade.2 - 3 336 c.331delG c.(331-333)GCGfs p.A111fs TNFRSF4_uc001adf.2_Frame_Shift_Del_p.A115fs NM_003327 NP_003318 P43489 TNR4_HUMAN tumor necrosis factor receptor superfamily, 111 TNFR-Cys 3; truncated.|Extracellular (Potential). immune response|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|positive regulation of B cell proliferation|positive regulation of immunoglobulin secretion|T cell proliferation integral to plasma membrane tumor necrosis factor receptor activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199) 0.000 0.30 1293 552 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH196_LUNG NA NCIH196_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.30 367 161 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH196_LUNG NA NCIH196_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 128 109 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH196_LUNG NA NCIH196_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.54 34 40 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH196_LUNG NA NCIH196_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.31 42 19 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH196_LUNG NA NCIH196_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.97 1 37 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH196_LUNG NA NCIH196_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 43 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 NCIH196_LUNG NA NCIH196_LUNG NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.56 16 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH196_LUNG NA NCIH196_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 348 95 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH196_LUNG NA NCIH196_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 2 32 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH196_LUNG NA NCIH196_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 34 161 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH196_LUNG NA NCIH196_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.33 54 27 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH196_LUNG NA NCIH196_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 71 454 FAM48B1 100130302 broad.mit.edu 37 X 24382374 24382400 + In_Frame_Del DEL TGCTGCTGCTGCTGCTGCTGCTGCTGC - - rs10560780;rs2525863 NCIH2023_LUNG NA NCIH2023_LUNG NA g.chrX:24382374_24382400delTGCTGCTGCTGCTGCTGCTGCTGCTGC uc011mjx.1 + 1 1497_1523 c.1497_1523delTGCTGCTGCTGCTGCTGCTGCTGCTGC c.(1495-1524)ATTGCTGCTGCTGCTGCTGCTGCTGCTGCT>ATT p.AAAAAAAAA509del NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 ctgctgctattgctgctgctgctgctgctgctgctgctgctgctgct 0.181 0.43 8 6 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes NCIH2023_LUNG NA NCIH2023_LUNG NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.70 3 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH2023_LUNG NA NCIH2023_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.17 33 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2023_LUNG NA NCIH2023_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 103 139 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2023_LUNG NA NCIH2023_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 39 68 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2023_LUNG NA NCIH2023_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 2 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2023_LUNG NA NCIH2023_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 534 89 FAM155A 728215 broad.mit.edu 37 13 108518686 108518687 + In_Frame_Ins INS - CTG CTG NCIH2023_LUNG NA NCIH2023_LUNG NA g.chr13:108518686_108518687insCTG uc001vql.2 - 1 774_775 c.258_259insCAG c.(256-261)insCAG p.86_87insQ NM_001080396 NP_001073865 B1AL88 F155A_HUMAN family with sequence similarity 155, member A 86_87 Poly-Gln. integral to membrane binding skin(1) 1 tgccgctgcctctgctgctgct 0.401 0.50 11 11 SMARCA4 6597 broad.mit.edu 37 19 11129671 11129671 + Frame_Shift_Del DEL C - - NCIH2023_LUNG NA NCIH2023_LUNG NA g.chr19:11129671delC uc002mqf.3 + 17 2761 c.2477delC c.(2476-2478)GCCfs p.A826fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.A826fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.A826fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.A826fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.A826fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.A826fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.A826fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.A826fs|SMARCA4_uc010dxt.1_Frame_Shift_Del_p.A46fs|SMARCA4_uc002mqh.3_5'Flank|SMARCA4_uc002mqi.1_5'Flank NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 826 Helicase ATP-binding. chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) GACAAGTGGGCCCCCTCCGTG 0.557 0.92 20 235 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2023_LUNG NA NCIH2023_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.45 133 108 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH2023_LUNG NA NCIH2023_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 76 9 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2023_LUNG NA NCIH2023_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 73 589 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2023_LUNG NA NCIH2023_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 7 103 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2029_LUNG NA NCIH2029_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 74 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 344 131 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.34 27 14 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.46 26 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 131 150 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 32 85 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.80 2 8 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.16 88 17 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 25 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.14 48 8 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.70 3 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 678 309 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.29 145 58 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.40 125 84 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 31 361 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 8 118 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 NCIH2029_LUNG NA NCIH2029_LUNG NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 0.000 0.10 330 36 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2030_LUNG NA NCIH2030_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 3 28 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 259 67 CABC1 56997 broad.mit.edu 37 1 227152918 227152919 + Frame_Shift_Ins INS - C C NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr1:227152918_227152919insC uc001hqm.1 + 8 3814_3815 c.395_396insC c.(394-396)GGCfs p.G132fs CABC1_uc010pvp.1_Frame_Shift_Ins_p.G95fs|CABC1_uc001hqn.1_Frame_Shift_Ins_p.G132fs|CABC1_uc009xeq.1_Frame_Shift_Ins_p.G80fs|CABC1_uc010pvq.1_Intron|CABC1_uc010pvr.1_5'Flank NM_020247 NP_064632 Q8NI60 ADCK3_HUMAN chaperone, ABC1 activity of bc1 complex like 132 cell death mitochondrion ATP binding|protein serine/threonine kinase activity 0 Prostate(94;0.0771) GGGTTCCCCGGCCAGGCCTCCT 0.653 0.11 108 13 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.47 20 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.60 6 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 60 105 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 1.00 0 11 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.40 33 22 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 2 12 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.10 175 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 4 54 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 333 37 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.13 156 23 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.36 7 4 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 812 444 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.45 6 5 TAF15 8148 broad.mit.edu 37 17 34171660 34171683 + In_Frame_Del DEL GGTGGCTATGGTGGGGACAGAGGC - - rs149167178;rs143659169;rs146792937 byFrequency;byFrequency NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr17:34171660_34171683delGGTGGCTATGGTGGGGACAGAGGC uc002hkd.2 + 15 1443_1466 c.1357_1380delGGTGGCTATGGTGGGGACAGAGGC c.(1357-1380)GGTGGCTATGGTGGGGACAGAGGCdel p.GGYGGDRG477del TAF15_uc002hkc.2_In_Frame_Del_p.GGYGGDRG474del NM_139215 NP_631961 Q92804 RBP56_HUMAN TBP-associated factor 15 isoform 1 477_484 Arg/Gly-rich.|10.|21 X approximate tandem repeats of D-R- [S,G](0,3)-G-G-Y-G-G. positive regulation of transcription, DNA-dependent cytoplasm|nucleus DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding TAF15/NR4A3(33) bone(33)|lung(1)|skin(1) 35 Ovarian(249;0.17) UCEC - Uterine corpus endometrioid carcinoma (308;0.0193) cagaagtgggggtggctatggtggggacagaggcggcggctatg 0.000 0.78 6 21 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 52 529 MCM3AP 8888 broad.mit.edu 37 21 47704116 47704116 + Frame_Shift_Del DEL T - - NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr21:47704116delT uc002zir.1 - 1 1121 c.1085delA c.(1084-1086)AAGfs p.K362fs C21orf57_uc002zit.1_5'Flank|C21orf57_uc002ziu.1_5'Flank|C21orf57_uc002ziv.2_5'Flank|C21orf57_uc002ziw.2_5'Flank|C21orf57_uc002zix.2_5'Flank|C21orf57_uc010gqh.2_5'Flank|C21orf57_uc002ziy.2_5'Flank NM_003906 NP_003897 O60318 MCM3A_HUMAN minichromosome maintenance complex component 3 362 DNA replication|protein import into nucleus cytosol|nucleus DNA binding|nucleotide binding large_intestine(2)|lung(1)|ovary(1)|skin(1) 5 Breast(49;0.112) GCCAGTTTCCTTTTTGGCCTC 0.493 0.50 158 157 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2030_LUNG NA NCIH2030_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 7 56 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.86 7 44 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.56 12 15 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.57 17 23 HTT 3064 broad.mit.edu 37 4 3076604 3076609 + In_Frame_Del DEL CAGCAG - - rs10618869 NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr4:3076604_3076609delCAGCAG uc011bvq.1 + 2 203_208 c.58_63delCAGCAG c.(58-63)CAGCAGdel p.QQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagc 0.330 0.25 59 20 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.68 102 213 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.39 152 97 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.60 16 24 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.99 1 93 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.51 871 893 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.36 16 9 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 20 194 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 45 177 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 69 454 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2052_PLEURA NA NCIH2052_PLEURA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 9 170 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 NCIH2066_LUNG NA NCIH2066_LUNG NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.27 176 66 HEPH 9843 broad.mit.edu 37 X 65393573 65393573 + Frame_Shift_Del DEL C - - NCIH2066_LUNG NA NCIH2066_LUNG NA g.chrX:65393573delC uc011moz.1 + 4 624 c.564delC c.(562-564)TACfs p.Y188fs HEPH_uc004dwn.2_Frame_Shift_Del_p.Y188fs|HEPH_uc004dwo.2_5'UTR|HEPH_uc010nkr.2_Frame_Shift_Del_p.Y188fs|HEPH_uc011mpa.1_Frame_Shift_Del_p.Y188fs NM_138737 NP_620074 Q9BQS7 HEPH_HUMAN hephaestin isoform a 185 Extracellular (Potential).|Plastocyanin-like 1. cellular iron ion homeostasis|copper ion transport|transmembrane transport integral to membrane|plasma membrane copper ion binding|oxidoreductase activity lung(5)|ovary(4) 9 CCTGGATCTACCATTCTCATG 0.532 0.27 213 77 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2066_LUNG NA NCIH2066_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 5 80 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 345 90 TTN 7273 broad.mit.edu 37 2 179505972 179505973 + Frame_Shift_Ins INS - G G NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr2:179505972_179505973insG uc010zfg.1 - 169 33148_33149 c.32924_32925insC c.(32923-32925)CCTfs p.P10975fs TTN_uc010zfh.1_Frame_Shift_Ins_p.P4670fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.P4603fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.P4478fs|TTN_uc010fre.1_Frame_Shift_Ins_p.P853fs|TTN_uc002umw.1_Intron|TTN_uc002umx.1_Intron NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 11902 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCCTACCTGCAGGTTTTTTAAC 0.277 0.15 79 14 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.26 35 12 RFC4 5984 broad.mit.edu 37 3 186522391 186522392 + Frame_Shift_Ins INS - G G NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr3:186522391_186522392insG uc003fqz.2 - 2 334_335 c.111_112insC c.(109-114)CCCGTTfs p.P37fs RFC4_uc011bsc.1_Frame_Shift_Ins_p.P37fs|RFC4_uc011bsd.1_Frame_Shift_Ins_p.P37fs NM_002916 NP_002907 P35249 RFC4_HUMAN replication factor C 4 37_38 cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|phosphatidylinositol-mediated signaling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair DNA replication factor C complex|nucleoplasm ATP binding|DNA clamp loader activity|protein binding breast(2)|upper_aerodigestive_tract(1)|ovary(1)|large_intestine(1) 5 all_cancers(143;2.92e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;7.41e-21) GBM - Glioblastoma multiforme(93;0.0739) ACCCAGGGAACGGGTTTGGCTT 0.401 0.15 57 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.45 31 25 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 98 135 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 15 24 CSF1R 1436 broad.mit.edu 37 5 149460397 149460397 + Frame_Shift_Del DEL C - - NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr5:149460397delC uc003lrl.2 - 2 435 c.240delG c.(238-240)GGGfs p.G80fs CSF1R_uc011dcd.1_5'UTR|CSF1R_uc010jhc.2_RNA|CSF1R_uc003lrm.2_Frame_Shift_Del_p.G80fs|CSF1R_uc011dce.1_Frame_Shift_Del_p.G80fs|CSF1R_uc011dcf.1_Frame_Shift_Del_p.G80fs NM_005211 NP_005202 P07333 CSF1R_HUMAN colony stimulating factor 1 receptor precursor 80 Ig-like C2-type 1.|Extracellular (Potential). cell proliferation|multicellular organismal development|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane|receptor complex ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity haematopoietic_and_lymphoid_tissue(38)|lung(6)|central_nervous_system(3)|liver(3)|breast(2)|endometrium(1)|ovary(1) 54 KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147) Imatinib(DB00619)|Sunitinib(DB01268) AGCGATAGGTCCCCGTGTTTT 0.612 0.92 22 257 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 1 14 MYST4 23522 broad.mit.edu 37 10 76788480 76788481 + Frame_Shift_Ins INS - C C NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr10:76788480_76788481insC uc001jwn.1 + 18 4391_4392 c.3898_3899insC c.(3898-3900)ACCfs p.T1300fs MYST4_uc001jwo.1_Frame_Shift_Ins_p.T1008fs|MYST4_uc001jwp.1_Frame_Shift_Ins_p.T1117fs NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1300 histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) AGAAGGAAAAACCAGCCCCAGT 0.510 0.14 107 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 595 331 NAV3 89795 broad.mit.edu 37 12 78604246 78604246 + Frame_Shift_Del DEL C - - NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr12:78604246delC uc001syp.2 + 40 7280 c.7107delC c.(7105-7107)AGCfs p.S2369fs NAV3_uc001syo.2_Frame_Shift_Del_p.S2347fs|NAV3_uc010sub.1_Frame_Shift_Del_p.S1826fs|NAV3_uc009zsf.2_Frame_Shift_Del_p.S1178fs NM_014903 NP_055718 Q8IVL0 NAV3_HUMAN neuron navigator 3 2369 nuclear outer membrane ATP binding|nucleoside-triphosphatase activity large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 17 ACAGCGAAAGCACCAGCCACC 0.393 0.32 69 32 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 5 59 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.37 31 18 ALPK2 115701 broad.mit.edu 37 18 56149057 56149058 + Frame_Shift_Ins INS - G G NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr18:56149057_56149058insG uc002lhj.3 - 13 6724_6725 c.6510_6511insC c.(6508-6513)ACCTAAfs p.T2170fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 2170_2171 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 CAGGGACGTTAGGTTTTCTTTT 0.495 0.13 127 19 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.40 83 56 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 64 442 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2066_LUNG NA NCIH2066_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 7 163 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2073_LUNG NA NCIH2073_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 67 ODZ1 10178 broad.mit.edu 37 X 123554591 123554591 + Frame_Shift_Del DEL C - - NCIH2073_LUNG NA NCIH2073_LUNG NA g.chrX:123554591delC uc004euj.2 - 24 4595 c.4531delG c.(4531-4533)GCAfs p.A1511fs ODZ1_uc011muj.1_Frame_Shift_Del_p.A1517fs|ODZ1_uc010nqy.2_Frame_Shift_Del_p.A1518fs NM_014253 NP_055068 Q9UKZ4 TEN1_HUMAN odz, odd Oz/ten-m homolog 1 isoform 3 1511 Extracellular (Potential).|NHL 5. immune response|negative regulation of cell proliferation|nervous system development|signal transduction extracellular region heparin binding ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1) 23 CCGAGGTCTGCCACATAGAGG 0.488 0.40 9 6 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH2073_LUNG NA NCIH2073_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.25 42 14 N4BP2 55728 broad.mit.edu 37 4 40099113 40099115 + In_Frame_Del DEL CAC - - NCIH2073_LUNG NA NCIH2073_LUNG NA g.chr4:40099113_40099115delCAC uc003guy.3 + 3 491_493 c.153_155delCAC c.(151-156)TTCACC>TTC p.T52del N4BP2_uc010ifq.2_5'UTR NM_018177 NP_060647 Q86UW6 N4BP2_HUMAN Nedd4 binding protein 2 52 CUE. cytoplasm ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding lung(3)|breast(2)|kidney(2)|ovary(1) 8 AAGAACTCTTCACCAGTATCTCA 0.414 0.43 13 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2073_LUNG NA NCIH2073_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 38 38 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2073_LUNG NA NCIH2073_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.40 35 23 ATXN1 6310 broad.mit.edu 37 6 16327898 16327909 + In_Frame_Del DEL TGCTGCTGCTGA - - rs71806515;rs66949327;rs3817753;rs59310777 by1000genomes NCIH2073_LUNG NA NCIH2073_LUNG NA g.chr6:16327898_16327909delTGCTGCTGCTGA uc003nbt.2 - 8 1604_1615 c.633_644delTCAGCAGCAGCA c.(631-645)CATCAGCAGCAGCAG>CAG p.HQQQ211del ATXN1_uc010jpi.2_In_Frame_Del_p.HQQQ211del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 211_214 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgctgctgctgctgatgctgatgct 0.392 0.38 8 5 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2073_LUNG NA NCIH2073_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 49 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2073_LUNG NA NCIH2073_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 133 36 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH2073_LUNG NA NCIH2073_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.31 9 4 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes NCIH2073_LUNG NA NCIH2073_LUNG NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.24 26 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2073_LUNG NA NCIH2073_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 10 25 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH2073_LUNG NA NCIH2073_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.34 25 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2073_LUNG NA NCIH2073_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 65 237 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2073_LUNG NA NCIH2073_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 47 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2081_LUNG NA NCIH2081_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 9 87 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH2081_LUNG NA NCIH2081_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.27 310 116 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2081_LUNG NA NCIH2081_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 51 63 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2081_LUNG NA NCIH2081_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 27 48 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH2081_LUNG NA NCIH2081_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.41 23 16 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH2081_LUNG NA NCIH2081_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.63 20 34 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH2081_LUNG NA NCIH2081_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.54 612 727 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH2081_LUNG NA NCIH2081_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 1.00 0 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2081_LUNG NA NCIH2081_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 203 105 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2081_LUNG NA NCIH2081_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.44 15 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2081_LUNG NA NCIH2081_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 85 343 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2081_LUNG NA NCIH2081_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 67 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2085_LUNG NA NCIH2085_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 3 34 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.59 30 44 TOPBP1 11073 broad.mit.edu 37 3 133342265 133342265 + Frame_Shift_Del DEL A - - NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr3:133342265delA uc003eps.2 - 18 3097 c.2965delT c.(2965-2967)TATfs p.Y989fs TOPBP1_uc003ept.1_5'UTR NM_007027 NP_008958 Q92547 TOPB1_HUMAN topoisomerase (DNA) II binding protein 1 989 BRCT 6. DNA repair|response to ionizing radiation microtubule organizing center|PML body|spindle pole DNA binding|protein C-terminus binding ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1) 7 GTATGTGGATAAAGAGATTCA 0.403 0.32 159 76 HTT 3064 broad.mit.edu 37 4 3076604 3076612 + In_Frame_Del DEL CAGCAGCAG - - rs10618869 NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr4:3076604_3076612delCAGCAGCAG uc011bvq.1 + 2 203_211 c.58_66delCAGCAGCAG c.(58-66)CAGCAGCAGdel p.QQQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagcagc 0.325 0.22 46 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.73 79 209 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 35 105 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.87 2 13 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.31 131 59 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.14 73 12 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 22 RECQL4 9401 broad.mit.edu 37 8 145738411 145738416 + In_Frame_Del DEL GGTGCA - - NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr8:145738411_145738416delGGTGCA uc003zdj.2 - 16 2601_2606 c.2569_2574delTGCACC c.(2569-2574)TGCACCdel p.CT857del NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 857_858 Missing. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) AGGGCGGCCTGGTGCAGGTGCAGGTG 0.665 0.52 13 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 29 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.51 589 622 HSP90AA1 3320 broad.mit.edu 37 14 102551254 102551255 + In_Frame_Ins INS - TTCTTT TTCTTT NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr14:102551254_102551255insTTCTTT uc001yku.3 - 5 934_935 c.744_745insAAAGAA c.(742-747)insAAAGAA p.248_249insKE HSP90AA1_uc001ykv.3_In_Frame_Ins_p.370_371insKE|HSP90AA1_uc001ykw.1_In_Frame_Ins_p.69_70insKE|HSP90AA1_uc001ykx.1_In_Frame_Ins_p.237_238insKE NM_005348 NP_005339 P07900 HS90A_HUMAN heat shock 90kDa protein 1, alpha isoform 2 248_249 axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction cytosol|melanosome|plasma membrane ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding ovary(2)|central_nervous_system(2)|prostate(1)|lung(1)|breast(1) 7 Rifabutin(DB00615) GACtctttctcttctttttctt 0.198 0.15 501 88 SRP14 6727 broad.mit.edu 37 15 40328596 40328597 + In_Frame_Ins INS - TGC TGC NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr15:40328596_40328597insTGC uc001zkq.2 - 5 420_421 c.348_349insGCA c.(346-351)insGCA p.116_117insA SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116_117 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) gctgcggcaggtgctgctgctg 0.228 0.21 64 17 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 1.00 0 13 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.25 24 8 HIPK4 147746 broad.mit.edu 37 19 40885531 40885532 + Frame_Shift_Ins INS - CC CC NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr19:40885531_40885532insCC uc002onp.2 - 4 2098_2099 c.1813_1814insGG c.(1813-1815)GCCfs p.A605fs NM_144685 NP_653286 Q8NE63 HIPK4_HUMAN homeodomain interacting protein kinase 4 605 cytoplasm ATP binding|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292) 0.000 0.61 134 209 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 45 191 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.94 14 212 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2085_LUNG NA NCIH2085_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 10 217 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2087_LUNG NA NCIH2087_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 40 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH2087_LUNG NA NCIH2087_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.36 21 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2087_LUNG NA NCIH2087_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.40 116 78 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2087_LUNG NA NCIH2087_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 48 76 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes NCIH2087_LUNG NA NCIH2087_LUNG NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.79 3 11 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH2087_LUNG NA NCIH2087_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.32 13 6 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2087_LUNG NA NCIH2087_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 23 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH2087_LUNG NA NCIH2087_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.42 33 24 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2087_LUNG NA NCIH2087_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 817 192 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH2087_LUNG NA NCIH2087_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 15 153 MYT1 4661 broad.mit.edu 37 20 62848495 62848496 + Frame_Shift_Ins INS - A A NCIH2087_LUNG NA NCIH2087_LUNG NA g.chr20:62848495_62848496insA uc002yii.2 + 11 2071_2072 c.1707_1708insA c.(1705-1710)CCCAGGfs p.P569fs MYT1_uc002yih.2_Frame_Shift_Ins_p.P271fs|MYT1_uc002yij.2_Frame_Shift_Ins_p.P201fs NM_004535 NP_004526 Q01538 MYT1_HUMAN myelin transcription factor 1 569_570 ATPRANLA -> RHTQGQLG (in Ref. 5; AAA59897). cell differentiation|nervous system development nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2) 2 all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09) CCGCCACACCCAGGGCCAACTT 0.584 0.75 14 42 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2087_LUNG NA NCIH2087_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 92 599 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2087_LUNG NA NCIH2087_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 89 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2106_LUNG NA NCIH2106_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.86 8 48 THRAP3 9967 broad.mit.edu 37 1 36769478 36769479 + Frame_Shift_Ins INS - G G NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr1:36769478_36769479insG uc001cae.3 + 12 2952_2953 c.2728_2729insG c.(2728-2730)CGGfs p.R910fs THRAP3_uc001caf.3_Frame_Shift_Ins_p.R910fs|C1orf113_uc010oia.1_5'Flank NM_005119 NP_005110 Q9Y2W1 TR150_HUMAN thyroid hormone receptor associated protein 3 910 androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter mediator complex ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding ovary(5)|lung(3)|breast(1) 9 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) GGGTCGGGGCCGGTTCATGTTC 0.594 0.14 96 15 TPRXL 348825 broad.mit.edu 37 3 14105886 14105897 + In_Frame_Del DEL CAGCAGCAGCCC - - NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr3:14105886_14105897delCAGCAGCAGCCC uc011avd.1 + 3 665_676 c.210_221delCAGCAGCAGCCC c.(208-222)AGCAGCAGCAGCCCC>AGC p.SSSP71del TPRXL_uc003byh.1_In_Frame_Del_p.SSSP71del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSP71del NR_002223 RecName: Full=Putative protein TPRXL; 0 gcagccccagcagcagcagccccagcagcagc 0.000 0.42 11 8 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.52 15 16 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.29 47 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 96 147 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.57 22 29 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.57 73 96 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 3 58 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 844 477 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.16 71 14 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.20 79 20 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.50 87 88 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 95 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 84 607 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2106_LUNG NA NCIH2106_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 8 101 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2110_LUNG NA NCIH2110_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.94 3 48 ARID1A 8289 broad.mit.edu 37 1 27023007 27023008 + In_Frame_Ins INS - GGC GGC NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr1:27023007_27023008insGGC uc001bmv.1 + 1 486_487 c.113_114insGGC c.(112-114)GAG>GAGGCG p.45_46insA ARID1A_uc001bmt.1_In_Frame_Ins_p.45_46insA|ARID1A_uc001bmu.1_In_Frame_Ins_p.45_46insA NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 45_46 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.35 172 92 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.27 284 107 SPEG 10290 broad.mit.edu 37 2 220331951 220331951 + Frame_Shift_Del DEL G - - NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr2:220331951delG uc010fwg.2 + 10 2937 c.2937delG c.(2935-2937)GTGfs p.V979fs NM_005876 NP_005867 Q15772 SPEG_HUMAN SPEG complex locus 979 Ig-like 4. muscle organ development|negative regulation of cell proliferation nucleus ATP binding|protein serine/threonine kinase activity stomach(9)|ovary(4)|central_nervous_system(1) 14 Renal(207;0.0183) Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163) ACGTGGACGTGGGGGCCGGGG 0.701 0.36 7 4 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. "regulation of transcription, DNA-dependent" membrane|nucleus "calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity" skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.36 0.3 31 13 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN "phosphoinositide-3-kinase, regulatory subunit 4" fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 48 10 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.33 141 68 BMP2K 55589 broad.mit.edu 37 4 79792119 79792136 + In_Frame_Del DEL CAGCAGCAGCAACAGCAA - - NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr4:79792119_79792136delCAGCAGCAGCAACAGCAA uc003hlk.2 + 11 1580_1597 c.1414_1431delCAGCAGCAGCAACAGCAA c.(1414-1431)CAGCAGCAGCAACAGCAAdel p.QQQQQQ478del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQQQQ478del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 478_483 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 acagcaacagcagcagcagcaacagcaacagcagcagc 0.206 0.12 201 27 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs "SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA;" GAAGAAGTCGATTAGGAGTTCA 0.545 0.55 14 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 76 125 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 5 15 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 "cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent" cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.43 24 18 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 2 20 PLAG1 5324 broad.mit.edu 37 8 57078886 57078886 + Frame_Shift_Del DEL C - - NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr8:57078886delC uc003xsq.3 - 3 1870 c.1419delG c.(1417-1419)GGGfs p.G473fs PLAG1_uc003xsr.3_Frame_Shift_Del_p.G473fs|PLAG1_uc010lyi.2_Frame_Shift_Del_p.G473fs|PLAG1_uc010lyj.2_Frame_Shift_Del_p.G391fs NM_001114635 NP_001108107 Q6DJT9 PLAG1_HUMAN pleiomorphic adenoma gene 1 isoform b 473 Activates transcription; Inhibition of nuclear import due to lack of NLS and KPNA2 interaction.|Massively activates transcription. nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding CTNNB1/PLAG1(60)|FGFR1_ENST00000447712/PLAG1(28)|CHCHD7/PLAG1(12)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|COL1A2/PLAG1(3)|TCEA1_ENST00000521604/PLAG1(3) salivary_gland(113)|soft_tissue(13)|lung(1)|central_nervous_system(1)|breast(1) 129 all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125) Epithelial(17;0.00179)|all cancers(17;0.0125) AGTGCAGAGACCCAAGCCCTA 0.493 0.21 165 44 CSPP1 79848 broad.mit.edu 37 8 68084649 68084655 + Splice_Site DEL AGGAAAA - - NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr8:68084649_68084655delAGGAAAA uc003xxi.2 + 25 2950 c.2919_splice c.e25-1 p.R973_splice CSPP1_uc003xxj.2_Splice_Site_p.R938_splice|CSPP1_uc003xxk.2_Splice_Site_p.R593_splice|CSPP1_uc010lyw.2_Splice_Site_p.R33_splice NM_001077204 NP_001070672 Q1MSJ5 CSPP1_HUMAN centrosome spindle pole associated protein 1 centrosome|microtubule|spindle ovary(3)|breast(2) 5 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153) ATTTATCTATAGGAAAAAGGAAAGGAA 0.382 0.43 30 23 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 3 88 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.55 236 294 CUBN 8029 broad.mit.edu 37 10 17113940 17113940 + Frame_Shift_Del DEL C - - NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr10:17113940delC uc001ioo.2 - 18 2384 c.2332delG c.(2332-2334)GTCfs p.V778fs NM_001081 NP_001072 O60494 CUBN_HUMAN cubilin precursor 778 CUB 3. cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1) 19 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) TTGCCACAGACTTTTCCAAGT 0.363 0.4 87 57 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.50 5 5 MAP2K5 5607 broad.mit.edu 37 15 68065065 68065066 + Frame_Shift_Ins INS - G G NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr15:68065065_68065066insG uc002aqu.2 + 21 1870_1871 c.1217_1218insG c.(1216-1218)GAAfs p.E406fs MAP2K5_uc002aqv.2_Frame_Shift_Ins_p.E396fs|MAP2K5_uc002aqw.2_Frame_Shift_Ins_p.E246fs|MAP2K5_uc002aqx.2_Frame_Shift_Ins_p.E216fs NM_145160 NP_660143 Q13163 MP2K5_HUMAN mitogen-activated protein kinase kinase 5 406 Protein kinase. nerve growth factor receptor signaling pathway ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(2) 2 CAGCCAAAAGAAAGGCCAGCAC 0.307 0.33 27 13 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.47 0.13 61 9 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.17 48 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.35 130 71 PRKCG 5582 broad.mit.edu 37 19 54392952 54392953 + Frame_Shift_Ins INS - A A NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr19:54392952_54392953insA uc002qcq.1 + 4 628_629 c.346_347insA c.(346-348)CACfs p.H116fs PRKCG_uc010eqz.1_Frame_Shift_Ins_p.H116fs|PRKCG_uc010yef.1_Frame_Shift_Ins_p.H116fs|PRKCG_uc010yeg.1_Frame_Shift_Ins_p.H116fs|PRKCG_uc010yeh.1_Intron NM_002739 NP_002730 P05129 KPCG_HUMAN "protein kinase C, gamma" 116 Phorbol-ester/DAG-type 2. activation of phospholipase C activity|cell death|intracellular signal transduction|negative regulation of protein catabolic process|negative regulation of protein ubiquitination|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of mismatch repair|synaptic transmission cytosol ATP binding|protein kinase C activity|zinc ion binding lung(4)|ovary(2)|pancreas(2)|large_intestine(1) 9 all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218) GBM - Glioblastoma multiforme(134;0.0521) CTTCTGCGACCACTGTGGCTCC 0.634 0.36 153 86 SULF2 55959 broad.mit.edu 37 20 46291876 46291876 + Frame_Shift_Del DEL G - - NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr20:46291876delG uc002xto.2 - 17 2638 c.2308delC c.(2308-2310)CTCfs p.L770fs SULF2_uc002xtr.2_Frame_Shift_Del_p.L770fs|SULF2_uc002xtq.2_Frame_Shift_Del_p.L770fs|SULF2_uc010zyd.1_Frame_Shift_Del_p.L49fs NM_018837 NP_061325 Q8IWU5 SULF2_HUMAN sulfatase 2 isoform a precursor 770 bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway cell surface|endoplasmic reticulum|extracellular space|Golgi stack arylsulfatase activity|calcium ion binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 TCACAGAAGAGGAAATTGTGA 0.527 0.28 125 48 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 58 245 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2110_LUNG NA NCIH2110_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.9 9 81 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH211_LUNG NA NCIH211_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.98 1 52 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH211_LUNG NA NCIH211_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.26 380 131 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes NCIH211_LUNG NA NCIH211_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0 0.5 6 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH211_LUNG NA NCIH211_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 43 55 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH211_LUNG NA NCIH211_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 9 16 EPHA7 2045 broad.mit.edu 37 6 93965609 93965609 + Frame_Shift_Del DEL T - - NCIH211_LUNG NA NCIH211_LUNG NA g.chr6:93965609delT uc003poe.2 - 13 2560 c.2319delA c.(2317-2319)AAAfs p.K773fs EPHA7_uc003pof.2_Frame_Shift_Del_p.K768fs|EPHA7_uc011eac.1_Frame_Shift_Del_p.K769fs NM_004440 NP_004431 Q15375 EPHA7_HUMAN ephrin receptor EphA7 precursor 773 Cytoplasmic (Potential).|Protein kinase. integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1) 28 all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142) BRCA - Breast invasive adenocarcinoma(108;0.0847) AATCTGACACTTTACAAACGA 0.408 0.25 45 15 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH211_LUNG NA NCIH211_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane "calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle" ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.67 4 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH211_LUNG NA NCIH211_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 38 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH211_LUNG NA NCIH211_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.34 444 230 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH211_LUNG NA NCIH211_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 673 245 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH211_LUNG NA NCIH211_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.34 19 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH211_LUNG NA NCIH211_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.61 34 53 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH211_LUNG NA NCIH211_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 155 443 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH211_LUNG NA NCIH211_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.96 3 67 HEPH 9843 broad.mit.edu 37 X 65393494 65393495 + Frame_Shift_Ins INS - C C NCIH2122_LUNG NA NCIH2122_LUNG NA g.chrX:65393494_65393495insC uc011moz.1 + 4 545_546 c.485_486insC c.(484-486)GGCfs p.G162fs HEPH_uc004dwn.2_Frame_Shift_Ins_p.G162fs|HEPH_uc004dwo.2_5'UTR|HEPH_uc010nkr.2_Frame_Shift_Ins_p.G162fs|HEPH_uc011mpa.1_Frame_Shift_Ins_p.G162fs NM_138737 NP_620074 Q9BQS7 HEPH_HUMAN hephaestin isoform a 159 Extracellular (Potential).|Plastocyanin-like 1. cellular iron ion homeostasis|copper ion transport|transmembrane transport integral to membrane|plasma membrane copper ion binding|oxidoreductase activity lung(5)|ovary(4) 9 CCCCCGGGGGGCAGCCATATCT 0.535 0.13 435 63 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2122_LUNG NA NCIH2122_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 10 195 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.30 1784 781 PARP1 142 broad.mit.edu 37 1 226551692 226551692 + Frame_Shift_Del DEL C - - NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr1:226551692delC uc001hqd.3 - 20 2909 c.2738delG c.(2737-2739)GGAfs p.G913fs NM_001618 NP_001609 P09874 PARP1_HUMAN poly (ADP-ribose) polymerase family, member 1 913 PARP catalytic. cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter nuclear envelope|nucleolus|transcription factor complex DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding p.G913fs*4(1) lung(3)|ovary(2)|breast(2)|skin(2)|upper_aerodigestive_tract(1) 10 Breast(184;0.133) GBM - Glioblastoma multiforme(131;0.0531) TATTGGGTCTCCCTGAGACGT 0.498 0.61 748 1171 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.25 100 34 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.48 76 71 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 211 306 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 196 95 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 22 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 532 247 RAGE 5891 broad.mit.edu 37 14 102695876 102695877 + Frame_Shift_Del DEL GT - - NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr14:102695876_102695877delGT uc001ylm.2 - 11 1325_1326 c.1099_1100delAC c.(1099-1101)ACGfs p.T367fs RAGE_uc010txv.1_Frame_Shift_Del_p.T337fs|RAGE_uc001yln.2_Frame_Shift_Del_p.T185fs|RAGE_uc001ylh.2_Intron|RAGE_uc001yli.2_RNA|RAGE_uc001yll.2_RNA|RAGE_uc001ylj.2_RNA|RAGE_uc001ylk.2_RNA NM_014226 NP_055041 Q9UQ07 MOK_HUMAN MAPK/MAK/MRK overlapping kinase 367 signal transduction Golgi apparatus ATP binding|cyclin-dependent protein kinase activity|protein binding ovary(2)|breast(1)|central_nervous_system(1) 4 GGACTGCAGCGTGGGGCTGGAG 0.569 0.57 666 878 CDH1 999 broad.mit.edu 37 16 68842427 68842444 + In_Frame_Del DEL GCCCAGAAAATGAAAAAG - - NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr16:68842427_68842444delGCCCAGAAAATGAAAAAG uc002ewg.1 + 4 612_629 c.488_505delGCCCAGAAAATGAAAAAG c.(487-507)TGCCCAGAAAATGAAAAAGGC>TGC p.PENEKG164del CDH1_uc010vlj.1_RNA|CDH1_uc010cfg.1_In_Frame_Del_p.PENEKG164del NM_004360 NP_004351 P12830 CADH1_HUMAN cadherin 1, type 1 preproprotein 164_169 Cadherin 1.|Extracellular (Potential). adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm cell adhesion molecule binding|gamma-catenin binding p.V157_Q177del(1)|p.E165_P170del(1) breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1) 243 all_neural(199;0.0189)|Ovarian(137;0.0563) Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261) CCCATCAGCTGCCCAGAAAATGAAAAAGGCCCATTTCC 0.477 0.50 112 113 STK11 6794 broad.mit.edu 37 19 1221314 1221314 + Frame_Shift_Del DEL C - - rs67873004 NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr19:1221314delC uc002lrl.1 + 6 1952 c.837delC c.(835-837)GGCfs p.G279fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 279 Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.P281fs*6(2)|p.?(2)|p.Y246fs*3(1)|p.G279F(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) GCGACTGTGGCCCCCCGCTCT 0.607 0.88 13 100 CYP24A1 1591 broad.mit.edu 37 20 52779369 52779377 + In_Frame_Del DEL ACTTCTCTA - - NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr20:52779369_52779377delACTTCTCTA uc002xwv.2 - 7 1267_1275 c.869_877delTAGAGAAGT c.(868-879)TTAGAGAAGTAT>TAT p.LEK290del CYP24A1_uc002xwu.1_In_Frame_Del_p.LEK148del|CYP24A1_uc002xww.2_In_Frame_Del_p.LEK290del NM_000782 NP_000773 Q07973 CP24A_HUMAN cytochrome P450 family 24 subfamily A 290_292 hormone biosynthetic process|osteoblast differentiation|vitamin D catabolic process|vitamin D receptor signaling pathway|xenobiotic metabolic process mitochondrial inner membrane 1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity|electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen p.L290_Y293>Y(1) upper_aerodigestive_tract(1)|ovary(1)|lung(1) 3 Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05) STAD - Stomach adenocarcinoma(23;0.206) Calcidiol(DB00146)|Calcitriol(DB00136)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Paricalcitol(DB00910) TGCTGAGAATACTTCTCTAACCGGTTGTC 0.431 0.17 338 69 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.36 310 176 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 54 308 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2122_LUNG NA NCIH2122_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 37 427 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2126_LUNG NA NCIH2126_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 7 54 PTCH2 8643 broad.mit.edu 37 1 45307582 45307582 + Frame_Shift_Del DEL C - - NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr1:45307582delC uc010olf.1 - 2 214 c.202delG c.(202-204)GCCfs p.A68fs PTCH2_uc010olg.1_5'UTR NM_003738 NP_003729 Q9Y6C5 PTC2_HUMAN patched 2 68 Helical; (Potential). protein complex assembly|spermatogenesis integral to plasma membrane hedgehog receptor activity p.A68fs*4(1) lung(6)|breast(6)|central_nervous_system(3)|skin(2)|ovary(1) 18 Acute lymphoblastic leukemia(166;0.155) AATGCCAGGGCCCCAAAGGCC 0.537 0.23 280 86 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.36 7 4 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 43 55 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.60 22 33 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.47 18 16 ADHFE1 137872 broad.mit.edu 37 8 67372670 67372670 + Frame_Shift_Del DEL C - - NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr8:67372670delC uc003xwb.3 + 13 1324 c.1290delC c.(1288-1290)ATCfs p.I430fs ADHFE1_uc003xwd.3_RNA|ADHFE1_uc003xwc.3_Frame_Shift_Del_p.I382fs|ADHFE1_uc003xwe.3_RNA|ADHFE1_uc003xwf.3_RNA|ADHFE1_uc011les.1_Frame_Shift_Del_p.I360fs NM_144650 NP_653251 Q8IWW8 HOT_HUMAN alcohol dehydrogenase, iron containing, 1 430 2-oxoglutarate metabolic process|molecular hydrogen transport mitochondrial matrix hydroxyacid-oxoacid transhydrogenase activity|metal ion binding ovary(1)|lung(1)|breast(1)|skin(1) 4 Lung NSC(129;0.197) Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226) AAGCTGATATCCCCGCACTAG 0.542 0.90 5 46 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.89 2 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 283 59 POLE 5426 broad.mit.edu 37 12 133257857 133257857 + Frame_Shift_Del DEL C - - NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr12:133257857delC uc001uks.1 - 2 115 c.71delG c.(70-72)GGCfs p.G24fs POLE_uc010tbq.1_RNA|POLE_uc009zyu.1_Frame_Shift_Del_p.G24fs NM_006231 NP_006222 Q07864 DPOE1_HUMAN DNA-directed DNA polymerase epsilon 24 base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair nucleoplasm chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding p.G24fs*30(1) ovary(3)|skin(3)|lung(1)|central_nervous_system(1) 8 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.0416) OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05) 0.000 0.26 521 183 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.19 51 12 ADAMTS18 170692 broad.mit.edu 37 16 77334227 77334228 + Frame_Shift_Ins INS - G G rs148849944 by1000genomes NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr16:77334227_77334228insG uc002ffc.3 - 17 3025_3026 c.2606_2607insC c.(2605-2607)CCAfs p.P869fs ADAMTS18_uc010chc.1_Frame_Shift_Ins_p.P457fs|ADAMTS18_uc002ffe.1_Frame_Shift_Ins_p.P565fs NM_199355 NP_955387 Q8TE60 ATS18_HUMAN ADAM metallopeptidase with thrombospondin type 1 869 Spacer. proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1) 18 TTTTTGTGGCTGGTGGAGTTCC 0.460 0.15 69 12 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 3 35 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.67 6 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 38 403 MCM3AP 8888 broad.mit.edu 37 21 47704276 47704276 + Frame_Shift_Del DEL C - - NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr21:47704276delC uc002zir.1 - 1 961 c.925delG c.(925-927)GCAfs p.A309fs C21orf57_uc002zit.1_5'Flank|C21orf57_uc002ziu.1_5'Flank|C21orf57_uc002ziv.2_5'Flank|C21orf57_uc002ziw.2_5'Flank|C21orf57_uc002zix.2_5'Flank|C21orf57_uc010gqh.2_5'Flank|C21orf57_uc002ziy.2_5'Flank NM_003906 NP_003897 O60318 MCM3A_HUMAN minichromosome maintenance complex component 3 309 DNA replication|protein import into nucleus cytosol|nucleus DNA binding|nucleotide binding p.A309fs*21(1) large_intestine(2)|lung(1)|ovary(1)|skin(1) 5 Breast(49;0.112) GAATCTTCTGCTGGCTCGTGG 0.562 0.66 42 81 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 5 49 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 NCIH2126_LUNG NA NCIH2126_LUNG NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.41 19 13 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2171_LUNG NA NCIH2171_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 3 31 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 265 85 LOC728989 728989 broad.mit.edu 37 1 146514520 146514520 + Frame_Shift_Del DEL G - - NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr1:146514520delG uc001epd.2 - 1 80 c.6delC c.(4-6)CCCfs p.P2fs NR_024442 SubName: Full=cDNA FLJ59595, highly similar to Homo sapiens phosphodiesterase 4D interacting protein, transcript variant 1, mRNA; 0 CTCTCTGGATGGGCATGGAAC 0.383 0.46 53 45 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 190 51 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.48 47 44 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.78 10 35 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.72 34 88 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.20 694 177 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.57 16 21 TGFBR1 7046 broad.mit.edu 37 9 101907057 101907058 + Frame_Shift_Ins INS - T T NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr9:101907057_101907058insT uc004azc.2 + 6 1093_1094 c.1017_1018insT c.(1015-1020)ATCTTGfs p.I339fs TGFBR1_uc004azd.2_Frame_Shift_Ins_p.I262fs|TGFBR1_uc011lvc.1_Frame_Shift_Ins_p.I270fs NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 339_340 Protein kinase.|Cytoplasmic (Potential). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) CAAAGAATATCTTGGTAAAGAA 0.371 0.55 59 71 PCDH15 65217 broad.mit.edu 37 10 55913017 55913017 + Frame_Shift_Del DEL C - - NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr10:55913017delC uc001jju.1 - 14 2022 c.1627delG c.(1627-1629)GAGfs p.E543fs PCDH15_uc010qhq.1_Frame_Shift_Del_p.E548fs|PCDH15_uc010qhr.1_Frame_Shift_Del_p.E543fs|PCDH15_uc010qhs.1_Frame_Shift_Del_p.E555fs|PCDH15_uc010qht.1_Frame_Shift_Del_p.E550fs|PCDH15_uc010qhu.1_Frame_Shift_Del_p.E543fs|PCDH15_uc001jjv.1_Frame_Shift_Del_p.E521fs|PCDH15_uc010qhv.1_Frame_Shift_Del_p.E543fs|PCDH15_uc010qhw.1_Frame_Shift_Del_p.E506fs|PCDH15_uc010qhx.1_Frame_Shift_Del_p.E543fs|PCDH15_uc010qhy.1_Frame_Shift_Del_p.E548fs|PCDH15_uc010qhz.1_Frame_Shift_Del_p.E543fs|PCDH15_uc010qia.1_Frame_Shift_Del_p.E521fs|PCDH15_uc010qib.1_Frame_Shift_Del_p.E521fs|PCDH15_uc001jjw.2_Frame_Shift_Del_p.E543fs NM_033056 NP_149045 Q96QU1 PCD15_HUMAN protocadherin 15 isoform CD1-4 precursor 543 Cadherin 5.|Extracellular (Potential). equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse calcium ion binding pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2) 13 Melanoma(3;0.117)|Lung SC(717;0.238) TATGTGATCTCCCCATTTGAC 0.458 0.96 4 98 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 282 86 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 92 1055 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 9 39 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 229 532 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2171_LUNG NA NCIH2171_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 76 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2172_LUNG NA NCIH2172_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 4 41 ARID1A 8289 broad.mit.edu 37 1 27105549 27105549 + Frame_Shift_Del DEL C - - NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr1:27105549delC uc001bmv.1 + 20 5533 c.5160delC c.(5158-5160)TTCfs p.F1720fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.F1503fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.F566fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.F48fs|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1720 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) TAGAATATTTCCGACGATGCC 0.443 0.98 2 114 DENND4B 9909 broad.mit.edu 37 1 153907279 153907281 + In_Frame_Del DEL CTG - - NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr1:153907279_153907281delCTG uc001fdd.1 - 18 3129_3131 c.2728_2730delCAG c.(2728-2730)CAGdel p.Q910del uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) ACACctgctcctgctgctgctgc 0.463 0.10 61 7 BIRC6 57448 broad.mit.edu 37 2 32740837 32740837 + Frame_Shift_Del DEL G - - NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr2:32740837delG uc010ezu.2 + 55 11483 c.11349delG c.(11347-11349)CAGfs p.Q3783fs NM_016252 NP_057336 Q9NR09 BIRC6_HUMAN baculoviral IAP repeat-containing 6 3783 anti-apoptosis|apoptosis intracellular acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1) 14 Acute lymphoblastic leukemia(172;0.155) TGATGGCACAGGTAAGACAAA 0.373 0.42 36 26 TTN 7273 broad.mit.edu 37 2 179427957 179427957 + Frame_Shift_Del DEL G - - NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr2:179427957delG uc010zfg.1 - 275 75422 c.75198delC c.(75196-75198)ACCfs p.T25066fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.T18761fs|TTN_uc010zfi.1_Frame_Shift_Del_p.T18694fs|TTN_uc010zfj.1_Frame_Shift_Del_p.T18569fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 25993 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CTTTAAGCTTGGTCACTGTGA 0.453 0.32 302 141 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 35 16 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.10 80 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.42 122 88 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.57 32 43 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.28 39 15 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 2 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.89 7 57 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.64 262 461 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.85 8 47 CNTN5 53942 broad.mit.edu 37 11 99715847 99715848 + Frame_Shift_Ins INS - T T NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr11:99715847_99715848insT uc001pga.2 + 6 769_770 c.430_431insT c.(430-432)CTGfs p.L144fs CNTN5_uc009ywv.1_Frame_Shift_Ins_p.L144fs|CNTN5_uc001pfz.2_Frame_Shift_Ins_p.L144fs|CNTN5_uc001pgb.2_Frame_Shift_Ins_p.L70fs NM_014361 NP_055176 O94779 CNTN5_HUMAN contactin 5 isoform long 144 Ig-like C2-type 1. cell adhesion anchored to membrane|plasma membrane protein binding skin(3)|ovary(2)|pancreas(2)|breast(1) 8 all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219) BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196) AGAAATAGATCTGGAAAGTGAT 0.366 0.68 41 89 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.29 40 16 RASA3 22821 broad.mit.edu 37 13 114748807 114748807 + Frame_Shift_Del DEL A - - NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr13:114748807delA uc001vui.2 - 24 2587 c.2456delT c.(2455-2457)TTCfs p.F819fs RASA3_uc010tkk.1_Frame_Shift_Del_p.F787fs|RASA3_uc001vuj.2_Frame_Shift_Del_p.F436fs NM_007368 NP_031394 Q14644 RASA3_HUMAN RAS p21 protein activator 3 819 intracellular signal transduction|negative regulation of Ras protein signal transduction cytoplasm|intrinsic to internal side of plasma membrane calcium-release channel activity|metal ion binding|Ras GTPase activator activity lung(3)|skin(1) 4 Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218) all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188) BRCA - Breast invasive adenocarcinoma(86;0.128) GTAGTTCTGGAAGCTCTTGTC 0.617 0.92 6 65 AKAP6 9472 broad.mit.edu 37 14 33291267 33291267 + Frame_Shift_Del DEL G - - NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr14:33291267delG uc001wrq.2 + 13 4418 c.4248delG c.(4246-4248)GAGfs p.E1416fs NM_004274 NP_004265 Q13023 AKAP6_HUMAN A-kinase anchor protein 6 1416 protein targeting calcium channel complex|nuclear membrane|sarcoplasmic reticulum protein kinase A binding|receptor binding breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1) 21 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) GBM - Glioblastoma multiforme(265;0.019) TTACAGATGAGGGGGAAAGCA 0.408 0.54 121 144 ATP10A 57194 broad.mit.edu 37 15 25971191 25971191 + Frame_Shift_Del DEL G - - rs147326935 NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr15:25971191delG uc010ayu.2 - 5 992 c.886delC c.(886-888)CGCfs p.R296fs NM_024490 NP_077816 O60312 AT10A_HUMAN ATPase, class V, type 10A 296 Cytoplasmic (Potential). ATP biosynthetic process|regulation of cell shape integral to membrane|plasma membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity pancreas(2)|ovary(1)|breast(1)|liver(1) 5 all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125) all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244) CGCTTGTAGCGGGGCCCACTG 0.552 0.41 146 102 CDH11 1009 broad.mit.edu 37 16 65025791 65025791 + Frame_Shift_Del DEL C - - NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr16:65025791delC uc002eoi.2 - 6 1125 c.691delG c.(691-693)GAGfs p.E231fs CDH11_uc010cdn.2_RNA|CDH11_uc002eoj.2_Frame_Shift_Del_p.E231fs|CDH11_uc010vin.1_Frame_Shift_Del_p.E105fs NM_001797 NP_001788 P55287 CAD11_HUMAN cadherin 11, type 2 preproprotein 231 Cadherin 2.|Extracellular (Potential). adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development integral to membrane|plasma membrane calcium ion binding|protein binding lung(10)|ovary(3)|skin(1) 14 Ovarian(137;0.0973) OV - Ovarian serous cystadenocarcinoma(108;0.205) ACGTGGTACTCCTCCTTGGCC 0.498 0.74 90 250 CDH11 1009 broad.mit.edu 37 16 65032684 65032684 + Frame_Shift_Del DEL C - - NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr16:65032684delC uc002eoi.2 - 4 738 c.304delG c.(304-306)GTGfs p.V102fs CDH11_uc010cdn.2_RNA|CDH11_uc002eoj.2_Frame_Shift_Del_p.V102fs|CDH11_uc010vin.1_5'UTR|CDH11_uc010vio.1_Frame_Shift_Del_p.V102fs NM_001797 NP_001788 P55287 CAD11_HUMAN cadherin 11, type 2 preproprotein 102 Extracellular (Potential).|Cadherin 1. adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development integral to membrane|plasma membrane calcium ion binding|protein binding lung(10)|ovary(3)|skin(1) 14 Ovarian(137;0.0973) OV - Ovarian serous cystadenocarcinoma(108;0.205) TCATCAATCACAAAAATGGTT 0.453 0.36 269 153 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 6 59 TP53 7157 broad.mit.edu 37 17 7579471 7579471 + Frame_Shift_Del DEL G - - rs56275308 NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr17:7579471delG uc002gim.2 - 4 410 c.216delC c.(214-216)CCCfs p.P72fs TP53_uc002gig.1_Frame_Shift_Del_p.P72fs|TP53_uc002gih.2_Frame_Shift_Del_p.P72fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.P72fs|TP53_uc010cni.1_Frame_Shift_Del_p.P72fs|TP53_uc002gij.2_Frame_Shift_Del_p.P72fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.P33fs|TP53_uc010cnk.1_Frame_Shift_Del_p.P87fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 72 Interaction with WWOX.|Interaction with HRMT1L2. P -> C (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> L (in a sporadic cancer; somatic mutation).|P -> H (in sporadic cancers; somatic mutation).|P -> G (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.R72fs*51(6)|p.G59fs*23(3)|p.R72C(2)|p.V73fs*76(2)|p.R72H(2)|p.V73fs*9(1)|p.R65fs*38(1)|p.E68fs*76(1)|p.V73fs*50(1)|p.D48fs*55(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.D57_A76del20(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.47 364 329 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.38 13 8 UBE2O 63893 broad.mit.edu 37 17 74392741 74392741 + Frame_Shift_Del DEL G - - NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr17:74392741delG uc002jrm.3 - 14 2342 c.2277delC c.(2275-2277)CCCfs p.P759fs UBE2O_uc002jrn.3_Frame_Shift_Del_p.P759fs|UBE2O_uc002jrl.3_Frame_Shift_Del_p.P363fs NM_022066 NP_071349 Q9C0C9 UBE2O_HUMAN ubiquitin-conjugating enzyme E2O 759 ATP binding|ubiquitin-protein ligase activity breast(2)|skin(2)|lung(1) 5 GGGGTGGGATGGGGGGCTCCT 0.642 0.91 7 67 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 144 94 MARK4 57787 broad.mit.edu 37 19 45762391 45762391 + Frame_Shift_Del DEL G - - NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr19:45762391delG uc002pbb.1 + 2 201 c.196delG c.(196-198)GGGfs p.G66fs MARK4_uc002paz.1_Intron|MARK4_uc002pba.1_Frame_Shift_Del_p.G66fs Q96L34 MARK4_HUMAN RecName: Full=MAP/microtubule affinity-regulating kinase 4; EC=2.7.11.1; AltName: Full=MAP/microtubule affinity-regulating kinase-like 1; 66 ATP (By similarity).|Protein kinase. microtubule bundle formation|nervous system development|positive regulation of programmed cell death centrosome|neuron projection ATP binding|gamma-tubulin binding|microtubule binding|protein serine/threonine kinase activity|tau-protein kinase activity|ubiquitin binding central_nervous_system(2)|large_intestine(1) 3 all_neural(266;0.224)|Ovarian(192;0.231) OV - Ovarian serous cystadenocarcinoma(262;0.0102) GAGGACCATTGGGAAGGGCAA 0.657 0.45 65 54 ERCC2 2068 broad.mit.edu 37 19 45867313 45867313 + Frame_Shift_Del DEL C - - NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr19:45867313delC uc002pbj.2 - 10 927 c.880delG c.(880-882)GAGfs p.E294fs ERCC2_uc002pbi.2_5'Flank|ERCC2_uc010ejz.2_Frame_Shift_Del_p.E216fs|ERCC2_uc002pbk.2_Frame_Shift_Del_p.E270fs|ERCC2_uc002pbl.3_Frame_Shift_Del_p.E270fs|ERCC2_uc010xxj.1_RNA NM_000400 NP_000391 P18074 ERCC2_HUMAN excision repair cross-complementing rodent 294 cell cycle checkpoint|chromosome segregation|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|UV protection|viral reproduction cytoplasm|holo TFIIH complex|MMXD complex 5'-3' DNA helicase activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding|protein C-terminus binding|protein N-terminus binding lung(2)|pancreas(1) 3 Ovarian(192;0.0728)|all_neural(266;0.112) OV - Ovarian serous cystadenocarcinoma(262;0.0226) GCGCTGGCCTCCCGCAGCCCC 0.731 0.47 26 23 ZNF331 55422 broad.mit.edu 37 19 54080223 54080223 + Frame_Shift_Del DEL G - - NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr19:54080223delG uc002qbx.1 + 7 1843 c.409delG c.(409-411)GGGfs p.G137fs ZNF331_uc002qby.1_Frame_Shift_Del_p.G137fs|ZNF331_uc002qbz.1_Frame_Shift_Del_p.G137fs|ZNF331_uc002qca.1_Frame_Shift_Del_p.G137fs|ZNF331_uc010eqr.1_Frame_Shift_Del_p.G137fs|ZNF331_uc002qcb.1_Frame_Shift_Del_p.G137fs|ZNF331_uc002qcc.1_Frame_Shift_Del_p.G137fs|ZNF331_uc002qcd.1_Frame_Shift_Del_p.G137fs NM_018555 NP_061025 Q9NQX6 ZN331_HUMAN zinc finger protein 331 137 C2H2-type 1. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding skin(3)|upper_aerodigestive_tract(1)|ovary(1)|lung(1) 6 GBM - Glioblastoma multiforme(134;0.00555) TAAGGACTGTGGGAAGGCCTT 0.413 0.95 7 134 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 144 873 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 7 121 MED15 51586 broad.mit.edu 37 22 20918916 20918918 + In_Frame_Del DEL CAG - - NCIH2172_LUNG NA NCIH2172_LUNG NA g.chr22:20918916_20918918delCAG uc002zsp.2 + 6 711_713 c.631_633delCAG c.(631-633)CAGdel p.Q218del MED15_uc002zsn.1_In_Frame_Del_p.Q137del|MED15_uc002zso.2_In_Frame_Del_p.Q147del|MED15_uc002zsq.2_In_Frame_Del_p.Q218del|MED15_uc010gso.2_In_Frame_Del_p.Q218del|MED15_uc002zsr.2_In_Frame_Del_p.Q192del|MED15_uc011ahs.1_In_Frame_Del_p.Q192del|MED15_uc011aht.1_In_Frame_Del_p.Q192del|MED15_uc002zss.2_In_Frame_Del_p.Q137del|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 218 Poly-Gln. Missing (in Ref. 4; CAG30423). regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) gcagcagctccagcagcagcagc 0.187 0.40 38 25 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2196_LUNG NA NCIH2196_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 3 46 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 471 136 YSK4 80122 broad.mit.edu 37 2 135757546 135757546 + Frame_Shift_Del DEL G - - NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr2:135757546delG uc002tue.1 - 4 306 c.275delC c.(274-276)CCTfs p.P92fs YSK4_uc010fne.1_Frame_Shift_Del_p.P64fs|YSK4_uc002tuf.1_Frame_Shift_Del_p.P92fs|YSK4_uc010fnc.1_Frame_Shift_Del_p.P92fs|YSK4_uc010fnd.1_Intron|YSK4_uc010zbg.1_Frame_Shift_Del_p.P92fs|YSK4_uc002tui.3_Frame_Shift_Del_p.P109fs NM_025052 NP_079328 Q56UN5 YSK4_HUMAN Yeast Sps1/Ste20-related kinase 4 isoform 1 92 ATP binding|protein serine/threonine kinase activity stomach(2)|urinary_tract(1)|ovary(1)|breast(1) 5 BRCA - Breast invasive adenocarcinoma(221;0.112) TTCTTGGGGAGGACTGACATC 0.368 0.43 125 93 PBRM1 55193 broad.mit.edu 37 3 52637580 52637580 + Frame_Shift_Del DEL T - - NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr3:52637580delT uc003des.2 - 17 2748 c.2736delA c.(2734-2736)AAAfs p.K912fs PBRM1_uc003dex.2_Intron|PBRM1_uc003deq.2_Frame_Shift_Del_p.K912fs|PBRM1_uc003der.2_Frame_Shift_Del_p.K880fs|PBRM1_uc003det.2_Frame_Shift_Del_p.K927fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.K927fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.K912fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.K912fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.K912fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.K912fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.K825fs|PBRM1_uc003dfa.1_Frame_Shift_Del_p.K258fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 912 chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 1.00 0 68 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.34 37 19 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.26 287 99 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.33 18 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 115 167 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 28 76 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 1 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 16 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 1030 117 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 413 200 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.25 46 15 RB1 5925 broad.mit.edu 37 13 49039128 49039134 + Splice_Site DEL CCTCAGA - - NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr13:49039128_49039134delCCTCAGA uc001vcb.2 + 22 2378 c.2212_splice c.e22-1 p.T738_splice NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.?(10) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) tACTGTTCTTCCTCAGACATTCAAACG 0.242 0.97 1 36 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 26 303 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 78 50 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 189 40 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 66 344 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 10 108 MED15 51586 broad.mit.edu 37 22 20920814 20920822 + In_Frame_Del DEL CAGCAGCAG - - rs11281025 NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr22:20920814_20920822delCAGCAGCAG uc002zsp.2 + 7 831_839 c.751_759delCAGCAGCAG c.(751-759)CAGCAGCAGdel p.QQQ260del MED15_uc002zso.2_In_Frame_Del_p.QQQ189del|MED15_uc002zsq.2_In_Frame_Del_p.QQQ260del|MED15_uc010gso.2_In_Frame_Del_p.QQQ260del|MED15_uc002zsr.2_In_Frame_Del_p.QQQ234del|MED15_uc011ahs.1_In_Frame_Del_p.QQQ234del|MED15_uc002zss.2_In_Frame_Del_p.QQQ179del|MED15_uc011ahu.1_5'UTR NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 260_262 Poly-Gln. Missing. Missing (in Ref. 3; BAB85034). regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) acaacagcaacagcagcagcagcagcagc 0.325 0.37 12 7 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 NCIH2196_LUNG NA NCIH2196_LUNG NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 0.000 0.12 268 37 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2227_LUNG NA NCIH2227_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.87 10 68 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.13 313 47 SOX11 6664 broad.mit.edu 37 2 5834002 5834002 + Frame_Shift_Del DEL C - - NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr2:5834002delC uc002qyj.2 + 1 1204 c.1149delC c.(1147-1149)GGCfs p.G383fs NM_003108 NP_003099 P35716 SOX11_HUMAN SRY-box 11 383 cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis cytoplasm|nucleolus enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding central_nervous_system(3) 3 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) OV - Ovarian serous cystadenocarcinoma(76;0.132) 0.000 0.30 765 326 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.57 6 8 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.64 4 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 74 105 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 17 34 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 2 25 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.23 27 8 PSKH2 85481 broad.mit.edu 37 8 87081752 87081753 + Frame_Shift_Ins INS - C C NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr8:87081752_87081753insC uc011lfy.1 - 1 99_100 c.99_100insG c.(97-102)GGGCCTfs p.G33fs NM_033126 NP_149117 Q96QS6 KPSH2_HUMAN protein serine kinase H2 33_34 ATP binding|protein serine/threonine kinase activity stomach(2)|lung(2)|ovary(1) 5 STAD - Stomach adenocarcinoma(118;0.129) TCGGGCCCAGGCCCCGCGCCTC 0.713 0.31 18 8 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.11 602 73 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.70 16 37 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 332 150 SRP14 6727 broad.mit.edu 37 15 40328564 40328575 + In_Frame_Del DEL TGCTGTTGTTGG - - rs16924521;rs8874;rs7535 by1000genomes NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr15:40328564_40328575delTGCTGTTGTTGG uc001zkq.2 - 5 442_453 c.370_381delCCAACAACAGCA c.(370-381)CCAACAACAGCAdel p.PTTA124del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 124_127 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgttgttgctgctgttgttggtgctgttgct 0.231 0.57 26 34 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 6 52 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.75 64 196 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 65 518 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2227_LUNG NA NCIH2227_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 9 124 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH226_LUNG NA NCIH226_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.61 40 63 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH226_LUNG NA NCIH226_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 88 94 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH226_LUNG NA NCIH226_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.85 19 111 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH226_LUNG NA NCIH226_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.21 30 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH226_LUNG NA NCIH226_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 55 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency NCIH226_LUNG NA NCIH226_LUNG NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.12 711 100 MUSK 4593 broad.mit.edu 37 9 113445078 113445081 + Splice_Site DEL TAAG - - NCIH226_LUNG NA NCIH226_LUNG NA g.chr9:113445078_113445081delTAAG uc004bey.2 + 2 304 c.206_splice c.e2+1 p.K69_splice MUSK_uc004bex.2_Splice_Site_p.K69_splice NM_005592 NP_005583 O15146 MUSK_HUMAN skeletal muscle receptor tyrosine kinase transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(3)|ovary(2)|central_nervous_system(1) 6 AAATTCTCATTAAGTAAGTATTCC 0.235 0.37 46 27 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH226_LUNG NA NCIH226_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 473 181 CSAD 51380 broad.mit.edu 37 12 53564286 53564287 + Splice_Site INS - C C NCIH226_LUNG NA NCIH226_LUNG NA g.chr12:53564286_53564287insC uc001sby.2 - 8 694 c.568_splice c.e8-1 p.C190_splice CSAD_uc001sbw.2_Splice_Site_p.C43_splice|CSAD_uc009zmt.2_Splice_Site|CSAD_uc010snx.1_Splice_Site_p.C217_splice|CSAD_uc001sbz.2_Splice_Site_p.C190_splice|CSAD_uc009zmu.2_Splice_Site_p.C43_splice|CSAD_uc001sca.3_Splice_Site NM_015989 NP_057073 Q9Y600 CSAD_HUMAN cysteine sulfinic acid decarboxylase carboxylic acid metabolic process pyridoxal phosphate binding|sulfinoalanine decarboxylase activity ovary(1) 1 L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114) 0.000 0.95 1 19 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH226_LUNG NA NCIH226_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.14 77 13 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH226_LUNG NA NCIH226_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.61 7 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH226_LUNG NA NCIH226_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 38 356 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH226_LUNG NA NCIH226_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.33 49 24 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH226_LUNG NA NCIH226_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.14 71 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH226_LUNG NA NCIH226_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 109 456 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH226_LUNG NA NCIH226_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 5 43 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2286_LUNG NA NCIH2286_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.80 6 24 ARID1A 8289 broad.mit.edu 37 1 27023909 27023910 + Frame_Shift_Ins INS - T T NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr1:27023909_27023910insT uc001bmv.1 + 1 1388_1389 c.1015_1016insT c.(1015-1017)GCTfs p.A339fs ARID1A_uc001bmt.1_Frame_Shift_Ins_p.A339fs|ARID1A_uc001bmu.1_Frame_Shift_Ins_p.A339fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 339 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.A339fs*24(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.50 88 87 ROR1 4919 broad.mit.edu 37 1 64606020 64606021 + Frame_Shift_Ins INS - A A NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr1:64606020_64606021insA uc001dbj.2 + 6 1238_1239 c.839_840insA c.(838-840)CCAfs p.P280fs ROR1_uc001dbi.3_Frame_Shift_Ins_p.P280fs|uc001dbl.2_Intron NM_005012 NP_005003 Q01973 ROR1_HUMAN receptor tyrosine kinase-like orphan receptor 1 280 FZ.|Extracellular (Potential). transmembrane receptor protein tyrosine kinase signaling pathway cytoplasm|integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1) 19 CTGAAACTGCCAAACTGTGAAG 0.450 0.44 44 34 GRM7 2917 broad.mit.edu 37 3 7620383 7620383 + Frame_Shift_Del DEL T - - NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr3:7620383delT uc003bqm.2 + 8 2064 c.1790delT c.(1789-1791)CTGfs p.L597fs GRM7_uc011ata.1_RNA|GRM7_uc011atb.1_RNA|GRM7_uc010hcf.2_RNA|GRM7_uc011atc.1_RNA|GRM7_uc010hcg.2_Frame_Shift_Del_p.L597fs|GRM7_uc003bql.2_Frame_Shift_Del_p.L597fs|GRM7_uc003bqn.1_Frame_Shift_Del_p.L180fs|GRM7_uc010hch.1_Frame_Shift_Del_p.L108fs NM_000844 NP_000835 Q14831 GRM7_HUMAN glutamate receptor, metabotropic 7 isoform a 597 Helical; Name=1; (Potential). negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding ovary(4)|lung(3) 7 L-Glutamic Acid(DB00142) 0.000 0.15 317 57 GRM7 2917 broad.mit.edu 37 3 7620384 7620384 + Frame_Shift_Del DEL G - - NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr3:7620384delG uc003bqm.2 + 8 2065 c.1791delG c.(1789-1791)CTGfs p.L597fs GRM7_uc011ata.1_RNA|GRM7_uc011atb.1_RNA|GRM7_uc010hcf.2_RNA|GRM7_uc011atc.1_RNA|GRM7_uc010hcg.2_Frame_Shift_Del_p.L597fs|GRM7_uc003bql.2_Frame_Shift_Del_p.L597fs|GRM7_uc003bqn.1_Frame_Shift_Del_p.L180fs|GRM7_uc010hch.1_Frame_Shift_Del_p.L108fs NM_000844 NP_000835 Q14831 GRM7_HUMAN glutamate receptor, metabotropic 7 isoform a 597 Helical; Name=1; (Potential). negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding ovary(4)|lung(3) 7 L-Glutamic Acid(DB00142) 0.000 0.80 74 298 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.43 12 9 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.60 4 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 54 81 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 19 31 MNX1 3110 broad.mit.edu 37 7 156802406 156802406 + Frame_Shift_Del DEL C - - NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr7:156802406delC uc003wnd.1 - 1 942 c.639delG c.(637-639)TGGfs p.W213fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.W213fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 213 humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.61 204 319 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 24 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 294 121 MMP20 9313 broad.mit.edu 37 11 102480729 102480729 + Frame_Shift_Del DEL G - - NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr11:102480729delG uc001phc.2 - 4 569 c.556delC c.(556-558)CGGfs p.R186fs NM_004771 NP_004762 O60882 MMP20_HUMAN matrix metalloproteinase 20 preproprotein 186 proteolysis|regulation of enamel mineralization extracellular space|proteinaceous extracellular matrix calcium ion binding|metalloendopeptidase activity|protein binding|zinc ion binding urinary_tract(1)|skin(1) 2 all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139) Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033) Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13) BRCA - Breast invasive adenocarcinoma(274;0.0161) AGAGTCCCCCGAGGCCCATCG 0.488 0.15 103 18 MMP1 4312 broad.mit.edu 37 11 102668123 102668124 + Frame_Shift_Ins INS - A A NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr11:102668123_102668124insA uc001phi.2 - 2 356_357 c.213_214insT c.(211-216)TTTGGGfs p.F71fs uc001phh.1_Intron|MMP1_uc010ruv.1_Frame_Shift_Ins_p.F5fs NM_002421 NP_002412 P03956 MMP1_HUMAN matrix metalloproteinase 1 isoform 1 71_72 blood coagulation|collagen catabolic process|interspecies interaction between organisms|leukocyte migration|proteolysis proteinaceous extracellular matrix calcium ion binding|metalloendopeptidase activity|zinc ion binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(12;0.0127) all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967) Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233) OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014) ACTTTCAGCCCAAAGAATTCCT 0.470 0.58 43 59 CASP1 834 broad.mit.edu 37 11 104905013 104905013 + Frame_Shift_Del DEL C - - NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr11:104905013delC uc010rve.1 - 2 213 c.196delG c.(196-198)GCAfs p.A66fs CASP1_uc001pig.2_Intron|CASP1_uc001pik.2_Frame_Shift_Del_p.A50fs|CASP1_uc010rvf.1_Intron|CASP1_uc010rvg.1_Frame_Shift_Del_p.A66fs|CASP1_uc010rvh.1_Intron|CASP1_uc010rvi.1_Intron|CASP1_uc001pim.3_Frame_Shift_Del_p.A66fs|CASP1_uc009yxi.2_Frame_Shift_Del_p.A66fs|CASP1_uc010rvj.1_Frame_Shift_Del_p.A66fs|CASP1_uc009yxj.2_5'UTR|CASP1_uc010rvk.1_Frame_Shift_Del_p.A27fs|CASP1_uc010rvl.1_Frame_Shift_Del_p.A66fs NM_033292 NP_150634 P29466 CASP1_HUMAN caspase 1 isoform alpha precursor 66 CARD. cellular response to mechanical stimulus|cellular response to organic substance|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis|signal transduction cytosol caspase activator activity|cysteine-type endopeptidase activity|protein binding ovary(2) 2 Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047) BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482) Minocycline(DB01017)|Penicillamine(DB00859) CATGCCTGTGCCCCTTTCGGA 0.463 0.60 25 38 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.43 8 6 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 71 612 NLK 51701 broad.mit.edu 37 17 26370116 26370130 + In_Frame_Del DEL GCGGCAGCCGCAGCA - - NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr17:26370116_26370130delGCGGCAGCCGCAGCA uc010crj.2 + 1 429_443 c.217_231delGCGGCAGCCGCAGCA c.(217-231)GCGGCAGCCGCAGCAdel p.AAAAA78del NLK_uc010cri.1_RNA NM_016231 NP_057315 Q9UBE8 NLK_HUMAN nemo like kinase 78_82 Poly-Ala. intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway cytoplasm|nucleus ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding ovary(1)|lung(1)|central_nervous_system(1) 3 all_lung(13;0.000343)|Lung NSC(42;0.00184) UCEC - Uterine corpus endometrioid carcinoma (53;0.168) TTcggcagctgcggcagccgcagcagcggctgcag 0.498 0.33 66 33 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.59 27 39 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 158 549 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2286_LUNG NA NCIH2286_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 7 54 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2291_LUNG NA NCIH2291_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 8 67 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.29 238 98 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 104 21 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 99 81 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 19 40 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 53 ANO1 55107 broad.mit.edu 37 11 70031773 70031773 + Frame_Shift_Del DEL C - - NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr11:70031773delC uc001opj.2 + 25 2971 c.2666delC c.(2665-2667)GCCfs p.A889fs ANO1_uc001opl.1_RNA|ANO1_uc010rqk.1_Frame_Shift_Del_p.A598fs|ANO1_uc010rql.1_Frame_Shift_Del_p.A63fs NM_018043 NP_060513 Q5XXA6 ANO1_HUMAN anoctamin 1, calcium activated chloride channel 889 Helical; (Potential). multicellular organismal development chloride channel complex|cytoplasm|plasma membrane intracellular calcium activated chloride channel activity ovary(1)|pancreas(1) 2 0.000 0.33 209 102 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 205 70 MMP1 4312 broad.mit.edu 37 11 102665959 102665959 + Frame_Shift_Del DEL A - - NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr11:102665959delA uc001phi.2 - 6 988 c.845delT c.(844-846)CTAfs p.L282fs uc001phh.1_Intron|MMP1_uc010ruv.1_Frame_Shift_Del_p.L216fs NM_002421 NP_002412 P03956 MMP1_HUMAN matrix metalloproteinase 1 isoform 1 282 blood coagulation|collagen catabolic process|interspecies interaction between organisms|leukocyte migration|proteolysis proteinaceous extracellular matrix calcium ion binding|metalloendopeptidase activity|zinc ion binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(12;0.0127) all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967) Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233) OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014) ATCAAAGGTTAGCTTACTGTC 0.403 0.35 119 64 DACH1 1602 broad.mit.edu 37 13 72440098 72440098 + Frame_Shift_Del DEL G - - NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr13:72440098delG uc010thn.1 - 2 1227 c.804delC c.(802-804)TCCfs p.S268fs DACH1_uc010tho.1_Frame_Shift_Del_p.S268fs|DACH1_uc010thp.1_Frame_Shift_Del_p.S268fs NM_080759 NP_542937 Q9UI36 DACH1_HUMAN dachshund homolog 1 isoform a 268 Interaction with SIX6 and HDAC3 (By similarity).|DACHbox-N. multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus DNA binding|nucleotide binding|protein binding breast(1) 1 Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198) GBM - Glioblastoma multiforme(99;0.00032) AGTCCTTCCTGGAGATGAGTT 0.637 0.98 1 41 MGA 23269 broad.mit.edu 37 15 42042673 42042673 + Frame_Shift_Del DEL G - - NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr15:42042673delG uc010ucy.1 + 17 7049 c.6868delG c.(6868-6870)GGGfs p.G2290fs MGA_uc010ucz.1_Frame_Shift_Del_p.G2081fs|MGA_uc010uda.1_Frame_Shift_Del_p.G906fs|MGA_uc001zoi.2_Frame_Shift_Del_p.G504fs NM_001164273 NP_001157745 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 1 2251 Basic motif. MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) GAAGAAGGGTGGGAGAAGCAG 0.418 0.94 6 93 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.25 52 17 THAP11 57215 broad.mit.edu 37 16 67876821 67876823 + In_Frame_Del DEL CAA - - rs34138555;rs28647874 byFrequency NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr16:67876821_67876823delCAA uc002euo.2 + 1 609_611 c.364_366delCAA c.(364-366)CAAdel p.Q132del CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 132 Gln-rich. Missing (in Ref. 2; AAH12182). regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) gcagcagcagcaacagcagcagc 0.305 0.19 39 9 CDH2 1000 broad.mit.edu 37 18 25572683 25572683 + Frame_Shift_Del DEL G - - NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr18:25572683delG uc002kwg.2 - 9 1739 c.1280delC c.(1279-1281)CCTfs p.P427fs CDH2_uc010xbn.1_Frame_Shift_Del_p.P396fs NM_001792 NP_001783 P19022 CADH2_HUMAN cadherin 2, type 1 preproprotein 427 Extracellular (Potential).|Cadherin 3. adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation catenin complex|integral to membrane alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding ovary(3)|lung(1) 4 CCGTCCAGTAGGATCTCCGCC 0.522 1.00 0 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 103 299 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2291_LUNG NA NCIH2291_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 8 117 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2342_LUNG NA NCIH2342_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.9 3 27 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.26 405 144 PTPRC 5788 broad.mit.edu 37 1 198668790 198668791 + Frame_Shift_Ins INS - A A NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr1:198668790_198668791insA uc001gur.1 + 5 570_571 c.390_391insA c.(388-393)GCCAATfs p.A130fs PTPRC_uc001gus.1_Frame_Shift_Ins_p.A130fs|PTPRC_uc001gut.1_Intron|PTPRC_uc009wze.1_Frame_Shift_Ins_p.A66fs|PTPRC_uc009wzf.1_Frame_Shift_Ins_p.A66fs|PTPRC_uc010ppg.1_Frame_Shift_Ins_p.A66fs|PTPRC_uc001guu.1_Frame_Shift_Ins_p.A173fs|PTPRC_uc001guv.1_RNA|PTPRC_uc001guw.1_RNA NM_002838 NP_002829 P08575 PTPRC_HUMAN "protein tyrosine phosphatase, receptor type, C" 130_131 Extracellular (Potential). axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway focal adhesion|integral to plasma membrane|membrane raft protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1) 12 GCTCCGCCGCCAATGCAAAACT 0.525 0.19 177 42 NLRP3 114548 broad.mit.edu 37 1 247587426 247587426 + Frame_Shift_Del DEL G - - NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr1:247587426delG uc001icr.2 + 5 819 c.681delG c.(679-681)GCGfs p.A227fs NLRP3_uc001ics.2_Frame_Shift_Del_p.A227fs|NLRP3_uc001icu.2_Frame_Shift_Del_p.A227fs|NLRP3_uc001icw.2_Frame_Shift_Del_p.A227fs|NLRP3_uc001icv.2_Frame_Shift_Del_p.A227fs|NLRP3_uc010pyw.1_Frame_Shift_Del_p.A225fs|NLRP3_uc001ict.1_Frame_Shift_Del_p.A225fs NM_001079821 NP_001073289 Q96P20 NALP3_HUMAN "NLR family, pyrin domain containing 3 isoform a" 227 ATP (Potential).|NACHT. detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction cytoplasm ATP binding|peptidoglycan binding|protein binding lung(8)|skin(8)|ovary(7)|upper_aerodigestive_tract(1)|breast(1)|pancreas(1) 26 all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) all_cancers(173;0.0172) OV - Ovarian serous cystadenocarcinoma(106;0.0141) TCCAGGGGGCGGCAGGGATTG 0.537 0.52 85 93 LRP2 4036 broad.mit.edu 37 2 170131619 170131620 + Frame_Shift_Ins INS - T T NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr2:170131619_170131620insT uc002ues.2 - 14 2114_2115 c.1901_1902insA c.(1900-1902)AACfs p.N634fs LRP2_uc010zdf.1_Frame_Shift_Ins_p.N565fs NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 634 LDL-receptor class B 5.|Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) "Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)" ACACTTGTGGGTTGGTCTCTGT 0.485 0.36 344 195 TTN 7273 broad.mit.edu 37 2 179577531 179577531 + Frame_Shift_Del DEL G - - NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr2:179577531delG uc010zfg.1 - 91 23713 c.23489delC c.(23488-23490)GCTfs p.A7830fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.A4491fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 8757 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CTCCAGTTCAGCAACTGAATC 0.428 0.24 440 138 TGFBR2 7048 broad.mit.edu 37 3 30691878 30691879 + Frame_Shift_Ins INS - G G NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr3:30691878_30691879insG uc003ceo.2 + 3 762_763 c.380_381insG c.(379-381)AAAfs p.K127fs TGFBR2_uc003cen.2_Frame_Shift_Ins_p.K152fs NM_003242 NP_003233 P37173 TGFR2_HUMAN "transforming growth factor, beta receptor II" 127 Extracellular (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane "ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding" pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 AAGGAAAAAAAAAAGCCTGGTG 0.426 0.59 80 113 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs "SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA;" GAAGAAGTCGATTAGGAGTTCA 0.545 0.14 50 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 32 37 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 46 89 FBN2 2201 broad.mit.edu 37 5 127730903 127730903 + Frame_Shift_Del DEL C - - NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr5:127730903delC uc003kuu.2 - 9 1582 c.1143delG c.(1141-1143)GGGfs p.G381fs FBN2_uc003kuv.2_Frame_Shift_Del_p.G348fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 381 TB 2. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) TCGTCATTCTCCCCGGGAGCT 0.547 1 0 21 GRM1 2911 broad.mit.edu 37 6 146755506 146755506 + Frame_Shift_Del DEL A - - NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr6:146755506delA uc010khw.1 + 9 3629 c.3159delA c.(3157-3159)GCAfs p.A1053fs GRM1_uc010khv.1_3'UTR|GRM1_uc003qll.2_3'UTR|GRM1_uc011edz.1_3'UTR|GRM1_uc011eea.1_3'UTR NM_000838 NP_000829 Q13255 GRM1_HUMAN glutamate receptor, metabotropic 1 isoform alpha 1053 Cytoplasmic (Potential). synaptic transmission integral to plasma membrane G-protein coupled receptor activity|glutamate receptor activity lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2) 19 Ovarian(120;0.0387) OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762) Acamprosate(DB00659)|L-Glutamic Acid(DB00142) 0.000 0.63 280 479 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.83 5 24 CSMD3 114788 broad.mit.edu 37 8 113988326 113988326 + Frame_Shift_Del DEL T - - rs138285672 NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr8:113988326delT uc003ynu.2 - 7 1241 c.1082delA c.(1081-1083)AACfs p.N361fs CSMD3_uc003ynt.2_Frame_Shift_Del_p.N321fs|CSMD3_uc011lhx.1_Intron NM_198123 NP_937756 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 isoform 1 361 Extracellular (Potential). integral to membrane|plasma membrane ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1) 63 GGTAGTCCTGTTATGCTCCTC 0.448 0.69 32 70 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1 0 13 TGFBR1 7046 broad.mit.edu 37 9 101867554 101867555 + Frame_Shift_Ins INS - T T rs67861970 NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr9:101867554_101867555insT uc004azc.2 + 1 143_144 c.67_68insT c.(67-69)GCGfs p.A23fs TGFBR1_uc004azd.2_Frame_Shift_Ins_p.A23fs NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 23 activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.33 8 4 TPH1 7166 broad.mit.edu 37 11 18054822 18054822 + Frame_Shift_Del DEL G - - NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr11:18054822delG uc001mnp.2 - 3 427 c.401delC c.(400-402)CCTfs p.P134fs TPH1_uc009yhe.2_RNA NM_004179 NP_004170 P17752 TPH1_HUMAN tryptophan hydroxylase 1 134 aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process cytosol amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity 0 L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360) aaTACTTACAGGATGGTCTGC 0.234 0.58 36 49 NR1H3 10062 broad.mit.edu 37 11 47283104 47283104 + Frame_Shift_Del DEL C - - NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr11:47283104delC uc009ylm.2 + 6 936 c.715delC c.(715-717)CCCfs p.P239fs NR1H3_uc009yll.1_Frame_Shift_Del_p.P245fs|NR1H3_uc010rhk.1_Frame_Shift_Del_p.P245fs|NR1H3_uc001nek.2_Frame_Shift_Del_p.P194fs|NR1H3_uc001nej.2_Intron|NR1H3_uc001nel.2_Frame_Shift_Del_p.P194fs|NR1H3_uc001nen.3_Intron|NR1H3_uc001nem.2_Frame_Shift_Del_p.P239fs|NR1H3_uc001nep.2_Intron NM_005693 NP_005684 Q13133 NR1H3_HUMAN "nuclear receptor subfamily 1, group H, member 3" 239 Ligand-binding (Potential). apoptotic cell clearance|cellular response to lipopolysaccharide|cholesterol homeostasis|negative regulation of cholesterol storage|negative regulation of inflammatory response|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of macrophage activation|negative regulation of pancreatic juice secretion|negative regulation of pinocytosis|negative regulation of secretion of lysosomal enzymes|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of cholesterol homeostasis|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of receptor biosynthetic process|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of circadian rhythm|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to progesterone stimulus|triglyceride homeostasis nuclear chromatin|nucleoplasm cholesterol binding|steroid hormone receptor activity|sterol response element binding|transcription coactivator activity|zinc ion binding ovary(2)|lung(1) 3 GTAGCCTTGGCCCATGGCACC 0.602 0.61 13 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 320 142 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.46 0.68 13 28 CREBBP 1387 broad.mit.edu 37 16 3781324 3781326 + In_Frame_Del DEL AGG - - NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr16:3781324_3781326delAGG uc002cvv.2 - 30 5243_5245 c.5039_5041delCCT c.(5038-5043)TCCTTG>TTG p.S1680del CREBBP_uc002cvw.2_In_Frame_Del_p.S1642del NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1680 Interaction with TRERF1. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) 0.000 0.51 232 246 MYH2 4620 broad.mit.edu 37 17 10433187 10433187 + Frame_Shift_Del DEL C - - NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr17:10433187delC uc010coi.2 - 23 3030 c.2902delG c.(2902-2904)GCCfs p.A968fs uc002gml.1_Intron|MYH2_uc002gmp.3_Frame_Shift_Del_p.A968fs|MYH2_uc010coj.2_Intron NM_001100112 NP_001093582 Q9UKX2 MYH2_HUMAN myosin heavy chain IIa 968 Potential. muscle filament sliding muscle myosin complex|myosin filament|sarcomere actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1) 14 TCAACCTTGGCCAGTGTCAGC 0.433 0.44 80 63 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.16 97 19 BAX 581 broad.mit.edu 37 19 49458963 49458971 + In_Frame_Del DEL GGGCGAATG - - rs141306106 byFrequency NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr19:49458963_49458971delGGGCGAATG uc002plk.2 + 3 175_183 c.106_114delGGGCGAATG c.(106-114)GGGCGAATGdel p.GRM36del BAX_uc002plf.1_In_Frame_Del_p.GRM36del|BAX_uc002plg.1_Translation_Start_Site|BAX_uc002plh.1_Intron|BAX_uc010xzx.1_RNA|BAX_uc002plj.2_In_Frame_Del_p.GRM36del|BAX_uc002pll.2_Intron|BAX_uc002plm.2_Intron NM_138761 NP_620116 Q07812 BAX_HUMAN BCL2-associated X protein isoform alpha 36_38 activation of caspase activity by cytochrome c|activation of pro-apoptotic gene products|B cell apoptosis|cleavage of lamin|DNA fragmentation involved in apoptotic nuclear change|establishment or maintenance of transmembrane electrochemical gradient|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|induction of retinal programmed cell death|mitochondrial fragmentation involved in apoptosis|mitochondrial fusion|negative regulation of protein binding|negative regulation of survival gene product expression|nuclear fragmentation involved in apoptotic nuclear change|positive regulation of neuron apoptosis|protein homooligomerization|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|release of cytochrome c from mitochondria|release of matrix enzymes from mitochondria|response to toxin|transformed cell apoptosis cytosol|endoplasmic reticulum membrane|mitochondrial outer membrane|mitochondrial permeability transition pore complex|nucleus BH3 domain binding|channel activity|lipid binding|protein heterodimerization activity|protein homodimerization activity lung(1)|central_nervous_system(1)|skin(1) 3 all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261) OV - Ovarian serous cystadenocarcinoma(262;0.000159)|all cancers(93;0.00047)|GBM - Glioblastoma multiforme(486;0.018)|Epithelial(262;0.0279) GGATCGAGCAGGGCGAATGGGGGGGGAGG 0.589 0.17 33 7 PTPRT 11122 broad.mit.edu 37 20 40827959 40827959 + Frame_Shift_Del DEL G - - NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr20:40827959delG uc002xkg.2 - 16 2596 c.2412delC c.(2410-2412)GCCfs p.A804fs PTPRT_uc010ggj.2_Frame_Shift_Del_p.A823fs|PTPRT_uc010ggi.2_Frame_Shift_Del_p.A7fs NM_007050 NP_008981 O14522 PTPRT_HUMAN "protein tyrosine phosphatase, receptor type, T" 804 Cytoplasmic (Potential). homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway cell surface|integral to membrane|plasma membrane alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity skin(8)|ovary(7)|lung(5) 20 Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783) TGGGTTTGTCGGCAGAGGCCA 0.557 0.47 67 59 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 134 369 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2342_LUNG NA NCIH2342_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.95 6 107 PRKX 5613 broad.mit.edu 37 X 3533862 3533862 + Frame_Shift_Del DEL T - - NCIH2347_LUNG NA NCIH2347_LUNG NA g.chrX:3533862delT uc010nde.2 - 7 1312 c.945delA c.(943-945)AAAfs p.K315fs NM_005044 NP_005035 P51817 PRKX_HUMAN "protein kinase, X-linked" 315 AGC-kinase C-terminal. ATP binding|cAMP-dependent protein kinase activity skin(2)|lung(1) 3 all_lung(23;0.000396)|Lung NSC(23;0.00123) GTACCTTCAGTTTTCTCTGCG 0.498 0.61 85 132 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2347_LUNG NA NCIH2347_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.97 2 73 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.34 338 178 EHBP1 23301 broad.mit.edu 37 2 63085639 63085643 + Frame_Shift_Del DEL TCTGA - - NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr2:63085639_63085643delTCTGA uc002sby.2 + 8 1215_1219 c.733_737delTCTGA c.(733-738)TCTGAAfs p.S245fs EHBP1_uc010fcp.2_Intron|EHBP1_uc002sbx.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron NM_015252 NP_056067 Q8NDI1 EHBP1_HUMAN EH domain binding protein 1 isoform 1 245_246 cytoplasm|membrane ovary(1)|breast(1) 2 Lung NSC(7;0.0951)|all_lung(7;0.169) LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189) AGCCAGTTCCTCTGAAGGTCTAAGA 0.405 0.49 35 34 GLI2 2736 broad.mit.edu 37 2 121747069 121747070 + Frame_Shift_Ins INS - A A NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr2:121747069_121747070insA uc010flp.2 + 13 3609_3610 c.3579_3580insA c.(3577-3582)GCTAGCfs p.A1193fs GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Frame_Shift_Ins_p.A865fs|GLI2_uc002tmu.3_Frame_Shift_Ins_p.A848fs NM_005270 NP_005261 P10070 GLI2_HUMAN GLI-Kruppel family member GLI2 1193_1194 axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis nucleus|nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1) 13 Renal(3;0.0496) Prostate(154;0.0623) GCCTACAGGCTAGCCCTGGGGG 0.663 0.33 8 4 NEK10 152110 broad.mit.edu 37 3 27243993 27243994 + Frame_Shift_Del DEL CT - - NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr3:27243993_27243994delCT uc010hfk.2 - 3 310_311 c.81_82delAG c.(79-84)GTAGGCfs p.V27fs NEK10_uc003cds.1_Frame_Shift_Del_p.V112fs|NEK10_uc010hfj.2_Frame_Shift_Del_p.V27fs Q6ZWH5 NEK10_HUMAN RecName: Full=Serine/threonine-protein kinase Nek10; EC=2.7.11.1; AltName: Full=NimA-related protein kinase 10; 715_716 ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1) 13 AGGATGCAGCCTACTGCCCAGA 0.495 0.56 15 19 MAML3 55534 broad.mit.edu 37 4 140641185 140641186 + Frame_Shift_Ins INS - G G NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr4:140641185_140641186insG uc003ihz.1 - 7 3445_3446 c.2693_2694insC c.(2692-2694)CCTfs p.P898fs MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_Frame_Shift_Ins_p.P366fs NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 899 Gln-rich. "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) GCCCAGAGGCAGGTTGCCTCGG 0.53 0.1 762 82 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 149 253 ADAM29 11086 broad.mit.edu 37 4 175897936 175897936 + Frame_Shift_Del DEL A - - NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr4:175897936delA uc003iuc.2 + 5 1930 c.1260delA c.(1258-1260)GCAfs p.A420fs ADAM29_uc003iud.2_Frame_Shift_Del_p.A420fs|ADAM29_uc010irr.2_Frame_Shift_Del_p.A420fs|ADAM29_uc011cki.1_Frame_Shift_Del_p.A420fs NM_014269 NP_055084 Q9UKF5 ADA29_HUMAN ADAM metallopeptidase domain 29 preproprotein 420 Disintegrin.|Extracellular (Potential). proteolysis|spermatogenesis integral to plasma membrane metalloendopeptidase activity|zinc ion binding skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1) 16 Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164) all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286) AGCATTGTGCAAAAGATCCCT 0.438 0.5 142 143 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.7 44 102 TRRAP 8295 broad.mit.edu 37 7 98515229 98515229 + Frame_Shift_Del DEL A - - NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr7:98515229delA uc003upp.2 + 20 2758 c.2549delA c.(2548-2550)GAGfs p.E850fs TRRAP_uc011kis.1_Frame_Shift_Del_p.E850fs|TRRAP_uc003upr.2_Frame_Shift_Del_p.E542fs NM_003496 NP_003487 Q9Y4A5 TRRAP_HUMAN transformation/transcription domain-associated 850 "histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent" NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex "phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity" ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1) 37 all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274) STAD - Stomach adenocarcinoma(171;0.215) AGGACGCTGGAGCTGTGTGTG 0.567 0.55 5 6 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.9 2 19 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane "calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle" ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.33 8 4 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 3 69 RET 5979 broad.mit.edu 37 10 43614979 43614980 + Frame_Shift_Ins INS - C C NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr10:43614979_43614980insC uc001jal.2 + 14 2583_2584 c.2393_2394insC c.(2392-2394)GGCfs p.G798fs RET_uc001jak.1_Frame_Shift_Ins_p.G798fs|RET_uc010qez.1_Frame_Shift_Ins_p.G544fs NM_020975 NP_066124 P07949 RET_HUMAN ret proto-oncogene isoform a 798 Protein kinase.|Cytoplasmic (Potential). "homophilic cell adhesion|positive regulation of metanephric glomerulus development|positive regulation of transcription, DNA-dependent|posterior midgut development" integral to membrane ATP binding|calcium ion binding|transmembrane receptor protein tyrosine kinase activity thyroid(404)|adrenal_gland(20)|lung(9)|large_intestine(5)|breast(4)|ovary(4)|central_nervous_system(3)|urinary_tract(1)|NS(1) 451 Ovarian(717;0.0423) Sunitinib(DB01268) CCGCCCCCAGGCCCGCTCCTCC 0.723 0.8 3 12 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.31 25 11 NYNRIN 57523 broad.mit.edu 37 14 24879251 24879252 + Frame_Shift_Ins INS - C C NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr14:24879251_24879252insC uc001wpf.3 + 4 2569_2570 c.2251_2252insC c.(2251-2253)GCCfs p.A751fs NM_025081 NP_079357 Q9P2P1 NYNRI_HUMAN hypothetical protein LOC57523 751 DNA integration integral to membrane DNA binding ovary(2)|central_nervous_system(1) 3 TTGGGAGGGGGCCCCAAGGCAG 0.639 0.14 62 10 MGA 23269 broad.mit.edu 37 15 41999999 41999999 + Frame_Shift_Del DEL G - - NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr15:41999999delG uc001zog.1 + 6 2353 c.2262delG c.(2260-2262)TTGfs p.L754fs MGA_uc010ucy.1_Frame_Shift_Del_p.L754fs|MGA_uc010ucz.1_Frame_Shift_Del_p.L754fs NM_001080541 NP_001074010 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 2 754 MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) AGTTACCTTTGGCTCCAGCTA 0.373 0.87 10 69 TOX3 27324 broad.mit.edu 37 16 52473512 52473513 + In_Frame_Ins INS - TGC TGC NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr16:52473512_52473513insTGC uc002egw.2 - 7 1526_1527 c.1355_1356insGCA c.(1354-1356)CAA>CAGCAA p.452_452Q>QQ TOX3_uc010vgt.1_In_Frame_Ins_p.447_447Q>QQ|TOX3_uc010vgu.1_In_Frame_Ins_p.452_452Q>QQ NM_001080430 NP_001073899 O15405 TOX3_HUMAN TOX high mobility group box family member 3 452 Gln-rich. "apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent" nucleus chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity 0 tctgttgttgttgctgctgctg 0.218 0.58 169 232 CBFA2T3 863 broad.mit.edu 37 16 89043085 89043085 + Frame_Shift_Del DEL C - - NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr16:89043085delC uc002fmm.1 - 1 317 c.131delG c.(130-132)GGTfs p.G44fs CBFA2T3_uc002fmn.1_Frame_Shift_Del_p.G44fs NM_005187 NP_005178 O75081 MTG16_HUMAN myeloid translocation gene on chromosome 16 44 Mediates localization to the nucleus (By similarity).|Pro-rich.|Mediates interaction with PDE7A (in isoform 2).|Required for nucleolar targeting (in isoform 1). cell proliferation|granulocyte differentiation Golgi membrane|nucleolus|nucleoplasm protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding large_intestine(3)|ovary(1) 4 BRCA - Breast invasive adenocarcinoma(80;0.0275) 0.000 0.92 43 520 MATK 4145 broad.mit.edu 37 19 3779060 3779061 + Frame_Shift_Ins INS - C C NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr19:3779060_3779061insC uc002lyt.2 - 12 1526_1527 c.1126_1127insG c.(1126-1128)GCCfs p.A376fs MATK_uc002lyv.2_Frame_Shift_Ins_p.A377fs|MATK_uc002lyu.2_Frame_Shift_Ins_p.A335fs|MATK_uc010dtq.2_Frame_Shift_Ins_p.A376fs NM_139355 NP_647612 P42679 MATK_HUMAN megakaryocyte-associated tyrosine kinase isoform 376 Protein kinase. cell proliferation|mesoderm development|positive regulation of cell proliferation cytoplasm|nucleus ATP binding|non-membrane spanning protein tyrosine kinase activity stomach(2)|ovary(1)|lung(1)|large_intestine(1) 5 Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18) CTTCCGCTCGGCTTTGGCCAGG 0.658 0.11 173 21 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 52 164 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 "B melanoma antigen family, member 2 precursor" 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.26 85 30 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 56 410 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2347_LUNG NA NCIH2347_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.93 10 141 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH23_LUNG NA NCIH23_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 0.97 3 89 TTN 7273 broad.mit.edu 37 2 179396824 179396825 + Frame_Shift_Ins INS - T T NCIH23_LUNG NA NCIH23_LUNG NA g.chr2:179396824_179396825insT uc010zfg.1 - 307 97037_97038 c.96813_96814insA c.(96811-96816)CGACGGfs p.R32271fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Ins_p.R25966fs|TTN_uc010zfi.1_Frame_Shift_Ins_p.R25899fs|TTN_uc010zfj.1_Frame_Shift_Ins_p.R25774fs|TTN_uc002umq.2_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 33198_33199 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AGGGAGCGCCGTCGTCTCAGTA 0.45 0.3 395 169 RPL14 9045 broad.mit.edu 37 3 40503519 40503521 + In_Frame_Del DEL TAC - - rs111899316;rs147295890 by1000genomes NCIH23_LUNG NA NCIH23_LUNG NA g.chr3:40503519_40503521delTAC uc003ckg.2 + 6 495_497 c.444_446delTAC c.(442-447)GGTACT>GGT p.T149del RPL14_uc003ckh.2_In_Frame_Del_p.T149del|RPL14_uc003cki.2_In_Frame_Del_p.T100del NM_003973 NP_003964 P50914 RL14_HUMAN ribosomal protein L14 149 endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription cytosolic large ribosomal subunit protein binding|RNA binding|structural constituent of ribosome 0 KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065) GTACTAAGGGTActgctgctgct 0.365 0.55 5 6 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH23_LUNG NA NCIH23_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.35 55 29 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH23_LUNG NA NCIH23_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.9 3 27 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH23_LUNG NA NCIH23_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1 0 20 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH23_LUNG NA NCIH23_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.64 97 169 PAPPA 5069 broad.mit.edu 37 9 119158809 119158809 + Frame_Shift_Del DEL T - - NCIH23_LUNG NA NCIH23_LUNG NA g.chr9:119158809delT uc004bjn.2 + 22 5179 c.4798delT c.(4798-4800)TGTfs p.C1600fs PAPPA_uc011lxq.1_Frame_Shift_Del_p.C975fs NM_002581 NP_002572 Q13219 PAPP1_HUMAN pregnancy-associated plasma protein A 1600 cell differentiation|female pregnancy cytoplasm|extracellular region|membrane metalloendopeptidase activity|zinc ion binding ovary(4)|skin(4)|pancreas(1) 9 CCCTATGTCCTGTGATCTACA 0.453 0.45 63 52 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH23_LUNG NA NCIH23_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 474 191 CNTN5 53942 broad.mit.edu 37 11 99872771 99872772 + Frame_Shift_Ins INS - T T NCIH23_LUNG NA NCIH23_LUNG NA g.chr11:99872771_99872772insT uc001pga.2 + 9 1222_1223 c.883_884insT c.(883-885)ATGfs p.M295fs CNTN5_uc009ywv.1_Frame_Shift_Ins_p.M295fs|CNTN5_uc001pfz.2_Frame_Shift_Ins_p.M295fs|CNTN5_uc001pgb.2_Frame_Shift_Ins_p.M221fs NM_014361 NP_055176 O94779 CNTN5_HUMAN contactin 5 isoform long 295 cell adhesion anchored to membrane|plasma membrane protein binding skin(3)|ovary(2)|pancreas(2)|breast(1) 8 all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219) BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196) CTAAGGTGTGATGGGAGAATAT 0.366 0.96 4 98 ATN1 1822 broad.mit.edu 37 12 7045892 7045903 + In_Frame_Del DEL CAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448 byFrequency;byFrequency;by1000genomes;byFrequency NCIH23_LUNG NA NCIH23_LUNG NA g.chr12:7045892_7045903delCAGCAGCAGCAG uc001qrw.1 + 5 1699_1710 c.1462_1473delCAGCAGCAGCAG c.(1462-1473)CAGCAGCAGCAGdel p.QQQQ496del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQ496del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 496_499 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagc 0.467 0.41 62 43 GRIN2B 2904 broad.mit.edu 37 12 13716189 13716189 + Frame_Shift_Del DEL C - - NCIH23_LUNG NA NCIH23_LUNG NA g.chr12:13716189delC uc001rbt.2 - 13 4162 c.3983delG c.(3982-3984)GGCfs p.G1328fs NM_000834 NP_000825 Q13224 NMDE2_HUMAN N-methyl-D-aspartate receptor subunit 2B 1328 Cytoplasmic (Potential). response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding central_nervous_system(4)|ovary(3)|skin(3)|lung(2) 12 Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043) CATGAATCGGCCCTTGTCTTT 0.602 0.72 15 38 CNGB1 1258 broad.mit.edu 37 16 57983287 57983292 + In_Frame_Del DEL TCCTCT - - NCIH23_LUNG NA NCIH23_LUNG NA g.chr16:57983287_57983292delTCCTCT uc002emt.2 - 14 1151_1156 c.1086_1091delAGAGGA c.(1084-1092)GAAGAGGAG>GAG p.362_364EEE>E CNGB1_uc010cdh.2_In_Frame_Del_p.356_358EEE>E NM_001297 NP_001288 Q14028 CNGB1_HUMAN cyclic nucleotide gated channel beta 1 isoform 362_364 Poly-Glu.|Cytoplasmic (Potential). sensory perception of smell intracellular cyclic nucleotide activated cation channel complex cAMP binding|intracellular cAMP activated cation channel activity breast(3)|pancreas(1) 4 ctcctcctcctcctcttcctcttcct 0.437 0.79 3 11 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 NCIH23_LUNG NA NCIH23_LUNG NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.44 32 25 TAF15 8148 broad.mit.edu 37 17 34171663 34171686 + In_Frame_Del DEL GGCTATGGTGGGGACAGAGGCGGC - - rs143659169;rs146792937 byFrequency NCIH23_LUNG NA NCIH23_LUNG NA g.chr17:34171663_34171686delGGCTATGGTGGGGACAGAGGCGGC uc002hkd.2 + 15 1446_1469 c.1360_1383delGGCTATGGTGGGGACAGAGGCGGC c.(1360-1383)GGCTATGGTGGGGACAGAGGCGGCdel p.GYGGDRGG478del TAF15_uc002hkc.2_In_Frame_Del_p.GYGGDRGG475del NM_139215 NP_631961 Q92804 RBP56_HUMAN TBP-associated factor 15 isoform 1 478_485 "Arg/Gly-rich.|10.|21 X approximate tandem repeats of D-R- [S,G](0,3)-G-G-Y-G-G." "positive regulation of transcription, DNA-dependent" cytoplasm|nucleus DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding TAF15/NR4A3(33) bone(33)|lung(1)|skin(1) 35 Ovarian(249;0.17) UCEC - Uterine corpus endometrioid carcinoma (308;0.0193) aagtgggggtggctatggtggggacagaggcggcggctatggtg 0 0.48 12 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH23_LUNG NA NCIH23_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.8 30 119 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH23_LUNG NA NCIH23_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 45 470 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH23_LUNG NA NCIH23_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.93 8 112 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2405_LUNG NA NCIH2405_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.75 11 33 SPEN 23013 broad.mit.edu 37 1 16258933 16258934 + Frame_Shift_Ins INS - C C NCIH2405_LUNG NA NCIH2405_LUNG NA g.chr1:16258933_16258934insC uc001axk.1 + 11 6402_6403 c.6198_6199insC c.(6196-6201)AAACCGfs p.K2066fs SPEN_uc010obp.1_Frame_Shift_Ins_p.K2025fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2066_2067 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) TAGAGAAAAAACCGGCCCCTGA 0.475 0.27 19 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 NCIH2405_LUNG NA NCIH2405_LUNG NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.44 10 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2405_LUNG NA NCIH2405_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.66 106 204 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2405_LUNG NA NCIH2405_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.78 13 45 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH2405_LUNG NA NCIH2405_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.28 28 11 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH2405_LUNG NA NCIH2405_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.87 3 20 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH2405_LUNG NA NCIH2405_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2405_LUNG NA NCIH2405_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 823 422 MEF2A 4205 broad.mit.edu 37 15 100252710 100252712 + In_Frame_Del DEL CAG - - NCIH2405_LUNG NA NCIH2405_LUNG NA g.chr15:100252710_100252712delCAG uc010urw.1 + 11 1617_1619 c.1258_1260delCAG c.(1258-1260)CAGdel p.Q430del MEF2A_uc010urv.1_In_Frame_Del_p.Q360del|MEF2A_uc010bos.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvf.2_In_Frame_Del_p.Q422del|MEF2A_uc002bve.2_In_Frame_Del_p.Q428del|MEF2A_uc002bvg.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvi.2_In_Frame_Del_p.Q420del|MEF2A_uc010bot.2_In_Frame_Del_p.Q352del NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 430 Gln/Pro-rich. Missing (in Ref. 4; AAB17195/AAB17196). apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) ATCGGGCTTCcagcagcagcagc 0.493 0.40 9 6 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2405_LUNG NA NCIH2405_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.32 169 81 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2405_LUNG NA NCIH2405_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 147 476 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2405_LUNG NA NCIH2405_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 70 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2444_LUNG NA NCIH2444_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 2 23 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH2444_LUNG NA NCIH2444_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.47 180 160 THBS3 7059 broad.mit.edu 37 1 155172174 155172175 + Frame_Shift_Del DEL AG - - NCIH2444_LUNG NA NCIH2444_LUNG NA g.chr1:155172174_155172175delAG uc001fix.2 - 9 998_999 c.975_976delCT c.(973-978)CCCTGTfs p.P325fs RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Frame_Shift_Del_p.P316fs|THBS3_uc001fiz.2_Frame_Shift_Del_p.P325fs|THBS3_uc001fiy.2_5'UTR|THBS3_uc010pfu.1_Frame_Shift_Del_p.P205fs|THBS3_uc010pfv.1_RNA|THBS3_uc001fja.2_RNA NM_007112 NP_009043 P49746 TSP3_HUMAN thrombospondin 3 precursor 325_326 EGF-like 2; calcium-binding (Potential). cell-matrix adhesion extracellular region|perinuclear region of cytoplasm calcium ion binding|heparin binding|structural molecule activity breast(3)|ovary(2) 5 all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) CCCGGGAAACAGGGGTCAGCGT 0.614 0.24 50 16 HOXD11 3237 broad.mit.edu 37 2 176973853 176973853 + Frame_Shift_Del DEL G - - NCIH2444_LUNG NA NCIH2444_LUNG NA g.chr2:176973853delG uc002uki.2 + 2 1000 c.1000delG c.(1000-1002)GGAfs p.G334fs HOXD11_uc010fqx.2_RNA NM_021192 NP_067015 P31277 HXD11_HUMAN homeobox D11 334 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678) GTATTTCACTGGAAACCCCTT 0.547 0.26 28 10 CNTN6 27255 broad.mit.edu 37 3 1427381 1427382 + Frame_Shift_Ins INS - T T NCIH2444_LUNG NA NCIH2444_LUNG NA g.chr3:1427381_1427382insT uc003boz.2 + 20 2871_2872 c.2604_2605insT c.(2602-2607)GGGCTGfs p.G868fs CNTN6_uc011asj.1_Frame_Shift_Ins_p.G796fs|CNTN6_uc003bpa.2_Frame_Shift_Ins_p.G868fs NM_014461 NP_055276 Q9UQ52 CNTN6_HUMAN contactin 6 precursor 868_869 Fibronectin type-III 3. axon guidance|cell adhesion|central nervous system development|Notch signaling pathway anchored to membrane|plasma membrane skin(3)|lung(2)|breast(2)|pancreas(1) 8 all_cancers(2;0.000164)|all_epithelial(2;0.107) Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139) 0.000 0.12 189 26 PBRM1 55193 broad.mit.edu 37 3 52598108 52598108 + Frame_Shift_Del DEL G - - NCIH2444_LUNG NA NCIH2444_LUNG NA g.chr3:52598108delG uc003des.2 - 23 3845 c.3833delC c.(3832-3834)TCAfs p.S1278fs PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.S1278fs|PBRM1_uc003der.2_Frame_Shift_Del_p.S1246fs|PBRM1_uc003det.2_Frame_Shift_Del_p.S1293fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.S1293fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.S1278fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.S1253fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.S1253fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.S1277fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 1278 chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.93 14 199 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH2444_LUNG NA NCIH2444_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 111 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2444_LUNG NA NCIH2444_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 45 45 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH2444_LUNG NA NCIH2444_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 16 36 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH2444_LUNG NA NCIH2444_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH2444_LUNG NA NCIH2444_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 1 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2444_LUNG NA NCIH2444_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 186 97 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH2444_LUNG NA NCIH2444_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 12 38 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2444_LUNG NA NCIH2444_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 36 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 39 ALK 238 broad.mit.edu 37 2 30143051 30143052 + Frame_Shift_Ins INS - G G NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr2:30143051_30143052insG uc002rmy.2 - 1 1381_1382 c.474_475insC c.(472-477)CCCGGGfs p.P158fs NM_004304 NP_004295 Q9UM73 ALK_HUMAN anaplastic lymphoma kinase precursor 158_159 Extracellular (Potential). protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2) haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1) 1218 Acute lymphoblastic leukemia(172;0.155) Adenosine triphosphate(DB00171) GCCGCCTCCCCGGGGGGCCCGA 0.673 0.12 52 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.40 15 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.58 5 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 58 71 MICA 4276 broad.mit.edu 37 6 31380161 31380162 + Splice_Site INS - CTGCTGCTGCT CTGCTGCTGCT rs72548004;rs9279200 NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr6:31380161_31380162insCTGCTGCTGCT uc003ntk.1 + 6 988 c.949_splice c.e6-1 p.A317_splice MICA_uc003rxz.1_Frame_Shift_Ins_p.G180fs RecName: Full=MHC class I polypeptide-related sequence A; Short=MIC-A; Flags: Precursor; 0 Ovarian(999;0.0253) TGTTGCTGCTGGCTGCTGCTAT 0.450 0.90 1 9 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.10 504 59 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.40 24 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 567 309 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.21 55 15 ZMYM2 7750 broad.mit.edu 37 13 20580662 20580662 + Frame_Shift_Del DEL T - - NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr13:20580662delT uc001umr.2 + 7 1746 c.1448delT c.(1447-1449)GTTfs p.V483fs ZMYM2_uc001umq.2_Frame_Shift_Del_p.V396fs|ZMYM2_uc001ums.2_Frame_Shift_Del_p.V483fs|ZMYM2_uc001umt.2_Frame_Shift_Del_p.V483fs|ZMYM2_uc010tco.1_Intron NM_003453 NP_003444 Q9UBW7 ZMYM2_HUMAN zinc finger protein 198 483 regulation of transcription, DNA-dependent|transcription, DNA-dependent PML body ubiquitin conjugating enzyme binding|zinc ion binding lung(3)|ovary(2)|prostate(1) 6 all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856) GGAAATAATGTTCTGGTGATT 0.363 0.55 122 147 Unknown 0 broad.mit.edu 37 14 28733863 28733864 + Frame_Shift_Ins INS - G G NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr14:28733863_28733864insG uc001wqd.2 + 1 244_245 c.104_105insG c.(103-105)TCGfs p.S35fs SubName: Full=cDNA FLJ60537, highly similar to BCL2/adenovirus E1B 19 kDa protein-interacting protein 3; GTTCCAGCCTCGGTTTCTATTT 0.535 0.10 69 8 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.59 9 13 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 7 70 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 131 612 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 7 150 CARD10 29775 broad.mit.edu 37 22 37906357 37906358 + Frame_Shift_Ins INS - G G NCIH2452_PLEURA NA NCIH2452_PLEURA NA g.chr22:37906357_37906358insG uc003asx.1 - 4 773_774 c.770_771insC c.(769-771)CCGfs p.P257fs CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_Frame_Shift_Ins_p.P257fs NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 257 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) CCCCAGGGGGCGGGCCCCTGGC 0.515 0.10 176 20 FAM48B1 100130302 broad.mit.edu 37 X 24382374 24382376 + In_Frame_Del DEL TGC - - NCIH28_PLEURA NA NCIH28_PLEURA NA g.chrX:24382374_24382376delTGC uc011mjx.1 + 1 1497_1499 c.1497_1499delTGC c.(1495-1500)ATTGCT>ATT p.A517del NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 ctgctgctattgctgctgctgct 0.202 0.23 54 16 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.59 44 64 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 57 DENND4B 9909 broad.mit.edu 37 1 153907278 153907279 + In_Frame_Ins INS - CTG CTG rs141373027 by1000genomes NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr1:153907278_153907279insCTG uc001fdd.1 - 18 3131_3132 c.2730_2731insCAG c.(2728-2733)insCAG p.910_911insQ uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910_911 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) GACACctgctcctgctgctgct 0.455 0.63 73 123 KCNN3 3782 broad.mit.edu 37 1 154842330 154842331 + In_Frame_Ins INS - TGC TGC NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr1:154842330_154842331insTGC uc001ffp.2 - 1 424_425 c.110_111insGCA c.(109-111)CAA>CAGCAA p.37_37Q>QQ KCNN3_uc009wox.1_In_Frame_Ins_p.37_37Q>QQ NM_002249 NP_002240 Q9UGI6 KCNN3_HUMAN small conductance calcium-activated potassium 37 Poly-Gln. integral to membrane calmodulin binding lung(1) 1 all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245) BRCA - Breast invasive adenocarcinoma(34;0.00819) gctgctgctgttgctgctgctg 0.233 0.22 105 30 TTN 7273 broad.mit.edu 37 2 179419423 179419425 + In_Frame_Del DEL TCT - - NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr2:179419423_179419425delTCT uc010zfg.1 - 281 81169_81171 c.80945_80947delAGA c.(80944-80949)AAGATC>ATC p.K26982del uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.K20677del|TTN_uc010zfi.1_In_Frame_Del_p.K20610del|TTN_uc010zfj.1_In_Frame_Del_p.K20485del NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 27909 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AGAAGGGTGATCTTCTCAGCAGT 0.468 0.41 295 206 IRS1 3667 broad.mit.edu 37 2 227661396 227661398 + In_Frame_Del DEL TGC - - NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr2:227661396_227661398delTGC uc002voh.3 - 1 2109_2111 c.2057_2059delGCA c.(2056-2061)AGCAAC>AAC p.S686del NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 686 Poly-Ser. fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) GGGACGGCGTtgctgctgctgct 0.547 0.43 182 135 BAP1 8314 broad.mit.edu 37 3 52441329 52441351 + Splice_Site DEL GGGCCTGGGGAAAAACAGAGTCA - - rs139750149;rs142131779 by1000genomes NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr3:52441329_52441351delGGGCCTGGGGAAAAACAGAGTCA uc003ddx.2 - 7 553 c.438_splice c.e7-1 p.R146_splice BAP1_uc010hmh.2_5'Flank NM_004656 NP_004647 Q92560 BAP1_HUMAN BRCA1 associated protein-1 monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process cytoplasm|nucleolus|PR-DUB complex chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity p.?(1) pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1) 65 BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277) GGCGTGGCTCGGGCCTGGGGAAAAACAGAGTCAGGGCCCAAAA 0.592 0.42 174 127 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.54 19 22 HTT 3064 broad.mit.edu 37 4 3076672 3076673 + In_Frame_Ins INS - CCGCCG CCGCCG rs76533208 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr4:3076672_3076673insCCGCCG uc011bvq.1 + 2 271_272 c.126_127insCCGCCG c.(124-129)insCCGCCG p.50_51insPP NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 48_49 Poly-Pro. establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) aacagccgccaccgccgccgcc 0.084 0.30 87 38 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.66 86 166 MAML3 55534 broad.mit.edu 37 4 140811064 140811072 + Splice_Site DEL TGCTGCTGC - - NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr4:140811064_140811072delTGCTGCTGC uc003ihz.1 - 3 2265 c.1513_splice c.e3-1 p.Q505_splice MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) TGAGtgctgttgctgctgctgctgctgct 0.263 0.16 351 65 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 24 53 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.56 8 10 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.53 23 26 KPNA5 3841 broad.mit.edu 37 6 117013462 117013464 + In_Frame_Del DEL GTT - - NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr6:117013462_117013464delGTT uc003pxh.2 + 4 378_380 c.247_249delGTT c.(247-249)GTTdel p.V84del NM_002269 NP_002260 O15131 IMA5_HUMAN karyopherin alpha 5 81 ARM 1; truncated. NLS-bearing substrate import into nucleus cytoplasm|nuclear pore protein binding|protein transporter activity breast(3)|skin(1) 4 all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234) GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212) TTAGGAAGAAGTTGTTACTACAG 0.271 0.42 96 70 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.14 232 39 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 15 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.50 10 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 2 29 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.83 5 25 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 679 195 ATN1 1822 broad.mit.edu 37 12 7045885 7045886 + In_Frame_Ins INS - CAG CAG NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr12:7045885_7045886insCAG uc001qrw.1 + 5 1692_1693 c.1455_1456insCAG c.(1453-1458)insCAG p.502_503insQ ATN1_uc001qrx.1_In_Frame_Ins_p.502_503insQ|ATN1_uc001qry.1_In_Frame_Ins_p.486_487insQ NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502_503 cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 ACCACcagcaacagcaacagca 0.441 0.55 38 47 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.53 7 8 SRP14 6727 broad.mit.edu 37 15 40328597 40328605 + In_Frame_Del DEL TGCTGCTGC - - NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr15:40328597_40328605delTGCTGCTGC uc001zkq.2 - 5 412_420 c.340_348delGCAGCAGCA c.(340-348)GCAGCAGCAdel p.AAA114del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 114_116 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgcggcaggtgctgctgctgctgctgct 0.239 0.13 135 21 SALL1 6299 broad.mit.edu 37 16 51175655 51175656 + In_Frame_Ins INS - GCT GCT rs113614842 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr16:51175655_51175656insGCT uc010vgs.1 - 2 508_509 c.477_478insAGC c.(475-480)insAGC p.159_160insS SALL1_uc010vgr.1_In_Frame_Ins_p.62_63insS|SALL1_uc010cbv.2_Intron NM_002968 NP_002959 Q9NSC2 SALL1_HUMAN sal-like 1 isoform a 159_160 Poly-Gly. adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development chromocenter|cytoplasm|heterochromatin|nucleus beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding skin(5)|ovary(3) 8 all_cancers(37;0.0322) COAD - Colon adenocarcinoma(2;0.24) ccgccgccgccgctgctgctgc 0.460 0.31 11 5 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.44 23 18 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.85 30 170 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.23 243 73 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 135 594 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH28_PLEURA NA NCIH28_PLEURA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 12 93 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 NCIH292_LUNG NA NCIH292_LUNG NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.22 117 33 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH292_LUNG NA NCIH292_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 74 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH292_LUNG NA NCIH292_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 417 142 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH292_LUNG NA NCIH292_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 14 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH292_LUNG NA NCIH292_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 95 227 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH292_LUNG NA NCIH292_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 46 90 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH292_LUNG NA NCIH292_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.33 37 18 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 NCIH292_LUNG NA NCIH292_LUNG NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.13 145 21 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH292_LUNG NA NCIH292_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.91 5 50 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH292_LUNG NA NCIH292_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 1220 278 ATN1 1822 broad.mit.edu 37 12 7045892 7045894 + In_Frame_Del DEL CAG - - rs66756893;rs67074116 NCIH292_LUNG NA NCIH292_LUNG NA g.chr12:7045892_7045894delCAG uc001qrw.1 + 5 1699_1701 c.1462_1464delCAG c.(1462-1464)CAGdel p.Q502del ATN1_uc001qrx.1_In_Frame_Del_p.Q502del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagc 0.458 0.29 89 36 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes NCIH292_LUNG NA NCIH292_LUNG NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.64 52 92 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH292_LUNG NA NCIH292_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.42 109 80 SALL1 6299 broad.mit.edu 37 16 51175655 51175656 + In_Frame_Ins INS - GCT GCT rs113614842 NCIH292_LUNG NA NCIH292_LUNG NA g.chr16:51175655_51175656insGCT uc010vgs.1 - 2 508_509 c.477_478insAGC c.(475-480)insAGC p.159_160insS SALL1_uc010vgr.1_In_Frame_Ins_p.62_63insS|SALL1_uc010cbv.2_Intron NM_002968 NP_002959 Q9NSC2 SALL1_HUMAN sal-like 1 isoform a 159_160 Poly-Gly. adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development chromocenter|cytoplasm|heterochromatin|nucleus beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding skin(5)|ovary(3) 8 all_cancers(37;0.0322) COAD - Colon adenocarcinoma(2;0.24) ccgccgccgccgctgctgctgc 0.460 0.41 10 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH292_LUNG NA NCIH292_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 32 298 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH292_LUNG NA NCIH292_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.79 32 121 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH292_LUNG NA NCIH292_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.34 146 75 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH292_LUNG NA NCIH292_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 126 574 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH292_LUNG NA NCIH292_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 58 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 NCIH292_LUNG NA NCIH292_LUNG NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 0.000 0.17 362 75 NF2 4771 broad.mit.edu 37 22 30074222 30074223 + Frame_Shift_Ins INS - A A NCIH292_LUNG NA NCIH292_LUNG NA g.chr22:30074222_30074223insA uc003age.3 + 14 1927_1928 c.1484_1485insA c.(1483-1485)ATAfs p.I495fs NF2_uc003afy.3_Frame_Shift_Ins_p.I495fs|NF2_uc003afz.3_Frame_Shift_Ins_p.I412fs|NF2_uc003agf.3_Frame_Shift_Ins_p.I495fs|NF2_uc003agb.3_Frame_Shift_Ins_p.I418fs|NF2_uc003agc.3_Frame_Shift_Ins_p.I457fs|NF2_uc003agd.3_RNA|NF2_uc003agg.3_Frame_Shift_Ins_p.I495fs|NF2_uc003aga.3_Frame_Shift_Ins_p.I453fs|NF2_uc003agh.3_Frame_Shift_Ins_p.I454fs|NF2_uc003agi.3_Frame_Shift_Ins_p.I412fs|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Frame_Shift_Ins_p.I457fs|NF2_uc010gvp.2_Frame_Shift_Ins_p.I159fs|NF2_uc011akq.1_Frame_Shift_Ins_p.I121fs NM_000268 NP_000259 P35240 MERL_HUMAN neurofibromin 2 isoform 1 495 actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane cytoskeletal protein binding|protein binding p.P483fs*17(1)|p.?(1) meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1) 728 CCTCCTGACATACCAAGCTTCA 0.460 0.65 56 103 FAM48B1 100130302 broad.mit.edu 37 X 24382373 24382374 + In_Frame_Ins INS - TGC TGC NCIH322_LUNG NA NCIH322_LUNG NA g.chrX:24382373_24382374insTGC uc011mjx.1 + 1 1496_1497 c.1496_1497insTGC c.(1495-1497)ATT>ATTGCT p.517_518insA NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 gctgctgctattgctgctgctg 0.208 0.24 71 23 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH322_LUNG NA NCIH322_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 34 CHD5 26038 broad.mit.edu 37 1 6206873 6206873 + Frame_Shift_Del DEL G - - NCIH322_LUNG NA NCIH322_LUNG NA g.chr1:6206873delG uc001amb.1 - 10 1542 c.1442delC c.(1441-1443)CCTfs p.P481fs CHD5_uc001ama.1_5'Flank|CHD5_uc001amc.1_RNA NM_015557 NP_056372 Q8TDI0 CHD5_HUMAN chromodomain helicase DNA binding protein 5 481 Pro-rich. chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1) 12 Ovarian(185;0.0634) all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15) Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193) GAAGGGGGCAGGGGGCTCCGT 0.647 0.85 8 44 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH322_LUNG NA NCIH322_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.57 29 38 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH322_LUNG NA NCIH322_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.74 109 315 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH322_LUNG NA NCIH322_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 43 89 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH322_LUNG NA NCIH322_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.58 20 28 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH322_LUNG NA NCIH322_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH322_LUNG NA NCIH322_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 66 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH322_LUNG NA NCIH322_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.89 2 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH322_LUNG NA NCIH322_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.51 921 971 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH322_LUNG NA NCIH322_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 61 204 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH322_LUNG NA NCIH322_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 155 397 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH322_LUNG NA NCIH322_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 8 191 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH3255_LUNG NA NCIH3255_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 35 PIP5K1A 8394 broad.mit.edu 37 1 151205030 151205031 + Frame_Shift_Ins INS - C C NCIH3255_LUNG NA NCIH3255_LUNG NA g.chr1:151205030_151205031insC uc001exj.2 + 7 942_943 c.490_491insC c.(490-492)TCCfs p.S164fs PIP5K1A_uc001exi.2_Frame_Shift_Ins_p.S151fs|PIP5K1A_uc010pcu.1_Frame_Shift_Ins_p.S152fs|PIP5K1A_uc001exk.2_Frame_Shift_Ins_p.S151fs|PIP5K1A_uc010pcv.1_5'Flank NM_001135638 NP_001129110 Q99755 PI51A_HUMAN phosphatidylinositol-4-phosphate 5-kinase, type 164 PIPK. phospholipid biosynthetic process|signal transduction endomembrane system|Golgi stack|lamellipodium|nuclear speck 1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|kinase binding ovary(1)|central_nervous_system(1)|skin(1) 3 Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.181) GCCCCAGTATTCCCTCTGCAGT 0.426 0.26 110 38 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH3255_LUNG NA NCIH3255_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.56 12 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH3255_LUNG NA NCIH3255_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.34 55 28 MAML3 55534 broad.mit.edu 37 4 140811064 140811096 + Splice_Site DEL TGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC - - rs72203913;rs13108712;rs12506879;rs67877726;rs72161425;rs79090010 by1000genomes;by1000genomes NCIH3255_LUNG NA NCIH3255_LUNG NA g.chr4:140811064_140811096delTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC uc003ihz.1 - 2 2264 c.1512_splice c.e2+1 p.Q504_splice MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) TGAGtgctgttgctgctgctgctgctgctgctgctgctgctgctgctgctgct 0.288 0.29 121 50 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 NCIH3255_LUNG NA NCIH3255_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.18 119 26 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH3255_LUNG NA NCIH3255_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.83 4 20 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH3255_LUNG NA NCIH3255_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.93 1 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH3255_LUNG NA NCIH3255_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH3255_LUNG NA NCIH3255_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 137 35 CCNA1 8900 broad.mit.edu 37 13 37012863 37012864 + Frame_Shift_Ins INS - G G rs140782401 by1000genomes NCIH3255_LUNG NA NCIH3255_LUNG NA g.chr13:37012863_37012864insG uc001uvr.3 + 5 1102_1103 c.752_753insG c.(751-753)CTGfs p.L251fs CCNA1_uc010teo.1_Frame_Shift_Ins_p.L207fs|CCNA1_uc010abq.2_Frame_Shift_Ins_p.L207fs|CCNA1_uc010abp.2_Frame_Shift_Ins_p.L207fs|CCNA1_uc001uvs.3_Frame_Shift_Ins_p.L250fs|CCNA1_uc010abr.2_Intron NM_003914 NP_003905 P78396 CCNA1_HUMAN cyclin A1 isoform a 251 cell division|G2/M transition of mitotic cell cycle|male meiosis I|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|spermatogenesis cytosol|microtubule cytoskeleton|nucleoplasm protein kinase binding lung(2)|skin(2)|ovary(1) 5 Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242) GTGGACTGGCTGGTGGAGGTTG 0.495 0.11 63 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH3255_LUNG NA NCIH3255_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 17 42 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH3255_LUNG NA NCIH3255_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.94 21 311 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH3255_LUNG NA NCIH3255_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 7 69 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH358_LUNG NA NCIH358_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 64 ELF4 2000 broad.mit.edu 37 X 129203441 129203441 + Frame_Shift_Del DEL G - - NCIH358_LUNG NA NCIH358_LUNG NA g.chrX:129203441delG uc004evd.3 - 8 1406 c.1021delC c.(1021-1023)CAGfs p.Q341fs ELF4_uc004eve.3_Frame_Shift_Del_p.Q341fs NM_001421 NP_001412 Q99607 ELF4_HUMAN E74-like factor 4 341 natural killer cell proliferation|NK T cell proliferation|positive regulation of transcription from RNA polymerase II promoter PML body protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity ovary(1) 1 CCCTTGCCCTGGGGGGCAGAT 0.617 0.79 10 38 CDC7 8317 broad.mit.edu 37 1 91989708 91989708 + Frame_Shift_Del DEL G - - NCIH358_LUNG NA NCIH358_LUNG NA g.chr1:91989708delG uc001doe.2 + 12 1606 c.1441delG c.(1441-1443)GGGfs p.G481fs CDC7_uc001dof.2_Frame_Shift_Del_p.G481fs|CDC7_uc010osw.1_Frame_Shift_Del_p.G453fs|CDC7_uc009wdc.2_Frame_Shift_Del_p.G481fs|CDC7_uc009wdd.2_Frame_Shift_Del_p.G124fs NM_003503 NP_003494 O00311 CDC7_HUMAN cell division cycle 7 481 Protein kinase. cell cycle checkpoint|cell division|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|positive regulation of cell proliferation|regulation of S phase cytoplasm|nucleoplasm ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity stomach(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 5 all_lung(203;0.0165)|Lung NSC(277;0.0562) all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124) TGATATACAAGGGCATGCTTC 0.363 0.17 109 22 TPR 7175 broad.mit.edu 37 1 186305687 186305687 + Frame_Shift_Del DEL T - - NCIH358_LUNG NA NCIH358_LUNG NA g.chr1:186305687delT uc001grv.2 - 33 4943 c.4646delA c.(4645-4647)AAGfs p.K1549fs NM_003292 NP_003283 P12270 TPR_HUMAN nuclear pore complex-associated protein TPR 1549 Potential. carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm ATP binding|protein binding|serine-tRNA ligase activity ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1) 7 Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157) Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553) TTTTTCTTCCTTTTCAGTTAT 0.403 0.21 154 40 NLRP3 114548 broad.mit.edu 37 1 247587856 247587857 + Frame_Shift_Ins INS - T T NCIH358_LUNG NA NCIH358_LUNG NA g.chr1:247587856_247587857insT uc001icr.2 + 5 1249_1250 c.1111_1112insT c.(1111-1113)CTGfs p.L371fs NLRP3_uc001ics.2_Frame_Shift_Ins_p.L371fs|NLRP3_uc001icu.2_Frame_Shift_Ins_p.L371fs|NLRP3_uc001icw.2_Frame_Shift_Ins_p.L371fs|NLRP3_uc001icv.2_Frame_Shift_Ins_p.L371fs|NLRP3_uc010pyw.1_Frame_Shift_Ins_p.L369fs|NLRP3_uc001ict.1_Frame_Shift_Ins_p.L369fs NM_001079821 NP_001073289 Q96P20 NALP3_HUMAN NLR family, pyrin domain containing 3 isoform a 371 NACHT. detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction cytoplasm ATP binding|peptidoglycan binding|protein binding lung(8)|skin(8)|ovary(7)|upper_aerodigestive_tract(1)|breast(1)|pancreas(1) 26 all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) all_cancers(173;0.0172) OV - Ovarian serous cystadenocarcinoma(106;0.0141) TGTGGAGATCCTGGGTTTCTCC 0.550 0.59 47 69 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH358_LUNG NA NCIH358_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.22 25 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH358_LUNG NA NCIH358_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 68 82 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH358_LUNG NA NCIH358_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 17 35 PIK3CG 5294 broad.mit.edu 37 7 106524645 106524646 + Frame_Shift_Del DEL TG - - NCIH358_LUNG NA NCIH358_LUNG NA g.chr7:106524645_106524646delTG uc003vdv.3 + 9 2891_2892 c.2806_2807delTG c.(2806-2808)TGTfs p.C936fs PIK3CG_uc003vdu.2_Frame_Shift_Del_p.C936fs|PIK3CG_uc003vdw.2_Frame_Shift_Del_p.C936fs NM_002649 NP_002640 P48736 PK3CG_HUMAN phosphoinositide-3-kinase, catalytic, gamma 936 PI3K/PI4K. G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation phosphatidylinositol 3-kinase complex 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding p.C936S(1) lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1) 38 TGCAGGCTACTGTGTGGCAACC 0.356 0.54 50 59 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH358_LUNG NA NCIH358_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.80 2 8 CSMD3 114788 broad.mit.edu 37 8 113347580 113347580 + Frame_Shift_Del DEL G - - NCIH358_LUNG NA NCIH358_LUNG NA g.chr8:113347580delG uc003ynu.2 - 45 7302 c.7143delC c.(7141-7143)GGCfs p.G2381fs CSMD3_uc003yns.2_Frame_Shift_Del_p.G1583fs|CSMD3_uc003ynt.2_Frame_Shift_Del_p.G2341fs|CSMD3_uc011lhx.1_Frame_Shift_Del_p.G2277fs|CSMD3_uc003ynw.1_Frame_Shift_Del_p.G92fs NM_198123 NP_937756 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 isoform 1 2381 Extracellular (Potential).|CUB 13. integral to membrane|plasma membrane ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1) 63 GCACAAAAAAGCCACTTGTTG 0.358 0.63 52 87 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH358_LUNG NA NCIH358_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 53 SPTAN1 6709 broad.mit.edu 37 9 131367409 131367410 + Frame_Shift_Ins INS - C C NCIH358_LUNG NA NCIH358_LUNG NA g.chr9:131367409_131367410insC uc004bvl.3 + 30 3929_3930 c.3816_3817insC c.(3814-3819)CAACGCfs p.Q1272fs SPTAN1_uc011mbh.1_Frame_Shift_Ins_p.Q1284fs|SPTAN1_uc004bvm.3_Frame_Shift_Ins_p.Q1272fs|SPTAN1_uc004bvn.3_Frame_Shift_Ins_p.Q1252fs NM_003127 NP_003118 Q13813 SPTA2_HUMAN spectrin, alpha, non-erythrocytic 1 1272_1273 Spectrin 14. actin filament capping|axon guidance|cellular component disassembly involved in apoptosis cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton breast(5)|ovary(4)|pancreas(1) 10 AGGCCCTGCAACGCAAGCATGA 0.490 0.13 164 24 INCENP 3619 broad.mit.edu 37 11 61914293 61914293 + Frame_Shift_Del DEL G - - NCIH358_LUNG NA NCIH358_LUNG NA g.chr11:61914293delG uc001nsw.1 + 15 2325 c.2123delG c.(2122-2124)CGGfs p.R708fs INCENP_uc009ynw.1_Frame_Shift_Del_p.R712fs|INCENP_uc001nsx.1_Frame_Shift_Del_p.R704fs|INCENP_uc001nsy.1_Frame_Shift_Del_p.R122fs NM_001040694 NP_001035784 Q9NQS7 INCE_HUMAN inner centromere protein antigens 135/155kDa 708 Potential. chromosome segregation|cytokinesis|mitotic prometaphase centromeric heterochromatin|condensed chromosome kinetochore|cytosol|microtubule|spindle protein binding lung(1) 1 0.000 0.80 5 20 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH358_LUNG NA NCIH358_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.53 8 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH358_LUNG NA NCIH358_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 465 70 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH358_LUNG NA NCIH358_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.67 5 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH358_LUNG NA NCIH358_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 13 37 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH358_LUNG NA NCIH358_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 218 495 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH358_LUNG NA NCIH358_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 80 SHROOM4 57477 broad.mit.edu 37 X 50350728 50350729 + In_Frame_Ins INS - TCC TCC rs143151534 NCIH441_LUNG NA NCIH441_LUNG NA g.chrX:50350728_50350729insTCC uc004dpe.2 - 6 3439_3440 c.3413_3414insGGA c.(3412-3414)GAA>GAGGAA p.1138_1138E>EE SHROOM4_uc004dpd.3_RNA NM_020717 NP_065768 Q9ULL8 SHRM4_HUMAN shroom family member 4 1138 Glu-rich. actin filament organization|brain development|cell morphogenesis|cognition apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus actin filament binding upper_aerodigestive_tract(1) 1 Ovarian(276;0.236) cttcttcttcttcctcctcctc 0.223 0.58 5 7 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH441_LUNG NA NCIH441_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 5 129 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH441_LUNG NA NCIH441_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.19 1396 326 FMN2 56776 broad.mit.edu 37 1 240370441 240370441 + Frame_Shift_Del DEL C - - NCIH441_LUNG NA NCIH441_LUNG NA g.chr1:240370441delC uc010pyd.1 + 5 2554 c.2329delC c.(2329-2331)CCTfs p.P777fs FMN2_uc010pye.1_Frame_Shift_Del_p.P781fs NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 777 Pro-rich.|FH1. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) TGAAAGTGGACCTCAGACAAA 0.577 0.13 244 35 FMN2 56776 broad.mit.edu 37 1 240370942 240370974 + In_Frame_Del DEL CCTCCGCCCCCTCTACCCGGAGCGGCAATACCC - - rs150891575;rs6143701;rs142725738;rs146070457;rs72444563;rs144739133;rs142178619 byFrequency;byFrequency;byFrequency;byFrequency NCIH441_LUNG NA NCIH441_LUNG NA g.chr1:240370942_240370974delCCTCCGCCCCCTCTACCCGGAGCGGCAATACCC uc010pyd.1 + 5 3055_3087 c.2830_2862delCCTCCGCCCCCTCTACCCGGAGCGGCAATACCC c.(2830-2862)CCTCCGCCCCCTCTACCCGGAGCGGCAATACCCdel p.PPPPLPGAAIP944del FMN2_uc010pye.1_In_Frame_Del_p.PPPPLPGAAIP948del NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 944_954 Pro-rich.|FH1. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) GGGAATACCTCCTCCGCCCCCTCTACCCGGAGCGGCAATACCCCCTCCGCCCC 0.700 0.62 18 29 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 NCIH441_LUNG NA NCIH441_LUNG NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.27 37 14 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH441_LUNG NA NCIH441_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.52 65 70 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH441_LUNG NA NCIH441_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.48 242 226 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH441_LUNG NA NCIH441_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 53 128 IKZF1 10320 broad.mit.edu 37 7 50444366 50444371 + In_Frame_Del DEL AAGGCA - - NCIH441_LUNG NA NCIH441_LUNG NA g.chr7:50444366_50444371delAAGGCA uc003tow.3 + 5 464_469 c.296_301delAAGGCA c.(295-303)CAAGGCAGC>CGC p.99_101QGS>R IKZF1_uc003tox.3_In_Frame_Del_p.99_101QGS>R|IKZF1_uc003toy.3_In_Frame_Del_p.99_101QGS>R|IKZF1_uc011kck.1_Intron|IKZF1_uc003toz.3_In_Frame_Del_p.69_71QGS>R|IKZF1_uc010kyx.2_Intron NM_006060 NP_006051 Q13422 IKZF1_HUMAN zinc finger protein, subfamily 1A, 1 (Ikaros) 99_101 cell cycle|chromatin modification|mesoderm development cytoplasm|nucleus zinc ion binding p.?(74) haematopoietic_and_lymphoid_tissue(147)|lung(1) 148 Glioma(55;0.08)|all_neural(89;0.245) Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07) CACAGGGACCAAGGCAGCTCGGCTTT 0.510 0.11 264 31 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH441_LUNG NA NCIH441_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 12 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH441_LUNG NA NCIH441_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.66 10 19 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH441_LUNG NA NCIH441_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 278 70 CARD17 440068 broad.mit.edu 37 11 104971279 104971279 + Frame_Shift_Del DEL C - - NCIH441_LUNG NA NCIH441_LUNG NA g.chr11:104971279delC uc001pir.1 - 2 252 c.235delG c.(235-237)GAAfs p.E79fs CASP1_uc010rve.1_Intron|CASP1_uc010rvf.1_Intron|CASP1_uc010rvg.1_Intron|CASP1_uc010rvh.1_Intron|CASP1_uc010rvi.1_Intron NM_001007232 NP_001007233 Q5XLA6 CAR17_HUMAN caspase recruitment domain family, member 17 79 CARD. proteolysis|regulation of apoptosis cytoplasm cysteine-type endopeptidase activity|cysteine-type endopeptidase inhibitor activity ovary(1) 1 TGACTGTCTTCTTCACAAATG 0.488 0.96 6 148 SRP14 6727 broad.mit.edu 37 15 40328596 40328597 + In_Frame_Ins INS - TGC TGC NCIH441_LUNG NA NCIH441_LUNG NA g.chr15:40328596_40328597insTGC uc001zkq.2 - 5 420_421 c.348_349insGCA c.(346-351)insGCA p.116_117insA SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116_117 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) gctgcggcaggtgctgctgctg 0.228 0.22 69 19 MAP2K7 5609 broad.mit.edu 37 19 7976202 7976202 + Frame_Shift_Del DEL T - - NCIH441_LUNG NA NCIH441_LUNG NA g.chr19:7976202delT uc002mit.2 + 8 988 c.923delT c.(922-924)CTGfs p.L308fs MAP2K7_uc002miv.2_Frame_Shift_Del_p.L308fs|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_Frame_Shift_Del_p.L308fs|MAP2K7_uc010dvv.2_Frame_Shift_Del_p.L183fs NM_145185 NP_660186 O14733 MP2K7_HUMAN mitogen-activated protein kinase kinase 7 308 Protein kinase. activation of JUN kinase activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleus ATP binding|JUN kinase kinase activity|magnesium ion binding|protein binding|protein kinase binding|protein phosphatase binding|protein serine/threonine kinase activity|protein tyrosine kinase activity large_intestine(7)|central_nervous_system(2)|ovary(1)|lung(1) 11 Etoposide(DB00773) GTATGGAGCCTGGGCATCTCG 0.637 0.87 26 170 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes NCIH441_LUNG NA NCIH441_LUNG NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.43 13 10 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH441_LUNG NA NCIH441_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.18 231 52 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH441_LUNG NA NCIH441_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 43 541 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH441_LUNG NA NCIH441_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 23 366 SHROOM4 57477 broad.mit.edu 37 X 50350758 50350759 + In_Frame_Ins INS - TGCTGCTGCTGT TGCTGCTGCTGT NCIH446_LUNG NA NCIH446_LUNG NA g.chrX:50350758_50350759insTGCTGCTGCTGT uc004dpe.2 - 6 3409_3410 c.3383_3384insACAGCAGCAGCA c.(3382-3384)CAG>CAACAGCAGCAGCAG p.1128_1128Q>QQQQQ SHROOM4_uc004dpd.3_RNA NM_020717 NP_065768 Q9ULL8 SHRM4_HUMAN shroom family member 4 1128 Gln-rich. actin filament organization|brain development|cell morphogenesis|cognition apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus actin filament binding upper_aerodigestive_tract(1) 1 Ovarian(276;0.236) cctgttgcttctgctgctgctg 0.252 0.57 6 8 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH446_LUNG NA NCIH446_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 3 87 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH446_LUNG NA NCIH446_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 1192 355 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT NCIH446_LUNG NA NCIH446_LUNG NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.44 499 392 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH446_LUNG NA NCIH446_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.20 78 20 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH446_LUNG NA NCIH446_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.53 47 54 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH446_LUNG NA NCIH446_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 188 263 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH446_LUNG NA NCIH446_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.82 16 74 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH446_LUNG NA NCIH446_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 2 19 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH446_LUNG NA NCIH446_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 2 32 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH446_LUNG NA NCIH446_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 456 53 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH446_LUNG NA NCIH446_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.62 17 28 ATP10A 57194 broad.mit.edu 37 15 25972393 25972393 + Frame_Shift_Del DEL T - - NCIH446_LUNG NA NCIH446_LUNG NA g.chr15:25972393delT uc010ayu.2 - 4 867 c.761delA c.(760-762)AAGfs p.K254fs NM_024490 NP_077816 O60312 AT10A_HUMAN ATPase, class V, type 10A 254 Cytoplasmic (Potential). ATP biosynthetic process|regulation of cell shape integral to membrane|plasma membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity pancreas(2)|ovary(1)|breast(1)|liver(1) 5 all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125) all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244) CAGCCCGGCCTTTTTCCCGTT 0.567 0.54 193 229 THAP11 57215 broad.mit.edu 37 16 67876824 67876832 + In_Frame_Del DEL CAGCAGCAG - - rs34213159;rs3982383;rs63117363;rs141903290 byFrequency;byFrequency NCIH446_LUNG NA NCIH446_LUNG NA g.chr16:67876824_67876832delCAGCAGCAG uc002euo.2 + 1 612_620 c.367_375delCAGCAGCAG c.(367-375)CAGCAGCAGdel p.QQQ129del CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 129_131 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) gcagcagcaacagcagcagcagcagcagc 0.311 0.49 36 35 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH446_LUNG NA NCIH446_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 28 355 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH446_LUNG NA NCIH446_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 100 74 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes NCIH446_LUNG NA NCIH446_LUNG NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.36 9 5 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH446_LUNG NA NCIH446_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.34 250 129 TMPRSS2 7113 broad.mit.edu 37 21 42866332 42866332 + Frame_Shift_Del DEL G - - rs61735792 byFrequency;by1000genomes NCIH446_LUNG NA NCIH446_LUNG NA g.chr21:42866332delG uc002yzj.2 - 3 323 c.189delC c.(187-189)CCCfs p.P63fs TMPRSS2_uc010gor.2_Frame_Shift_Del_p.P100fs|TMPRSS2_uc010gos.1_Frame_Shift_Del_p.P63fs NM_005656 NP_005647 O15393 TMPS2_HUMAN transmembrane protease, serine 2 isoform 2 63 Cytoplasmic (Potential). proteolysis cytoplasm|extracellular region|integral to plasma membrane scavenger receptor activity|serine-type endopeptidase activity TMPRSS2/ERG(2499)|TMPRSS2/ETV1(24) prostate(2523)|central_nervous_system(1) 2524 Prostate(19;4.48e-07)|all_epithelial(19;0.031) TGCAGACGACGGGGTTGGAAG 0.607 0.27 161 60 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH446_LUNG NA NCIH446_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 222 625 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH446_LUNG NA NCIH446_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 27 375 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH460_LUNG NA NCIH460_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.49 28 27 ARID1A 8289 broad.mit.edu 37 1 27106789 27106794 + In_Frame_Del DEL CTGATT - - NCIH460_LUNG NA NCIH460_LUNG NA g.chr1:27106789_27106794delCTGATT uc001bmv.1 + 20 6773_6778 c.6400_6405delCTGATT c.(6400-6405)CTGATTdel p.LI2134del ARID1A_uc001bmu.1_In_Frame_Del_p.LI1917del|ARID1A_uc001bmx.1_In_Frame_Del_p.LI980del|ARID1A_uc009vsm.1_In_Frame_Del_p.LI462del|ARID1A_uc009vsn.1_In_Frame_Del_p.LI376del NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 2134_2135 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CAATGTGGACCTGATTCTGGCCACAC 0.587 0.89 17 137 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH460_LUNG NA NCIH460_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 37 87 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH460_LUNG NA NCIH460_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.30 103 45 EPHA7 2045 broad.mit.edu 37 6 93956546 93956546 + Frame_Shift_Del DEL G - - NCIH460_LUNG NA NCIH460_LUNG NA g.chr6:93956546delG uc003poe.2 - 15 2931 c.2690delC c.(2689-2691)CCAfs p.P897fs EPHA7_uc003pof.2_Frame_Shift_Del_p.P892fs|EPHA7_uc011eac.1_Frame_Shift_Del_p.P893fs NM_004440 NP_004431 Q15375 EPHA7_HUMAN ephrin receptor EphA7 precursor 897 Cytoplasmic (Potential). integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1) 28 all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142) BRCA - Breast invasive adenocarcinoma(108;0.0847) CAGACTATTTGGGTTTCGAAT 0.393 0.43 120 91 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH460_LUNG NA NCIH460_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 15 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH460_LUNG NA NCIH460_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.53 14 16 SMC2 10592 broad.mit.edu 37 9 106877063 106877064 + Frame_Shift_Ins INS - AATT AATT NCIH460_LUNG NA NCIH460_LUNG NA g.chr9:106877063_106877064insAATT uc004bbv.2 + 13 1912_1913 c.1624_1625insAATT c.(1624-1626)GAAfs p.E542fs SMC2_uc004bbu.1_Frame_Shift_Ins_p.E542fs|SMC2_uc004bbw.2_Frame_Shift_Ins_p.E542fs|SMC2_uc011lvl.1_Frame_Shift_Ins_p.E542fs|SMC2_uc004bbx.2_Frame_Shift_Ins_p.E542fs NM_001042551 NP_001036016 O95347 SMC2_HUMAN structural maintenance of chromosomes 2 542 Flexible hinge. cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism condensin complex|cytoplasm|nuclear chromosome ATP binding|protein heterodimerization activity ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1) 9 CACAGCTTTAGAATTAGTGGCT 0.351 0.28 83 32 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH460_LUNG NA NCIH460_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.93 1 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH460_LUNG NA NCIH460_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 221 98 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH460_LUNG NA NCIH460_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.17 59 12 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH460_LUNG NA NCIH460_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 16 138 SMURF2 64750 broad.mit.edu 37 17 62551021 62551022 + Frame_Shift_Ins INS - T T NCIH460_LUNG NA NCIH460_LUNG NA g.chr17:62551021_62551022insT uc002jep.1 - 15 2088_2089 c.1700_1701insA c.(1699-1701)AATfs p.N567fs SMURF2_uc002jeq.1_Frame_Shift_Ins_p.N326fs|SMURF2_uc002jer.1_Frame_Shift_Ins_p.N326fs NM_022739 NP_073576 Q9HAU4 SMUF2_HUMAN SMAD specific E3 ubiquitin protein ligase 2 567 HECT. BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex identical protein binding|SMAD binding|ubiquitin-protein ligase activity skin(3)|lung(1) 4 Breast(5;1.32e-14) BRCA - Breast invasive adenocarcinoma(8;9.88e-12) TACTTTTGCCATTTGGTTTAAG 0.327 0.35 251 137 CSNK2A1 1457 broad.mit.edu 37 20 468160 468160 + Frame_Shift_Del DEL G - - NCIH460_LUNG NA NCIH460_LUNG NA g.chr20:468160delG uc002wdw.1 - 12 1277 c.884delC c.(883-885)CCTfs p.P295fs CSNK2A1_uc002wdx.1_Frame_Shift_Del_p.P295fs|CSNK2A1_uc002wdy.1_Frame_Shift_Del_p.P159fs NM_177559 NP_808227 P68400 CSK21_HUMAN casein kinase II alpha 1 subunit isoform a 295 Protein kinase. axon guidance|Wnt receptor signaling pathway cytosol|NuRD complex|plasma membrane|Sin3 complex ATP binding|protein N-terminus binding|protein serine/threonine kinase activity ovary(1) 1 Breast(17;0.231) OV - Ovarian serous cystadenocarcinoma(29;0.0969) CAAGGCCTCAGGGCTGACAAG 0.532 0.62 49 80 ZNF217 7764 broad.mit.edu 37 20 52193208 52193208 + Frame_Shift_Del DEL C - - NCIH460_LUNG NA NCIH460_LUNG NA g.chr20:52193208delC uc002xwq.3 - 3 2366 c.2095delG c.(2095-2097)GCAfs p.A699fs ZNF217_uc010gij.1_Frame_Shift_Del_p.A691fs NM_006526 NP_006517 O75362 ZN217_HUMAN zinc finger protein 217 699 negative regulation of transcription, DNA-dependent histone deacetylase complex protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding skin(2)|ovary(1)|large_intestine(1)|lung(1)|breast(1) 6 all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398) BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198) AAAGAAATTGCCGGGCAATTG 0.428 0.64 189 331 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH460_LUNG NA NCIH460_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.14 82 13 TIAM1 7074 broad.mit.edu 37 21 32508286 32508286 + Frame_Shift_Del DEL C - - NCIH460_LUNG NA NCIH460_LUNG NA g.chr21:32508286delC uc002yow.1 - 24 4320 c.3848delG c.(3847-3849)GGCfs p.G1283fs TIAM1_uc011adk.1_Frame_Shift_Del_p.G1283fs|TIAM1_uc011adl.1_Frame_Shift_Del_p.G1223fs NM_003253 NP_003244 Q13009 TIAM1_HUMAN T-cell lymphoma invasion and metastasis 1 1283 PH 2. apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cell-cell junction|cytosol receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity lung(3)|breast(3)|ovary(2)|large_intestine(2) 10 TTTCCACTTGCCCAGCGAGGC 0.493 0.43 41 31 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH460_LUNG NA NCIH460_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 125 357 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH460_LUNG NA NCIH460_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 3 42 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 3 23 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.35 13 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.30 31 13 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.15 70 12 TOPBP1 11073 broad.mit.edu 37 3 133376643 133376644 + Frame_Shift_Ins INS - T T NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr3:133376643_133376644insT uc003eps.2 - 4 493_494 c.361_362insA c.(361-363)AGGfs p.R121fs NM_007027 NP_008958 Q92547 TOPB1_HUMAN topoisomerase (DNA) II binding protein 1 121 BRCT 1. DNA repair|response to ionizing radiation microtubule organizing center|PML body|spindle pole DNA binding|protein C-terminus binding ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1) 7 AATATCTACCCTTTTTTCTTTT 0.218 0.59 41 60 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 89 113 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 24 38 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.62 6 10 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 19 PAXIP1 22976 broad.mit.edu 37 7 154760540 154760541 + In_Frame_Ins INS - TGC TGC NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr7:154760540_154760541insTGC uc003wlp.2 - 7 1413_1414 c.1370_1371insGCA c.(1369-1371)CAA>CAGCAA p.457_457Q>QQ PAXIP1_uc003wlq.1_In_Frame_Ins_p.423_423Q>QQ|PAXIP1_uc011kvs.1_In_Frame_Ins_p.421_421Q>QQ|PAXIP1_uc003wlr.1_In_Frame_Ins_p.366_366Q>QQ NM_007349 NP_031375 Q6ZW49 PAXI1_HUMAN PAX interacting protein 1 457 Gln-rich. DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent histone methyltransferase complex|nuclear matrix p.F457C(1) lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_neural(206;0.119) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.0296) UCEC - Uterine corpus endometrioid carcinoma (81;0.178) GCGGATGGGCTtgctgctgctg 0.203 0.12 61 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 31 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 794 84 CREBBP 1387 broad.mit.edu 37 16 3786145 3786145 + Frame_Shift_Del DEL A - - NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr16:3786145delA uc002cvv.2 - 28 4824 c.4620delT c.(4618-4620)TTTfs p.F1540fs CREBBP_uc002cvw.2_Frame_Shift_Del_p.F1502fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1540 Interaction with TRERF1. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) AATCACCTTCAAAATAGGGCA 0.463 0.46 163 139 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 7 49 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.75 35 105 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 47 321 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH508_LARGE_INTESTINE NA NCIH508_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 4 118 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH510_LUNG NA NCIH510_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 74 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH510_LUNG NA NCIH510_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 254 97 CDC42BPA 8476 broad.mit.edu 37 1 227335146 227335146 + Frame_Shift_Del DEL C - - NCIH510_LUNG NA NCIH510_LUNG NA g.chr1:227335146delC uc001hqr.2 - 7 1751 c.808delG c.(808-810)GTCfs p.V270fs CDC42BPA_uc001hqs.2_Frame_Shift_Del_p.V270fs|CDC42BPA_uc009xes.2_Frame_Shift_Del_p.V270fs|CDC42BPA_uc010pvs.1_Frame_Shift_Del_p.V270fs NM_003607 NP_003598 Q5VT25 MRCKA_HUMAN CDC42-binding protein kinase alpha isoform B 270 Protein kinase. actin cytoskeleton reorganization|intracellular signal transduction cell leading edge|cell-cell junction|cytoplasm ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1) 11 all_cancers(173;0.156)|Prostate(94;0.0792) TACATACAGACCCCCAAAGAC 0.418 0.30 119 50 ACVR2A 92 broad.mit.edu 37 2 148657074 148657074 + Frame_Shift_Del DEL G - - NCIH510_LUNG NA NCIH510_LUNG NA g.chr2:148657074delG uc002twg.2 + 4 580 c.311delG c.(310-312)TGCfs p.C104fs ACVR2A_uc010zbn.1_5'UTR|ACVR2A_uc002twh.2_Frame_Shift_Del_p.C104fs NM_001616 NP_001607 P27037 AVR2A_HUMAN activin A receptor, type IIA precursor 104 Extracellular (Potential). activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1) 13 BRCA - Breast invasive adenocarcinoma(221;0.0969) TATTTTTGTTGCTGTGAGGGC 0.333 0.97 1 33 PDK1 5163 broad.mit.edu 37 2 173429749 173429749 + Frame_Shift_Del DEL A - - NCIH510_LUNG NA NCIH510_LUNG NA g.chr2:173429749delA uc002uhr.2 + 5 739 c.639delA c.(637-639)CGAfs p.R213fs PDK1_uc010zdz.1_Frame_Shift_Del_p.R58fs|PDK1_uc010zea.1_RNA|PDK1_uc002uhq.1_Frame_Shift_Del_p.R233fs|PDK1_uc002uhs.2_Frame_Shift_Del_p.R213fs|PDK1_uc010zeb.1_Frame_Shift_Del_p.R233fs NM_002610 NP_002601 Q15118 PDK1_HUMAN pyruvate dehydrogenase kinase 1 precursor 213 Histidine kinase. glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate|small GTPase mediated signal transduction mitochondrial matrix ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity lung(3)|central_nervous_system(1) 4 OV - Ovarian serous cystadenocarcinoma(117;0.12) CATCTCATCGAAAACACATTG 0.323 0.11 131 17 PHOX2B 8929 broad.mit.edu 37 4 41748014 41748028 + In_Frame_Del DEL GCCGCCGCTGCCGCG - - rs17882335 NCIH510_LUNG NA NCIH510_LUNG NA g.chr4:41748014_41748028delGCCGCCGCTGCCGCG uc003gwf.3 - 3 1101_1115 c.741_755delCGCGGCAGCGGCGGC c.(739-756)GCCGCGGCAGCGGCGGCG>GCG p.247_252AAAAAA>A NM_003924 NP_003915 Q99453 PHX2B_HUMAN paired-like homeobox 2b 247_252 Poly-Ala. positive regulation of transcription from RNA polymerase II promoter nuclear chromatin RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity p.A241fs*64(1) autonomic_ganglia(7)|lung(2)|ovary(2)|central_nervous_system(1) 12 0.000 0.16 134 26 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH510_LUNG NA NCIH510_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.33 18 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH510_LUNG NA NCIH510_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 91 142 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH510_LUNG NA NCIH510_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.56 18 23 FBN2 2201 broad.mit.edu 37 5 127653882 127653882 + Frame_Shift_Del DEL G - - NCIH510_LUNG NA NCIH510_LUNG NA g.chr5:127653882delG uc003kuu.2 - 36 5115 c.4676delC c.(4675-4677)CCAfs p.P1559fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 1559 EGF-like 26; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) AAAATCGGGTGGGCAGTTACA 0.398 0.42 44 32 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH510_LUNG NA NCIH510_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH510_LUNG NA NCIH510_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 27 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - NCIH510_LUNG NA NCIH510_LUNG NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.12 361 48 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH510_LUNG NA NCIH510_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 1002 461 ADAMTS20 80070 broad.mit.edu 37 12 43770101 43770101 + Frame_Shift_Del DEL C - - NCIH510_LUNG NA NCIH510_LUNG NA g.chr12:43770101delC uc010skx.1 - 34 5158 c.5158delG c.(5158-5160)GTGfs p.V1720fs NM_025003 NP_079279 P59510 ATS20_HUMAN a disintegrin-like and metalloprotease with 1720 GON. proteinaceous extracellular matrix zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1) 19 all_cancers(12;2.6e-05)|Lung SC(27;0.184) Lung NSC(34;0.0569)|all_lung(34;0.129) GBM - Glioblastoma multiforme(48;0.0473) TGGTTTTTCACTTGAATTTCT 0.294 0.28 28 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH510_LUNG NA NCIH510_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 1 16 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 NCIH510_LUNG NA NCIH510_LUNG NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.10 74 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH510_LUNG NA NCIH510_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.25 162 53 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH510_LUNG NA NCIH510_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 89 517 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH510_LUNG NA NCIH510_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 82 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH522_LUNG NA NCIH522_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 1833 380 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH522_LUNG NA NCIH522_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.14 78 13 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH522_LUNG NA NCIH522_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.55 55 68 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH522_LUNG NA NCIH522_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 228 195 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH522_LUNG NA NCIH522_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 40 104 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT NCIH522_LUNG NA NCIH522_LUNG NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.11 678 86 KCNH2 3757 broad.mit.edu 37 7 150656676 150656676 + Frame_Shift_Del DEL G - - NCIH522_LUNG NA NCIH522_LUNG NA g.chr7:150656676delG uc003wic.2 - 3 469 c.456delC c.(454-456)ACCfs p.T152fs KCNH2_uc011kux.1_Frame_Shift_Del_p.T56fs|KCNH2_uc003wie.2_Frame_Shift_Del_p.T152fs NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 152 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) CCAGCCAGCTGGTGGGGGGGC 0.587 0.33 111 54 TP53 7157 broad.mit.edu 37 17 7578277 7578277 + Frame_Shift_Del DEL G - - NCIH522_LUNG NA NCIH522_LUNG NA g.chr17:7578277delG uc002gim.2 - 6 766 c.572delC c.(571-573)CCTfs p.P191fs TP53_uc002gig.1_Frame_Shift_Del_p.P191fs|TP53_uc002gih.2_Frame_Shift_Del_p.P191fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.P59fs|TP53_uc010cng.1_Frame_Shift_Del_p.P59fs|TP53_uc002gii.1_Frame_Shift_Del_p.P59fs|TP53_uc010cnh.1_Frame_Shift_Del_p.P191fs|TP53_uc010cni.1_Frame_Shift_Del_p.P191fs|TP53_uc002gij.2_Frame_Shift_Del_p.P191fs|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Frame_Shift_Del_p.P98fs|TP53_uc002gio.2_Frame_Shift_Del_p.P59fs|TP53_uc010vug.1_Frame_Shift_Del_p.P152fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 191 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). P -> R (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> H (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.P191del(5)|p.A189_V197delAPPQHLIRV(4)|p.P191fs*56(3)|p.P191L(2)|p.P191fs*53(2)|p.P191R(2)|p.P191S(2)|p.G187fs*16(2)|p.K164_P219del(1)|p.P191fs*6(1)|p.A189_Q192>E(1)|p.P191fs*15(1)|p.P191H(1)|p.P191fs*57(1)|p.P191fs*18(1)|p.P191P(1)|p.P191T(1)|p.P191_Q192delPQ(1)|p.D186_P191delDGLAPP(1)|p.A189fs*53(1)|p.Q192fs*56(1)|p.L188_P191del(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) AAGATGCTGAGGAGGGGCCAG 0.557 0.96 7 191 SMARCA4 6597 broad.mit.edu 37 19 11097625 11097626 + Frame_Shift_Del DEL CC - - NCIH522_LUNG NA NCIH522_LUNG NA g.chr19:11097625_11097626delCC uc002mqf.3 + 5 1089_1090 c.805_806delCC c.(805-807)CCCfs p.P269fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.P269fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.P269fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.P269fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.P269fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.P269fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.P269fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.P269fs|SMARCA4_uc002mqe.2_Frame_Shift_Del_p.P269fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 269 Necessary for interaction with SS18L1/CREST (By similarity). chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.P270fs*16(1)|p.M272fs*31(1)|p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) CTCGGGCGTGCCCCCCGGGATG 0.629 0.95 1 21 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH522_LUNG NA NCIH522_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 43 386 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH522_LUNG NA NCIH522_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 20 300 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH524_LUNG NA NCIH524_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.51 31 32 CDK15 65061 broad.mit.edu 37 2 202719637 202719637 + Frame_Shift_Del DEL C - - NCIH524_LUNG NA NCIH524_LUNG NA g.chr2:202719637delC uc002uyt.2 + 10 1035 c.986delC c.(985-987)TCCfs p.S329fs CDK15_uc010ftm.2_Frame_Shift_Del_p.S194fs|CDK15_uc002uys.2_Frame_Shift_Del_p.S278fs|CDK15_uc010ftn.1_Frame_Shift_Del_p.S278fs|CDK15_uc010fto.1_Frame_Shift_Del_p.S308fs|CDK15_uc002uyu.1_RNA NM_139158 NP_631897 Q96Q40 CDK15_HUMAN PFTAIRE protein kinase 2 329 Protein kinase. ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding breast(2)|ovary(1)|lung(1)|kidney(1) 5 Adenosine triphosphate(DB00171) CCGGGAGTCTCCAAGCTACCT 0.458 0.51 116 119 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH524_LUNG NA NCIH524_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.44 32 25 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH524_LUNG NA NCIH524_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.23 41 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH524_LUNG NA NCIH524_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 63 103 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH524_LUNG NA NCIH524_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.85 23 132 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT NCIH524_LUNG NA NCIH524_LUNG NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.17 690 139 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH524_LUNG NA NCIH524_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH524_LUNG NA NCIH524_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 259 132 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH524_LUNG NA NCIH524_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.21 34 9 CDX2 1045 broad.mit.edu 37 13 28542788 28542788 + Frame_Shift_Del DEL G - - NCIH524_LUNG NA NCIH524_LUNG NA g.chr13:28542788delG uc001urv.2 - 1 530 c.356delC c.(355-357)CCGfs p.P119fs NM_001265 NP_001256 Q99626 CDX2_HUMAN caudal type homeobox 2 119 organ morphogenesis|transcription from RNA polymerase II promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity lung(1) 1 all_cancers(110;0.191)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155) Lung SC(185;0.0156) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199) 0.000 0.36 467 260 RASGRF1 5923 broad.mit.edu 37 15 79277398 79277398 + Frame_Shift_Del DEL C - - NCIH524_LUNG NA NCIH524_LUNG NA g.chr15:79277398delC uc002beq.2 - 24 3788 c.3413delG c.(3412-3414)CGCfs p.R1138fs RASGRF1_uc002bep.2_Frame_Shift_Del_p.R1122fs|RASGRF1_uc010blm.1_Frame_Shift_Del_p.R1047fs|RASGRF1_uc002ber.3_Frame_Shift_Del_p.R1122fs|RASGRF1_uc002beo.2_Frame_Shift_Del_p.R354fs NM_002891 NP_002882 Q13972 RGRF1_HUMAN Ras protein-specific guanine 1140 Ras-GEF. activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission cytosol|growth cone|plasma membrane|synaptosome Rho guanyl-nucleotide exchange factor activity skin(4)|ovary(1)|central_nervous_system(1) 6 GATTGCACTGCGGTTCATGGA 0.597 0.29 389 161 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH524_LUNG NA NCIH524_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.94 23 348 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH524_LUNG NA NCIH524_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 66 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 NCIH524_LUNG NA NCIH524_LUNG NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.27 48 18 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH526_LUNG NA NCIH526_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 38 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH526_LUNG NA NCIH526_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 71 104 AIM1 202 broad.mit.edu 37 6 107009321 107009322 + Frame_Shift_Ins INS - G G NCIH526_LUNG NA NCIH526_LUNG NA g.chr6:107009321_107009322insG uc003prh.2 + 18 5347_5348 c.4860_4861insG c.(4858-4863)GATGTCfs p.D1620fs AIM1_uc003pri.2_Frame_Shift_Ins_p.D424fs NM_001624 NP_001615 Q9Y4K1 AIM1_HUMAN absent in melanoma 1 1620_1621 Ricin B-type lectin. sugar binding breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1) 9 Breast(9;0.0138)|all_epithelial(6;0.169) all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473) Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305) all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858) TCATGGAGGATGTCGGGGCCGA 0.455 0.31 242 110 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH526_LUNG NA NCIH526_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 1 12 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH526_LUNG NA NCIH526_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.17 44 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH526_LUNG NA NCIH526_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 422 197 GRIN2B 2904 broad.mit.edu 37 12 13722817 13722817 + Frame_Shift_Del DEL T - - NCIH526_LUNG NA NCIH526_LUNG NA g.chr12:13722817delT uc001rbt.2 - 11 2485 c.2306delA c.(2305-2307)GATfs p.D769fs NM_000834 NP_000825 Q13224 NMDE2_HUMAN N-methyl-D-aspartate receptor subunit 2B 769 Extracellular (Potential). response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding central_nervous_system(4)|ovary(3)|skin(3)|lung(2) 12 Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043) CCACCCAGAATCTTTTTGGAT 0.517 0.21 71 19 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH526_LUNG NA NCIH526_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 4 70 MKNK2 2872 broad.mit.edu 37 19 2046394 2046398 + Frame_Shift_Del DEL GGCCC - - rs142517981 NCIH526_LUNG NA NCIH526_LUNG NA g.chr19:2046394_2046398delGGCCC uc002lus.2 - 4 454_458 c.209_213delGGGCC c.(208-213)CGGGCCfs p.R70fs MKNK2_uc010xgu.1_5'UTR|MKNK2_uc010xgv.1_5'UTR|MKNK2_uc002lur.2_Frame_Shift_Del_p.R70fs NM_199054 NP_951009 Q9HBH9 MKNK2_HUMAN MAP kinase-interacting serine/threonine kinase 2 70_71 cell surface receptor linked signaling pathway|intracellular protein kinase cascade|regulation of translation ATP binding|metal ion binding|protein serine/threonine kinase activity lung(1)|breast(1) 2 Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.70 10 23 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH526_LUNG NA NCIH526_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.60 28 42 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH526_LUNG NA NCIH526_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 10 40 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH526_LUNG NA NCIH526_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 4 46 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH647_LUNG NA NCIH647_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 47 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH647_LUNG NA NCIH647_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 88 72 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH647_LUNG NA NCIH647_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 26 37 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH647_LUNG NA NCIH647_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 2 29 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH647_LUNG NA NCIH647_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.85 4 23 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH647_LUNG NA NCIH647_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 304 102 NAV3 89795 broad.mit.edu 37 12 78591116 78591118 + In_Frame_Del DEL TCT - - NCIH647_LUNG NA NCIH647_LUNG NA g.chr12:78591116_78591118delTCT uc001syp.2 + 35 6554_6556 c.6381_6383delTCT c.(6379-6384)AATCTT>AAT p.L2128del NAV3_uc001syo.2_In_Frame_Del_p.L2106del|NAV3_uc010sub.1_In_Frame_Del_p.L1585del|NAV3_uc009zsf.2_In_Frame_Del_p.L937del NM_014903 NP_055718 Q8IVL0 NAV3_HUMAN neuron navigator 3 2128 nuclear outer membrane ATP binding|nucleoside-triphosphatase activity large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 17 TTCTTGATAATCTTCATCATGTG 0.330 0.96 6 149 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH647_LUNG NA NCIH647_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 38 350 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH647_LUNG NA NCIH647_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 19 63 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH647_LUNG NA NCIH647_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 184 589 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH647_LUNG NA NCIH647_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 71 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH650_LUNG NA NCIH650_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 33 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH650_LUNG NA NCIH650_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.47 187 164 AFF3 3899 broad.mit.edu 37 2 100218011 100218013 + In_Frame_Del DEL GCT - - NCIH650_LUNG NA NCIH650_LUNG NA g.chr2:100218011_100218013delGCT uc002tag.2 - 13 1491_1493 c.1255_1257delAGC c.(1255-1257)AGCdel p.S419del AFF3_uc002taf.2_In_Frame_Del_p.S444del|AFF3_uc010fiq.1_In_Frame_Del_p.S419del|AFF3_uc010yvr.1_In_Frame_Del_p.S572del|AFF3_uc002tah.1_In_Frame_Del_p.S444del NM_002285 NP_002276 P51826 AFF3_HUMAN AF4/FMR2 family, member 3 isoform 1 419 Poly-Ser. multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1) 6 tgctgctgccgctgctgctgctg 0.562 0.10 70 8 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT NCIH650_LUNG NA NCIH650_LUNG NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.41 104 73 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH650_LUNG NA NCIH650_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.50 21 21 KIT 3815 broad.mit.edu 37 4 55561731 55561731 + Frame_Shift_Del DEL C - - NCIH650_LUNG NA NCIH650_LUNG NA g.chr4:55561731delC uc010igr.2 + 2 208 c.121delC c.(121-123)CCAfs p.P41fs KIT_uc010igs.2_Frame_Shift_Del_p.P41fs NM_000222 NP_000213 P10721 KIT_HUMAN v-kit Hardy-Zuckerman 4 feline sarcoma viral 41 Extracellular (Potential).|Ig-like C2-type 1. male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway extracellular space|integral to membrane ATP binding|protein binding|receptor signaling protein tyrosine kinase activity soft_tissue(3273)|haematopoietic_and_lymphoid_tissue(1572)|skin(99)|testis(49)|bone(21)|genital_tract(18)|kidney(17)|ovary(16)|salivary_gland(15)|large_intestine(11)|thymus(6)|lung(6)|central_nervous_system(4)|NS(3)|eye(2)|endometrium(2)|breast(1)|stomach(1)|autonomic_ganglia(1)|pancreas(1) 5118 all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101) LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209) Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171) Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268) ATCCATCCATCCAGGAAAATC 0.483 0.54 115 135 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH650_LUNG NA NCIH650_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.38 13 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH650_LUNG NA NCIH650_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.66 94 180 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH650_LUNG NA NCIH650_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.58 21 29 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes NCIH650_LUNG NA NCIH650_LUNG NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.56 7 9 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH650_LUNG NA NCIH650_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.48 32 29 FANCE 2178 broad.mit.edu 37 6 35423790 35423791 + Frame_Shift_Ins INS - C C NCIH650_LUNG NA NCIH650_LUNG NA g.chr6:35423790_35423791insC uc003oko.1 + 2 700_701 c.515_516insC c.(514-516)GGCfs p.G172fs FANCE_uc010jvw.1_Frame_Shift_Ins_p.G172fs NM_021922 NP_068741 Q9HB96 FANCE_HUMAN Fanconi anemia, complementation group E 172 Interaction with FANCC. DNA repair nucleoplasm protein binding ovary(1)|lung(1)|skin(1) 3 AGGGGGCTGGGCCTGGGGGGCA 0.594 0.60 10 15 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH650_LUNG NA NCIH650_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 21 ERLIN2 11160 broad.mit.edu 37 8 37602210 37602214 + Frame_Shift_Del DEL GTTTG - - NCIH650_LUNG NA NCIH650_LUNG NA g.chr8:37602210_37602214delGTTTG uc003xke.3 + 6 535_539 c.420_424delGTTTG c.(418-426)CTGTTTGATfs p.L140fs ERLIN2_uc003xkc.3_Frame_Shift_Del_p.L140fs|ERLIN2_uc003xkd.2_Frame_Shift_Del_p.L140fs|ERLIN2_uc003xkf.3_Frame_Shift_Del_p.L140fs|ERLIN2_uc003xkg.2_Frame_Shift_Del_p.L140fs NM_007175 NP_009106 O94905 ERLN2_HUMAN ER lipid raft associated 2 isoform 1 140_142 Lumenal (Potential). ER-associated protein catabolic process endoplasmic reticulum membrane|integral to membrane|plasma membrane protein binding 0 Lung NSC(58;0.174) BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10) ACATTGAGCTGTTTGGTAAGAAAGT 0.527 0.67 47 97 VPS13B 157680 broad.mit.edu 37 8 100123462 100123462 + Frame_Shift_Del DEL T - - NCIH650_LUNG NA NCIH650_LUNG NA g.chr8:100123462delT uc003yiv.2 + 6 828 c.717delT c.(715-717)CATfs p.H239fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.H239fs|VPS13B_uc003yit.2_Frame_Shift_Del_p.H239fs|VPS13B_uc003yiu.1_Frame_Shift_Del_p.H239fs|VPS13B_uc003yis.2_Frame_Shift_Del_p.H239fs|VPS13B_uc011lgy.1_Frame_Shift_Del_p.H115fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 239 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) CTCGTCTTCATTTTACATATG 0.318 0.40 44 29 POU5F1B 5462 broad.mit.edu 37 8 128428367 128428367 + Frame_Shift_Del DEL C - - NCIH650_LUNG NA NCIH650_LUNG NA g.chr8:128428367delC uc003ysf.2 + 1 511 c.256delC c.(256-258)CCCfs p.P86fs uc003ysc.1_Intron|uc003ysd.1_Intron|LOC727677_uc003yse.1_Intron|uc011liu.1_RNA NM_001159542 NP_001153014 Q06416 P5F1B_HUMAN POU class 5 homeobox 1B 86 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 GGGGCTAGTGCCCCAAGGCGG 0.667 0.18 136 30 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH650_LUNG NA NCIH650_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.31 73 33 TRAF2 7186 broad.mit.edu 37 9 139804423 139804425 + In_Frame_Del DEL AAG - - NCIH650_LUNG NA NCIH650_LUNG NA g.chr9:139804423_139804425delAAG uc010nbu.2 + 7 753_755 c.580_582delAAG c.(580-582)AAGdel p.K196del TRAF2_uc010nbv.1_In_Frame_Del_p.K248del|TRAF2_uc004cjv.2_In_Frame_Del_p.K196del|TRAF2_uc011mek.1_In_Frame_Del_p.K185del|TRAF2_uc010nbw.2_Intron NM_021138 NP_066961 Q12933 TRAF2_HUMAN TNF receptor-associated factor 2 196 TRAF-type 2. activation of caspase activity|activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cellular protein complex assembly|induction of apoptosis by extracellular signals|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|protein autoubiquitination|protein homotrimerization|protein K63-linked ubiquitination|tumor necrosis factor-mediated signaling pathway CD40 receptor complex|cytosol|internal side of plasma membrane CD40 receptor binding|enzyme binding|protein binding|signal transducer activity|sphingolipid binding|ubiquitin-protein ligase activity|zinc ion binding ovary(1)|lung(1)|breast(1)|skin(1) 4 all_cancers(76;0.11) Myeloproliferative disorder(178;0.0511) STAD - Stomach adenocarcinoma(284;0.229) OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06) CGGCTGCGGCAAGAAGAAGATCC 0.631 0.16 41 8 CSNK2A1P 283106 broad.mit.edu 37 11 11374137 11374137 + Frame_Shift_Del DEL C - - NCIH650_LUNG NA NCIH650_LUNG NA g.chr11:11374137delC uc001mjp.2 - 1 768 c.530delG c.(529-531)GGTfs p.G177fs GALNTL4_uc001mjo.2_Intron NM_177559 NP_808227 casein kinase II alpha 1 subunit isoform a 0 CTCAGCCAAACCCCAGTCTAT 0.428 0.45 117 96 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 NCIH650_LUNG NA NCIH650_LUNG NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.62 6 10 MRE11A 4361 broad.mit.edu 37 11 94212901 94212901 + Frame_Shift_Del DEL C - - NCIH650_LUNG NA NCIH650_LUNG NA g.chr11:94212901delC uc001peu.2 - 5 530 c.341delG c.(340-342)GGCfs p.G114fs MRE11A_uc001pev.2_Frame_Shift_Del_p.G114fs|MRE11A_uc009ywj.2_Frame_Shift_Del_p.G117fs NM_005591 NP_005582 P49959 MRE11_HUMAN meiotic recombination 11 homolog A isoform 1 114 DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase Mre11 complex|nucleoplasm 3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity breast(4)|lung(1) 5 Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824) GTTGAGGTTGCCATCTTGATA 0.348 0.20 159 40 GUCY1A2 2977 broad.mit.edu 37 11 106810362 106810362 + Frame_Shift_Del DEL C - - NCIH650_LUNG NA NCIH650_LUNG NA g.chr11:106810362delC uc001pjg.1 - 4 1420 c.1030delG c.(1030-1032)GAAfs p.E344fs GUCY1A2_uc010rvo.1_Frame_Shift_Del_p.E344fs|GUCY1A2_uc009yxn.1_Frame_Shift_Del_p.E344fs NM_000855 NP_000846 P33402 GCYA2_HUMAN guanylate cyclase 1, soluble, alpha 2 344 intracellular signal transduction|platelet activation cytoplasm GTP binding|guanylate cyclase activity|heme binding large_intestine(3)|lung(2)|pancreas(2)|ovary(1) 8 all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068) BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476) CTTAGACCTTCCCCCAACTGA 0.473 0.31 303 135 ATN1 1822 broad.mit.edu 37 12 7045892 7045894 + In_Frame_Del DEL CAG - - rs66756893;rs67074116 NCIH650_LUNG NA NCIH650_LUNG NA g.chr12:7045892_7045894delCAG uc001qrw.1 + 5 1699_1701 c.1462_1464delCAG c.(1462-1464)CAGdel p.Q502del ATN1_uc001qrx.1_In_Frame_Del_p.Q502del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagc 0.458 0.21 147 40 DTX1 1840 broad.mit.edu 37 12 113532936 113532936 + Frame_Shift_Del DEL C - - NCIH650_LUNG NA NCIH650_LUNG NA g.chr12:113532936delC uc001tuk.1 + 7 1812 c.1476delC c.(1474-1476)ATCfs p.I492fs NM_004416 NP_004407 Q86Y01 DTX1_HUMAN deltex homolog 1 492 negative regulation of neuron differentiation|Notch signaling pathway|regulation of Notch signaling pathway|transcription from RNA polymerase II promoter cytoplasm|nucleus Notch binding|SH3 domain binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding lung(2)|ovary(1)|central_nervous_system(1) 4 TCCACCTCATCCCCCACTCGC 0.657 0.43 44 33 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 NCIH650_LUNG NA NCIH650_LUNG NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.16 81 15 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH650_LUNG NA NCIH650_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.79 51 187 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH650_LUNG NA NCIH650_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 68 290 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH650_LUNG NA NCIH650_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 15 205 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH660_PROSTATE NA NCIH660_PROSTATE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH660_PROSTATE NA NCIH660_PROSTATE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 44 61 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH660_PROSTATE NA NCIH660_PROSTATE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 18 42 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH660_PROSTATE NA NCIH660_PROSTATE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 3 78 MYST4 23522 broad.mit.edu 37 10 76736014 76736014 + Frame_Shift_Del DEL C - - NCIH660_PROSTATE NA NCIH660_PROSTATE NA g.chr10:76736014delC uc001jwn.1 + 8 2412 c.1919delC c.(1918-1920)ACCfs p.T640fs MYST4_uc001jwm.1_Intron|MYST4_uc001jwo.1_Intron|MYST4_uc001jwp.1_Intron NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 640 Negatively regulates HAT activity. histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) TATAAAGTGACCCCTCAGATG 0.458 0.54 181 214 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH660_PROSTATE NA NCIH660_PROSTATE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 263 104 HNF1A 6927 broad.mit.edu 37 12 121431966 121431966 + Splice_Site DEL G - - NCIH660_PROSTATE NA NCIH660_PROSTATE NA g.chr12:121431966delG uc001tzg.2 + 4 737 c.714_splice c.e4-1 p.R238_splice HNF1A_uc001tze.1_Splice_Site_p.R238_splice|HNF1A_uc001tzf.2_Splice_Site_p.R238_splice|HNF1A_uc010szn.1_Splice_Site_p.R238_splice NM_000545 NP_000536 P20823 HNF1A_HUMAN hepatic nuclear factor-1-alpha glucose homeostasis|glucose import|insulin secretion|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|renal glucose absorption cytoplasm|nucleus|protein complex DNA binding|protein dimerization activity|protein heterodimerization activity|protein homodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding liver(92)|large_intestine(15)|endometrium(6)|breast(2)|lung(1) 116 all_neural(191;0.0684)|Medulloblastoma(191;0.0922) 0.000 0.23 239 70 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - NCIH660_PROSTATE NA NCIH660_PROSTATE NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 0.77 7 24 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH660_PROSTATE NA NCIH660_PROSTATE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 1 27 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH661_LUNG NA NCIH661_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 4 70 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH661_LUNG NA NCIH661_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.13 261 38 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes NCIH661_LUNG NA NCIH661_LUNG NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.69 5 11 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH661_LUNG NA NCIH661_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.40 15 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH661_LUNG NA NCIH661_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 66 76 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH661_LUNG NA NCIH661_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 18 37 WNK2 65268 broad.mit.edu 37 9 95947400 95947400 + Frame_Shift_Del DEL G - - NCIH661_LUNG NA NCIH661_LUNG NA g.chr9:95947400delG uc004ati.1 + 1 189 c.189delG c.(187-189)CCGfs p.P63fs WNK2_uc011lud.1_Frame_Shift_Del_p.P63fs|WNK2_uc004atj.2_Frame_Shift_Del_p.P63fs|WNK2_uc010mrc.1_Frame_Shift_Del_p.P63fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 63 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 0.000 0.98 16 649 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - NCIH661_LUNG NA NCIH661_LUNG NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.11 116 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH661_LUNG NA NCIH661_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 680 306 IRAK3 11213 broad.mit.edu 37 12 66641621 66641621 + Frame_Shift_Del DEL C - - NCIH661_LUNG NA NCIH661_LUNG NA g.chr12:66641621delC uc001sth.2 + 12 1563 c.1461delC c.(1459-1461)AACfs p.N487fs IRAK3_uc010ssy.1_Frame_Shift_Del_p.N426fs NM_007199 NP_009130 Q9Y616 IRAK3_HUMAN interleukin-1 receptor-associated kinase 3 487 interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|negative regulation of innate immune response|negative regulation of interleukin-12 production|negative regulation of interleukin-6 production|negative regulation of macrophage cytokine production|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein catabolic process|negative regulation of protein complex disassembly|negative regulation of toll-like receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of macrophage tolerance induction|positive regulation of NF-kappaB transcription factor activity|response to exogenous dsRNA|response to lipopolysaccharide|response to peptidoglycan cytoplasm|nucleus ATP binding|magnesium ion binding|protein heterodimerization activity|protein homodimerization activity|protein serine/threonine kinase activity lung(3)|ovary(2)|breast(2)|central_nervous_system(1) 8 GBM - Glioblastoma multiforme(28;0.0203) GCCAGAATAACAATTTACTAC 0.428 0.45 68 56 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH661_LUNG NA NCIH661_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.13 86 13 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH661_LUNG NA NCIH661_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.37 26 15 KIAA1409 57578 broad.mit.edu 37 14 94039081 94039081 + Frame_Shift_Del DEL G - - NCIH661_LUNG NA NCIH661_LUNG NA g.chr14:94039081delG uc001ybv.1 + 13 1541 c.1458delG c.(1456-1458)ATGfs p.M486fs KIAA1409_uc001ybs.1_Frame_Shift_Del_p.M486fs NM_020818 NP_065869 Q9P2D8 UNC79_HUMAN hypothetical protein LOC57578 663 integral to membrane ovary(10)|skin(4)|large_intestine(3) 17 all_cancers(154;0.0354)|all_epithelial(191;0.216) Epithelial(152;0.188) CTTTCTCAATGGAGGAGATGT 0.408 0.54 86 101 SMARCA4 6597 broad.mit.edu 37 19 11141498 11141498 + Frame_Shift_Del DEL G - - NCIH661_LUNG NA NCIH661_LUNG NA g.chr19:11141498delG uc002mqf.3 + 25 3759 c.3475delG c.(3475-3477)GGGfs p.G1159fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.G1159fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.G1159fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.G1159fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.G1159fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.G1159fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.G1159fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.G1159fs|SMARCA4_uc010dxt.1_Frame_Shift_Del_p.G379fs|SMARCA4_uc002mqh.3_Frame_Shift_Del_p.G282fs|SMARCA4_uc002mqi.1_Frame_Shift_Del_p.G362fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 1159 Helicase C-terminal. chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) CACCCGGGCTGGGGGGCTCGG 0.622 0.93 1 13 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH661_LUNG NA NCIH661_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 54 185 MYT1 4661 broad.mit.edu 37 20 62839408 62839410 + In_Frame_Del DEL GAG - - NCIH661_LUNG NA NCIH661_LUNG NA g.chr20:62839408_62839410delGAG uc002yii.2 + 7 1223_1225 c.859_861delGAG c.(859-861)GAGdel p.E306del MYT1_uc002yih.2_Intron|MYT1_uc002yij.2_5'UTR NM_004535 NP_004526 Q01538 MYT1_HUMAN myelin transcription factor 1 306 Glu-rich. cell differentiation|nervous system development nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2) 2 all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09) ggaagaggaagaggaggaggagg 0.138 0.61 7 11 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH661_LUNG NA NCIH661_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 58 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH661_LUNG NA NCIH661_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.25 434 141 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH661_LUNG NA NCIH661_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 101 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH684_LIVER NA NCIH684_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.49 19 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCIH684_LIVER NA NCIH684_LIVER NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.11 62 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH684_LIVER NA NCIH684_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.34 77 40 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH684_LIVER NA NCIH684_LIVER NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.27 44 16 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 NCIH684_LIVER NA NCIH684_LIVER NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.88 4 29 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes NCIH684_LIVER NA NCIH684_LIVER NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.70 3 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH684_LIVER NA NCIH684_LIVER NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.60 6 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH684_LIVER NA NCIH684_LIVER NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 18 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH684_LIVER NA NCIH684_LIVER NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.11 198 24 TOX3 27324 broad.mit.edu 37 16 52473512 52473513 + In_Frame_Ins INS - TGC TGC NCIH684_LIVER NA NCIH684_LIVER NA g.chr16:52473512_52473513insTGC uc002egw.2 - 7 1526_1527 c.1355_1356insGCA c.(1354-1356)CAA>CAGCAA p.452_452Q>QQ TOX3_uc010vgt.1_In_Frame_Ins_p.447_447Q>QQ|TOX3_uc010vgu.1_In_Frame_Ins_p.452_452Q>QQ NM_001080430 NP_001073899 O15405 TOX3_HUMAN TOX high mobility group box family member 3 452 Gln-rich. apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity 0 tctgttgttgttgctgctgctg 0.218 0.25 127 43 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH684_LIVER NA NCIH684_LIVER NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 23 325 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH684_LIVER NA NCIH684_LIVER NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.15 50 9 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH684_LIVER NA NCIH684_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 12 58 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH684_LIVER NA NCIH684_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 3 44 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH69_LUNG NA NCIH69_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 4 52 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes NCIH69_LUNG NA NCIH69_LUNG NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.85 2 11 PIK3CA 5290 broad.mit.edu 37 3 178916929 178916937 + In_Frame_Del DEL GGCAACCGT - - NCIH69_LUNG NA NCIH69_LUNG NA g.chr3:178916929_178916937delGGCAACCGT uc003fjk.2 + 2 473_481 c.316_324delGGCAACCGT c.(316-324)GGCAACCGTdel p.GNR106del NM_006218 NP_006209 P42336 PK3CA_HUMAN phosphoinositide-3-kinase, catalytic, alpha 106_108 PI3K-ABD. epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity p.R108H(5)|p.G106V(4)|p.G106_R108del(2)|p.G106R(1)|p.P104_G106>R(1)|p.R108P(1)|p.R108del(1) breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1) 3553 all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155) OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282) TGAACCAGTAGGCAACCGTGAAGAAAAGA 0.335 0.35 11 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH69_LUNG NA NCIH69_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 100 149 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH69_LUNG NA NCIH69_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 27 67 STK10 6793 broad.mit.edu 37 5 171583770 171583771 + Frame_Shift_Ins INS - C C NCIH69_LUNG NA NCIH69_LUNG NA g.chr5:171583770_171583771insC uc003mbo.1 - 2 478_479 c.178_179insG c.(178-180)GCTfs p.A60fs NM_005990 NP_005981 O94804 STK10_HUMAN serine/threonine kinase 10 60 Protein kinase. ATP binding|protein serine/threonine kinase activity ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1) 8 Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094) Medulloblastoma(196;0.00868)|all_neural(177;0.026) Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516) CGCAGCCAAAGCACCCGTCTCC 0.554 0.12 121 16 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIH69_LUNG NA NCIH69_LUNG NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.20 36 9 PHIP 55023 broad.mit.edu 37 6 79692608 79692609 + Frame_Shift_Ins INS - T T NCIH69_LUNG NA NCIH69_LUNG NA g.chr6:79692608_79692609insT uc003pir.2 - 23 2989_2990 c.2763_2764insA c.(2761-2766)AAACAAfs p.K921fs PHIP_uc003piq.2_5'UTR|PHIP_uc011dyp.1_Frame_Shift_Ins_p.K920fs NM_017934 NP_060404 Q8WWQ0 PHIP_HUMAN pleckstrin homology domain interacting protein 921_922 Lys-rich. insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis nucleus insulin receptor binding large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1) 6 all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219) BRCA - Breast invasive adenocarcinoma(397;0.231) CAAACCttttgttttctttctt 0.149 0.19 48 11 PMS2 5395 broad.mit.edu 37 7 6026614 6026614 + Frame_Shift_Del DEL T - - rs63750593 NCIH69_LUNG NA NCIH69_LUNG NA g.chr7:6026614delT uc003spl.2 - 11 1869 c.1782delA c.(1780-1782)TTAfs p.L594fs PMS2_uc003spj.2_Frame_Shift_Del_p.L488fs|PMS2_uc003spk.2_Frame_Shift_Del_p.L459fs|PMS2_uc011jwl.1_Frame_Shift_Del_p.L459fs|PMS2_uc010ktg.2_Frame_Shift_Del_p.L283fs|PMS2_uc010kte.2_Intron|PMS2_uc010ktf.1_Intron NM_000535 NP_000526 P54278 PMS2_HUMAN PMS2 postmeiotic segregation increased 2 isoform 594 mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes MutLalpha complex ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding lung(1)|central_nervous_system(1) 2 Ovarian(82;0.0694) UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15) GAGTATTTACTAACTTTTGAC 0.373 0.47 136 121 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH69_LUNG NA NCIH69_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 22 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G NCIH69_LUNG NA NCIH69_LUNG NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.11 336 43 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency NCIH69_LUNG NA NCIH69_LUNG NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) agcagcagcaacagcagcagca 0.267 0.11 77 10 MYST4 23522 broad.mit.edu 37 10 76788480 76788481 + Frame_Shift_Ins INS - C C NCIH69_LUNG NA NCIH69_LUNG NA g.chr10:76788480_76788481insC uc001jwn.1 + 18 4391_4392 c.3898_3899insC c.(3898-3900)ACCfs p.T1300fs MYST4_uc001jwo.1_Frame_Shift_Ins_p.T1008fs|MYST4_uc001jwp.1_Frame_Shift_Ins_p.T1117fs NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1300 histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) AGAAGGAAAAACCAGCCCCAGT 0.510 0.12 67 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH69_LUNG NA NCIH69_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 834 435 HSP90AA1 3320 broad.mit.edu 37 14 102551075 102551077 + In_Frame_Del DEL CTC - - NCIH69_LUNG NA NCIH69_LUNG NA g.chr14:102551075_102551077delCTC uc001yku.3 - 5 1112_1114 c.922_924delGAG c.(922-924)GAGdel p.E308del HSP90AA1_uc001ykv.3_In_Frame_Del_p.E430del|HSP90AA1_uc001ykw.1_In_Frame_Del_p.E129del|HSP90AA1_uc001ykx.1_In_Frame_Del_p.E297del NM_005348 NP_005339 P07900 HS90A_HUMAN heat shock 90kDa protein 1, alpha isoform 2 308 axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction cytosol|melanosome|plasma membrane ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding ovary(2)|central_nervous_system(2)|prostate(1)|lung(1)|breast(1) 7 Rifabutin(DB00615) ATTCTCCGTACTCCTCATTAGTA 0.374 0.41 243 168 AURKB 9212 broad.mit.edu 37 17 8108582 8108583 + Frame_Shift_Ins INS - G G NCIH69_LUNG NA NCIH69_LUNG NA g.chr17:8108582_8108583insG uc002gkm.2 - 8 873_874 c.812_813insC c.(811-813)CCAfs p.P271fs AURKB_uc010cnu.2_Frame_Shift_Ins_p.P91fs|AURKB_uc002gkn.2_Frame_Shift_Ins_p.P272fs|AURKB_uc010vuu.1_Frame_Shift_Ins_p.P230fs|AURKB_uc002gko.2_RNA NM_004217 NP_004208 Q96GD4 AURKB_HUMAN aurora kinase B 271 Protein kinase. Missing (in Ref. 3; BAA82709). anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|mitotic prometaphase|protein localization to kinetochore chromosome passenger complex|condensed nuclear chromosome, centromeric region|cytosol|spindle ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity lung(2)|breast(1)|central_nervous_system(1) 4 TCTCAAAGGGTGGGTTCCCCAC 0.599 0.16 102 20 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH69_LUNG NA NCIH69_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 37 149 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH69_LUNG NA NCIH69_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 81 737 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH69_LUNG NA NCIH69_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 13 169 SMARCB1 6598 broad.mit.edu 37 22 24134068 24134069 + Frame_Shift_Ins INS - C C NCIH69_LUNG NA NCIH69_LUNG NA g.chr22:24134068_24134069insC uc002zyb.2 + 2 426_427 c.219_220insC c.(217-222)AAACCTfs p.K73fs SMARCB1_uc002zyg.2_Frame_Shift_Ins_p.K73fs|SMARCB1_uc011ajb.1_Intron|SMARCB1_uc002zya.2_Frame_Shift_Ins_p.K73fs|SMARCB1_uc002zyc.2_Intron|SMARCB1_uc002zyd.2_Intron|SMARCB1_uc002zye.1_Frame_Shift_Ins_p.K36fs|SMARCB1_uc002zyf.1_Intron|SMARCB1_uc010gue.1_Intron NM_003073 NP_003064 Q12824 SNF5_HUMAN SWI/SNF related, matrix associated, actin 73_74 cell cycle|chromatin remodeling|DNA integration|interspecies interaction between organisms|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|retroviral genome replication|transcription, DNA-dependent nBAF complex|npBAF complex|nucleolus|nucleoplasm|SWI/SNF complex p53 binding p.?(2) soft_tissue(193)|central_nervous_system(172)|haematopoietic_and_lymphoid_tissue(23)|meninges(5)|skin(5)|bone(4)|ovary(2)|endometrium(1)|lung(1)|pancreas(1) 407 Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05) AAAAAACAAAACCTAACACTAA 0.436 0.15 63 11 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 57 IRS1 3667 broad.mit.edu 37 2 227661396 227661398 + In_Frame_Del DEL TGC - - NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chr2:227661396_227661398delTGC uc002voh.3 - 1 2109_2111 c.2057_2059delGCA c.(2056-2061)AGCAAC>AAC p.S686del NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 686 Poly-Ser. fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) GGGACGGCGTtgctgctgctgct 0.547 0.41 117 81 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.13 76 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 131 163 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.17 106 22 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.31 18 8 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.40 32 21 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.87 2 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 265 120 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 16 160 RNF43 54894 broad.mit.edu 37 17 56435721 56435721 + Frame_Shift_Del DEL A - - NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chr17:56435721delA uc002iwf.2 - 8 3372 c.1416delT c.(1414-1416)CATfs p.H472fs RNF43_uc010wnv.1_Frame_Shift_Del_p.H431fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.H472fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.H472fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.H345fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 472 Cytoplasmic (Potential).|Ser-rich. endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.88 60 437 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 66 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 84 325 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH716_LARGE_INTESTINE NA NCIH716_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 79 GUCY2F 2986 broad.mit.edu 37 X 108719148 108719148 + Frame_Shift_Del DEL C - - NCIH727_LUNG NA NCIH727_LUNG NA g.chrX:108719148delC uc004eod.3 - 2 294 c.18delG c.(16-18)GGGfs p.G6fs GUCY2F_uc011msq.1_RNA NM_001522 NP_001513 P51841 GUC2F_HUMAN guanylate cyclase 2F precursor 6 intracellular signal transduction|receptor guanylyl cyclase signaling pathway|visual perception integral to plasma membrane|nuclear outer membrane ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity lung(4)|breast(3)|central_nervous_system(1) 8 0.000 0.97 20 585 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH727_LUNG NA NCIH727_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 73 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH727_LUNG NA NCIH727_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 39 71 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH727_LUNG NA NCIH727_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 15 23 NUP153 9972 broad.mit.edu 37 6 17633077 17633078 + Splice_Site INS - AA AA rs36027788;rs147103527 NCIH727_LUNG NA NCIH727_LUNG NA g.chr6:17633077_17633078insAA uc003ncd.1 - 17 2665 c.2465_splice c.e17-1 p.G822_splice NUP153_uc011dje.1_Splice_Site_p.G853_splice|NUP153_uc010jpl.1_Splice_Site_p.G780_splice NM_005124 NP_005115 P49790 NU153_HUMAN nucleoporin 153kDa carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm DNA binding|protein binding|transporter activity|zinc ion binding lung(4)|ovary(2)|breast(2)|skin(1) 9 Breast(50;0.0259)|Ovarian(93;0.0584) all_hematologic(90;0.125) all cancers(50;0.0981)|Epithelial(50;0.112) CTGAACTTCCTAAAAAAAAAAA 0.406 0.22 29 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH727_LUNG NA NCIH727_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 23 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIH727_LUNG NA NCIH727_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.62 92 152 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NCIH727_LUNG NA NCIH727_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.82 3 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH727_LUNG NA NCIH727_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 420 162 IDH2 3418 broad.mit.edu 37 15 90631943 90631943 + Frame_Shift_Del DEL C - - NCIH727_LUNG NA NCIH727_LUNG NA g.chr15:90631943delC uc002box.2 - 4 496 c.410delG c.(409-411)GGAfs p.G137fs IDH2_uc010uqb.1_Frame_Shift_Del_p.G85fs|IDH2_uc010uqc.1_Frame_Shift_Del_p.G7fs|IDH2_uc010bnu.2_Intron NM_002168 NP_002159 P48735 IDHP_HUMAN isocitrate dehydrogenase 2 (NADP+), 137 Substrate binding (By similarity). 2-oxoglutarate metabolic process|glyoxylate cycle|isocitrate metabolic process|tricarboxylic acid cycle mitochondrial matrix isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding haematopoietic_and_lymphoid_tissue(621)|central_nervous_system(80)|bone(7)|skin(3) 711 Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04) BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106) CCGGATAGTTCCATTGGGACT 0.522 0.45 21 17 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH727_LUNG NA NCIH727_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 26 195 TP53 7157 broad.mit.edu 37 17 7578433 7578434 + In_Frame_Ins INS - ACTGCTTGT ACTGCTTGT NCIH727_LUNG NA NCIH727_LUNG NA g.chr17:7578433_7578434insACTGCTTGT uc002gim.2 - 5 690_691 c.496_497insACAAGCAGT c.(496-498)TCA>TACAAGCAGTCA p.165_166insYKQ TP53_uc002gig.1_In_Frame_Ins_p.165_166insYKQ|TP53_uc002gih.2_In_Frame_Ins_p.165_166insYKQ|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_In_Frame_Ins_p.33_34insYKQ|TP53_uc010cng.1_In_Frame_Ins_p.33_34insYKQ|TP53_uc002gii.1_In_Frame_Ins_p.33_34insYKQ|TP53_uc010cnh.1_In_Frame_Ins_p.165_166insYKQ|TP53_uc010cni.1_In_Frame_Ins_p.165_166insYKQ|TP53_uc002gij.2_In_Frame_Ins_p.165_166insYKQ|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_In_Frame_Ins_p.72_73insYKQ|TP53_uc002gio.2_In_Frame_Ins_p.33_34insYKQ|TP53_uc010vug.1_In_Frame_Ins_p.126_127insYKQ NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 165_166 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). S -> T (in sporadic cancers; somatic mutation).|S -> L (in sporadic cancers; somatic mutation).|S -> A (in sporadic cancers; somatic mutation).|S -> P (in sporadic cancers; somatic mutation).|S -> G (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.Q165*(22)|p.S166*(19)|p.0?(7)|p.S166P(5)|p.S166L(4)|p.Q167fs*14(4)|p.Q165L(3)|p.Q165P(2)|p.S166fs*15(2)|p.S166A(2)|p.Q165R(2)|p.K164fs*3(2)|p.V157_C176del20(1)|p.K164_P219del(1)|p.Y163fs*1(1)|p.K164_Q165insXXX(1)|p.Y163_Q165delYKQ(1)|p.P151_V173del23(1)|p.Q165E(1)|p.Q165H(1)|p.Q165fs*16(1)|p.S166G(1)|p.Q165del(1)|p.S166T(1)|p.Q165fs*4(1)|p.S149fs*72(1)|p.Q165_S166insXXX(1)|p.Q165_S166insYKQ(1)|p.Q165_M169delQSQHM(1)|p.Y163fs*14(1)|p.A159_Q167delAMAIYKQSQ(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) CATGTGCTGTGACTGCTTGTAG 0.634 0.32 77 37 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 NCIH727_LUNG NA NCIH727_LUNG NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.31 9 4 STAC2 342667 broad.mit.edu 37 17 37371466 37371473 + Frame_Shift_Del DEL CCACCTTC - - NCIH727_LUNG NA NCIH727_LUNG NA g.chr17:37371466_37371473delCCACCTTC uc002hrs.2 - 5 816_823 c.597_604delGAAGGTGG c.(595-606)GGGAAGGTGGACfs p.G199fs STAC2_uc010cvt.2_Frame_Shift_Del_p.G57fs NM_198993 NP_945344 Q6ZMT1 STAC2_HUMAN SH3 and cysteine rich domain 2 199_202 intracellular signal transduction metal ion binding pancreas(1) 1 TAGACAGGGTCCACCTTCCCACTGTCCC 0.519 0.36 73 41 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH727_LUNG NA NCIH727_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 4 19 LMTK3 114783 broad.mit.edu 37 19 49000829 49000829 + Frame_Shift_Del DEL G - - NCIH727_LUNG NA NCIH727_LUNG NA g.chr19:49000829delG uc002pjk.2 - 12 3584 c.3584delC c.(3583-3585)CCGfs p.P1195fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.14 1248 203 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH727_LUNG NA NCIH727_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 87 233 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH727_LUNG NA NCIH727_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 106 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH747_LARGE_INTESTINE NA NCIH747_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 55 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 NCIH747_LARGE_INTESTINE NA NCIH747_LARGE_INTESTINE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.46 13 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH747_LARGE_INTESTINE NA NCIH747_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 58 68 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH747_LARGE_INTESTINE NA NCIH747_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.39 82 53 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH747_LARGE_INTESTINE NA NCIH747_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 465 156 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH747_LARGE_INTESTINE NA NCIH747_LARGE_INTESTINE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.24 25 8 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCIH747_LARGE_INTESTINE NA NCIH747_LARGE_INTESTINE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.65 6 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH747_LARGE_INTESTINE NA NCIH747_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.58 35 48 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH747_LARGE_INTESTINE NA NCIH747_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 52 221 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH747_LARGE_INTESTINE NA NCIH747_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 31 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH838_LUNG NA NCIH838_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 23 ARID1A 8289 broad.mit.edu 37 1 27106010 27106017 + Frame_Shift_Del DEL GCCCACCA - - rs138605055 by1000genomes NCIH838_LUNG NA NCIH838_LUNG NA g.chr1:27106010_27106017delGCCCACCA uc001bmv.1 + 20 5994_6001 c.5621_5628delGCCCACCA c.(5620-5628)TGCCCACCAfs p.C1874fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.C1657fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.C720fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.C202fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.C116fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1874_1876 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CACGCACCCTGCCCACCAGCCCCTCGGA 0.620 0.52 214 230 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes NCIH838_LUNG NA NCIH838_LUNG NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.43 32 24 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIH838_LUNG NA NCIH838_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.21 38 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH838_LUNG NA NCIH838_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 103 124 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH838_LUNG NA NCIH838_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 21 33 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCIH838_LUNG NA NCIH838_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 21 WRN 7486 broad.mit.edu 37 8 30925776 30925777 + Frame_Shift_Ins INS - G G NCIH838_LUNG NA NCIH838_LUNG NA g.chr8:30925776_30925777insG uc003xio.3 + 7 1445_1446 c.657_658insG c.(655-660)GCTGGTfs p.A219fs NM_000553 NP_000544 Q14191 WRN_HUMAN Werner syndrome protein 219_220 Interaction with WRNIP1 (By similarity).|3'-5' exonuclease. base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance centrosome|nucleolus|nucleoplasm 3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1) 7 Breast(100;0.195) KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192) TTTTATAGGCTGGTTTTATTAT 0.277 0.33 14 7 CSMD3 114788 broad.mit.edu 37 8 113326771 113326771 + Frame_Shift_Del DEL G - - NCIH838_LUNG NA NCIH838_LUNG NA g.chr8:113326771delG uc003ynu.2 - 48 7595 c.7436delC c.(7435-7437)CCAfs p.P2479fs CSMD3_uc003yns.2_Frame_Shift_Del_p.P1681fs|CSMD3_uc003ynt.2_Frame_Shift_Del_p.P2439fs|CSMD3_uc011lhx.1_Frame_Shift_Del_p.P2375fs|CSMD3_uc003ynw.1_Frame_Shift_Del_p.P190fs NM_198123 NP_937756 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 isoform 1 2479 CUB 14.|Extracellular (Potential). integral to membrane|plasma membrane ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1) 63 TTGAAGATTTGGGTAACTGTC 0.378 0.25 77 26 BLNK 29760 broad.mit.edu 37 10 97967646 97967647 + Frame_Shift_Ins INS - G G NCIH838_LUNG NA NCIH838_LUNG NA g.chr10:97967646_97967647insG uc001kls.3 - 10 933_934 c.755_756insC c.(754-756)CCAfs p.P252fs BLNK_uc001kme.3_Frame_Shift_Ins_p.P147fs|BLNK_uc001klt.3_Frame_Shift_Ins_p.P143fs|BLNK_uc009xvc.2_RNA|BLNK_uc001klu.3_Frame_Shift_Ins_p.P170fs|BLNK_uc001klv.3_Frame_Shift_Ins_p.P147fs|BLNK_uc001klw.3_RNA|BLNK_uc001klx.3_Frame_Shift_Ins_p.P229fs|BLNK_uc001kly.3_Frame_Shift_Ins_p.P252fs|BLNK_uc001klz.3_RNA|BLNK_uc001kma.3_Frame_Shift_Ins_p.P229fs|BLNK_uc001kmb.3_Frame_Shift_Ins_p.P48fs|BLNK_uc001kmc.3_RNA|BLNK_uc001kmd.3_Frame_Shift_Ins_p.P170fs|BLNK_uc009xvd.2_RNA NM_013314 NP_037446 Q8WV28 BLNK_HUMAN B-cell linker isoform 1 252 Pro-rich. B cell differentiation|humoral immune response|inflammatory response|intracellular signal transduction cytoplasm|plasma membrane SH3/SH2 adaptor activity|transmembrane receptor protein tyrosine kinase adaptor activity skin(2) 2 Colorectal(252;0.083) Epithelial(162;7.89e-08)|all cancers(201;2.27e-06) GTGGTGTCGTTGGTTTTTTCCT 0.307 0.10 90 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825377 + In_Frame_Del DEL TGC - - rs11277537 NCIH838_LUNG NA NCIH838_LUNG NA g.chr11:95825375_95825377delTGC uc001pfw.1 - 2 3103_3105 c.1818_1820delGCA c.(1816-1821)CAGCAA>CAA p.606_607QQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 606_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgct 0.113 0.25 683 230 PLEKHA5 54477 broad.mit.edu 37 12 19512448 19512449 + Frame_Shift_Ins INS - C C NCIH838_LUNG NA NCIH838_LUNG NA g.chr12:19512448_19512449insC uc001reb.2 + 22 3039_3040 c.2953_2954insC c.(2953-2955)ACCfs p.T985fs PLEKHA5_uc010sie.1_Frame_Shift_Ins_p.T1146fs|PLEKHA5_uc001rea.2_Frame_Shift_Ins_p.T1043fs|PLEKHA5_uc009zin.2_Frame_Shift_Ins_p.T743fs|PLEKHA5_uc010sif.1_Frame_Shift_Ins_p.T974fs|PLEKHA5_uc010sig.1_Frame_Shift_Ins_p.T967fs|PLEKHA5_uc010sih.1_Frame_Shift_Ins_p.T940fs|PLEKHA5_uc001rec.1_Frame_Shift_Ins_p.T794fs|PLEKHA5_uc009zio.2_Frame_Shift_Ins_p.T251fs NM_019012 NP_061885 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A 985 1-phosphatidylinositol binding|protein binding ovary(1)|kidney(1)|skin(1) 3 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) ACTAAAAGAAACCGAACCCCAA 0.386 0.15 46 8 RARG 5916 broad.mit.edu 37 12 53605487 53605488 + Frame_Shift_Ins INS - C C NCIH838_LUNG NA NCIH838_LUNG NA g.chr12:53605487_53605488insC uc001sce.2 - 10 1822_1823 c.1337_1338insG c.(1336-1338)GGCfs p.G446fs RARG_uc001scd.2_Frame_Shift_Ins_p.G435fs|RARG_uc010sob.1_Frame_Shift_Ins_p.G424fs|RARG_uc001scf.2_Frame_Shift_Ins_p.G446fs|RARG_uc001scg.2_Frame_Shift_Ins_p.G374fs|RARG_uc010soc.1_Frame_Shift_Ins_p.G325fs NM_000966 NP_000957 P13631 RARG_HUMAN retinoic acid receptor, gamma isoform 1 446 canonical Wnt receptor signaling pathway|embryonic eye morphogenesis|embryonic hindlimb morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|regulation of cell size|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid integral to membrane|transcription factor complex retinoic acid receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding breast(2)|ovary(1)|lung(1) 4 Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tazarotene(DB00799)|Tretinoin(DB00755) GGCCCCCTTTGCCCTGGCCCCC 0.644 0.13 72 11 LRP1 4035 broad.mit.edu 37 12 57573916 57573917 + Frame_Shift_Ins INS - C C NCIH838_LUNG NA NCIH838_LUNG NA g.chr12:57573916_57573917insC uc001snd.2 + 31 5694_5695 c.5228_5229insC c.(5227-5229)GGCfs p.G1743fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 1743 LDL-receptor class B 15.|Extracellular (Potential). G -> S (in Ref. 8; AA sequence). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) GGCCAGAAGGGCCCCGTGGGTA 0.624 0.10 74 8 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH838_LUNG NA NCIH838_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.38 48 30 DACH1 1602 broad.mit.edu 37 13 72053357 72053358 + Frame_Shift_Ins INS - C C NCIH838_LUNG NA NCIH838_LUNG NA g.chr13:72053357_72053358insC uc010thn.1 - 9 2236_2237 c.1813_1814insG c.(1813-1815)GAAfs p.E605fs DACH1_uc010tho.1_Frame_Shift_Ins_p.E457fs|DACH1_uc010thp.1_Frame_Shift_Ins_p.E403fs NM_080759 NP_542937 Q9UI36 DACH1_HUMAN dachshund homolog 1 isoform a 657 DACHbox-C.|Potential.|Interaction with SIN3A (By similarity). multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus DNA binding|nucleotide binding|protein binding breast(1) 1 Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198) GBM - Glioblastoma multiforme(99;0.00032) TAGTTCTCTTTCCCTTAAAAAA 0.366 0.89 8 67 STK11 6794 broad.mit.edu 37 19 1220614 1220614 + Frame_Shift_Del DEL G - - NCIH838_LUNG NA NCIH838_LUNG NA g.chr19:1220614delG uc002lrl.1 + 5 1747 c.632delG c.(631-633)CGGfs p.R211fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 211 Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.?(2) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.99 6 462 ID1 3397 broad.mit.edu 37 20 30193544 30193545 + Frame_Shift_Ins INS - G G rs11545371 NCIH838_LUNG NA NCIH838_LUNG NA g.chr20:30193544_30193545insG uc002wwg.1 + 1 453_454 c.354_355insG c.(352-357)CCCGGGfs p.P118fs ID1_uc002wwh.1_Frame_Shift_Ins_p.P118fs|hsa-mir-3193|MI0014238_5'Flank NM_002165 NP_002156 P41134 ID1_HUMAN inhibitor of DNA binding 1 isoform a 118_119 angiogenesis|blood vessel endothelial cell migration|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by transcription factor localization|transforming growth factor beta receptor signaling pathway cytoplasm protein binding ovary(1) 1 all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198) Epithelial(4;1.99e-05)|all cancers(5;0.000169)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264) TTGGAACCCCCGGGGGCCGAGG 0.614 0.18 56 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH838_LUNG NA NCIH838_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 44 613 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH838_LUNG NA NCIH838_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 68 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH854_LUNG NA NCIH854_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 25 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCIH854_LUNG NA NCIH854_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.38 183 114 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH854_LUNG NA NCIH854_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.28 67 26 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH854_LUNG NA NCIH854_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 11 24 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NCIH854_LUNG NA NCIH854_LUNG NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.49 29 28 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH854_LUNG NA NCIH854_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 1 21 PCDH15 65217 broad.mit.edu 37 10 55973727 55973728 + Frame_Shift_Del DEL TC - - NCIH854_LUNG NA NCIH854_LUNG NA g.chr10:55973727_55973728delTC uc001jju.1 - 10 1461_1462 c.1066_1067delGA c.(1066-1068)GACfs p.D356fs PCDH15_uc010qhq.1_Frame_Shift_Del_p.D361fs|PCDH15_uc010qhr.1_Frame_Shift_Del_p.D356fs|PCDH15_uc010qhs.1_Frame_Shift_Del_p.D361fs|PCDH15_uc010qht.1_Frame_Shift_Del_p.D356fs|PCDH15_uc010qhu.1_Frame_Shift_Del_p.D356fs|PCDH15_uc001jjv.1_Frame_Shift_Del_p.D334fs|PCDH15_uc010qhv.1_Frame_Shift_Del_p.D356fs|PCDH15_uc010qhw.1_Frame_Shift_Del_p.D319fs|PCDH15_uc010qhx.1_Frame_Shift_Del_p.D356fs|PCDH15_uc010qhy.1_Frame_Shift_Del_p.D361fs|PCDH15_uc010qhz.1_Frame_Shift_Del_p.D356fs|PCDH15_uc010qia.1_Frame_Shift_Del_p.D334fs|PCDH15_uc010qib.1_Frame_Shift_Del_p.D334fs|PCDH15_uc001jjw.2_Frame_Shift_Del_p.D356fs NM_033056 NP_149045 Q96QU1 PCD15_HUMAN protocadherin 15 isoform CD1-4 precursor 356 Cadherin 3.|Extracellular (Potential). equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse calcium ion binding pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2) 13 Melanoma(3;0.117)|Lung SC(717;0.238) CTGGTGAAAGTCTCTGTTTACT 0.381 0.38 45 27 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NCIH854_LUNG NA NCIH854_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 146 43 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH854_LUNG NA NCIH854_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 48 748 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIH854_LUNG NA NCIH854_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.24 53 17 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIH854_LUNG NA NCIH854_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.39 60 38 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH854_LUNG NA NCIH854_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 80 260 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH854_LUNG NA NCIH854_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 52 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 5 142 KIAA1804 84451 broad.mit.edu 37 1 233515217 233515217 + Frame_Shift_Del DEL T - - NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:233515217delT uc001hvt.3 + 9 2726 c.2465delT c.(2464-2466)GTGfs p.V822fs KIAA1804_uc001hvu.3_Frame_Shift_Del_p.V268fs NM_032435 NP_115811 Q5TCX8 M3KL4_HUMAN mixed lineage kinase 4 822 activation of JUN kinase activity|protein autophosphorylation ATP binding|MAP kinase kinase kinase activity|protein homodimerization activity lung(5)|central_nervous_system(2)|skin(1) 8 all_cancers(173;0.000405)|all_epithelial(177;0.0345)|Prostate(94;0.122) GATCCACTGGTGGACAGTGCA 0.567 0.13 124 18 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.33 176 87 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 104 121 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 32 71 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.41 246 174 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 1 11 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.21 37 10 CSNK1G1 53944 broad.mit.edu 37 15 64497103 64497103 + Frame_Shift_Del DEL T - - NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:64497103delT uc002anf.2 - 8 1291 c.811delA c.(811-813)AGGfs p.R271fs CSNK1G1_uc002ane.2_RNA|CSNK1G1_uc002ang.1_Frame_Shift_Del_p.R271fs|CSNK1G1_uc002anh.1_Frame_Shift_Del_p.R271fs|CSNK1G1_uc002anj.2_Frame_Shift_Del_p.R253fs NM_022048 NP_071331 Q9HCP0 KC1G1_HUMAN casein kinase 1, gamma 1 271 Protein kinase. Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity 0 GGAGTATTCCTTTTGGTGTCA 0.403 0.42 107 78 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 6 54 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 40 530 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 102 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 NCIN87_STOMACH NA NCIN87_STOMACH NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.36 113 64 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCIN87_STOMACH NA NCIN87_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 4 118 CTNNA2 1496 broad.mit.edu 37 2 80782932 80782932 + Frame_Shift_Del DEL A - - NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr2:80782932delA uc010ysh.1 + 11 1660 c.1655delA c.(1654-1656)CACfs p.H552fs CTNNA2_uc010yse.1_Frame_Shift_Del_p.H552fs|CTNNA2_uc010ysf.1_Frame_Shift_Del_p.H552fs|CTNNA2_uc010ysg.1_Frame_Shift_Del_p.H552fs|CTNNA2_uc010ysi.1_Frame_Shift_Del_p.H184fs NM_004389 NP_004380 P26232 CTNA2_HUMAN catenin, alpha 2 isoform 1 552 axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity actin cytoskeleton|axon|cytosol cadherin binding|structural constituent of cytoskeleton pancreas(4)|lung(3)|breast(1)|skin(1) 9 CGAGTCATACACATCATCAAT 0.507 0.47 279 250 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.30 80 35 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 262 65 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 216 255 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.44 15 12 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.38 10 6 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 3 32 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.61 275 433 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.27 148 55 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.56 14 18 HSP90AB4P 664618 broad.mit.edu 37 15 58983757 58983759 + In_Frame_Del DEL TAA - - NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr15:58983757_58983759delTAA uc002afh.1 - 3 1061_1063 c.1061_1063delTTA c.(1060-1065)ATTAAC>AAC p.I354del ADAM10_uc002afd.1_Intron|ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron|ADAM10_uc002afg.2_Intron NR_002927 RecName: Full=Putative heat shock protein HSP 90-beta 4; 0 TGTCGCCAGTTAATAGAGTCCTC 0.463 0.44 123 98 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 17 171 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.47 75 66 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.47 10 9 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.37 311 184 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 53 142 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 15 299 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes NCIN87_STOMACH NA NCIN87_STOMACH NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.10 388 41 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 9 73 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.46 323 275 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.56 15 19 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.38 16 10 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.23 172 51 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.41 48 33 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 182 249 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 4 41 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 4 89 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.42 38 28 BLM 641 broad.mit.edu 37 15 91292816 91292817 + Frame_Shift_Ins INS - T T NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:91292816_91292817insT uc002bpr.2 + 3 415_416 c.318_319insT c.(316-321)TCATTAfs p.S106fs BLM_uc010uqh.1_Frame_Shift_Ins_p.S106fs|BLM_uc010uqi.1_5'UTR|BLM_uc010bnx.2_Frame_Shift_Ins_p.S106fs NM_000057 NP_000048 P54132 BLM_HUMAN Bloom syndrome protein 106_107 double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray cytoplasm|lateral element|nuclear matrix|nucleolus|PML body ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding ovary(3)|skin(2)|breast(1) 6 Lung NSC(78;0.0875)|all_lung(78;0.109) Lung(145;0.189) GATCAAAATCATTATTGCCAGA 0.431 0.96 13 304 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 17 220 TAF15 8148 broad.mit.edu 37 17 34171795 34171815 + In_Frame_Del DEL CGAGGAGGCTATGGAGGAGAT - - NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:34171795_34171815delCGAGGAGGCTATGGAGGAGAT uc002hkd.2 + 15 1578_1598 c.1492_1512delCGAGGAGGCTATGGAGGAGAT c.(1492-1512)CGAGGAGGCTATGGAGGAGATdel p.RGGYGGD519del TAF15_uc002hkc.2_In_Frame_Del_p.RGGYGGD516del NM_139215 NP_631961 Q92804 RBP56_HUMAN TBP-associated factor 15 isoform 1 519_525 Arg/Gly-rich.|16.|21 X approximate tandem repeats of D-R- [S,G](0,3)-G-G-Y-G-G. positive regulation of transcription, DNA-dependent cytoplasm|nucleus DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding TAF15/NR4A3(33) bone(33)|lung(1)|skin(1) 35 Ovarian(249;0.17) UCEC - Uterine corpus endometrioid carcinoma (308;0.0193) tggtggagaccgaggaggctatggaggagatcgaggaggtt 0.118 0.79 5 19 ZNF573 126231 broad.mit.edu 37 19 38229950 38229951 + Frame_Shift_Ins INS - A A NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:38229950_38229951insA uc002ohe.2 - 4 1462_1463 c.1440_1441insT c.(1438-1443)AGTACTfs p.S480fs ZNF573_uc010efs.2_Frame_Shift_Ins_p.S393fs|ZNF573_uc002ohd.2_Frame_Shift_Ins_p.S478fs|ZNF573_uc002ohf.2_Frame_Shift_Ins_p.S422fs|ZNF573_uc002ohg.2_Frame_Shift_Ins_p.S392fs NM_152360 NP_689573 Q86YE8 ZN573_HUMAN zinc finger protein 573 460_461 C2H2-type 13. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1) 1 UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146) TTTGAGCCAGTACTATAGGCCT 0.361 0.50 10 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 119 382 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.26 122 42 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 271 1068 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 24 335 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 62 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.26 25 9 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 44 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 111 187 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 20 46 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.80 3 12 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.35 15 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 18 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.63 16 27 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 3 31 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.15 106 19 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.43 8 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 754 277 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 34 148 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.13 73 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 130 576 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NH6_AUTONOMIC_GANGLIA NA NH6_AUTONOMIC_GANGLIA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 7 114 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 58 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 33 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 122 98 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 13 32 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.60 4 6 POU3F2 5454 broad.mit.edu 37 6 99283172 99283173 + In_Frame_Ins INS - CAG CAG NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr6:99283172_99283173insCAG uc003ppe.2 + 1 593_594 c.423_424insCAG c.(421-426)insCAG p.149_150insQ NM_005604 NP_005595 P20265 PO3F2_HUMAN POU domain, class 3, transcription factor 2 149_150 positive regulation of cell proliferation identical protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197) BRCA - Breast invasive adenocarcinoma(108;0.0355) aacagcagcaacagcagcagca 0.465 0.34 52 27 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 1 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 28 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.62 5 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 305 83 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.12 52 7 FOS 2353 broad.mit.edu 37 14 75747842 75747846 + Frame_Shift_Del DEL CCGCT - - rs146332374 byFrequency NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr14:75747842_75747846delCCGCT uc001xrn.2 + 4 1063_1067 c.858_862delCCGCT c.(856-864)GCCCGCTCCfs p.A286fs FOS_uc010tva.1_Frame_Shift_Del_p.A250fs|FOS_uc010asi.2_Frame_Shift_Del_p.A172fs|FOS_uc001xro.2_Frame_Shift_Del_p.A138fs NM_005252 NP_005243 P01100 FOS_HUMAN v-fos FBJ murine osteosarcoma viral oncogene 286_288 cellular response to reactive oxygen species|DNA methylation|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|SMAD protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter|transforming growth factor beta receptor signaling pathway protein dimerization activity|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding lung(2)|ovary(1) 3 all_lung(585;0.0138)|all_epithelial(191;0.0263)|all_neural(303;0.112) BRCA - Breast invasive adenocarcinoma(234;0.0117) CTGAGACAGCCCGCTCCGTGCCAGA 0.600 0.10 327 38 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.33 26 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 51 508 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NIHOVCAR3_OVARY NA NIHOVCAR3_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 83 MAGEB16 139604 broad.mit.edu 37 X 35820679 35820679 + Frame_Shift_Del DEL T - - NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chrX:35820679delT uc010ngt.1 + 2 645 c.366delT c.(364-366)AATfs p.N122fs NM_001099921 NP_001093391 A2A368 MAGBG_HUMAN melanoma antigen family B, 16 122 MAGE. lung(3)|ovary(2)|breast(1)|skin(1) 7 TTTTGGTGAATTTCATGCTGC 0.443 0.34 587 300 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 8 389 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.45 928 772 FMO4 2329 broad.mit.edu 37 1 171289040 171289041 + Frame_Shift_Ins INS - TGGA TGGA NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr1:171289040_171289041insTGGA uc001gho.2 + 3 293_294 c.76_77insTGGA c.(76-78)CTGfs p.L26fs NM_002022 NP_002013 P31512 FMO4_HUMAN flavin containing monooxygenase 4 26 xenobiotic metabolic process integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding kidney(2)|skin(1) 3 all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181) GGATGAGGACCTGGAGCCCACC 0.480 0.77 155 516 NCL 4691 broad.mit.edu 37 2 232325415 232325417 + In_Frame_Del DEL TCA - - NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr2:232325415_232325417delTCA uc002vru.2 - 4 915_917 c.774_776delTGA c.(772-777)GATGAA>GAA p.D258del SNORD82_uc010fxw.1_5'Flank NM_005381 NP_005372 P19338 NUCL_HUMAN nucleolin 258 Asp/Glu-rich (acidic). angiogenesis cell cortex|nucleolus|ribonucleoprotein complex nucleotide binding|protein C-terminus binding|RNA binding|telomeric DNA binding ovary(2)|pancreas(1) 3 Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167) Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18) Ctcatcatcttcatcatcatcat 0.246 0.60 4 6 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.16 56 11 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.36 63 35 ALPK1 80216 broad.mit.edu 37 4 113360940 113360941 + Frame_Shift_Del DEL AG - - NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr4:113360940_113360941delAG uc003iap.3 + 14 3729_3730 c.3450_3451delAG c.(3448-3453)ACAGAAfs p.T1150fs ALPK1_uc003ian.3_Frame_Shift_Del_p.T1150fs|ALPK1_uc011cfx.1_Frame_Shift_Del_p.T1072fs|ALPK1_uc003iao.3_RNA|ALPK1_uc010imo.2_Frame_Shift_Del_p.T978fs NM_025144 NP_079420 Q96QP1 ALPK1_HUMAN alpha-kinase 1 1150_1151 Alpha-type protein kinase. ATP binding|protein serine/threonine kinase activity ovary(5) 5 Ovarian(17;0.0446)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.00325) TGGTGAAAACAGAATACAAAGC 0.366 0.99 2 192 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 234 190 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 58 135 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.18 37 8 PTK7 5754 broad.mit.edu 37 6 43109757 43109758 + Frame_Shift_Ins INS - A A NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr6:43109757_43109758insA uc003oub.1 + 12 2055_2056 c.1857_1858insA c.(1855-1860)CCCAAGfs p.P619fs PTK7_uc003ouc.1_Frame_Shift_Ins_p.P619fs|PTK7_uc003oud.1_Frame_Shift_Ins_p.P579fs|PTK7_uc003oue.1_Frame_Shift_Ins_p.P489fs|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Frame_Shift_Ins_p.P627fs|PTK7_uc010jyj.1_Intron NM_002821 NP_002812 Q13308 PTK7_HUMAN PTK7 protein tyrosine kinase 7 isoform a 619_620 Ig-like C2-type 7.|Extracellular (Potential). actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration cell-cell junction|integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ovary(2)|large_intestine(1) 3 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423) AGGGGGACCCCAAGCCGCTGAT 0.599 0.13 197 29 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.79 3 11 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.60 93 137 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.61 257 394 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 323 54 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.35 11 6 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.76 5 16 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.42 7 5 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.13 512 74 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 100 525 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 14 280 NF2 4771 broad.mit.edu 37 22 30000081 30000082 + Frame_Shift_Ins INS - A A NMCG1_CENTRAL_NERVOUS_SYSTEM NA NMCG1_CENTRAL_NERVOUS_SYSTEM NA g.chr22:30000081_30000082insA uc003age.3 + 1 537_538 c.94_95insA c.(94-96)GAGfs p.E32fs NF2_uc003afy.3_Frame_Shift_Ins_p.E32fs|NF2_uc003afz.3_Frame_Shift_Ins_p.E32fs|NF2_uc003agf.3_Frame_Shift_Ins_p.E32fs|NF2_uc003agb.3_5'UTR|NF2_uc003agc.3_5'UTR|NF2_uc003agd.3_RNA|NF2_uc003agg.3_Frame_Shift_Ins_p.E32fs|NF2_uc003aga.3_Frame_Shift_Ins_p.E32fs|NF2_uc003agh.3_Frame_Shift_Ins_p.E32fs|NF2_uc003agi.3_Frame_Shift_Ins_p.E32fs|NF2_uc003agj.3_Frame_Shift_Ins_p.E32fs NM_000268 NP_000259 P35240 MERL_HUMAN neurofibromin 2 isoform 1 32 FERM. actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane cytoskeletal protein binding|protein binding p.D30fs*15(2)|p.E32*(1)|p.?(1)|p.E32fs*16(1)|p.M33fs*16(1)|p.D30fs*3(1) meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1) 728 0.000 0.95 22 443 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.71 11 27 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.45 18 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.68 79 171 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 14 41 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 12 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.91 1 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.59 7 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 763 339 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 53 338 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 0.82 6 27 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.65 61 111 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 107 302 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.84 9 48 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.63 13 22 F8 2157 broad.mit.edu 37 X 154156923 154156924 + Frame_Shift_Ins INS - G G NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:154156923_154156924insG uc004fmt.2 - 14 5312_5313 c.5141_5142insC c.(5140-5142)ACAfs p.T1714fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1714 F5/8 type A 3.|Plastocyanin-like 5. T -> S (in HEMA; moderate). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AATAGTGTCGTGTTTTCTTTTG 0.396 0.14 75 12 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.37 19 11 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.23 27 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 90 133 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.84 14 71 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 3 42 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 375 40 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 595 329 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 7 116 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.38 16 10 COL1A1 1277 broad.mit.edu 37 17 48265889 48265890 + Splice_Site DEL AC - - NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:48265889_48265890delAC uc002iqm.2 - 43 3333 c.3207_splice c.e43+1 p.T1069_splice NM_000088 NP_000079 P02452 CO1A1_HUMAN alpha 1 type I collagen preproprotein axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception collagen type I|extracellular space|plasma membrane identical protein binding|platelet-derived growth factor binding COL1A1/PDGFB(372) soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1) 382 Collagenase(DB00048)|Palifermin(DB00039) 0.000 0.42 486 359 STXBP2 6813 broad.mit.edu 37 19 7707005 7707006 + Splice_Site DEL GT - - NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:7707005_7707006delGT uc002mha.3 + 8 708 c.663_splice c.e8+1 p.E221_splice STXBP2_uc002mhb.3_Splice_Site_p.E218_splice|STXBP2_uc010dvj.2_Splice_Site|STXBP2_uc010xjr.1_Splice_Site_p.E232_splice|STXBP2_uc010dvk.2_Splice_Site_p.E189_splice|STXBP2_uc002mhc.3_Splice_Site|STXBP2_uc002mhe.1_5'Flank NM_006949 NP_008880 Q15833 STXB2_HUMAN syntaxin binding protein 2 isoform a leukocyte mediated cytotoxicity|neutrophil degranulation|protein transport|regulation of mast cell degranulation|vesicle docking involved in exocytosis azurophil granule|cytolytic granule|cytosol|specific granule|tertiary granule syntaxin-3 binding central_nervous_system(1) 1 0.000 1.00 0 16 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.60 56 83 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 110 837 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.87 8 52 SHROOM4 57477 broad.mit.edu 37 X 50350728 50350729 + In_Frame_Ins INS - TCC TCC rs143151534 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chrX:50350728_50350729insTCC uc004dpe.2 - 6 3439_3440 c.3413_3414insGGA c.(3412-3414)GAA>GAGGAA p.1138_1138E>EE SHROOM4_uc004dpd.3_RNA NM_020717 NP_065768 Q9ULL8 SHRM4_HUMAN shroom family member 4 1138 Glu-rich. actin filament organization|brain development|cell morphogenesis|cognition apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus actin filament binding upper_aerodigestive_tract(1) 1 Ovarian(276;0.236) cttcttcttcttcctcctcctc 0.223 0.67 4 8 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 6 163 F8 2157 broad.mit.edu 37 X 154157685 154157686 + Frame_Shift_Ins INS - T T NUGC3_STOMACH NA NUGC3_STOMACH NA g.chrX:154157685_154157686insT uc004fmt.2 - 14 4550_4551 c.4379_4380insA c.(4378-4380)AATfs p.N1460fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1460 B. N -> K (in HEMA). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AAGAAAGGTTATTTTTTTTGGC 0.416 0.76 185 591 TRIM33 51592 broad.mit.edu 37 1 114952840 114952842 + In_Frame_Del DEL AGA - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr1:114952840_114952842delAGA uc001eew.2 - 12 2242_2244 c.2158_2160delTCT c.(2158-2160)TCTdel p.S720del TRIM33_uc010owr.1_In_Frame_Del_p.S334del|TRIM33_uc010ows.1_In_Frame_Del_p.S352del|TRIM33_uc001eex.2_In_Frame_Del_p.S720del NM_015906 NP_056990 Q9UPN9 TRI33_HUMAN tripartite motif-containing 33 protein isoform 720 negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent nucleus co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 11 all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184) all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05) Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133) AGGGACCTGGAGAAGGATTCATG 0.419 0.95 3 62 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.35 1098 580 CLK2 1196 broad.mit.edu 37 1 155233768 155233769 + Frame_Shift_Del DEL AT - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr1:155233768_155233769delAT uc001fjy.2 - 12 1579_1580 c.1289_1290delAT c.(1288-1290)TATfs p.Y430fs RAG1AP1_uc010pey.1_Intron|SCAMP3_uc001fjs.2_5'Flank|SCAMP3_uc001fju.2_5'Flank|SCAMP3_uc001fjv.2_5'Flank|SCAMP3_uc001fjt.2_5'Flank|CLK2_uc001fjw.2_Frame_Shift_Del_p.Y429fs|CLK2_uc001fjx.2_Frame_Shift_Del_p.Y202fs|CLK2_uc009wqm.2_Frame_Shift_Del_p.Y430fs NM_003993 NP_003984 P49760 CLK2_HUMAN CDC-like kinase 2 430 Protein kinase. nucleus ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity 0 all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088) Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) TCTCACGAACATAGCGCCCAGC 0.545 0.57 326 437 PRRX1 5396 broad.mit.edu 37 1 170688888 170688888 + Frame_Shift_Del DEL A - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr1:170688888delA uc001ghf.2 + 2 310 c.263delA c.(262-264)GAAfs p.E88fs PRRX1_uc001ghe.2_Frame_Shift_Del_p.E88fs NM_022716 NP_073207 P54821 PRRX1_HUMAN paired mesoderm homeobox 1 isoform pmx-1b 88 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity ovary(1) 1 all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181) AACTCAGAAGAAAAAAAGAAG 0.423 0.30 412 178 TPO 7173 broad.mit.edu 37 2 1499906 1499907 + Frame_Shift_Del DEL TT - - rs148431413 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr2:1499906_1499907delTT uc002qww.2 + 12 2243_2244 c.2152_2153delTT c.(2152-2154)TTTfs p.F718fs TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Frame_Shift_Del_p.F661fs|TPO_uc002qwr.2_Frame_Shift_Del_p.F718fs|TPO_uc002qwx.2_Frame_Shift_Del_p.F661fs|TPO_uc010yio.1_Frame_Shift_Del_p.F545fs|TPO_uc010yip.1_Frame_Shift_Del_p.F718fs|TPO_uc002qwy.1_Frame_Shift_Del_p.F58fs|TPO_uc002qwz.2_Intron NM_000547 NP_000538 P07202 PERT_HUMAN thyroid peroxidase isoform a 718 Extracellular (Potential). cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process cell surface|cytoplasm|integral to plasma membrane calcium ion binding|heme binding|iodide peroxidase activity ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1) 20 all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627) all_cancers(51;0.0338) all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12) Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550) CCCCGAAGACTTTGAGTCTTGT 0.554 0.47 130 114 SOX11 6664 broad.mit.edu 37 2 5833525 5833526 + In_Frame_Ins INS - GAC GAC NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr2:5833525_5833526insGAC uc002qyj.2 + 1 727_728 c.672_673insGAC c.(670-675)insGAC p.233_234insD NM_003108 NP_003099 P35716 SOX11_HUMAN SRY-box 11 233_234 cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis cytoplasm|nucleolus enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding central_nervous_system(3) 3 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) OV - Ovarian serous cystadenocarcinoma(76;0.132) 0.000 0.25 91 31 CTLA4 1493 broad.mit.edu 37 2 204737476 204737476 + Frame_Shift_Del DEL C - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr2:204737476delC uc002vak.1 + 4 770 c.613delC c.(613-615)CCCfs p.P205fs CTLA4_uc002val.1_Frame_Shift_Del_p.A168fs|CTLA4_uc010fty.1_Frame_Shift_Del_p.A73fs|CTLA4_uc010ftz.1_RNA NM_005214 NP_005205 P16410 CTLA4_HUMAN cytotoxic T-lymphocyte-associated protein 4 205 Cytoplasmic (Potential). B cell receptor signaling pathway|immune response|negative regulation of B cell proliferation|negative regulation of regulatory T cell differentiation|positive regulation of apoptosis|response to DNA damage stimulus|T cell costimulation clathrin-coated endocytic vesicle|external side of plasma membrane|Golgi apparatus|integral to plasma membrane|perinuclear region of cytoplasm 0 Abatacept(DB01281) TGTGAAAATGCCCCCAACAGA 0.378 0.27 558 206 SPEG 10290 broad.mit.edu 37 2 220326765 220326765 + Frame_Shift_Del DEL C - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr2:220326765delC uc010fwg.2 + 7 2602 c.2602delC c.(2602-2604)CCCfs p.P868fs SPEG_uc002vlm.2_RNA|SPEG_uc010fwh.1_Frame_Shift_Del_p.P76fs|SPEG_uc002vln.1_Frame_Shift_Del_p.P76fs|SPEG_uc002vlp.1_Frame_Shift_Del_p.P76fs|SPEG_uc002vlq.2_Frame_Shift_Del_p.P19fs NM_005876 NP_005867 Q15772 SPEG_HUMAN SPEG complex locus 868 muscle organ development|negative regulation of cell proliferation nucleus ATP binding|protein serine/threonine kinase activity stomach(9)|ovary(4)|central_nervous_system(1) 14 Renal(207;0.0183) Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163) CTCCAAGGCACCCCCCACCTT 0.647 0.59 13 19 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.36 9 5 TGFBR2 7048 broad.mit.edu 37 3 30691871 30691872 + Frame_Shift_Ins INS - A A NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr3:30691871_30691872insA uc003ceo.2 + 3 755_756 c.373_374insA c.(373-375)GAAfs p.E125fs TGFBR2_uc003cen.2_Frame_Shift_Ins_p.E150fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 125 Extracellular (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 CATTATGAAGGAAAAAAAAAAG 0.421 0.33 392 196 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.38 63 38 BMP2K 55589 broad.mit.edu 37 4 79792137 79792139 + In_Frame_Del DEL CAG - - rs17855588 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr4:79792137_79792139delCAG uc003hlk.2 + 11 1598_1600 c.1432_1434delCAG c.(1432-1434)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 gcaacagcaacagcagcagcagc 0.167 0.16 114 21 NFKB1 4790 broad.mit.edu 37 4 103534740 103534741 + Splice_Site INS - AA AA rs148268461;rs35795162 by1000genomes NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr4:103534740_103534741insAA uc011ceq.1 + 23 3213 c.2746_splice c.e23+2 p.D916_splice NFKB1_uc011cep.1_Splice_Site_p.D917_splice|NFKB1_uc011cer.1_Splice_Site_p.D736_splice NM_003998 NP_003989 P19838 NFKB1_HUMAN nuclear factor kappa-B, subunit 1 isoform 1 anti-apoptosis|apoptosis|cellular response to mechanical stimulus|inflammatory response|innate immune response|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of calcidiol 1-monooxygenase activity|nerve growth factor receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter cytosol|I-kappaB/NF-kappaB complex|mitochondrion|nucleoplasm protein binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding ovary(2)|breast(2)|skin(1) 5 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;6.59e-08) Dexamethasone(DB01234)|Pranlukast(DB01411)|Thalidomide(DB01041) AGCAAATAGGTAAAAAAAAAGA 0.500 0.21 30 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 198 268 ADAM29 11086 broad.mit.edu 37 4 175898788 175898788 + Frame_Shift_Del DEL A - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr4:175898788delA uc003iuc.2 + 5 2782 c.2112delA c.(2110-2112)ATAfs p.I704fs ADAM29_uc003iud.2_Frame_Shift_Del_p.I704fs|ADAM29_uc010irr.2_Frame_Shift_Del_p.I704fs|ADAM29_uc011cki.1_Frame_Shift_Del_p.I704fs NM_014269 NP_055084 Q9UKF5 ADA29_HUMAN ADAM metallopeptidase domain 29 preproprotein 704 Cytoplasmic (Potential). proteolysis|spermatogenesis integral to plasma membrane metalloendopeptidase activity|zinc ion binding skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1) 16 Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164) all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286) GTAAACCAATAAAAAAGCAGC 0.343 0.12 272 37 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 43 89 DDR1 780 broad.mit.edu 37 6 30863251 30863251 + Frame_Shift_Del DEL C - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr6:30863251delC uc003nrr.2 + 13 1843 c.1584delC c.(1582-1584)GGCfs p.G528fs DDR1_uc010jse.2_Intron|DDR1_uc003nrq.2_Intron|DDR1_uc003nrs.2_Frame_Shift_Del_p.G528fs|DDR1_uc003nrt.2_Intron|DDR1_uc011dms.1_Intron|DDR1_uc003nru.2_Intron|DDR1_uc003nrv.2_Frame_Shift_Del_p.G528fs|DDR1_uc003nrw.1_Frame_Shift_Del_p.A300fs|DDR1_uc003nry.1_Intron|DDR1_uc003nrx.1_Intron|DDR1_uc003nrz.1_5'Flank NM_013993 NP_054699 Q08345 DDR1_HUMAN discoidin domain receptor family, member 1 528 Gly/Pro-rich.|Cytoplasmic (Potential). cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway extracellular region|integral to plasma membrane ATP binding|protein binding|protein binding|transmembrane receptor protein tyrosine kinase activity lung(4)|central_nervous_system(3)|large_intestine(1)|ovary(1) 9 Imatinib(DB00619) GAGGCCCGGGCCCCCCCACAC 0.682 0.30 142 62 TNRC18 84629 broad.mit.edu 37 7 5352636 5352641 + In_Frame_Del DEL GAGGAG - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr7:5352636_5352641delGAGGAG uc003soi.3 - 27 8230_8235 c.7881_7886delCTCCTC c.(7879-7887)TCCTCCTCA>TCA p.2627_2629SSS>S NM_001080495 NP_001073964 O15417 TNC18_HUMAN trinucleotide repeat containing 18 2627_2629 Ser-rich. DNA binding 0 Ovarian(82;0.142) UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15) agaggaggatgaggaggaggaggagg 0.214 0.36 9 5 GRM3 2913 broad.mit.edu 37 7 86415912 86415913 + Frame_Shift_Del DEL CG - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr7:86415912_86415913delCG uc003uid.2 + 3 1903_1904 c.804_805delCG c.(802-807)AACGCGfs p.N268fs GRM3_uc010lef.2_Frame_Shift_Del_p.N266fs|GRM3_uc010leg.2_Frame_Shift_Del_p.N140fs|GRM3_uc010leh.2_Intron NM_000840 NP_000831 Q14832 GRM3_HUMAN glutamate receptor, metabotropic 3 precursor 268_269 Extracellular (Potential). synaptic transmission integral to plasma membrane lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1) 13 Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142) Acamprosate(DB00659)|Nicotine(DB00184) 0.000 0.15 431 76 CYP3A4 1576 broad.mit.edu 37 7 99377640 99377640 + Frame_Shift_Del DEL A - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr7:99377640delA uc003urv.1 - 2 244 c.140delT c.(139-141)TTGfs p.L47fs CYP3A4_uc003urw.1_Frame_Shift_Del_p.L47fs|CYP3A4_uc011kiz.1_Frame_Shift_Del_p.L47fs|CYP3A4_uc011kja.1_Intron|CYP3A4_uc011kjb.1_Intron NM_017460 NP_059488 P08684 CP3A4_HUMAN cytochrome P450, family 3, subfamily A, 47 alkaloid catabolic process|androgen metabolic process|exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid catabolic process|xenobiotic metabolic process cell surface|endoplasmic reticulum membrane|integral to membrane|microsome albendazole monooxygenase activity|caffeine oxidase activity|electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding|quinine 3-monooxygenase activity|steroid binding|taurochenodeoxycholate 6alpha-hydroxylase activity|testosterone 6-beta-hydroxylase activity|vitamin D 24-hydroxylase activity|vitamin D3 25-hydroxylase activity central_nervous_system(3)|ovary(1) 4 Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228) Albendazole(DB00518)|Alclometasone(DB00240)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Aliskiren(DB01258)|Almotriptan(DB00918)|Alosetron(DB00969)|Alprazolam(DB00404)|Amlodipine(DB00381)|Amprenavir(DB00701)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Benazepril(DB00542)|Bepridil(DB01244)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bortezomib(DB00188)|Bosentan(DB00559)|Bromocriptine(DB01200)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Buspirone(DB00490)|Busulfan(DB01008)|Carbamazepine(DB00564)|Cevimeline(DB00185)|Chlorpheniramine(DB01114)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cinacalcet(DB01012)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clindamycin(DB01190)|Clofibrate(DB00636)|Clonazepam(DB01068)|Clopidogrel(DB00758)|Cocaine(DB00907)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cyproterone(DB04839)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Delavirdine(DB00705)|Desogestrel(DB00304)|Dexamethasone(DB01234)|Diazepam(DB00829)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dofetilide(DB00204)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Doxorubicin(DB00997)|Drospirenone(DB01395)|Dutasteride(DB01126)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Epirubicin(DB00445)|Eplerenone(DB00700)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Exemestane(DB00990)|Felodipine(DB01023)|Fentanyl(DB00813)|Fexofenadine(DB00950)|Finasteride(DB01216)|Fluconazole(DB00196)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Fosamprenavir(DB01319)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Granisetron(DB00889)|Grepafloxacin(DB00365)|Halofantrine(DB01218)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Imatinib(DB00619)|Indinavir(DB00224)|Ipratropium(DB00332)|Irinotecan(DB00762)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levomethadyl Acetate(DB01227)|Levothyroxine(DB00451)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Maraviroc(DB04835)|Marinol(DB00470)|Mebendazole(DB00643)|Medroxyprogesterone(DB00603)|Methadone(DB00333)|Methylprednisolone(DB00959)|Metyrapone(DB01011)|Mibefradil(DB01388)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirtazapine(DB00370)|Modafinil(DB00745)|Mometasone(DB00764)|Montelukast(DB00471)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norgestrel(DB00506)|Nystatin(DB00646)|Ondansetron(DB00904)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paricalcitol(DB00910)|Phenmetrazine(DB00830)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prednisolone(DB00860)|Prednisone(DB00635)|Prochlorperazine(DB00433)|Quetiapine(DB01224)|Quinapril(DB00881)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranolazine(DB00243)|Reboxetine(DB00234)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampin(DB01045)|Rimonabant(DB06155)|Ritonavir(DB00503)|Rofecoxib(DB00533)|Roxithromycin(DB00778)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sertindole(DB06144)|Sibutramine(DB01105)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Terconazole(DB00251)|Terfenadine(DB00342)|Testosterone(DB00624)|Tiagabine(DB00906)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tiotropium(DB01409)|Tipranavir(DB00932)|Toremifene(DB00539)|Triazolam(DB00897)|Trimetrexate(DB01157)|Troglitazone(DB00197)|Valdecoxib(DB00580)|Vardenafil(DB00862)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Voriconazole(DB00582)|Zaleplon(DB00962)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909) AATATTTCCCAAAAAAGGCAG 0.403 0.10 309 34 EPHB6 2051 broad.mit.edu 37 7 142561448 142561448 + Frame_Shift_Del DEL G - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr7:142561448delG uc011kst.1 + 6 947 c.160delG c.(160-162)GGGfs p.G54fs EPHB6_uc011ksu.1_Frame_Shift_Del_p.G54fs|EPHB6_uc003wbs.2_Intron|EPHB6_uc003wbt.2_5'UTR|EPHB6_uc003wbu.2_Intron NM_004445 NP_004436 O15197 EPHB6_HUMAN ephrin receptor EphB6 precursor 54 Extracellular (Potential). extracellular region|integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1) 19 Melanoma(164;0.059) CTACCCACCAGGGGGGGTGAG 0.572 0.45 11 9 EZH2 2146 broad.mit.edu 37 7 148525902 148525903 + In_Frame_Ins INS - TCA TCA rs137864062 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr7:148525902_148525903insTCA uc003wfd.1 - 6 720_721 c.554_555insTGA c.(553-555)GAC>GATGAC p.185_185D>DD EZH2_uc011kug.1_In_Frame_Ins_p.176_176D>DD|EZH2_uc003wfb.1_In_Frame_Ins_p.185_185D>DD|EZH2_uc003wfc.1_In_Frame_Ins_p.146_146D>DD|EZH2_uc011kuh.1_In_Frame_Ins_p.176_176D>DD|EZH2_uc011kui.1_In_Frame_Ins_p.185_185D>DD|EZH2_uc011kuj.1_RNA NM_004456 NP_004447 Q15910 EZH2_HUMAN enhancer of zeste 2 isoform a 185 Interaction with DNMT1, DNMT3A and DNMT3B. negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent ESC/E(Z) complex DNA binding|histone-lysine N-methyltransferase activity|protein binding haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1) 183 Melanoma(164;0.15) OV - Ovarian serous cystadenocarcinoma(82;0.00239) 0.000 0.86 22 137 TCEA1 6917 broad.mit.edu 37 8 54934627 54934629 + In_Frame_Del DEL TTC - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr8:54934627_54934629delTTC uc003xru.2 - 1 380_382 c.57_59delGAA c.(55-60)AAGAAC>AAC p.K19del TCEA1_uc003xrv.2_In_Frame_Del_p.K19del|TCEA1_uc011ldw.1_In_Frame_Del_p.K19del|TCEA1_uc003xrw.1_RNA NM_006756 NP_006747 P23193 TCEA1_HUMAN transcription elongation factor A 1 isoform 1 19 TFIIS N-terminal. positive regulation of viral transcription|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction nucleoplasm DNA binding|translation elongation factor activity|zinc ion binding 0 Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181) OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699) gcTCACCGCGTTCTTCTTCTGCA 0.429 0.33 84 42 PLAG1 5324 broad.mit.edu 37 8 57080711 57080712 + Frame_Shift_Del DEL CA - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr8:57080711_57080712delCA uc003xsq.3 - 2 568_569 c.117_118delTG c.(115-120)TGTGACfs p.C39fs PLAG1_uc003xsr.3_Frame_Shift_Del_p.C39fs|PLAG1_uc010lyi.2_Frame_Shift_Del_p.C39fs|PLAG1_uc010lyj.2_Intron NM_001114635 NP_001108107 Q6DJT9 PLAG1_HUMAN pleiomorphic adenoma gene 1 isoform b 39_40 Interacts with KPNA2.|C2H2-type 1. nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding CTNNB1/PLAG1(60)|FGFR1_ENST00000447712/PLAG1(28)|CHCHD7/PLAG1(12)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|COL1A2/PLAG1(3)|TCEA1_ENST00000521604/PLAG1(3) salivary_gland(113)|soft_tissue(13)|lung(1)|central_nervous_system(1)|breast(1) 129 all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125) Epithelial(17;0.00179)|all cancers(17;0.0125) AAGGCCTTGTCACACAGTTGGC 0.450 0.44 502 399 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 28 MAMDC4 158056 broad.mit.edu 37 9 139751386 139751387 + Frame_Shift_Ins INS - C C NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr9:139751386_139751387insC uc004cjs.2 + 16 1915_1916 c.1865_1866insC c.(1864-1866)GACfs p.D622fs MAMDC4_uc011mej.1_5'UTR NM_206920 NP_996803 Q6UXC1 AEGP_HUMAN apical early endosomal glycoprotein precursor 701 MAM 4.|Extracellular (Potential). protein transport integral to membrane breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1) 7 all_cancers(76;0.0763)|all_epithelial(76;0.198) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171) GACCCCACAGACCCCCTGGCCT 0.683 0.21 31 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 533 247 SNX19 399979 broad.mit.edu 37 11 130775936 130775936 + Frame_Shift_Del DEL T - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr11:130775936delT uc001qgk.3 - 7 2903 c.2355delA c.(2353-2355)AAAfs p.K785fs SNX19_uc009zcw.2_Frame_Shift_Del_p.K22fs|SNX19_uc010sce.1_Frame_Shift_Del_p.K165fs|SNX19_uc010scf.1_Frame_Shift_Del_p.K228fs|SNX19_uc010scg.1_Frame_Shift_Del_p.K22fs|SNX19_uc001qgl.3_Frame_Shift_Del_p.K768fs|SNX19_uc009zcx.1_RNA NM_014758 NP_055573 Q92543 SNX19_HUMAN sorting nexin 19 785 cell communication|protein transport cytoplasmic vesicle membrane phosphatidylinositol binding|protein binding ovary(2)|lung(2) 4 all_hematologic(175;0.0597) Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425) OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233) GTTCAGGATCTTTTTCTGGGG 0.493 0.64 94 168 ATN1 1822 broad.mit.edu 37 12 7045892 7045894 + In_Frame_Del DEL CAG - - rs66756893;rs67074116 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr12:7045892_7045894delCAG uc001qrw.1 + 5 1699_1701 c.1462_1464delCAG c.(1462-1464)CAGdel p.Q502del ATN1_uc001qrx.1_In_Frame_Del_p.Q502del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagc 0.458 0.11 66 8 ADAMTS20 80070 broad.mit.edu 37 12 43763167 43763167 + Frame_Shift_Del DEL A - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr12:43763167delA uc010skx.1 - 37 5464 c.5464delT c.(5464-5466)TCCfs p.S1822fs NM_025003 NP_079279 P59510 ATS20_HUMAN a disintegrin-like and metalloprotease with 1822 GON. proteinaceous extracellular matrix zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1) 19 all_cancers(12;2.6e-05)|Lung SC(27;0.184) Lung NSC(34;0.0569)|all_lung(34;0.129) GBM - Glioblastoma multiforme(48;0.0473) ATTGTTTTGGAAAAAAGAAGG 0.333 0.92 36 395 MLL2 8085 broad.mit.edu 37 12 49416586 49416586 + Frame_Shift_Del DEL G - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr12:49416586delG uc001rta.3 - 51 16125 c.16125delC c.(16123-16125)CCCfs p.P5375fs NM_003482 NP_003473 O14686 MLL2_HUMAN myeloid/lymphoid or mixed-lineage leukemia 2 5375 chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent histone methyltransferase complex histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2) 41 GCTTGCTGTAGGGGGTGTTGG 0.557 0.53 9 10 TMPO 7112 broad.mit.edu 37 12 98941486 98941486 + Frame_Shift_Del DEL A - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr12:98941486delA uc001tfj.2 + 9 1452 c.1215delA c.(1213-1215)ACAfs p.T405fs TMPO_uc001tfk.2_Frame_Shift_Del_p.T296fs|TMPO_uc001tfl.2_RNA NM_001032283 NP_001027454 P42167 LAP2B_HUMAN thymopoietin isoform beta 405 Nucleoplasmic (Potential). integral to membrane|nuclear inner membrane DNA binding|lamin binding ovary(2) 2 CAGAAAAGACAAAAAAGGGAC 0.398 0.95 24 477 CIT 11113 broad.mit.edu 37 12 120172022 120172022 + Frame_Shift_Del DEL A - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr12:120172022delA uc001txi.1 - 25 3224 c.3171delT c.(3169-3171)TTTfs p.F1057fs CIT_uc001txh.1_Frame_Shift_Del_p.F591fs|CIT_uc001txj.1_Frame_Shift_Del_p.F1099fs NM_007174 NP_009105 O14578 CTRO_HUMAN citron 1057 Potential. intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) CCCGACACTCAAACTGGGATT 0.547 0.28 1534 603 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.37 12 7 KIAA1409 57578 broad.mit.edu 37 14 94060136 94060137 + Frame_Shift_Ins INS - A A NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr14:94060136_94060137insA uc001ybv.1 + 20 2695_2696 c.2612_2613insA c.(2611-2613)ATAfs p.I871fs KIAA1409_uc001ybs.1_Frame_Shift_Ins_p.I871fs NM_020818 NP_065869 Q9P2D8 UNC79_HUMAN hypothetical protein LOC57578 1048 integral to membrane ovary(10)|skin(4)|large_intestine(3) 17 all_cancers(154;0.0354)|all_epithelial(191;0.216) Epithelial(152;0.188) TGGACAATCATAAATGGCAATT 0.480 0.46 622 520 SRP14 6727 broad.mit.edu 37 15 40328597 40328599 + In_Frame_Del DEL TGC - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr15:40328597_40328599delTGC uc001zkq.2 - 5 418_420 c.346_348delGCA c.(346-348)GCAdel p.A116del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgcggcaggtgctgctgctgct 0.227 0.22 118 34 CLK3 1198 broad.mit.edu 37 15 74912490 74912490 + Frame_Shift_Del DEL G - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr15:74912490delG uc010uln.1 + 3 1198 c.737delG c.(736-738)AGGfs p.R246fs CLK3_uc002ayg.3_Frame_Shift_Del_p.R98fs|CLK3_uc002ayh.3_5'UTR|CLK3_uc010ulm.1_Frame_Shift_Del_p.R246fs|CLK3_uc002ayj.3_Frame_Shift_Del_p.R98fs|CLK3_uc002ayk.3_5'UTR NM_001130028 NP_001123500 P49761 CLK3_HUMAN CDC-like kinase 3 isoform a 246 Arg-rich. acrosomal vesicle|nucleus ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity stomach(2) 2 TCGCGGGAGAGGGGGCCATAC 0.612 0.38 155 97 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.28 71 28 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.41 23 16 PTPRT 11122 broad.mit.edu 37 20 40733244 40733244 + Frame_Shift_Del DEL G - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr20:40733244delG uc002xkg.2 - 25 3689 c.3505delC c.(3505-3507)CAGfs p.Q1169fs PTPRT_uc010ggj.2_Frame_Shift_Del_p.Q1188fs|PTPRT_uc010ggi.2_Frame_Shift_Del_p.Q372fs NM_007050 NP_008981 O14522 PTPRT_HUMAN protein tyrosine phosphatase, receptor type, T 1169 Cytoplasmic (Potential). homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway cell surface|integral to membrane|plasma membrane alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity skin(8)|ovary(7)|lung(5) 20 Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783) GAGTTTGTCTGGGGGTCCAGC 0.428 0.20 433 109 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.18 299 67 TIAM1 7074 broad.mit.edu 37 21 32492712 32492713 + Frame_Shift_Ins INS - G G NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr21:32492712_32492713insG uc002yow.1 - 29 5221_5222 c.4749_4750insC c.(4747-4752)CCCTCCfs p.P1583fs TIAM1_uc011adk.1_3'UTR|TIAM1_uc011adl.1_Frame_Shift_Ins_p.P1523fs NM_003253 NP_003244 Q13009 TIAM1_HUMAN T-cell lymphoma invasion and metastasis 1 1583_1584 apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cell-cell junction|cytosol receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity lung(3)|breast(3)|ovary(2)|large_intestine(2) 10 AGTTTCCTGGAGGGGGCAAAGT 0.564 0.10 548 58 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.95 5 90 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 16 304 NF2 4771 broad.mit.edu 37 22 30057197 30057197 + Frame_Shift_Del DEL A - - NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr22:30057197delA uc003age.3 + 8 1122 c.679delA c.(679-681)AAAfs p.K227fs NF2_uc003afy.3_Frame_Shift_Del_p.K227fs|NF2_uc003afz.3_Frame_Shift_Del_p.K144fs|NF2_uc003agf.3_Frame_Shift_Del_p.K227fs|NF2_uc003agb.3_Frame_Shift_Del_p.K150fs|NF2_uc003agc.3_Frame_Shift_Del_p.K189fs|NF2_uc003agd.3_RNA|NF2_uc003agg.3_Frame_Shift_Del_p.K227fs|NF2_uc003aga.3_Frame_Shift_Del_p.K185fs|NF2_uc003agh.3_Frame_Shift_Del_p.K186fs|NF2_uc003agi.3_Frame_Shift_Del_p.K144fs|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Frame_Shift_Del_p.K189fs NM_000268 NP_000259 P35240 MERL_HUMAN neurofibromin 2 isoform 1 227 FERM. actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane cytoskeletal protein binding|protein binding p.?(2)|p.L127_D382del(1)|p.N226_E270del(1)|p.L140_P252del(1) meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1) 728 TCCACAGAATAAAAAGGGCAC 0.483 0.96 14 381 EP300 2033 broad.mit.edu 37 22 41558756 41558757 + Frame_Shift_Ins INS - A A NUGC3_STOMACH NA NUGC3_STOMACH NA g.chr22:41558756_41558757insA uc003azl.3 + 21 4096_4097 c.3701_3702insA c.(3700-3702)AGAfs p.R1234fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1234 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding p.Y1198_L1243del(1) haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 TTTTCCAAGAGAAAAAATGACA 0.366 0.90 38 339 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 NUGC4_STOMACH NA NUGC4_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 34 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.44 131 105 ZMYND10 51364 broad.mit.edu 37 3 50380780 50380781 + Frame_Shift_Ins INS - C C NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr3:50380780_50380781insC uc003dag.1 - 5 613_614 c.467_468insG c.(466-468)GGCfs p.G156fs RASSF1_uc003dad.1_5'Flank|RASSF1_uc003dae.1_5'Flank|RASSF1_uc010hlk.1_5'Flank|RASSF1_uc003daf.1_5'Flank|RASSF1_uc011bdq.1_5'Flank|ZMYND10_uc010hll.1_Frame_Shift_Ins_p.G156fs|ZMYND10_uc003dah.1_Frame_Shift_Ins_p.G77fs|ZMYND10_uc010hlm.1_Frame_Shift_Ins_p.G113fs NM_015896 NP_056980 O75800 ZMY10_HUMAN zinc finger, MYND domain-containing 10 156 cytoplasm protein binding|zinc ion binding lung(4)|ovary(1) 5 BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607) CCTCAGGGGGGCCACCACAGCC 0.604 0.12 61 8 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.25 27 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 48 62 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.62 285 460 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.83 3 15 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.50 16 16 TNFRSF10B 8795 broad.mit.edu 37 8 22885917 22885917 + Frame_Shift_Del DEL C - - NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr8:22885917delC uc003xcu.2 - 5 968 c.675delG c.(673-675)TTGfs p.L225fs TNFRSF10B_uc003xcs.1_5'Flank|TNFRSF10B_uc003xct.2_Frame_Shift_Del_p.L196fs|TNFRSF10B_uc011kzq.1_Frame_Shift_Del_p.L45fs|TNFRSF10B_uc003xcv.2_Frame_Shift_Del_p.L123fs NM_003842 NP_003833 O14763 TR10B_HUMAN tumor necrosis factor receptor superfamily, 225 Helical; (Potential). activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cell surface receptor linked signaling pathway|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|positive regulation of I-kappaB kinase/NF-kappaB cascade plasma membrane caspase activator activity|receptor activity|TRAIL binding 0 Prostate(55;0.0421)|Breast(100;0.067) Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703) CAGCCACAATCAAGACTACGG 0.552 0.46 20 17 FNBP1 23048 broad.mit.edu 37 9 132689471 132689472 + Splice_Site INS - A A NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr9:132689471_132689472insA uc004byw.1 - 8 1008 c.789_splice c.e8+1 p.N263_splice FNBP1_uc011mbv.1_Splice_Site_p.N263_splice|FNBP1_uc011mbw.1_Splice_Site_p.N263_splice|FNBP1_uc004bza.2_Splice_Site_p.N263_splice|FNBP1_uc004byz.1_Splice_Site_p.N263_splice|FNBP1_uc004byx.1_Splice_Site_p.N184_splice|FNBP1_uc004byy.1_Splice_Site_p.N184_splice NM_015033 NP_055848 Q96RU3 FNBP1_HUMAN formin binding protein 1 endocytosis cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane identical protein binding|lipid binding 0 Ovarian(14;0.000536) GBM - Glioblastoma multiforme(294;0.0378) TGGCAATACTTACATTTTTCTG 0.416 0.47 102 89 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 198 61 NEK3 4752 broad.mit.edu 37 13 52725278 52725279 + Splice_Site INS - A A NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr13:52725278_52725279insA uc001vgi.2 - 7 783 c.548_splice c.e7+1 p.S183_splice NEK3_uc001vgg.2_Splice_Site_p.S177_splice|NEK3_uc001vgh.2_Splice_Site_p.S204_splice|NEK3_uc010tgx.1_Splice_Site|NEK3_uc010tgy.1_Splice_Site_p.S183_splice NM_152720 NP_689933 P51956 NEK3_HUMAN NIMA-related kinase 3 isoform a cell division|mitosis nucleus ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173) GBM - Glioblastoma multiforme(99;2.81e-08) ATGCAGCACTCACCTTTTATTG 0.421 0.49 56 54 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.82 9 41 COL18A1 80781 broad.mit.edu 37 21 46911151 46911151 + Frame_Shift_Del DEL A - - NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr21:46911151delA uc011afs.1 + 21 3346 c.3325delA c.(3325-3327)AAGfs p.K1109fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.K694fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.K874fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1109 Triple-helical region 4 (COL4). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.40 367 243 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 106 380 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 NUGC4_STOMACH NA NUGC4_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 63 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OAW28_OVARY NA OAW28_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.43 17 13 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - OAW28_OVARY NA OAW28_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 258 53 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 OAW28_OVARY NA OAW28_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.28 26 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 OAW28_OVARY NA OAW28_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.53 9 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OAW28_OVARY NA OAW28_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 72 118 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OAW28_OVARY NA OAW28_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 10 26 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 OAW28_OVARY NA OAW28_OVARY NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.38 34 21 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes OAW28_OVARY NA OAW28_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.73 7 19 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - OAW28_OVARY NA OAW28_OVARY NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.42 18 13 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 OAW28_OVARY NA OAW28_OVARY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.59 7 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OAW28_OVARY NA OAW28_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 5 50 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 OAW28_OVARY NA OAW28_OVARY NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.73 6 16 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes OAW28_OVARY NA OAW28_OVARY NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.74 5 14 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes OAW28_OVARY NA OAW28_OVARY NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.43 45 34 TP53 7157 broad.mit.edu 37 17 7578475 7578475 + Frame_Shift_Del DEL G - - OAW28_OVARY NA OAW28_OVARY NA g.chr17:7578475delG uc002gim.2 - 5 649 c.455delC c.(454-456)CCGfs p.P152fs TP53_uc002gig.1_Frame_Shift_Del_p.P152fs|TP53_uc002gih.2_Frame_Shift_Del_p.P152fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.P20fs|TP53_uc010cng.1_Frame_Shift_Del_p.P20fs|TP53_uc002gii.1_Frame_Shift_Del_p.P20fs|TP53_uc010cnh.1_Frame_Shift_Del_p.P152fs|TP53_uc010cni.1_Frame_Shift_Del_p.P152fs|TP53_uc002gij.2_Frame_Shift_Del_p.P152fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.P59fs|TP53_uc002gio.2_Frame_Shift_Del_p.P20fs|TP53_uc010vug.1_Frame_Shift_Del_p.P113fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 152 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). P -> R (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|P -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> A (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.P152L(57)|p.P152S(21)|p.P152fs*18(17)|p.P152T(7)|p.0?(7)|p.P152fs*29(5)|p.P152P(5)|p.P152Q(4)|p.P153fs*28(4)|p.P152fs*14(4)|p.P152fs*28(3)|p.P152R(3)|p.T150fs*16(3)|p.P152A(2)|p.P153fs*16(1)|p.P151_V173del23(1)|p.P152_P153del(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.D148fs*23(1)|p.P152del(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.Q144_G154del11(1)|p.P152_P153insXXX(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGTGCCGGGCGGGGGTGTGGA 0.612 0.91 11 112 ROCK1 6093 broad.mit.edu 37 18 18690846 18690847 + Frame_Shift_Ins INS - T T OAW28_OVARY NA OAW28_OVARY NA g.chr18:18690846_18690847insT uc002kte.2 - 1 966_967 c.25_26insA c.(25-27)ACTfs p.T9fs NM_005406 NP_005397 Q13464 ROCK1_HUMAN Rho-associated, coiled-coil containing protein 9 actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction centriole|cytosol|Golgi membrane ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity lung(2)|breast(2)|central_nervous_system(1) 5 Melanoma(1;0.165) TTCAAATCGAGTCTCAAAACTG 0.505 0.38 10 6 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 OAW28_OVARY NA OAW28_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.35 131 70 ID1 3397 broad.mit.edu 37 20 30193544 30193545 + Frame_Shift_Ins INS - G G rs11545371 OAW28_OVARY NA OAW28_OVARY NA g.chr20:30193544_30193545insG uc002wwg.1 + 1 453_454 c.354_355insG c.(352-357)CCCGGGfs p.P118fs ID1_uc002wwh.1_Frame_Shift_Ins_p.P118fs|hsa-mir-3193|MI0014238_5'Flank NM_002165 NP_002156 P41134 ID1_HUMAN inhibitor of DNA binding 1 isoform a 118_119 angiogenesis|blood vessel endothelial cell migration|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by transcription factor localization|transforming growth factor beta receptor signaling pathway cytoplasm protein binding ovary(1) 1 all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198) Epithelial(4;1.99e-05)|all cancers(5;0.000169)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264) TTGGAACCCCCGGGGGCCGAGG 0.614 0.13 118 18 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 OAW28_OVARY NA OAW28_OVARY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.26 25 9 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OAW28_OVARY NA OAW28_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 58 229 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OAW42_OVARY NA OAW42_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 61 ARID1A 8289 broad.mit.edu 37 1 27057967 27057968 + Frame_Shift_Del DEL CC - - OAW42_OVARY NA OAW42_OVARY NA g.chr1:27057967_27057968delCC uc001bmv.1 + 3 2048_2049 c.1675_1676delCC c.(1675-1677)CCTfs p.P559fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.P559fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.P559fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.P176fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 559 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GGCTCAGTCTCCTTACCAGCAG 0.634 0.61 24 38 ARID1A 8289 broad.mit.edu 37 1 27097762 27097763 + Frame_Shift_Ins INS - T T OAW42_OVARY NA OAW42_OVARY NA g.chr1:27097762_27097763insT uc001bmv.1 + 12 3724_3725 c.3351_3352insT c.(3349-3354)ATCTTTfs p.I1117fs ARID1A_uc001bmt.1_Frame_Shift_Ins_p.I1117fs|ARID1A_uc001bmu.1_Frame_Shift_Ins_p.I1117fs|ARID1A_uc001bmw.1_Frame_Shift_Ins_p.I734fs|ARID1A_uc001bmx.1_5'UTR|ARID1A_uc009vsm.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1117_1118 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CCCCAGACATCTTTGCAGCTGC 0.550 0.24 76 24 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 OAW42_OVARY NA OAW42_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.21 27 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OAW42_OVARY NA OAW42_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.38 41 25 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OAW42_OVARY NA OAW42_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 19 34 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 OAW42_OVARY NA OAW42_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.74 59 165 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes OAW42_OVARY NA OAW42_OVARY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.65 6 11 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - OAW42_OVARY NA OAW42_OVARY NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 160 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OAW42_OVARY NA OAW42_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 107 24 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C OAW42_OVARY NA OAW42_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 8 48 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 OAW42_OVARY NA OAW42_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.72 14 36 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes OAW42_OVARY NA OAW42_OVARY NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.40 6 4 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OAW42_OVARY NA OAW42_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 135 449 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OAW42_OVARY NA OAW42_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 61 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 4 51 SPEN 23013 broad.mit.edu 37 1 16261409 16261410 + Frame_Shift_Del DEL AC - - rs144461687 OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:16261409_16261410delAC uc001axk.1 + 11 8878_8879 c.8674_8675delAC c.(8674-8676)ACAfs p.T2892fs SPEN_uc010obp.1_Frame_Shift_Del_p.T2851fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2892 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) GACCGCCCAGACATATAATGCC 0.574 0.44 235 184 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.50 7 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.43 12 9 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 109 21 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.24 34 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 122 194 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 34 70 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.35 311 171 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 573 234 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.49 43 41 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 40 294 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 5 149 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 3 32 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.17 35 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 108 161 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.32 50 24 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.32 94 45 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.20 35 9 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.13 384 57 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 2 23 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.12 293 40 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 4 64 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 1000 207 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.17 50 10 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 173 383 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 124 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 4 32 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.33 275 135 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.48 13 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.44 86 68 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.79 15 57 HOXA13 3209 broad.mit.edu 37 7 27239311 27239340 + In_Frame_Del DEL GCGGCGGCTGCAGCGGCAGCCGCGGCAGCA - - rs34856009;rs35861510 OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:27239311_27239340delGCGGCGGCTGCAGCGGCAGCCGCGGCAGCA uc003szb.1 - 1 386_415 c.357_386delTGCTGCCGCGGCTGCCGCTGCAGCCGCCGC c.(355-387)GCTGCTGCCGCGGCTGCCGCTGCAGCCGCCGCC>GCC p.119_129AAAAAAAAAAA>A uc003szc.1_5'Flank NM_000522 NP_000513 P31271 HXA13_HUMAN homeobox A13 119_129 Poly-Ala. A -> AAAAAAAAA (in HFGS). skeletal system development nucleus sequence-specific DNA binding breast(1) 1 0.000 0.58 140 192 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 193 30 TRIM37 4591 broad.mit.edu 37 17 57141768 57141769 + Splice_Site INS - A A rs147621691 OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:57141768_57141769insA uc002iwy.3 - 10 1254 c.810_splice c.e10-1 p.S270_splice TRIM37_uc002iwz.3_Splice_Site_p.S270_splice|TRIM37_uc002ixa.3_Splice_Site_p.S148_splice|TRIM37_uc010woc.1_Splice_Site_p.S236_splice NM_001005207 NP_001005207 O94972 TRI37_HUMAN tripartite motif-containing 37 protein perinuclear region of cytoplasm|peroxisome ligase activity|protein binding|zinc ion binding lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1) 7 Medulloblastoma(34;0.0922)|all_neural(34;0.101) ACTAATTCACTAAAAAAAAAAA 0.272 0.50 10 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.70 7 16 NCOA3 8202 broad.mit.edu 37 20 46279858 46279866 + In_Frame_Del DEL CAGCAGCAA - - rs151060280;rs3092460;rs67218125;rs11472494;rs112826888 byFrequency OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:46279858_46279866delCAGCAGCAA uc002xtk.2 + 20 3989_3997 c.3784_3792delCAGCAGCAA c.(3784-3792)CAGCAGCAAdel p.QQQ1274del NCOA3_uc010ght.1_In_Frame_Del_p.QQQ1265del|NCOA3_uc002xtl.2_In_Frame_Del_p.QQQ1270del|NCOA3_uc002xtm.2_In_Frame_Del_p.QQQ1269del|NCOA3_uc002xtn.2_In_Frame_Del_p.QQQ1273del|NCOA3_uc010zyc.1_In_Frame_Del_p.QQQ1069del NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 1274_1276 Poly-Gln.|Acetyltransferase. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 gcagcagcagcagcagcaacagcaacagc 0.321 0.47 62 56 RUNX1 861 broad.mit.edu 37 21 36252919 36252920 + Frame_Shift_Ins INS - TAGCA TAGCA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:36252919_36252920insTAGCA uc002yuh.2 - 2 1939_1940 c.361_362insTGCTA c.(361-363)ACCfs p.T121fs RUNX1_uc002yui.2_Frame_Shift_Ins_p.T121fs|RUNX1_uc010gmu.2_Frame_Shift_Ins_p.T148fs|RUNX1_uc010gmv.2_Frame_Shift_Ins_p.T148fs|RUNX1_uc002yuj.3_Frame_Shift_Ins_p.T16fs|RUNX1_uc002yuk.3_Frame_Shift_Ins_p.T148fs|RUNX1_uc002yum.1_Frame_Shift_Ins_p.T16fs|RUNX1_uc010gmw.1_Frame_Shift_Ins_p.T148fs|RUNX1_uc002yuo.1_Frame_Shift_Ins_p.T121fs|RUNX1_uc002yur.1_Frame_Shift_Ins_p.T16fs NM_001001890 NP_001001890 Q01196 RUNX1_HUMAN runt-related transcription factor 1 isoform 121 Runt. myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent nucleus|nucleus ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding p.L121fs*2(1)|p.T148fs*2(1) haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1) 387 CATGGCTGCGGTAGCATTTCTC 0.485 0.31 125 56 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 89 329 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 66 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 6 44 ARID1A 8289 broad.mit.edu 37 1 27089496 27089496 + Frame_Shift_Del DEL T - - OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:27089496delT uc001bmv.1 + 8 2825 c.2452delT c.(2452-2454)TTGfs p.L818fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.L818fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.L818fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.L435fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 818 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CTATAATGCCTTGCCCAATGC 0.537 0.56 7 9 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 318 103 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.45 24 20 MAML3 55534 broad.mit.edu 37 4 140641185 140641186 + Frame_Shift_Ins INS - G G OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140641185_140641186insG uc003ihz.1 - 7 3445_3446 c.2693_2694insC c.(2692-2694)CCTfs p.P898fs MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_Frame_Shift_Ins_p.P366fs NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 899 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) GCCCAGAGGCAGGTTGCCTCGG 0.530 0.12 566 74 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.67 94 192 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.35 54 29 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 2 22 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.90 1 9 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.13 443 65 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 37 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 757 431 PLEKHA5 54477 broad.mit.edu 37 12 19427887 19427888 + Frame_Shift_Ins INS - G G OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:19427887_19427888insG uc001reb.2 + 10 1351_1352 c.1265_1266insG c.(1264-1266)AAGfs p.K422fs PLEKHA5_uc010sie.1_Frame_Shift_Ins_p.K428fs|PLEKHA5_uc001rea.2_Frame_Shift_Ins_p.K422fs|PLEKHA5_uc009zin.2_Frame_Shift_Ins_p.K180fs|PLEKHA5_uc010sif.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc010sig.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc010sih.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc001rec.1_Frame_Shift_Ins_p.K110fs NM_019012 NP_061885 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A 422 1-phosphatidylinositol binding|protein binding ovary(1)|kidney(1)|skin(1) 3 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) AAAATCCAGAAGGGGAGGGGTC 0.470 0.14 69 11 MEF2A 4205 broad.mit.edu 37 15 100252710 100252712 + In_Frame_Del DEL CAG - - OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:100252710_100252712delCAG uc010urw.1 + 11 1617_1619 c.1258_1260delCAG c.(1258-1260)CAGdel p.Q430del MEF2A_uc010urv.1_In_Frame_Del_p.Q360del|MEF2A_uc010bos.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvf.2_In_Frame_Del_p.Q422del|MEF2A_uc002bve.2_In_Frame_Del_p.Q428del|MEF2A_uc002bvg.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvi.2_In_Frame_Del_p.Q420del|MEF2A_uc010bot.2_In_Frame_Del_p.Q352del NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 430 Gln/Pro-rich. Missing (in Ref. 4; AAB17195/AAB17196). apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) ATCGGGCTTCcagcagcagcagc 0.493 0.33 10 5 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.17 58 12 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.46 113 97 PIGU 128869 broad.mit.edu 37 20 33169374 33169374 + Frame_Shift_Del DEL G - - OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:33169374delG uc002xas.2 - 10 1229 c.1029delC c.(1027-1029)CCCfs p.P343fs PIGU_uc010zul.1_Frame_Shift_Del_p.P343fs|PIGU_uc002xat.2_Frame_Shift_Del_p.P323fs NM_080476 NP_536724 Q9H490 PIGU_HUMAN phosphatidylinositol glycan anchor biosynthesis, 343 attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade GPI-anchor transamidase complex|plasma membrane 0 GGTTCCACACGGGGAAGAAGG 0.532 0.42 26 19 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.10 104 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 135 414 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 108 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 5 41 TNFRSF4 7293 broad.mit.edu 37 1 1147169 1147169 + Frame_Shift_Del DEL C - - OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:1147169delC uc001ade.2 - 6 683 c.678delG c.(676-678)GGGfs p.G226fs TNFRSF4_uc001adf.2_Frame_Shift_Del_p.G230fs NM_003327 NP_003318 P43489 TNR4_HUMAN tumor necrosis factor receptor superfamily, 226 Helical; (Potential). immune response|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|positive regulation of B cell proliferation|positive regulation of immunoglobulin secretion|T cell proliferation integral to plasma membrane tumor necrosis factor receptor activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199) GGCCCAGCAGCCCCAGCACCA 0.731 0.47 8 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.39 22 14 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 163 32 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 144 200 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.79 23 88 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.70 93 215 RNF5P1 286140 broad.mit.edu 37 8 38458552 38458553 + In_Frame_Ins INS - TCT TCT rs138778842;rs142618177 by1000genomes OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:38458552_38458553insTCT uc003xly.2 - 1 223_224 c.166_167insAGA c.(166-168)GCA>GAGACA p.56_56A>ET NR_003129 SubName: Full=Putative uncharacterized protein RNF5; 0 TTCTGGCCGTGCCAGCCACTGA 0.554 0.80 5 20 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.21 52 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 1 21 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 427 168 SACS 26278 broad.mit.edu 37 13 23904581 23904582 + Frame_Shift_Ins INS - T T OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:23904581_23904582insT uc001uon.2 - 10 14022_14023 c.13433_13434insA c.(13432-13434)TACfs p.Y4478fs SACS_uc001uoo.2_Frame_Shift_Ins_p.Y4331fs|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 4478 HEPN. cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) TGGTAGAAAGGTAACATTTAAA 0.431 0.51 202 208 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.68 41 89 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 227 646 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 9 120 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.10 134 15 MAGEB16 139604 broad.mit.edu 37 X 35820679 35820679 + Frame_Shift_Del DEL T - - OCUM1_STOMACH NA OCUM1_STOMACH NA g.chrX:35820679delT uc010ngt.1 + 2 645 c.366delT c.(364-366)AATfs p.N122fs NM_001099921 NP_001093391 A2A368 MAGBG_HUMAN melanoma antigen family B, 16 122 MAGE. lung(3)|ovary(2)|breast(1)|skin(1) 7 TTTTGGTGAATTTCATGCTGC 0.443 0.57 58 77 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OCUM1_STOMACH NA OCUM1_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 59 ARID1A 8289 broad.mit.edu 37 1 27097801 27097801 + Frame_Shift_Del DEL C - - OCUM1_STOMACH NA OCUM1_STOMACH NA g.chr1:27097801delC uc001bmv.1 + 12 3763 c.3390delC c.(3388-3390)ATCfs p.I1130fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.I1130fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.I1130fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.I747fs|ARID1A_uc001bmx.1_5'UTR|ARID1A_uc009vsm.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1130 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) AGCCCAAGATCCAGCCTCCCT 0.542 0.95 3 62 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A OCUM1_STOMACH NA OCUM1_STOMACH NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 127 24 BMP2K 55589 broad.mit.edu 37 4 79792137 79792145 + In_Frame_Del DEL CAGCAGCAG - - rs17855588 OCUM1_STOMACH NA OCUM1_STOMACH NA g.chr4:79792137_79792145delCAGCAGCAG uc003hlk.2 + 11 1598_1606 c.1432_1440delCAGCAGCAG c.(1432-1440)CAGCAGCAGdel p.QQQ484del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQ484del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 484_486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 gcaacagcaacagcagcagcagcagcagc 0.177 0.32 45 21 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OCUM1_STOMACH NA OCUM1_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 50 57 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OCUM1_STOMACH NA OCUM1_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.26 63 22 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - OCUM1_STOMACH NA OCUM1_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.60 4 6 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OCUM1_STOMACH NA OCUM1_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OCUM1_STOMACH NA OCUM1_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 260 112 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C OCUM1_STOMACH NA OCUM1_STOMACH NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 39 382 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OCUM1_STOMACH NA OCUM1_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 81 484 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OCUM1_STOMACH NA OCUM1_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 3 51 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.59 20 29 TSSK3 81629 broad.mit.edu 37 1 32828364 32828368 + Frame_Shift_Del DEL ACTCA - - ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr1:32828364_32828368delACTCA uc001bvf.2 + 1 503_507 c.62_66delACTCA c.(61-66)TACTCAfs p.Y21fs uc001bve.1_RNA NM_052841 NP_443073 Q96PN8 TSSK3_HUMAN testis-specific serine kinase 3 21_22 ATP (By similarity).|Protein kinase. cell differentiation|multicellular organismal development|spermatogenesis ATP binding|magnesium ion binding|protein serine/threonine kinase activity stomach(1) 1 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.17)|Breast(348;0.212) GAAGGGACCTACTCAAAAGTCAAAG 0.502 0.39 105 66 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.47 139 125 C1orf85 112770 broad.mit.edu 37 1 156265382 156265382 + Frame_Shift_Del DEL G - - ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr1:156265382delG uc001foh.2 - 1 68 c.55delC c.(55-57)CTGfs p.L19fs C1orf85_uc001fof.3_5'Flank|C1orf85_uc001fog.1_RNA|C1orf85_uc001foi.2_Frame_Shift_Del_p.L19fs|C1orf85_uc009wrx.2_Frame_Shift_Del_p.L19fs|C1orf85_uc001foj.2_Frame_Shift_Del_p.L19fs NM_144580 NP_653181 Q8WWB7 NCUG1_HUMAN kidney predominant protein NCU-G1 precursor 19 positive regulation of transcription from RNA polymerase II promoter cytosol|integral to membrane|lysosomal membrane|nucleus ligand-dependent nuclear receptor activity|protein binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding ovary(2) 2 Hepatocellular(266;0.158) 0.000 1.00 0 17 CDKL4 344387 broad.mit.edu 37 2 39414801 39414802 + Frame_Shift_Ins INS - AA AA ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr2:39414801_39414802insAA uc002rrm.2 - 6 701_702 c.701_702insTT c.(700-702)TTCfs p.F234fs CDKL4_uc010fal.1_Frame_Shift_Ins_p.F234fs NM_001009565 NP_001009565 Q5MAI5 CDKL4_HUMAN cyclin-dependent kinase-like 4 234 Protein kinase. cytoplasm ATP binding|cyclin-dependent protein kinase activity ovary(1) 1 all_hematologic(82;0.248) TGATGCCATGGAAAAACCCGTT 0.327 0.44 28 22 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.39 25 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 27 32 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.17 52 11 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.48 63 58 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.64 9 16 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 2 37 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.29 903 369 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 257 98 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.55 13 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 31 356 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.64 16 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 49 149 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ONS76_CENTRAL_NERVOUS_SYSTEM NA ONS76_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 3 22 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 7 77 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.10 554 60 TNN 63923 broad.mit.edu 37 1 175048491 175048498 + Frame_Shift_Del DEL CCACGGGA - - OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:175048491_175048498delCCACGGGA uc001gkl.1 + 3 545_552 c.432_439delCCACGGGA c.(430-441)GGCCACGGGACCfs p.G144fs TNN_uc010pmx.1_Frame_Shift_Del_p.G144fs NM_022093 NP_071376 Q9UQP3 TENN_HUMAN tenascin N precursor 144_147 cell growth|cell migration|signal transduction extracellular space|proteinaceous extracellular matrix large_intestine(5)|ovary(3)|central_nervous_system(1) 9 Breast(1374;0.000962) KIRC - Kidney renal clear cell carcinoma(1967;0.00198) 0.000 0.21 266 71 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 135 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 138 194 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 34 69 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.84 3 16 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.87 2 13 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.30 62 27 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 12 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.24 293 93 DAPK1 1612 broad.mit.edu 37 9 90219945 90219947 + In_Frame_Del DEL AGG - - OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:90219945_90219947delAGG uc004apc.2 + 3 277_279 c.139_141delAGG c.(139-141)AGGdel p.R48del DAPK1_uc004ape.2_In_Frame_Del_p.R48del|DAPK1_uc004apd.2_In_Frame_Del_p.R48del|DAPK1_uc011ltg.1_In_Frame_Del_p.R48del|DAPK1_uc011lth.1_5'UTR NM_004938 NP_004929 P53355 DAPK1_HUMAN death-associated protein kinase 1 48 Protein kinase. apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade actin cytoskeleton|cytoplasm ATP binding|calmodulin binding|protein serine/threonine kinase activity ovary(1)|breast(1) 2 CATCAAGAAAAGGAGGACTAAGT 0.552 0.56 49 63 DRD4 1815 broad.mit.edu 37 11 640446 640446 + Frame_Shift_Del DEL C - - OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:640446delC uc001lqp.1 + 4 1103 c.1103delC c.(1102-1104)ACGfs p.T368fs NM_000797 NP_000788 P21917 DRD4_HUMAN dopamine receptor D4 416 Helical; Name=6; (Potential). activation of MAPK activity|adult locomotory behavior|arachidonic acid secretion|behavioral fear response|behavioral response to cocaine|behavioral response to ethanol|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cAMP biosynthetic process|negative regulation of protein secretion|positive regulation of sodium:hydrogen antiporter activity|regulation of dopamine metabolic process|regulation of inhibitory postsynaptic membrane potential|response to amphetamine|response to histamine|social behavior integral to plasma membrane dopamine D4 receptor activity|drug binding|potassium channel regulator activity|SH3 domain binding 0 all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136) all cancers(45;4.36e-28)|Epithelial(43;2.59e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.0703) Apomorphine(DB00714)|Clozapine(DB00363)|Olanzapine(DB00334)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Ropinirole(DB00268)|Thiethylperazine(DB00372)|Ziprasidone(DB00246) GTGCACATCACGCAGGCGCTG 0.711 0.45 18 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 499 187 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.67 8 16 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.24 102 32 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.66 193 376 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 96 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 23 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 134 27 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.30 28 12 FBXW7 55294 broad.mit.edu 37 4 153332604 153332605 + In_Frame_Ins INS - CTCCTC CTCCTC OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr4:153332604_153332605insCTCCTC uc003ims.2 - 2 500_501 c.351_352insGAGGAG c.(349-354)insGAGGAG p.117_118insEE FBXW7_uc011cii.1_In_Frame_Ins_p.117_118insEE|FBXW7_uc003imt.2_In_Frame_Ins_p.117_118insEE|FBXW7_uc003imu.2_In_Frame_Ins_p.117_118insEE NM_033632 NP_361014 Q969H0 FBXW7_HUMAN F-box and WD repeat domain containing 7 isoform 117_118 interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex protein binding|protein binding p.E117del(2) haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1) 308 all_hematologic(180;0.093) Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067) TCCTGGTCCATctcctcctcct 0.366 0.60 32 49 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.25 208 71 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 11 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.53 7 8 PTEN 5728 broad.mit.edu 37 10 89712013 89712028 + Splice_Site DEL TGCAGTAAGTGCTTGA - - rs121909232;rs138336847 OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr10:89712013_89712028delTGCAGTAAGTGCTTGA uc001kfb.2 + 7 1665 c.634_splice c.e7+1 p.N212_splice NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.?(13)|p.R55fs*1(4)|p.G165fs*9(3)|p.Y27fs*1(2)|p.C211Y(1)|p.C211fs*11(1)|p.G165_*404del(1)|p.C211*(1)|p.C211fs*32(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) TGGCGGAACTTGCAGTAAGTGCTTGAAATTCTCATC 0.333 0.72 8 21 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 100 37 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.27 27 10 THAP11 57215 broad.mit.edu 37 16 67876824 67876832 + In_Frame_Del DEL CAGCAGCAG - - rs34213159;rs3982383;rs63117363;rs141903290 byFrequency;byFrequency OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr16:67876824_67876832delCAGCAGCAG uc002euo.2 + 1 612_620 c.367_375delCAGCAGCAG c.(367-375)CAGCAGCAGdel p.QQQ129del CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 129_131 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) gcagcagcaacagcagcagcagcagcagc 0.311 0.19 50 12 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.21 445 115 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.67 16 32 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 100 447 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OSRC2_KIDNEY NA OSRC2_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 44 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 25 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.31 223 98 ALK 238 broad.mit.edu 37 2 29456506 29456508 + In_Frame_Del DEL TTC - - OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr2:29456506_29456508delTTC uc002rmy.2 - 14 3317_3319 c.2410_2412delGAA c.(2410-2412)GAAdel p.E804del NM_004304 NP_004295 Q9UM73 ALK_HUMAN anaplastic lymphoma kinase precursor 804 Extracellular (Potential). protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2) haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1) 1218 Acute lymphoblastic leukemia(172;0.155) Adenosine triphosphate(DB00171) TCACACGGATTTCTTCTTCTATC 0.483 0.27 296 107 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 44 57 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 13 38 APC 324 broad.mit.edu 37 5 112173260 112173261 + Frame_Shift_Del DEL AG - - OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr5:112173260_112173261delAG uc010jby.2 + 16 2349_2350 c.1969_1970delAG c.(1969-1971)AGAfs p.R657fs APC_uc011cvt.1_Frame_Shift_Del_p.R639fs|APC_uc003kpz.3_Frame_Shift_Del_p.R657fs|APC_uc003kpy.3_Frame_Shift_Del_p.R657fs|APC_uc010jbz.2_Frame_Shift_Del_p.R374fs|APC_uc010jca.2_5'UTR NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 657 Leu-rich.|ARM 5. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.?(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GCAAATCCTAAGAGAGAACAAC 0.322 0.41 30 21 APC 324 broad.mit.edu 37 5 112175951 112175952 + Frame_Shift_Ins INS - A A OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr5:112175951_112175952insA uc010jby.2 + 16 5040_5041 c.4660_4661insA c.(4660-4662)GAAfs p.E1554fs APC_uc011cvt.1_Frame_Shift_Ins_p.E1536fs|APC_uc003kpz.3_Frame_Shift_Ins_p.E1554fs|APC_uc003kpy.3_Frame_Shift_Ins_p.E1554fs|APC_uc010jbz.2_Frame_Shift_Ins_p.E1271fs|APC_uc010jca.2_Frame_Shift_Ins_p.E854fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1554 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.T1556fs*3(35)|p.E1554fs*5(2)|p.E1554*(2)|p.?(1)|p.T1556fs*9(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1554fs*11(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GAAAGAGGCAGAAAAAACTATT 0.342 0.44 20 16 FLT4 2324 broad.mit.edu 37 5 180055897 180055897 + Frame_Shift_Del DEL G - - OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr5:180055897delG uc003mma.3 - 8 1167 c.1088delC c.(1087-1089)CCGfs p.P363fs FLT4_uc003mlz.3_Frame_Shift_Del_p.P363fs|FLT4_uc003mmb.1_5'UTR|FLT4_uc011dgy.1_Frame_Shift_Del_p.P363fs|FLT4_uc011dgz.1_3'UTR NM_002020 NP_002011 P35916 VGFR3_HUMAN fms-related tyrosine kinase 4 isoform 2 363 Ig-like C2-type 4.|Extracellular (Potential). positive regulation of cell proliferation integral to plasma membrane ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1) 15 all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114) all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) all cancers(165;0.134) Sorafenib(DB00398)|Sunitinib(DB01268) GAACTCGGGCGGGGGGTACGC 0.637 0.36 25 14 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.56 8 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.45 36 29 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 14 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.72 282 713 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 262 140 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.27 19 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 30 376 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.28 42 16 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 86 458 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OUMS23_LARGE_INTESTINE NA OUMS23_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 32 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OUMS27_BONE NA OUMS27_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 16 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - OUMS27_BONE NA OUMS27_BONE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.53 140 155 HOXD11 3237 broad.mit.edu 37 2 176972369 176972371 + In_Frame_Del DEL GGC - - OUMS27_BONE NA OUMS27_BONE NA g.chr2:176972369_176972371delGGC uc002uki.2 + 1 286_288 c.286_288delGGC c.(286-288)GGCdel p.G99del HOXD11_uc010fqx.2_Intron NM_021192 NP_067015 P31277 HXD11_HUMAN homeobox D11 99 Poly-Gly. nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678) 0.000 0.12 80 11 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A OUMS27_BONE NA OUMS27_BONE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.25 82 28 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OUMS27_BONE NA OUMS27_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.34 41 21 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OUMS27_BONE NA OUMS27_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 18 38 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 OUMS27_BONE NA OUMS27_BONE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.76 66 214 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes OUMS27_BONE NA OUMS27_BONE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 12 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 OUMS27_BONE NA OUMS27_BONE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.59 30 44 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OUMS27_BONE NA OUMS27_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.89 2 16 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 OUMS27_BONE NA OUMS27_BONE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.28 23 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OUMS27_BONE NA OUMS27_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 132 30 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C OUMS27_BONE NA OUMS27_BONE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 3 36 TP53 7157 broad.mit.edu 37 17 7578479 7578480 + Frame_Shift_Del DEL GT - - rs28934874 OUMS27_BONE NA OUMS27_BONE NA g.chr17:7578479_7578480delGT uc002gim.2 - 5 644_645 c.450_451delAC c.(448-453)ACACCCfs p.T150fs TP53_uc002gig.1_Frame_Shift_Del_p.T150fs|TP53_uc002gih.2_Frame_Shift_Del_p.T150fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.T18fs|TP53_uc010cng.1_Frame_Shift_Del_p.T18fs|TP53_uc002gii.1_Frame_Shift_Del_p.T18fs|TP53_uc010cnh.1_Frame_Shift_Del_p.T150fs|TP53_uc010cni.1_Frame_Shift_Del_p.T150fs|TP53_uc002gij.2_Frame_Shift_Del_p.T150fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.T57fs|TP53_uc002gio.2_Frame_Shift_Del_p.T18fs|TP53_uc010vug.1_Frame_Shift_Del_p.T111fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 150_151 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). P -> R (in sporadic cancers; somatic mutation).|P -> A (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> H (in sporadic cancers; somatic mutation).|P -> T (in LFS; germline mutation and in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.P151S(61)|p.P151T(13)|p.P152fs*18(11)|p.P151A(10)|p.0?(7)|p.P151fs*30(7)|p.T150I(4)|p.T150fs*16(3)|p.P151_V173del23(1)|p.P152_P153del(1)|p.T150R(1)|p.P152fs*28(1)|p.T150fs*23(1)|p.T150K(1)|p.P151del(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.P58A(1)|p.D148fs*23(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.Q144_G154del11(1)|p.P19A(1)|p.T150fs*31(1)|p.P152fs*14(1)|p.T150_P151delTP(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.41 874 620 TP53 7157 broad.mit.edu 37 17 7578483 7578484 + Frame_Shift_Del DEL GG - - OUMS27_BONE NA OUMS27_BONE NA g.chr17:7578483_7578484delGG uc002gim.2 - 5 640_641 c.446_447delCC c.(445-447)TCCfs p.S149fs TP53_uc002gig.1_Frame_Shift_Del_p.S149fs|TP53_uc002gih.2_Frame_Shift_Del_p.S149fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.S17fs|TP53_uc010cng.1_Frame_Shift_Del_p.S17fs|TP53_uc002gii.1_Frame_Shift_Del_p.S17fs|TP53_uc010cnh.1_Frame_Shift_Del_p.S149fs|TP53_uc010cni.1_Frame_Shift_Del_p.S149fs|TP53_uc002gij.2_Frame_Shift_Del_p.S149fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.S56fs|TP53_uc002gio.2_Frame_Shift_Del_p.S17fs|TP53_uc010vug.1_Frame_Shift_Del_p.S110fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 149 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). S -> P (in sporadic cancers; somatic mutation).|S -> T (in sporadic cancers; somatic mutation).|S -> F (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.S149S(6)|p.S149F(6)|p.S149fs*32(5)|p.S149P(4)|p.S149fs*21(3)|p.S149T(2)|p.D148_T155delDSTPPPGT(1)|p.Q144_G154del11(1)|p.W146_S149>C(1)|p.T150fs*31(1)|p.T150fs*23(1)|p.D148fs*23(1)|p.S149fs*31(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.V143_S149del(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.56 650 843 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 OUMS27_BONE NA OUMS27_BONE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.10 70 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OUMS27_BONE NA OUMS27_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 234 1053 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OUMS27_BONE NA OUMS27_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 53 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OV56_OVARY NA OV56_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.63 23 40 ARID1A 8289 broad.mit.edu 37 1 27106916 27106917 + Frame_Shift_Ins INS - G G OV56_OVARY NA OV56_OVARY NA g.chr1:27106916_27106917insG uc001bmv.1 + 20 6900_6901 c.6527_6528insG c.(6526-6528)CAGfs p.Q2176fs ARID1A_uc001bmu.1_Frame_Shift_Ins_p.Q1959fs|ARID1A_uc001bmx.1_Frame_Shift_Ins_p.Q1022fs|ARID1A_uc009vsm.1_Frame_Shift_Ins_p.Q504fs|ARID1A_uc009vsn.1_Frame_Shift_Ins_p.Q418fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 2176 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) AACCTGGCTCAGGGGGACAGCC 0.609 0.85 9 50 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OV56_OVARY NA OV56_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 42 58 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OV56_OVARY NA OV56_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.85 7 39 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - OV56_OVARY NA OV56_OVARY NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.82 2 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OV56_OVARY NA OV56_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 25 CDKN2A 1029 broad.mit.edu 37 9 21974776 21974804 + Frame_Shift_Del DEL GGCCAGCCAGTCAGCCGAAGGCTCCATGC - - rs138677674;rs141798398;rs145445140 OV56_OVARY NA OV56_OVARY NA g.chr9:21974776_21974804delGGCCAGCCAGTCAGCCGAAGGCTCCATGC uc003zpk.2 - 1 235_263 c.23_51delGCATGGAGCCTTCGGCTGACTGGCTGGCC c.(22-51)AGCATGGAGCCTTCGGCTGACTGGCTGGCCfs p.S8fs MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_Frame_Shift_Del_p.S8fs|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Intron NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 8_17 ANK 1. cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.?(23)|p.A4_P11del(12)|p.W15*(7)|p.L16fs*9(4)|p.S12*(3)|p.P3_P11del(2)|p.M9I(2)|p.L16P(2)|p.D14E(2)|p.P11S(1)|p.W15L(1)|p.P11_S12insAAGSSMEP(1)|p.S12fs*20(1)|p.S7_A19del(1)|p.S12fs*6(1)|p.A17_T18insTA(1)|p.S12fs*14(1)|p.L16_A17insAT(1)|p.D14V(1)|p.A17fs*5(1)|p.S8fs*18(1)|p.M9fs*1(1)|p.A17T(1)|p.L16R(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) 0.000 0.17 34 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OV56_OVARY NA OV56_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 368 141 TP53 7157 broad.mit.edu 37 17 7579383 7579384 + Frame_Shift_Del DEL TT - - OV56_OVARY NA OV56_OVARY NA g.chr17:7579383_7579384delTT uc002gim.2 - 4 497_498 c.303_304delAA c.(301-306)AAAACCfs p.K101fs TP53_uc002gig.1_Frame_Shift_Del_p.K101fs|TP53_uc002gih.2_Frame_Shift_Del_p.K101fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.K101fs|TP53_uc010cni.1_Frame_Shift_Del_p.K101fs|TP53_uc002gij.2_Frame_Shift_Del_p.K101fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.K62fs|TP53_uc010cnk.1_Frame_Shift_Del_p.K116fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 101_102 Interaction with HIPK1 (By similarity).||Interaction with WWOX. T -> I (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.K101R(3)|p.G59fs*23(3)|p.V73fs*9(1)|p.K101fs*48(1)|p.T102fs*21(1)|p.?fs(1)|p.K101N(1)|p.W91fs*13(1)|p.K101*(1)|p.P13fs*18(1)|p.S33fs*23(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.77 50 166 NOTCH3 4854 broad.mit.edu 37 19 15288536 15288536 + Frame_Shift_Del DEL G - - OV56_OVARY NA OV56_OVARY NA g.chr19:15288536delG uc002nan.2 - 24 4279 c.4203delC c.(4201-4203)TGCfs p.C1401fs NOTCH3_uc002nao.1_Frame_Shift_Del_p.C1349fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 1401 Extracellular (Potential).|LNR 1. Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.29 211 85 NCOA3 8202 broad.mit.edu 37 20 46279837 46279851 + In_Frame_Del DEL CAGCAGCAGCAGCAG - - rs3830809;rs2664555;rs141751959;rs147099949 byFrequency OV56_OVARY NA OV56_OVARY NA g.chr20:46279837_46279851delCAGCAGCAGCAGCAG uc002xtk.2 + 20 3968_3982 c.3763_3777delCAGCAGCAGCAGCAG c.(3763-3777)CAGCAGCAGCAGCAGdel p.QQQQQ1270del NCOA3_uc010ght.1_In_Frame_Del_p.QQQQQ1261del|NCOA3_uc002xtl.2_In_Frame_Del_p.QQQQQ1266del|NCOA3_uc002xtm.2_In_Frame_Del_p.QQQQQ1265del|NCOA3_uc002xtn.2_In_Frame_Del_p.QQQQQ1269del|NCOA3_uc010zyc.1_In_Frame_Del_p.QQQQQ1065del NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 1270_1274 Poly-Gln.|Acetyltransferase. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 gcagcagcaacagcagcagcagcagcagcagcagc 0.321 0.40 65 44 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OV56_OVARY NA OV56_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 19 42 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OV90_OVARY NA OV90_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 6 112 FMN2 56776 broad.mit.edu 37 1 240370942 240370974 + In_Frame_Del DEL CCTCCGCCCCCTCTACCCGGAGCGGCAATACCC - - rs150891575;rs6143701;rs142725738;rs146070457;rs72444563;rs144739133;rs142178619 byFrequency;byFrequency;byFrequency;byFrequency OV90_OVARY NA OV90_OVARY NA g.chr1:240370942_240370974delCCTCCGCCCCCTCTACCCGGAGCGGCAATACCC uc010pyd.1 + 5 3055_3087 c.2830_2862delCCTCCGCCCCCTCTACCCGGAGCGGCAATACCC c.(2830-2862)CCTCCGCCCCCTCTACCCGGAGCGGCAATACCCdel p.PPPPLPGAAIP944del FMN2_uc010pye.1_In_Frame_Del_p.PPPPLPGAAIP948del NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 944_954 Pro-rich.|FH1. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) GGGAATACCTCCTCCGCCCCCTCTACCCGGAGCGGCAATACCCCCTCCGCCCC 0.700 0.48 34 32 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 OV90_OVARY NA OV90_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.15 47 8 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 OV90_OVARY NA OV90_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.33 32 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OV90_OVARY NA OV90_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.43 143 106 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OV90_OVARY NA OV90_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 28 44 ARID1B 57492 broad.mit.edu 37 6 157099426 157099427 + In_Frame_Ins INS - CAG CAG rs78253128 OV90_OVARY NA OV90_OVARY NA g.chr6:157099426_157099427insCAG uc003qqn.2 + 1 341_342 c.189_190insCAG c.(187-192)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) agcagcagcaacagcagcagca 0.193 0.21 48 13 BRAF 673 broad.mit.edu 37 7 140477837 140477851 + In_Frame_Del DEL TAGGTGCTGTCACAT - - OV90_OVARY NA OV90_OVARY NA g.chr7:140477837_140477851delTAGGTGCTGTCACAT uc003vwc.3 - 12 1518_1532 c.1457_1471delATGTGACAGCACCTA c.(1456-1473)AATGTGACAGCACCTACA>ACA p.NVTAP486del NM_004333 NP_004324 P15056 BRAF_HUMAN B-Raf 486_490 Protein kinase. activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission cytosol|nucleus|plasma membrane ATP binding|metal ion binding p.L485_P490>Y(2)|p.N486_P490del(1) KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2) thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1) 18290 Melanoma(164;0.00956) Sorafenib(DB00398) TGCTGAGGTGTAGGTGCTGTCACATTCAACATTTT 0.349 0.28 137 52 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes OV90_OVARY NA OV90_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 2 25 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OV90_OVARY NA OV90_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 47 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 OV90_OVARY NA OV90_OVARY NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.94 5 77 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OV90_OVARY NA OV90_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 510 130 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 OV90_OVARY NA OV90_OVARY NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.38 16 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C OV90_OVARY NA OV90_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 10 123 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 OV90_OVARY NA OV90_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.27 101 37 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 OV90_OVARY NA OV90_OVARY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.31 93 42 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OV90_OVARY NA OV90_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 112 937 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OVCAR8_OVARY NA OVCAR8_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 34 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.40 15 10 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.50 13 13 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.20 37 9 MAML3 55534 broad.mit.edu 37 4 140641185 140641186 + Frame_Shift_Ins INS - G G OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr4:140641185_140641186insG uc003ihz.1 - 7 3445_3446 c.2693_2694insC c.(2692-2694)CCTfs p.P898fs MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_Frame_Shift_Ins_p.P366fs NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 899 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) GCCCAGAGGCAGGTTGCCTCGG 0.530 0.13 770 117 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 164 293 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 37 72 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.80 2 8 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.13 136 21 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.37 36 21 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.87 3 20 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.29 27 11 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.42 14 10 STAT6 6778 broad.mit.edu 37 12 57490894 57490895 + Frame_Shift_Ins INS - G G OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr12:57490894_57490895insG uc009zpe.2 - 20 2432_2433 c.2181_2182insC c.(2179-2184)CCCAGCfs p.P727fs STAT6_uc009zpf.2_Frame_Shift_Ins_p.P727fs|STAT6_uc001sna.2_Frame_Shift_Ins_p.P727fs|STAT6_uc010srb.1_Frame_Shift_Ins_p.P617fs|STAT6_uc010src.1_Frame_Shift_Ins_p.P617fs|STAT6_uc010srd.1_Frame_Shift_Ins_p.P617fs|STAT6_uc009zpg.2_Frame_Shift_Ins_p.P776fs NM_003153 NP_003144 P42226 STAT6_HUMAN signal transducer and activator of transcription 727_728 regulation of transcription from RNA polymerase II promoter cytosol|nucleus calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity ovary(2)|lung(1)|skin(1) 4 TGGCCCAGGCTGGGGGGCATCT 0.515 0.15 192 35 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.11 195 24 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.12 124 17 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 20 131 ID1 3397 broad.mit.edu 37 20 30193544 30193545 + Frame_Shift_Ins INS - G G rs11545371 OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr20:30193544_30193545insG uc002wwg.1 + 1 453_454 c.354_355insG c.(352-357)CCCGGGfs p.P118fs ID1_uc002wwh.1_Frame_Shift_Ins_p.P118fs|hsa-mir-3193|MI0014238_5'Flank NM_002165 NP_002156 P41134 ID1_HUMAN inhibitor of DNA binding 1 isoform a 118_119 angiogenesis|blood vessel endothelial cell migration|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by transcription factor localization|transforming growth factor beta receptor signaling pathway cytoplasm protein binding ovary(1) 1 all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198) Epithelial(4;1.99e-05)|all cancers(5;0.000169)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264) TTGGAACCCCCGGGGGCCGAGG 0.614 0.11 59 7 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.10 205 22 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 179 842 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 133 EP300 2033 broad.mit.edu 37 22 41572902 41572902 + Frame_Shift_Del DEL T - - OVCAR8_OVARY NA OVCAR8_OVARY NA g.chr22:41572902delT uc003azl.3 + 31 5582 c.5187delT c.(5185-5187)GATfs p.D1729fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1729 Binding region for E1A adenovirus.|TAZ-type 2. apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 GCCCAGGCGATTCTCGCCGCC 0.532 0.50 78 79 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OVISE_OVARY NA OVISE_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.46 36 31 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 OVISE_OVARY NA OVISE_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.21 31 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OVISE_OVARY NA OVISE_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 45 74 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OVISE_OVARY NA OVISE_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.87 13 87 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 OVISE_OVARY NA OVISE_OVARY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.45 164 136 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OVISE_OVARY NA OVISE_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 26 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OVISE_OVARY NA OVISE_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 316 132 ITPR2 3709 broad.mit.edu 37 12 26869133 26869141 + In_Frame_Del DEL CTGCATTCA - - OVISE_OVARY NA OVISE_OVARY NA g.chr12:26869133_26869141delCTGCATTCA uc001rhg.2 - 6 977_985 c.560_568delTGAATGCAG c.(559-570)GTGAATGCAGGG>GGG p.VNA187del ITPR2_uc001rhh.1_In_Frame_Del_p.VNA125del NM_002223 NP_002214 Q14571 ITPR2_HUMAN inositol 1,4,5-triphosphate receptor, type 2 187_189 Cytoplasmic (Potential).|MIR 2. activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 14 Colorectal(261;0.0847) AGTGGCTGCCCTGCATTCACAGGCATCAA 0.402 0.38 67 41 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 OVISE_OVARY NA OVISE_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.63 52 89 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 OVISE_OVARY NA OVISE_OVARY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.24 42 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OVISE_OVARY NA OVISE_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 111 383 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OVISE_OVARY NA OVISE_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 2 38 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OVK18_OVARY NA OVK18_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 37 ARID1A 8289 broad.mit.edu 37 1 27058064 27058064 + Frame_Shift_Del DEL C - - OVK18_OVARY NA OVK18_OVARY NA g.chr1:27058064delC uc001bmv.1 + 3 2145 c.1772delC c.(1771-1773)GCCfs p.A591fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.A591fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.A591fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.A208fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 591 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CAGCAAACTGCCTATTCCCAG 0.597 0.49 27 26 MYCL1 4610 broad.mit.edu 37 1 40366654 40366654 + Frame_Shift_Del DEL G - - OVK18_OVARY NA OVK18_OVARY NA g.chr1:40366654delG uc001cer.1 - 2 670 c.453delC c.(451-453)CCCfs p.P151fs MYCL1_uc001ces.1_Frame_Shift_Del_p.P151fs|MYCL1_uc001cet.1_Frame_Shift_Del_p.P151fs NM_001033082 NP_001028254 P12524 MYCL1_HUMAN l-myc-1 proto-oncogene isoform 1 151 nucleus DNA binding|sequence-specific DNA binding transcription factor activity lung(1)|liver(1) 2 all_cancers(7;1.73e-14)|all_lung(5;2.77e-17)|all_epithelial(6;6.81e-17)|Lung SC(1;2.85e-13)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;1.51e-19)|Epithelial(16;3.36e-18)|all cancers(16;8.43e-17)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457) 0.000 0.17 879 174 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - OVK18_OVARY NA OVK18_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 193 50 ITGA10 8515 broad.mit.edu 37 1 145534122 145534122 + Frame_Shift_Del DEL C - - rs147270843 OVK18_OVARY NA OVK18_OVARY NA g.chr1:145534122delC uc001eoa.2 + 14 1703 c.1627delC c.(1627-1629)CCCfs p.P543fs NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Frame_Shift_Del_p.P412fs|ITGA10_uc009wiw.2_Frame_Shift_Del_p.P400fs|ITGA10_uc010oyw.1_Frame_Shift_Del_p.P488fs NM_003637 NP_003628 O75578 ITA10_HUMAN integrin, alpha 10 precursor 543 Extracellular (Potential).|FG-GAP 6. cell-matrix adhesion|integrin-mediated signaling pathway integrin complex collagen binding|receptor activity lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1) 8 all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786) TCAGCCAGAACCCCCCCAGGA 0.552 0.24 42 13 RGL1 23179 broad.mit.edu 37 1 183854006 183854006 + Frame_Shift_Del DEL G - - OVK18_OVARY NA OVK18_OVARY NA g.chr1:183854006delG uc001gqo.2 + 7 1042 c.885delG c.(883-885)CTGfs p.L295fs RGL1_uc010pof.1_Frame_Shift_Del_p.L100fs|RGL1_uc001gqm.2_Frame_Shift_Del_p.L330fs|RGL1_uc010pog.1_Frame_Shift_Del_p.L293fs|RGL1_uc010poh.1_Frame_Shift_Del_p.L293fs|RGL1_uc010poi.1_Frame_Shift_Del_p.L295fs NM_015149 NP_055964 Q9NZL6 RGL1_HUMAN ral guanine nucleotide dissociation 295 Ras-GEF. cellular lipid metabolic process|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction intracellular protein binding|Ral guanyl-nucleotide exchange factor activity breast(5)|ovary(4)|lung(2) 11 GCACCATCCTGGGGGGCAAAG 0.418 0.29 95 39 EGLN1 54583 broad.mit.edu 37 1 231557319 231557319 + Frame_Shift_Del DEL C - - OVK18_OVARY NA OVK18_OVARY NA g.chr1:231557319delC uc001huv.2 - 1 3472 c.316delG c.(316-318)GACfs p.D106fs EGLN1_uc001huu.3_5'Flank NM_022051 NP_071334 Q9GZT9 EGLN1_HUMAN egl nine homolog 1 106 negative regulation of sequence-specific DNA binding transcription factor activity|oxygen homeostasis|response to hypoxia cytosol iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptidyl-proline dioxygenase activity|protein binding|zinc ion binding 0 Prostate(94;0.194)|Acute lymphoblastic leukemia(190;0.244) Vitamin C(DB00126) 0.000 0.35 887 484 YSK4 80122 broad.mit.edu 37 2 135743471 135743471 + Frame_Shift_Del DEL T - - OVK18_OVARY NA OVK18_OVARY NA g.chr2:135743471delT uc002tue.1 - 7 3002 c.2971delA c.(2971-2973)ATGfs p.M991fs YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Frame_Shift_Del_p.M878fs|YSK4_uc010zbg.1_Intron|YSK4_uc002tuh.3_Frame_Shift_Del_p.M719fs|YSK4_uc002tui.3_Frame_Shift_Del_p.M1008fs NM_025052 NP_079328 Q56UN5 YSK4_HUMAN Yeast Sps1/Ste20-related kinase 4 isoform 1 991 ATP binding|protein serine/threonine kinase activity stomach(2)|urinary_tract(1)|ovary(1)|breast(1) 5 BRCA - Breast invasive adenocarcinoma(221;0.112) TCATTTGCCATTTTTTGGCAA 0.368 0.40 49 33 TTN 7273 broad.mit.edu 37 2 179456385 179456385 + Frame_Shift_Del DEL T - - OVK18_OVARY NA OVK18_OVARY NA g.chr2:179456385delT uc010zfg.1 - 252 52681 c.52457delA c.(52456-52458)AACfs p.N17486fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.N11181fs|TTN_uc010zfi.1_Frame_Shift_Del_p.N11114fs|TTN_uc010zfj.1_Frame_Shift_Del_p.N10989fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 18413 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) ACCCACAATGTTTTCAGCTTT 0.373 0.35 110 59 CXCR2P1 3580 broad.mit.edu 37 2 218925641 218925641 + Frame_Shift_Del DEL C - - OVK18_OVARY NA OVK18_OVARY NA g.chr2:218925641delC uc002vgx.2 - 1 373 c.80delG c.(79-81)GGTfs p.G27fs RUFY4_uc002vgw.2_Intron NR_002712 Homo sapiens interleukin 8 receptor, beta pseudogene, mRNA (cDNA clone IMAGE:5450999), with apparent retained intron. 0 GTTCCACAAACCCAGACATAT 0.537 0.31 42 19 CAMKV 79012 broad.mit.edu 37 3 49897964 49897965 + Frame_Shift_Ins INS - T T rs140497968 OVK18_OVARY NA OVK18_OVARY NA g.chr3:49897964_49897965insT uc003cxt.1 - 9 986_987 c.793_794insA c.(793-795)AGGfs p.R265fs CAMKV_uc011bcy.1_Frame_Shift_Ins_p.R190fs|CAMKV_uc003cxv.1_Frame_Shift_Ins_p.R237fs|CAMKV_uc003cxw.1_Frame_Shift_Ins_p.R97fs|CAMKV_uc003cxx.1_Frame_Shift_Ins_p.R97fs|CAMKV_uc003cxu.2_Frame_Shift_Ins_p.R265fs|CAMKV_uc011bcz.1_Frame_Shift_Ins_p.R228fs|CAMKV_uc011bda.1_Frame_Shift_Ins_p.R222fs|CAMKV_uc011bdb.1_RNA NM_024046 NP_076951 Q8NCB2 CAMKV_HUMAN CaM kinase-like vesicle-associated 265 Protein kinase. cytoplasmic vesicle membrane|plasma membrane ATP binding|protein serine/threonine kinase activity ovary(2)|lung(2)|large_intestine(2)|central_nervous_system(1) 7 BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621) CTCCATCAGCCTTGTGACCAGG 0.579 0.43 27 20 PPARGC1A 10891 broad.mit.edu 37 4 23830061 23830061 + Frame_Shift_Del DEL T - - OVK18_OVARY NA OVK18_OVARY NA g.chr4:23830061delT uc003gqs.2 - 5 839 c.719delA c.(718-720)AAGfs p.K240fs PPARGC1A_uc003gqt.2_RNA|PPARGC1A_uc011bxp.1_RNA|PPARGC1A_uc010ier.1_RNA NM_013261 NP_037393 Q9UBK2 PRGC1_HUMAN peroxisome proliferator-activated receptor 240 androgen receptor signaling pathway|brown fat cell differentiation|cellular glucose homeostasis|digestion|fatty acid oxidation|gluconeogenesis|mitochondrion organization|mRNA processing|neuron death|positive regulation of fatty acid oxidation|positive regulation of gluconeogenesis|positive regulation of histone acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization|response to muscle activity|response to starvation|RNA splicing|temperature homeostasis|transcription initiation from RNA polymerase II promoter DNA-directed RNA polymerase II, core complex androgen receptor binding|DNA binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|RNA binding|RNA polymerase II transcription cofactor activity|transcription factor binding ovary(2)|lung(2)|kidney(2)|skin(2) 8 Breast(46;0.0503) GTGGGACTTCTTTTTGGAGGT 0.498 0.51 72 75 AFF1 4299 broad.mit.edu 37 4 88035996 88035996 + Frame_Shift_Del DEL C - - OVK18_OVARY NA OVK18_OVARY NA g.chr4:88035996delC uc003hqj.3 + 11 2397 c.1990delC c.(1990-1992)CCCfs p.P664fs AFF1_uc011ccz.1_Frame_Shift_Del_p.P671fs|AFF1_uc003hqk.3_Frame_Shift_Del_p.P664fs|AFF1_uc011cda.1_Frame_Shift_Del_p.P302fs NM_005935 NP_005926 P51825 AFF1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 664 nucleus sequence-specific DNA binding transcription factor activity breast(1) 1 Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114) OV - Ovarian serous cystadenocarcinoma(123;0.000233) GCCAGCAGTGCCCCCCTCCAG 0.612 0.62 14 23 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 OVK18_OVARY NA OVK18_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.18 31 7 CFI 3426 broad.mit.edu 37 4 110662155 110662155 + Frame_Shift_Del DEL T - - OVK18_OVARY NA OVK18_OVARY NA g.chr4:110662155delT uc003hzr.3 - 13 1854 c.1646delA c.(1645-1647)AACfs p.N549fs CFI_uc003hzq.2_Frame_Shift_Del_p.N346fs|CFI_uc011cft.1_Frame_Shift_Del_p.N557fs|CFI_uc003hzs.3_Frame_Shift_Del_p.N542fs NM_000204 NP_000195 P05156 CFAI_HUMAN complement factor I preproprotein 549 Peptidase S1. complement activation, classical pathway|innate immune response|proteolysis extracellular space|membrane scavenger receptor activity|serine-type endopeptidase activity 0 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.000331) TTTTCCACAGTTTTCCCCCCA 0.463 0.53 54 61 ALPK1 80216 broad.mit.edu 37 4 113360940 113360941 + Frame_Shift_Del DEL AG - - OVK18_OVARY NA OVK18_OVARY NA g.chr4:113360940_113360941delAG uc003iap.3 + 14 3729_3730 c.3450_3451delAG c.(3448-3453)ACAGAAfs p.T1150fs ALPK1_uc003ian.3_Frame_Shift_Del_p.T1150fs|ALPK1_uc011cfx.1_Frame_Shift_Del_p.T1072fs|ALPK1_uc003iao.3_RNA|ALPK1_uc010imo.2_Frame_Shift_Del_p.T978fs NM_025144 NP_079420 Q96QP1 ALPK1_HUMAN alpha-kinase 1 1150_1151 Alpha-type protein kinase. ATP binding|protein serine/threonine kinase activity ovary(5) 5 Ovarian(17;0.0446)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.00325) TGGTGAAAACAGAATACAAAGC 0.366 0.52 16 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OVK18_OVARY NA OVK18_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.30 58 25 TRIO 7204 broad.mit.edu 37 5 14477003 14477004 + Frame_Shift_Ins INS - T T OVK18_OVARY NA OVK18_OVARY NA g.chr5:14477003_14477004insT uc003jff.2 + 41 6090_6091 c.6084_6085insT c.(6082-6087)GACTTTfs p.D2028fs TRIO_uc003jfg.2_RNA|TRIO_uc003jfh.1_Frame_Shift_Ins_p.D1677fs NM_007118 NP_009049 O75962 TRIO_HUMAN triple functional domain (PTPRF interacting) 2028_2029 DH 2. apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway cytosol ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1) 18 Lung NSC(4;0.000742) TTCTTTCCAGCTTTTTTTTAGG 0.292 0.40 29 19 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OVK18_OVARY NA OVK18_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.27 37 14 PIK3R1 5295 broad.mit.edu 37 5 67589019 67589020 + Frame_Shift_Ins INS - A A OVK18_OVARY NA OVK18_OVARY NA g.chr5:67589019_67589020insA uc003jva.2 + 9 1670_1671 c.1110_1111insA c.(1108-1113)CTTACAfs p.L370fs PIK3R1_uc003jvb.2_Frame_Shift_Ins_p.L370fs|PIK3R1_uc003jvc.2_Frame_Shift_Ins_p.L70fs|PIK3R1_uc003jvd.2_Frame_Shift_Ins_p.L100fs|PIK3R1_uc003jve.2_Frame_Shift_Ins_p.L49fs|PIK3R1_uc011crb.1_Frame_Shift_Ins_p.L40fs NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 370_371 SH2 1. epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.?(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) ATTATACTCTTACACTAAGGTA 0.342 0.50 48 48 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 OVK18_OVARY NA OVK18_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.39 206 130 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes OVK18_OVARY NA OVK18_OVARY NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.51 30 31 DDR1 780 broad.mit.edu 37 6 30862379 30862379 + Frame_Shift_Del DEL C - - OVK18_OVARY NA OVK18_OVARY NA g.chr6:30862379delC uc003nrr.2 + 12 1703 c.1444delC c.(1444-1446)CCCfs p.P482fs DDR1_uc010jse.2_Frame_Shift_Del_p.P482fs|DDR1_uc003nrq.2_Frame_Shift_Del_p.P482fs|DDR1_uc003nrs.2_Frame_Shift_Del_p.P482fs|DDR1_uc003nrt.2_Frame_Shift_Del_p.P482fs|DDR1_uc011dms.1_Frame_Shift_Del_p.P500fs|DDR1_uc003nru.2_Frame_Shift_Del_p.P482fs|DDR1_uc003nrv.2_Frame_Shift_Del_p.P482fs|DDR1_uc003nrw.1_Frame_Shift_Del_p.H253fs|DDR1_uc003nry.1_RNA|DDR1_uc003nrx.1_RNA|DDR1_uc003nrz.1_5'Flank NM_013993 NP_054699 Q08345 DDR1_HUMAN discoidin domain receptor family, member 1 482 PPxY motif.|Cytoplasmic (Potential).|Gly/Pro-rich. cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway extracellular region|integral to plasma membrane ATP binding|protein binding|protein binding|transmembrane receptor protein tyrosine kinase activity lung(4)|central_nervous_system(3)|large_intestine(1)|ovary(1) 9 Imatinib(DB00619) TAGAGAGCCACCCCCGTACCA 0.622 0.48 23 21 BRD2 6046 broad.mit.edu 37 6 32945713 32945714 + In_Frame_Ins INS - GAA GAA rs144872939 by1000genomes OVK18_OVARY NA OVK18_OVARY NA g.chr6:32945713_32945714insGAA uc003ocn.3 + 9 3210_3211 c.1509_1510insGAA c.(1507-1512)insGAA p.506_507insE BRD2_uc003oco.2_RNA|BRD2_uc003ocq.3_In_Frame_Ins_p.506_507insE|BRD2_uc003ocp.3_In_Frame_Ins_p.386_387insE|BRD2_uc010juh.2_In_Frame_Ins_p.506_507insE NM_005104 NP_005095 P25440 BRD2_HUMAN bromodomain containing 2 506_507 Glu/Ser-rich. spermatogenesis nucleus protein serine/threonine kinase activity central_nervous_system(3)|stomach(2) 5 aggacgaggaggaagaagagAG 0.371 0.30 19 8 XPO5 57510 broad.mit.edu 37 6 43521153 43521153 + Frame_Shift_Del DEL A - - OVK18_OVARY NA OVK18_OVARY NA g.chr6:43521153delA uc003ovp.2 - 14 1740 c.1529delT c.(1528-1530)TTGfs p.L510fs NM_020750 NP_065801 Q9HAV4 XPO5_HUMAN exportin 5 510 gene silencing by RNA cytosol|nucleoplasm protein binding|tRNA binding skin(2)|breast(1)|kidney(1) 4 all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243) all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524) AACACTTTCCAAAAAAAGAGT 0.368 0.48 48 44 MAP3K5 4217 broad.mit.edu 37 6 136913692 136913694 + In_Frame_Del DEL CTG - - OVK18_OVARY NA OVK18_OVARY NA g.chr6:136913692_136913694delCTG uc003qhc.2 - 22 3298_3300 c.2937_2939delCAG c.(2935-2940)AGCAGT>AGT p.979_980SS>S MAP3K5_uc011edj.1_In_Frame_Del_p.226_227SS>S|MAP3K5_uc011edk.1_In_Frame_Del_p.825_826SS>S NM_005923 NP_005914 Q99683 M3K5_HUMAN mitogen-activated protein kinase kinase kinase 979_980 activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding ovary(2)|skin(2)|lung(1) 5 Colorectal(23;0.24) GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569) GCCGTACTCACTGCTGCTGCTGG 0.483 0.36 81 45 CDK13 8621 broad.mit.edu 37 7 40102647 40102647 + Frame_Shift_Del DEL A - - OVK18_OVARY NA OVK18_OVARY NA g.chr7:40102647delA uc003thh.3 + 9 3010 c.2728delA c.(2728-2730)AAAfs p.K910fs CDK13_uc003thi.3_Frame_Shift_Del_p.K910fs|CDK13_uc011kbf.1_Frame_Shift_Del_p.K296fs|CDK13_uc003thj.2_5'UTR NM_003718 NP_003709 Q14004 CDK13_HUMAN cell division cycle 2-like 5 isoform 1 910 Protein kinase. alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity lung(2)|skin(2)|ovary(1) 5 ACTCTTCACTAAAAAACCTAT 0.333 0.37 74 43 MLL3 58508 broad.mit.edu 37 7 151845524 151845524 + Frame_Shift_Del DEL A - - OVK18_OVARY NA OVK18_OVARY NA g.chr7:151845524delA uc003wla.2 - 52 13707 c.13488delT c.(13486-13488)TTTfs p.F4496fs MLL3_uc003wkz.2_Frame_Shift_Del_p.F3614fs|MLL3_uc003wkx.2_Frame_Shift_Del_p.F654fs|MLL3_uc003wky.2_Frame_Shift_Del_p.F2060fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 4496 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTTTGTCCTTAAAAAACATGC 0.433 0.48 84 77 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - OVK18_OVARY NA OVK18_OVARY NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.27 41 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039782 + In_Frame_Del DEL CAGCAG - - rs113070757;rs62639301;rs139102413 byFrequency;byFrequency OVK18_OVARY NA OVK18_OVARY NA g.chr9:2039777_2039782delCAGCAG uc003zhc.2 + 4 766_771 c.667_672delCAGCAG c.(667-672)CAGCAGdel p.QQ237del SMARCA2_uc003zhd.2_In_Frame_Del_p.QQ237del|SMARCA2_uc010mha.2_In_Frame_Del_p.QQ228del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 237_238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.18 766 164 ROR2 4920 broad.mit.edu 37 9 94486232 94486233 + Frame_Shift_Ins INS - G G OVK18_OVARY NA OVK18_OVARY NA g.chr9:94486232_94486233insG uc004arj.1 - 9 2742_2743 c.2543_2544insC c.(2542-2544)CCGfs p.P848fs ROR2_uc004ari.1_Intron NM_004560 NP_004551 Q01974 ROR2_HUMAN receptor tyrosine kinase-like orphan receptor 2 848 Cytoplasmic (Potential).|Pro-rich. negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1) 20 GCACCTGCTGCGGGGCCATCTG 0.653 0.53 7 8 TRAF2 7186 broad.mit.edu 37 9 139793212 139793212 + Frame_Shift_Del DEL C - - OVK18_OVARY NA OVK18_OVARY NA g.chr9:139793212delC uc010nbu.2 + 3 193 c.20delC c.(19-21)ACCfs p.T7fs TRAF2_uc010nbv.1_Frame_Shift_Del_p.T7fs|TRAF2_uc004cjv.2_Frame_Shift_Del_p.T7fs|TRAF2_uc011mek.1_Frame_Shift_Del_p.T7fs|TRAF2_uc010nbw.2_Frame_Shift_Del_p.T7fs NM_021138 NP_066961 Q12933 TRAF2_HUMAN TNF receptor-associated factor 2 7 activation of caspase activity|activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cellular protein complex assembly|induction of apoptosis by extracellular signals|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|protein autoubiquitination|protein homotrimerization|protein K63-linked ubiquitination|tumor necrosis factor-mediated signaling pathway CD40 receptor complex|cytosol|internal side of plasma membrane CD40 receptor binding|enzyme binding|protein binding|signal transducer activity|sphingolipid binding|ubiquitin-protein ligase activity|zinc ion binding ovary(1)|lung(1)|breast(1)|skin(1) 4 all_cancers(76;0.11) Myeloproliferative disorder(178;0.0511) STAD - Stomach adenocarcinoma(284;0.229) OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06) GCTAGCGTGACCCCCCCTGGC 0.592 0.57 10 13 CACNB2 783 broad.mit.edu 37 10 18828599 18828599 + Frame_Shift_Del DEL A - - OVK18_OVARY NA OVK18_OVARY NA g.chr10:18828599delA uc001ipr.2 + 14 1989 c.1929delA c.(1927-1929)TCAfs p.S643fs CACNB2_uc009xjz.1_Frame_Shift_Del_p.S393fs|CACNB2_uc001ips.2_Frame_Shift_Del_p.S619fs|CACNB2_uc001ipt.2_Frame_Shift_Del_p.S605fs|CACNB2_uc001ipu.2_Frame_Shift_Del_p.S615fs|CACNB2_uc001ipv.2_Frame_Shift_Del_p.S591fs|CACNB2_uc009xka.1_Frame_Shift_Del_p.S577fs|CACNB2_uc001ipw.2_Frame_Shift_Del_p.S550fs|CACNB2_uc001ipx.2_Frame_Shift_Del_p.S588fs|CACNB2_uc001ipz.2_Frame_Shift_Del_p.S565fs|CACNB2_uc001ipy.2_Frame_Shift_Del_p.S589fs|CACNB2_uc010qco.1_Frame_Shift_Del_p.S557fs|CACNB2_uc001iqa.2_Frame_Shift_Del_p.S595fs|NSUN6_uc001iqb.2_Intron NM_201596 NP_963890 Q08289 CACB2_HUMAN calcium channel, voltage-dependent, beta 2 643 axon guidance|neuromuscular junction development integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity large_intestine(1)|central_nervous_system(1)|skin(1) 3 Magnesium Sulfate(DB00653)|Verapamil(DB00661) AAGTGATATCAAAAAAACGGA 0.448 0.61 72 111 PTEN 5728 broad.mit.edu 37 10 89692981 89692982 + Frame_Shift_Ins INS - G G OVK18_OVARY NA OVK18_OVARY NA g.chr10:89692981_89692982insG uc001kfb.2 + 6 1496_1497 c.465_466insG c.(463-468)TATGGGfs p.Y155fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 155_156 Phosphatase tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R55fs*1(4)|p.Y155C(3)|p.Y155H(3)|p.?(2)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.Y155N(1)|p.G156R(1)|p.F56fs*2(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) TAGATTTCTATGGGGAAGTAAG 0.371 0.58 77 108 PTEN 5728 broad.mit.edu 37 10 89720712 89720712 + Frame_Shift_Del DEL A - - OVK18_OVARY NA OVK18_OVARY NA g.chr10:89720712delA uc001kfb.2 + 9 1894 c.863delA c.(862-864)GAAfs p.E288fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 288 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.E288fs*3(6)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.E288*(2)|p.G165_*404del(1)|p.S287fs*1(1)|p.G165_K342del(1)|p.E288fs*8(1)|p.S287fs*8(1)|p.W274_F341del(1)|p.E288K(1)|p.E288fs*9(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GAAACCTCAGAAAAAGTAGAA 0.299 0.33 139 67 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 OVK18_OVARY NA OVK18_OVARY NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.76 7 22 MARK2 2011 broad.mit.edu 37 11 63667483 63667484 + Frame_Shift_Ins INS - A A OVK18_OVARY NA OVK18_OVARY NA g.chr11:63667483_63667484insA uc001nxw.2 + 8 1248_1249 c.669_670insA c.(667-672)GGCAAAfs p.G223fs MARK2_uc001nxx.2_Frame_Shift_Ins_p.G223fs|MARK2_uc001nxy.2_Frame_Shift_Ins_p.G223fs|MARK2_uc001nxv.3_Frame_Shift_Ins_p.G223fs|MARK2_uc001nxz.3_Frame_Shift_Ins_p.G190fs|MARK2_uc009yoy.2_Frame_Shift_Ins_p.G190fs NM_001039469 NP_001034558 Q7KZI7 MARK2_HUMAN MAP/microtubule affinity-regulating kinase 2 223_224 Protein kinase. cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress plasma membrane ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity stomach(1)|ovary(1)|lung(1) 3 TCTTCCAGGGCAAAAAATATGA 0.505 0.39 85 54 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OVK18_OVARY NA OVK18_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.11 92 11 POU2AF1 5450 broad.mit.edu 37 11 111224988 111224988 + Frame_Shift_Del DEL A - - OVK18_OVARY NA OVK18_OVARY NA g.chr11:111224988delA uc001plg.3 - 5 1024 c.769delT c.(769-771)TAGfs p.*257fs NM_006235 NP_006226 Q16633 OBF1_HUMAN POU class 2 associating factor 1 257 humoral immune response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter nucleus protein binding|transcription coactivator activity kidney(1) 1 all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389) Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;3.12e-06)|all cancers(92;1.8e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0364) AGCCACGCCTAAAAGCCTTCC 0.512 0.58 13 18 GRAMD1B 57476 broad.mit.edu 37 11 123489886 123489886 + Frame_Shift_Del DEL A - - OVK18_OVARY NA OVK18_OVARY NA g.chr11:123489886delA uc001pyx.2 + 19 2410 c.2081delA c.(2080-2082)CAAfs p.Q694fs GRAMD1B_uc001pyw.2_Frame_Shift_Del_p.Q701fs|GRAMD1B_uc010rzw.1_Frame_Shift_Del_p.Q650fs|GRAMD1B_uc010rzx.1_Frame_Shift_Del_p.Q654fs|GRAMD1B_uc001pyy.2_Frame_Shift_Del_p.Q381fs NM_020716 NP_065767 Q3KR37 GRM1B_HUMAN GRAM domain containing 1B 694 integral to membrane ovary(1) 1 Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394) ACTGAGCTCCAAAAATGGAGG 0.537 0.51 45 46 LRRK2 120892 broad.mit.edu 37 12 40760816 40760816 + Frame_Shift_Del DEL A - - OVK18_OVARY NA OVK18_OVARY NA g.chr12:40760816delA uc001rmg.3 + 50 7520 c.7399delA c.(7399-7401)AAAfs p.K2467fs LRRK2_uc009zjw.2_Frame_Shift_Del_p.K1305fs|LRRK2_uc001rmi.2_3'UTR NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 2467 activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) AGGAAGCCTTAAAAATGTCAT 0.323 0.40 52 35 IRAK3 11213 broad.mit.edu 37 12 66610954 66610954 + Frame_Shift_Del DEL A - - OVK18_OVARY NA OVK18_OVARY NA g.chr12:66610954delA uc001sth.2 + 6 694 c.592delA c.(592-594)AAAfs p.K198fs IRAK3_uc010ssy.1_Frame_Shift_Del_p.K137fs NM_007199 NP_009130 Q9Y616 IRAK3_HUMAN interleukin-1 receptor-associated kinase 3 198 Protein kinase. interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|negative regulation of innate immune response|negative regulation of interleukin-12 production|negative regulation of interleukin-6 production|negative regulation of macrophage cytokine production|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein catabolic process|negative regulation of protein complex disassembly|negative regulation of toll-like receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of macrophage tolerance induction|positive regulation of NF-kappaB transcription factor activity|response to exogenous dsRNA|response to lipopolysaccharide|response to peptidoglycan cytoplasm|nucleus ATP binding|magnesium ion binding|protein heterodimerization activity|protein homodimerization activity|protein serine/threonine kinase activity lung(3)|ovary(2)|breast(2)|central_nervous_system(1) 8 GBM - Glioblastoma multiforme(28;0.0203) TATGTAGGAGAAAAAAATGCA 0.303 0.18 115 25 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency OVK18_OVARY NA OVK18_OVARY NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.31 20 9 SACS 26278 broad.mit.edu 37 13 23915644 23915644 + Frame_Shift_Del DEL A - - OVK18_OVARY NA OVK18_OVARY NA g.chr13:23915644delA uc001uon.2 - 10 2960 c.2371delT c.(2371-2373)TCAfs p.S791fs SACS_uc001uoo.2_Frame_Shift_Del_p.S644fs|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Frame_Shift_Del_p.S644fs NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 791 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) AAATCCTCTGAAAAATGTATA 0.363 0.45 47 39 NEK3 4752 broad.mit.edu 37 13 52715206 52715207 + Splice_Site INS - T T OVK18_OVARY NA OVK18_OVARY NA g.chr13:52715206_52715207insT uc001vgi.2 - 13 1113 c.878_splice c.e13-1 p.T293_splice NEK3_uc001vgg.2_Intron|NEK3_uc001vgh.2_Intron|NEK3_uc010tgx.1_Splice_Site|NEK3_uc010tgy.1_Intron NM_152720 NP_689933 P51956 NEK3_HUMAN NIMA-related kinase 3 isoform a cell division|mitosis nucleus ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173) GBM - Glioblastoma multiforme(99;2.81e-08) CTGGGGTTTGCTTTTAAAAGAG 0.381 0.51 28 29 CYFIP1 23191 broad.mit.edu 37 15 22999510 22999511 + Frame_Shift_Del DEL CA - - OVK18_OVARY NA OVK18_OVARY NA g.chr15:22999510_22999511delCA uc001yus.2 + 29 3486_3487 c.3382_3383delCA c.(3382-3384)CACfs p.H1128fs CYFIP1_uc001yut.2_Frame_Shift_Del_p.H1128fs|CYFIP1_uc001yuu.2_Frame_Shift_Del_p.H697fs|CYFIP1_uc001yuv.2_Frame_Shift_Del_p.H322fs NM_014608 NP_055423 Q7L576 CYFP1_HUMAN cytoplasmic FMR1 interacting protein 1 isoform 1128 axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome actin filament binding|Rac GTPase binding ovary(4)|pancreas(3)|liver(1)|skin(1) 9 all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488) all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101) TGTGGAGTTTCACAGACTGTGG 0.574 0.52 15 16 HERC2 8924 broad.mit.edu 37 15 28525279 28525279 + Frame_Shift_Del DEL A - - OVK18_OVARY NA OVK18_OVARY NA g.chr15:28525279delA uc001zbj.2 - 5 583 c.477delT c.(475-477)TTTfs p.F159fs HERC2_uc001zbl.1_5'UTR NM_004667 NP_004658 O95714 HERC2_HUMAN hect domain and RLD 2 159 DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process nucleus guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1) 13 all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227) all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199) CATTCTCCTGAAAAACGGTTC 0.483 0.42 37 27 UNC13C 440279 broad.mit.edu 37 15 54305720 54305720 + Frame_Shift_Del DEL G - - OVK18_OVARY NA OVK18_OVARY NA g.chr15:54305720delG uc002ack.2 + 1 620 c.620delG c.(619-621)TGGfs p.W207fs NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 207 exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) AAAAAATCCTGGGGAATAAGA 0.438 0.41 50 35 SOCS1 8651 broad.mit.edu 37 16 11348742 11348742 + Frame_Shift_Del DEL G - - rs144893532 OVK18_OVARY NA OVK18_OVARY NA g.chr16:11348742delG uc002dar.1 - 2 748 c.594delC c.(592-594)CCCfs p.P198fs C16orf75_uc002daq.1_Intron NM_003745 NP_003736 O15524 SOCS1_HUMAN suppressor of cytokine signaling 1 198 SOCS box. interferon-gamma-mediated signaling pathway|JAK-STAT cascade|negative regulation of insulin receptor signaling pathway|negative regulation of tyrosine phosphorylation of Stat3 protein|regulation of growth|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway cytosol insulin-like growth factor receptor binding|protein kinase binding|protein kinase inhibitor activity p.P198S(2)|p.R127_*212del(1) haematopoietic_and_lymphoid_tissue(64)|lung(3)|breast(1)|central_nervous_system(1) 69 0.000 0.38 1347 827 NFAT5 10725 broad.mit.edu 37 16 69727530 69727532 + In_Frame_Del DEL CAG - - OVK18_OVARY NA OVK18_OVARY NA g.chr16:69727530_69727532delCAG uc002exm.1 + 12 4956_4958 c.3748_3750delCAG c.(3748-3750)CAGdel p.Q1266del NFAT5_uc002exi.2_In_Frame_Del_p.Q1190del|NFAT5_uc002exj.1_In_Frame_Del_p.Q1190del|NFAT5_uc002exk.1_In_Frame_Del_p.Q1190del|NFAT5_uc002exl.1_In_Frame_Del_p.Q1284del|NFAT5_uc002exn.1_In_Frame_Del_p.Q1283del|NFAT5_uc002exo.1_RNA NM_006599 NP_006590 O94916 NFAT5_HUMAN nuclear factor of activated T-cells 5 isoform c 1266 Poly-Gln. excretion|signal transduction|transcription from RNA polymerase II promoter nucleus DNA binding|sequence-specific DNA binding transcription factor activity 0 ATCCCAGGAAcagcagcagcagc 0.345 0.32 13 6 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C OVK18_OVARY NA OVK18_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 75 759 TP53 7157 broad.mit.edu 37 17 7578475 7578475 + Frame_Shift_Del DEL G - - OVK18_OVARY NA OVK18_OVARY NA g.chr17:7578475delG uc002gim.2 - 5 649 c.455delC c.(454-456)CCGfs p.P152fs TP53_uc002gig.1_Frame_Shift_Del_p.P152fs|TP53_uc002gih.2_Frame_Shift_Del_p.P152fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.P20fs|TP53_uc010cng.1_Frame_Shift_Del_p.P20fs|TP53_uc002gii.1_Frame_Shift_Del_p.P20fs|TP53_uc010cnh.1_Frame_Shift_Del_p.P152fs|TP53_uc010cni.1_Frame_Shift_Del_p.P152fs|TP53_uc002gij.2_Frame_Shift_Del_p.P152fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.P59fs|TP53_uc002gio.2_Frame_Shift_Del_p.P20fs|TP53_uc010vug.1_Frame_Shift_Del_p.P113fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 152 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). P -> R (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|P -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> A (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.P152L(57)|p.P152S(21)|p.P152fs*18(17)|p.P152T(7)|p.0?(7)|p.P152fs*29(5)|p.P152P(5)|p.P152Q(4)|p.P153fs*28(4)|p.P152fs*14(4)|p.P152fs*28(3)|p.P152R(3)|p.T150fs*16(3)|p.P152A(2)|p.P153fs*16(1)|p.P151_V173del23(1)|p.P152_P153del(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.D148fs*23(1)|p.P152del(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.Q144_G154del11(1)|p.P152_P153insXXX(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGTGCCGGGCGGGGGTGTGGA 0.612 0.42 15 11 SOCS3 9021 broad.mit.edu 37 17 76354904 76354905 + Frame_Shift_Ins INS - T T OVK18_OVARY NA OVK18_OVARY NA g.chr17:76354904_76354905insT uc002jvl.2 - 2 688_689 c.272_273insA c.(271-273)AAGfs p.K91fs NM_003955 NP_003946 O14543 SOCS3_HUMAN suppressor of cytokine signaling 3 91 SH2. anti-apoptosis|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|regulation of growth|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway cytosol protein kinase inhibitor activity ovary(1) 1 BRCA - Breast invasive adenocarcinoma(99;0.000688)|OV - Ovarian serous cystadenocarcinoma(97;0.0554) TGCGCAGGTTCTTGGTCCCAGA 0.658 0.40 6 4 SMAD2 4087 broad.mit.edu 37 18 45372073 45372073 + Frame_Shift_Del DEL A - - OVK18_OVARY NA OVK18_OVARY NA g.chr18:45372073delA uc002lcy.2 - 9 1344 c.1096delT c.(1096-1098)TATfs p.Y366fs SMAD2_uc002lcz.2_Frame_Shift_Del_p.Y366fs|SMAD2_uc010xdc.1_Frame_Shift_Del_p.Y336fs|SMAD2_uc010xdd.1_Frame_Shift_Del_p.Y336fs NM_005901 NP_005892 Q15796 SMAD2_HUMAN Sma- and Mad-related protein 2 isoform 1 366 MH2. anterior/posterior pattern formation|cell fate commitment|common-partner SMAD protein phosphorylation|intracellular signal transduction|mesoderm formation|negative regulation of transcription, DNA-dependent|palate development|paraxial mesoderm morphogenesis|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|regulation of binding|regulation of transforming growth factor beta receptor signaling pathway|response to cholesterol|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|zygotic specification of dorsal/ventral axis activin responsive factor complex|cytosol activating transcription factor binding|co-SMAD binding|double-stranded DNA binding|I-SMAD binding|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding large_intestine(3)|lung(1)|central_nervous_system(1) 5 TGCCAGCCATATCTCTGATTA 0.418 0.59 33 47 SMAD7 4092 broad.mit.edu 37 18 46476568 46476568 + Frame_Shift_Del DEL T - - OVK18_OVARY NA OVK18_OVARY NA g.chr18:46476568delT uc002ldg.2 - 1 514 c.227delA c.(226-228)CACfs p.H76fs SMAD7_uc010xde.1_5'Flank NM_005904 NP_005895 O15105 SMAD7_HUMAN SMAD family member 7 76 MH1. adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding 0 Colorectal(1;0.0518) 0.000 0.23 468 141 ALPK2 115701 broad.mit.edu 37 18 56196451 56196451 + Frame_Shift_Del DEL C - - rs7236563 byFrequency;by1000genomes OVK18_OVARY NA OVK18_OVARY NA g.chr18:56196451delC uc002lhj.3 - 6 5587 c.5373delG c.(5371-5373)AAGfs p.K1791fs ALPK2_uc002lhk.1_Frame_Shift_Del_p.K1122fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 1791 Ig-like 2. ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 CAGCTTGGATCTTTTTCAGTA 0.254 0.12 84 12 SMARCA4 6597 broad.mit.edu 37 19 11096048 11096048 + Frame_Shift_Del DEL C - - OVK18_OVARY NA OVK18_OVARY NA g.chr19:11096048delC uc002mqf.3 + 3 606 c.322delC c.(322-324)CCCfs p.P108fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.P108fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.P108fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.P108fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.P108fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.P108fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.P108fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.P108fs|SMARCA4_uc002mqe.2_Frame_Shift_Del_p.P108fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 108 Necessary for interaction with SS18L1/CREST (By similarity). chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) 0.000 0.49 895 843 SMARCA4 6597 broad.mit.edu 37 19 11141498 11141498 + Frame_Shift_Del DEL G - - OVK18_OVARY NA OVK18_OVARY NA g.chr19:11141498delG uc002mqf.3 + 25 3759 c.3475delG c.(3475-3477)GGGfs p.G1159fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.G1159fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.G1159fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.G1159fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.G1159fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.G1159fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.G1159fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.G1159fs|SMARCA4_uc010dxt.1_Frame_Shift_Del_p.G379fs|SMARCA4_uc002mqh.3_Frame_Shift_Del_p.G282fs|SMARCA4_uc002mqi.1_Frame_Shift_Del_p.G362fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 1159 Helicase C-terminal. chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) 0.000 0.56 579 723 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 OVK18_OVARY NA OVK18_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.30 16 7 MYLK2 85366 broad.mit.edu 37 20 30407987 30407987 + Frame_Shift_Del DEL C - - OVK18_OVARY NA OVK18_OVARY NA g.chr20:30407987delC uc002wwq.2 + 3 213 c.111delC c.(109-111)GGCfs p.G37fs NM_033118 NP_149109 Q9H1R3 MYLK2_HUMAN skeletal myosin light chain kinase 37 cardiac muscle tissue morphogenesis|regulation of muscle filament sliding ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity lung(2)|skin(2)|ovary(1)|central_nervous_system(1) 6 Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347) 0.000 0.49 517 499 ZNF217 7764 broad.mit.edu 37 20 52194917 52194917 + Frame_Shift_Del DEL A - - OVK18_OVARY NA OVK18_OVARY NA g.chr20:52194917delA uc002xwq.3 - 2 1710 c.1439delT c.(1438-1440)TTCfs p.F480fs ZNF217_uc010gij.1_Frame_Shift_Del_p.F472fs NM_006526 NP_006517 O75362 ZN217_HUMAN zinc finger protein 217 480 C2H2-type 6. negative regulation of transcription, DNA-dependent histone deacetylase complex protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding skin(2)|ovary(1)|large_intestine(1)|lung(1)|breast(1) 6 all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398) BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198) ATTTGAACGGAAAAACTTTCC 0.254 0.39 34 22 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OVK18_OVARY NA OVK18_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 298 766 TSSK2 23617 broad.mit.edu 37 22 19119731 19119732 + Frame_Shift_Ins INS - C C OVK18_OVARY NA OVK18_OVARY NA g.chr22:19119731_19119732insC uc002zow.2 + 1 1411_1412 c.819_820insC c.(817-822)CAGCCCfs p.Q273fs DGCR14_uc002zot.2_3'UTR|DGCR14_uc002zou.2_3'UTR|DGCR14_uc002zov.2_RNA NM_053006 NP_443732 Q96PF2 TSSK2_HUMAN testis-specific serine kinase 2 273_274 cell differentiation|multicellular organismal development|spermatogenesis cytoplasm ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity stomach(1) 1 Colorectal(54;0.0993) CGTGGCTGCAGCCCCCCAAGCC 0.624 0.26 28 10 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OVK18_OVARY NA OVK18_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 47 TNRC6B 23112 broad.mit.edu 37 22 40669453 40669453 + Frame_Shift_Del DEL G - - OVK18_OVARY NA OVK18_OVARY NA g.chr22:40669453delG uc011aor.1 + 7 3201 c.2990delG c.(2989-2991)TGGfs p.W997fs TNRC6B_uc003aym.2_Frame_Shift_Del_p.W250fs|TNRC6B_uc003ayn.3_Frame_Shift_Del_p.W944fs|TNRC6B_uc003ayo.2_Frame_Shift_Del_p.W801fs NM_001162501 NP_001155973 Q9UPQ9 TNR6B_HUMAN trinucleotide repeat containing 6B isoform 1 997 gene silencing by RNA|regulation of translation cytoplasmic mRNA processing body nucleotide binding|RNA binding 0 CAAGACGGCTGGGGGGAGAGT 0.483 0.54 16 19 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OVKATE_OVARY NA OVKATE_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 59 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - OVKATE_OVARY NA OVKATE_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.19 413 96 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes OVKATE_OVARY NA OVKATE_OVARY NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.41 10 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 OVKATE_OVARY NA OVKATE_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.24 26 8 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A OVKATE_OVARY NA OVKATE_OVARY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.14 61 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OVKATE_OVARY NA OVKATE_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 131 173 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 OVKATE_OVARY NA OVKATE_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.30 56 24 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 OVKATE_OVARY NA OVKATE_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.35 247 135 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes OVKATE_OVARY NA OVKATE_OVARY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.50 9 9 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes OVKATE_OVARY NA OVKATE_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 5 30 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 OVKATE_OVARY NA OVKATE_OVARY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.30 19 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OVKATE_OVARY NA OVKATE_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 54 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 OVKATE_OVARY NA OVKATE_OVARY NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.51 28 29 CHD8 57680 broad.mit.edu 37 14 21853994 21853995 + In_Frame_Ins INS - TGGTGATGG TGGTGATGG OVKATE_OVARY NA OVKATE_OVARY NA g.chr14:21853994_21853995insTGGTGATGG uc001was.1 - 38 6780_6781 c.6686_6687insCCATCACCA c.(6685-6687)CAT>CACCATCACCAT p.2229_2229H>HHHH CHD8_uc001war.1_In_Frame_Ins_p.2125_2125H>HHHH|SUPT16H_uc001wao.2_5'Flank|SUPT16H_uc001wap.2_5'Flank|SUPT16H_uc001waq.1_5'Flank NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 2508 His-rich. ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) TCAAGCCTGGAtggtgatggtg 0.391 0.18 171 38 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 OVKATE_OVARY NA OVKATE_OVARY NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.35 39 21 BCL11B 64919 broad.mit.edu 37 14 99641272 99641272 + Frame_Shift_Del DEL C - - OVKATE_OVARY NA OVKATE_OVARY NA g.chr14:99641272delC uc001yga.2 - 4 2168 c.1901delG c.(1900-1902)GGCfs p.G634fs BCL11B_uc001ygb.2_Frame_Shift_Del_p.G563fs NM_138576 NP_612808 Q9C0K0 BC11B_HUMAN B-cell CLL/lymphoma 11B isoform 1 634 Gly-rich. nucleus zinc ion binding central_nervous_system(8)|large_intestine(1)|lung(1) 10 Melanoma(154;0.0866)|all_epithelial(191;0.241) COAD - Colon adenocarcinoma(157;0.103) 0.000 0.13 62 9 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes OVKATE_OVARY NA OVKATE_OVARY NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.16 81 15 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C OVKATE_OVARY NA OVKATE_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 5 45 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 OVKATE_OVARY NA OVKATE_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 48 198 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OVKATE_OVARY NA OVKATE_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 93 620 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OVKATE_OVARY NA OVKATE_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 79 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OVMANA_OVARY NA OVMANA_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 27 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - OVMANA_OVARY NA OVMANA_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 295 83 CCNA2 890 broad.mit.edu 37 4 122743803 122743804 + Splice_Site INS - A A OVMANA_OVARY NA OVMANA_OVARY NA g.chr4:122743803_122743804insA uc003iec.3 - 2 519 c.214_splice c.e2-1 p.V72_splice NM_001237 NP_001228 P20248 CCNA2_HUMAN cyclin A cell division|mitosis|mitotic cell cycle G2/M transition DNA damage checkpoint|Ras protein signal transduction|regulation of cyclin-dependent protein kinase activity cytoplasm|nucleoplasm protein kinase binding ovary(1) 1 GGGTGCAACCTAAAAAAAAATT 0.406 0.25 85 28 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OVMANA_OVARY NA OVMANA_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 53 67 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - OVMANA_OVARY NA OVMANA_OVARY NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.91 1 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 OVMANA_OVARY NA OVMANA_OVARY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.50 9 9 PREX2 80243 broad.mit.edu 37 8 68942743 68942744 + Frame_Shift_Ins INS - CGGAC CGGAC OVMANA_OVARY NA OVMANA_OVARY NA g.chr8:68942743_68942744insCGGAC uc003xxv.1 + 6 582_583 c.555_556insCGGAC c.(553-558)AAGCGGfs p.K185fs PREX2_uc003xxu.1_Frame_Shift_Ins_p.K185fs|PREX2_uc011lez.1_Frame_Shift_Ins_p.K120fs NM_024870 NP_079146 Q70Z35 PREX2_HUMAN DEP domain containing 2 isoform a 185_186 DH. G-protein coupled receptor protein signaling pathway|intracellular signal transduction intracellular protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1) 17 AGTTGCTGAAGCGGACTCCACG 0.460 0.44 14 11 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 OVMANA_OVARY NA OVMANA_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 20 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency OVMANA_OVARY NA OVMANA_OVARY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.55 248 306 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OVMANA_OVARY NA OVMANA_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 284 107 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes OVMANA_OVARY NA OVMANA_OVARY NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.16 58 11 CDK12 51755 broad.mit.edu 37 17 37618866 37618868 + In_Frame_Del DEL AGG - - OVMANA_OVARY NA OVMANA_OVARY NA g.chr17:37618866_37618868delAGG uc010cvv.2 + 1 1128_1130 c.542_544delAGG c.(541-546)AAGGAG>AAG p.E182del CDK12_uc010wef.1_In_Frame_Del_p.E182del|CDK12_uc002hrw.3_In_Frame_Del_p.E182del NM_016507 NP_057591 Q9NYV4 CDK12_HUMAN Cdc2-related kinase, arginine/serine-rich 182 mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1) 19 AAGCTCCACAAGGAGAAGACCAG 0.493 0.23 27 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 OVMANA_OVARY NA OVMANA_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.50 28 28 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 OVMANA_OVARY NA OVMANA_OVARY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.13 104 16 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OVMANA_OVARY NA OVMANA_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 167 391 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OVMANA_OVARY NA OVMANA_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 4 40 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 OVTOKO_OVARY NA OVTOKO_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 65 SPEN 23013 broad.mit.edu 37 1 16259828 16259828 + Frame_Shift_Del DEL G - - OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr1:16259828delG uc001axk.1 + 11 7297 c.7093delG c.(7093-7095)GAGfs p.E2365fs SPEN_uc010obp.1_Frame_Shift_Del_p.E2324fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2365 RID.|Interaction with MSX2 (By similarity). interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) AGCTCAAGGTGAGAGTCCTGC 0.537 0.33 109 53 ARID1A 8289 broad.mit.edu 37 1 27107013 27107013 + Frame_Shift_Del DEL C - - OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr1:27107013delC uc001bmv.1 + 20 6997 c.6624delC c.(6622-6624)TTCfs p.F2208fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.F1991fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.F1054fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.F536fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.F450fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 2208 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CCACACAGTTCCAGCAGAGCC 0.637 0.29 93 38 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.46 158 133 CAD 790 broad.mit.edu 37 2 27461412 27461414 + In_Frame_Del DEL GGA - - OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr2:27461412_27461414delGGA uc002rji.2 + 31 5136_5138 c.4974_4976delGGA c.(4972-4977)GGGGAG>GGG p.E1659del CAD_uc010eyw.2_In_Frame_Del_p.E1596del NM_004341 NP_004332 P27708 PYR1_HUMAN carbamoylphosphate synthetase 2/aspartate 1659 DHOase (dihydroorotase). 'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process cytosol|neuronal cell body|nuclear matrix|terminal button aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1) 10 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) L-Aspartic Acid(DB00128)|L-Glutamine(DB00130) CTGGGAAGGGGGAGGTCCGGCCT 0.626 0.44 145 112 CCNA2 890 broad.mit.edu 37 4 122743803 122743804 + Splice_Site INS - A A OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr4:122743803_122743804insA uc003iec.3 - 2 519 c.214_splice c.e2-1 p.V72_splice NM_001237 NP_001228 P20248 CCNA2_HUMAN cyclin A cell division|mitosis|mitotic cell cycle G2/M transition DNA damage checkpoint|Ras protein signal transduction|regulation of cyclin-dependent protein kinase activity cytoplasm|nucleoplasm protein kinase binding ovary(1) 1 GGGTGCAACCTAAAAAAAAATT 0.406 0.48 62 58 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 112 143 PIK3R1 5295 broad.mit.edu 37 5 67589593 67589594 + In_Frame_Ins INS - AAC AAC OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr5:67589593_67589594insAAC uc003jva.2 + 11 1916_1917 c.1356_1357insAAC c.(1354-1359)insAAC p.453_454insN PIK3R1_uc003jvb.2_In_Frame_Ins_p.453_454insN|PIK3R1_uc003jvc.2_In_Frame_Ins_p.153_154insN|PIK3R1_uc003jvd.2_In_Frame_Ins_p.183_184insN|PIK3R1_uc003jve.2_In_Frame_Ins_p.132_133insN|PIK3R1_uc011crb.1_In_Frame_Ins_p.123_124insN NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 453_454 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.N453_T454insN(2)|p.D434_Q475del(2)|p.E451_Y452del(1)|p.?(1)|p.Y452_Q455>SGGSRIK(1) endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) 0.000 0.95 7 123 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.50 137 135 ARID1B 57492 broad.mit.edu 37 6 157099402 157099403 + In_Frame_Ins INS - CAG CAG OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr6:157099402_157099403insCAG uc003qqn.2 + 1 317_318 c.165_166insCAG c.(163-168)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) TAAACCAGTTCcagcagcagca 0.124 0.14 77 13 DLL1 28514 broad.mit.edu 37 6 170592478 170592478 + Frame_Shift_Del DEL T - - OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr6:170592478delT uc003qxm.2 - 9 2359 c.1889delA c.(1888-1890)AATfs p.N630fs NM_005618 NP_005609 O00548 DLL1_HUMAN delta-like 1 precursor 630 Cytoplasmic (Potential). cell communication|cell fate determination|hemopoiesis|Notch receptor processing|Notch signaling pathway|regulation of cell adhesion extracellular region|integral to plasma membrane calcium ion binding|Notch binding lung(4)|ovary(1) 5 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584) CTTGAAGCCATTCTTGTCGGC 0.607 0.63 46 77 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.42 7 5 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 662 70 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.55 10 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 408 160 ATN1 1822 broad.mit.edu 37 12 7045892 7045903 + In_Frame_Del DEL CAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448 byFrequency;byFrequency;by1000genomes;byFrequency OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr12:7045892_7045903delCAGCAGCAGCAG uc001qrw.1 + 5 1699_1710 c.1462_1473delCAGCAGCAGCAG c.(1462-1473)CAGCAGCAGCAGdel p.QQQQ496del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQ496del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 496_499 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagc 0.467 0.16 90 17 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.50 64 63 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.79 3 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.52 75 82 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.10 85 9 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.96 22 534 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 OVTOKO_OVARY NA OVTOKO_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 6 127 FIGF 2277 broad.mit.edu 37 X 15365364 15365364 + Frame_Shift_Del DEL T - - P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:15365364delT uc004cwt.1 - 6 1369 c.860delA c.(859-861)AACfs p.N287fs NM_004469 NP_004460 O43915 VEGFD_HUMAN vascular endothelial growth factor D 287 4 X 16 AA repeats of C-X(10)-C-X-C- X(1,3)-C.|3. angiogenesis|cell differentiation|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of mast cell chemotaxis|vascular endothelial growth factor receptor signaling pathway extracellular space|membrane|platelet alpha granule lumen chemoattractant activity|growth factor activity|platelet-derived growth factor receptor binding ovary(1)|breast(1)|central_nervous_system(1) 3 Hepatocellular(33;0.183) GCAACTGCAGTTTTTGGGGTG 0.483 0.94 8 132 ATRX 546 broad.mit.edu 37 X 76855019 76855019 + Frame_Shift_Del DEL T - - P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:76855019delT uc004ecp.3 - 25 6049 c.5817delA c.(5815-5817)AAAfs p.K1939fs ATRX_uc004ecq.3_Frame_Shift_Del_p.K1901fs|ATRX_uc004eco.3_Frame_Shift_Del_p.K1724fs NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 1939 Poly-Lys. DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) AGCTACTATCTTTTTTCCCCT 0.323 0.92 10 108 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 35 ARID1A 8289 broad.mit.edu 37 1 27101259 27101259 + Frame_Shift_Del DEL C - - P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:27101259delC uc001bmv.1 + 18 4914 c.4541delC c.(4540-4542)ACGfs p.T1514fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.T1513fs|ARID1A_uc001bmu.1_Intron|ARID1A_uc001bmw.1_Frame_Shift_Del_p.T1131fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.T360fs|ARID1A_uc009vsm.1_Intron|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1514 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) AGGCAGAGCACGGGCTCTGCC 0.592 0.48 137 129 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.45 195 160 ITGA10 8515 broad.mit.edu 37 1 145537734 145537735 + Splice_Site INS - AG AG P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:145537734_145537735insAG uc001eoa.2 + 21 2651 c.2575_splice c.e21-2 p.R859_splice NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Splice_Site_p.R728_splice|ITGA10_uc009wiw.2_Splice_Site_p.R716_splice|ITGA10_uc010oyw.1_Splice_Site_p.R804_splice NM_003637 NP_003628 O75578 ITA10_HUMAN integrin, alpha 10 precursor cell-matrix adhesion|integrin-mediated signaling pathway integrin complex collagen binding|receptor activity lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1) 8 all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786) CCCCTGCCCTCAGAGAGAGAGC 0.579 0.37 95 55 ATIC 471 broad.mit.edu 37 2 216197144 216197145 + Frame_Shift_Ins INS - T T P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:216197144_216197145insT uc002vex.3 + 8 902_903 c.728_729insT c.(727-729)GCTfs p.A243fs ATIC_uc010zjo.1_Frame_Shift_Ins_p.A184fs|ATIC_uc002vey.3_Frame_Shift_Ins_p.A242fs NM_004044 NP_004035 P31939 PUR9_HUMAN 5-aminoimidazole-4-carboxamide ribonucleotide 243 IMP biosynthetic process|purine base metabolic process cytosol IMP cyclohydrolase activity|phosphoribosylaminoimidazolecarboxamide formyltransferase activity|protein homodimerization activity ATIC/ALK(24) haematopoietic_and_lymphoid_tissue(22)|ovary(2)|lung(2)|soft_tissue(2)|skin(1) 29 Renal(323;0.229) Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097) Tetrahydrofolic acid(DB00116) TTGTGCGATGCTTTGAACGCCT 0.450 0.47 26 23 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.22 98 27 ALPK1 80216 broad.mit.edu 37 4 113360940 113360941 + Frame_Shift_Del DEL AG - - P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:113360940_113360941delAG uc003iap.3 + 14 3729_3730 c.3450_3451delAG c.(3448-3453)ACAGAAfs p.T1150fs ALPK1_uc003ian.3_Frame_Shift_Del_p.T1150fs|ALPK1_uc011cfx.1_Frame_Shift_Del_p.T1072fs|ALPK1_uc003iao.3_RNA|ALPK1_uc010imo.2_Frame_Shift_Del_p.T978fs NM_025144 NP_079420 Q96QP1 ALPK1_HUMAN alpha-kinase 1 1150_1151 Alpha-type protein kinase. ATP binding|protein serine/threonine kinase activity ovary(5) 5 Ovarian(17;0.0446)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.00325) TGGTGAAAACAGAATACAAAGC 0.366 0.53 9 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 49 68 CDC25C 995 broad.mit.edu 37 5 137627689 137627690 + Frame_Shift_Ins INS - T T P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:137627689_137627690insT uc003lcp.1 - 8 1002_1003 c.731_732insA c.(730-732)AAGfs p.K244fs CDC25C_uc003lcq.1_Frame_Shift_Ins_p.K171fs|CDC25C_uc003lcr.1_Frame_Shift_Ins_p.K244fs|CDC25C_uc011cyp.1_Frame_Shift_Ins_p.K261fs|CDC25C_uc003lcs.1_Frame_Shift_Ins_p.K322fs NM_001790 NP_001781 P30307 MPIP3_HUMAN cell division cycle 25C isoform a 244 cell cycle checkpoint|cell division|cell proliferation|DNA replication|G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis|traversing start control point of mitotic cell cycle cytosol|nucleoplasm protein tyrosine phosphatase activity|WW domain binding lung(3) 3 KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592) CAGAAAAATACTTTTTTTTAAC 0.386 0.16 218 41 LRGUK 136332 broad.mit.edu 37 7 133812358 133812359 + In_Frame_Ins INS - AGGGCG AGGGCG P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:133812358_133812359insAGGGCG uc003vrm.1 + 1 254_255 c.238_239insAGGGCG c.(238-240)CAG>CAGGGCGAG p.84_85insGE NM_144648 NP_653249 Q96M69 LRGUK_HUMAN leucine-rich repeats and guanylate kinase domain 84_85 ATP binding|kinase activity lung(2)|skin(2)|kidney(1) 5 AGATGAGGACCAGGGCGAGGGC 0.619 0.23 251 73 EZH2 2146 broad.mit.edu 37 7 148504789 148504790 + Frame_Shift_Ins INS - T T P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:148504789_148504790insT uc003wfd.1 - 20 2355_2356 c.2189_2190insA c.(2188-2190)CAGfs p.Q730fs EZH2_uc011kug.1_Frame_Shift_Ins_p.Q679fs|EZH2_uc003wfb.1_Frame_Shift_Ins_p.Q735fs|EZH2_uc003wfc.1_Frame_Shift_Ins_p.Q691fs|EZH2_uc011kuh.1_Frame_Shift_Ins_p.Q721fs NM_004456 NP_004447 Q15910 EZH2_HUMAN enhancer of zeste 2 isoform a 730 SET. negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent ESC/E(Z) complex DNA binding|histone-lysine N-methyltransferase activity|protein binding p.D730fs*1(2) haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1) 183 Melanoma(164;0.15) OV - Ovarian serous cystadenocarcinoma(82;0.00239) 0.000 0.93 48 673 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 1 14 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.33 609 296 PTEN 5728 broad.mit.edu 37 10 89717671 89717672 + Frame_Shift_Ins INS - G G rs121909219 P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:89717671_89717672insG uc001kfb.2 + 8 1727_1728 c.696_697insG c.(694-699)ACACGAfs p.T232fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 232_233 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R233*(57)|p.R55fs*1(4)|p.R233fs*10(3)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)|p.R233fs*12(1)|p.R233fs*20(1)|p.R233fs*25(1)|p.R233fs*23(1)|p.R233R(1)|p.G165_K342del(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) CAGGACCCACACGACGGGAAGA 0.421 0.42 144 105 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 398 197 MLL 4297 broad.mit.edu 37 11 118339529 118339530 + Frame_Shift_Ins INS - TTCC TTCC P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:118339529_118339530insTTCC uc001pta.2 + 2 495_496 c.472_473insTTCC c.(472-474)AGAfs p.R158fs MLL_uc001ptb.2_Frame_Shift_Ins_p.R158fs|MLL_uc001psz.1_Frame_Shift_Ins_p.R191fs|MLL_uc001ptd.1_5'UTR NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 158 apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) TGAAGAAGTCAGAGTGCGAAGT 0.411 0.40 113 74 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.16 53 10 CREBBP 1387 broad.mit.edu 37 16 3807363 3807364 + Frame_Shift_Ins INS - G G P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:3807363_3807364insG uc002cvv.2 - 19 3827_3828 c.3623_3624insC c.(3622-3624)CCAfs p.P1208fs CREBBP_uc002cvw.2_Frame_Shift_Ins_p.P1170fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1208 Cys/His-rich. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) ACAAAGTCTGTGGGGAAAACTC 0.386 0.38 10 6 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 10 143 MYH8 4626 broad.mit.edu 37 17 10314206 10314206 + Frame_Shift_Del DEL A - - P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:10314206delA uc002gmm.2 - 15 1570 c.1475delT c.(1474-1476)TTCfs p.F492fs uc002gml.1_Intron NM_002472 NP_002463 P13535 MYH8_HUMAN myosin, heavy chain 8, skeletal muscle, 492 Myosin head-like. muscle filament sliding cytosol|muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle skin(6)|ovary(3)|breast(2) 11 GTGGTGGTTGAAAAACTGTTG 0.443 0.47 64 56 RPTOR 57521 broad.mit.edu 37 17 78704393 78704400 + Frame_Shift_Del DEL GACCTGCA - - P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:78704393_78704400delGACCTGCA uc002jyt.1 + 5 1346_1353 c.541_548delGACCTGCA c.(541-549)GACCTGCAGfs p.D181fs RPTOR_uc002jys.2_Frame_Shift_Del_p.D181fs|RPTOR_uc010wuf.1_Translation_Start_Site|RPTOR_uc010wug.1_Frame_Shift_Del_p.D181fs NM_020761 NP_065812 Q8N122 RPTOR_HUMAN raptor isoform 1 181_183 cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade cytosol|lysosome|TORC1 complex protein complex binding lung(4)|urinary_tract(1)|ovary(1) 6 GTCCATATATGACCTGCAGACGTGGATG 0.529 0.29 98 41 FASN 2194 broad.mit.edu 37 17 80041166 80041167 + Frame_Shift_Ins INS - G G P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:80041166_80041167insG uc002kdu.2 - 32 5593_5594 c.5476_5477insC c.(5476-5478)CTCfs p.L1826fs FASN_uc002kdv.1_5'Flank NM_004104 NP_004095 P49327 FAS_HUMAN fatty acid synthase 1826 Enoyl reductase (By similarity). energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process cytosol|Golgi apparatus|melanosome|plasma membrane 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding central_nervous_system(1) 1 all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246) OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237) Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339) CGTGCACTTGAGGGGCCGTACC 0.644 0.43 90 69 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.52 65 71 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 102 505 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 9 81 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 3 37 MERTK 10461 broad.mit.edu 37 2 112722854 112722854 + Frame_Shift_Del DEL G - - rs7588635 byFrequency;by1000genomes P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:112722854delG uc002thk.1 + 5 966 c.844delG c.(844-846)GCAfs p.A282fs MERTK_uc002thl.1_Frame_Shift_Del_p.A106fs NM_006343 NP_006334 Q12866 MERTK_HUMAN MER receptor tyrosine kinase precursor 282 Extracellular (Potential). cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration integral to plasma membrane|soluble fraction ATP binding|transmembrane receptor protein tyrosine kinase activity lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1) 9 0.000 0.45 192 159 CXCR4 7852 broad.mit.edu 37 2 136872618 136872619 + In_Frame_Ins INS - GAA GAA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:136872618_136872619insGAA uc002tuz.2 - 2 974_975 c.879_880insTTC c.(877-882)insTTC p.293_294insF CXCR4_uc002tuy.2_In_Frame_Ins_p.297_298insF|CXCR4_uc010fnk.2_In_Frame_Ins_p.278_279insF NM_003467 NP_003458 P61073 CXCR4_HUMAN chemokine (C-X-C motif) receptor 4 isoform b 293_294 Helical; Name=7. activation of MAPK activity|apoptosis|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|inflammatory response|initiation of viral infection|regulation of chemotaxis|response to hypoxia|response to virus cell leading edge|cell surface|cytoplasmic membrane-bounded vesicle|integral to membrane|plasma membrane actin binding|C-X-C chemokine receptor activity|coreceptor activity|myosin light chain binding|ubiquitin binding|ubiquitin protein ligase binding upper_aerodigestive_tract(1)|large_intestine(1)|lung(1) 3 BRCA - Breast invasive adenocarcinoma(221;0.155) Framycetin(DB00452) AGACAACAGTGGAAGAAAGCTA 0.510 0.36 664 379 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.22 89 25 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.34 51 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.23 150 46 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.35 48 26 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.25 494 169 SMARCA2 6595 broad.mit.edu 37 9 2039806 2039807 + In_Frame_Ins INS - CAA CAA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039806_2039807insCAA uc003zhc.2 + 4 795_796 c.696_697insCAA c.(694-699)insCAA p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.13 448 66 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 251 90 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.39 17 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.78 11 39 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.36 71 40 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 61 248 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 5 57 ZNRF3 84133 broad.mit.edu 37 22 29445524 29445526 + In_Frame_Del DEL GTG - - P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:29445524_29445526delGTG uc003aeg.2 + 8 1220_1222 c.1055_1057delGTG c.(1054-1059)AGTGGC>AGC p.G353del ZNRF3_uc003aeh.1_In_Frame_Del_p.G353del NM_032173 NP_115549 Q9ULT6 ZNRF3_HUMAN zinc and ring finger 3 453 Cytoplasmic (Potential). integral to membrane zinc ion binding ovary(1) 1 0.000 0.36 337 193 Unknown 0 broad.mit.edu 37 X 80185321 80185321 + Frame_Shift_Del DEL A - - PANC0213_PANCREAS NA PANC0213_PANCREAS NA g.chrX:80185321delA uc004eec.1 + 1 394 c.220delA c.(220-222)AAAfs p.K74fs SubName: Full=cDNA FLJ16670 fis, clone THYMU3001133, highly similar to Voltage-dependent anion-selective channel protein 1; SubName: Full=Voltage-dependent anion channel 1, isoform CRA_a; TAACACTGGGAAAAAAAATGC 0.483 0.35 121 66 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PANC0213_PANCREAS NA PANC0213_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 80 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PANC0213_PANCREAS NA PANC0213_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 41 55 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PANC0213_PANCREAS NA PANC0213_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.60 17 26 BLK 640 broad.mit.edu 37 8 11412347 11412348 + Frame_Shift_Ins INS - C C PANC0213_PANCREAS NA PANC0213_PANCREAS NA g.chr8:11412347_11412348insC uc003wty.2 + 7 1149_1150 c.568_569insC c.(568-570)TCCfs p.S190fs BLK_uc003wtz.2_Frame_Shift_Ins_p.S119fs NM_001715 NP_001706 P51451 BLK_HUMAN B lymphoid tyrosine kinase 190 SH2. intracellular protein kinase cascade|positive regulation of insulin secretion ATP binding|non-membrane spanning protein tyrosine kinase activity large_intestine(1)|stomach(1)|ovary(1) 3 STAD - Stomach adenocarcinoma(15;0.00391) COAD - Colon adenocarcinoma(149;0.207) CTACTACATCTCCCCCCGGATC 0.604 0.34 84 44 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 PANC0213_PANCREAS NA PANC0213_PANCREAS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.37 38 22 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PANC0213_PANCREAS NA PANC0213_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PANC0213_PANCREAS NA PANC0213_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 186 58 IRS2 8660 broad.mit.edu 37 13 110436296 110436297 + In_Frame_Ins INS - CGG CGG rs34412495 PANC0213_PANCREAS NA PANC0213_PANCREAS NA g.chr13:110436296_110436297insCGG uc001vqv.2 - 1 2618_2619 c.2104_2105insCCG c.(2104-2106)GTG>GCCGTG p.701_702insA NM_003749 NP_003740 Q9Y4H2 IRS2_HUMAN insulin receptor substrate 2 701_702 fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus cytosol|plasma membrane insulin receptor binding|signal transducer activity large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|skin(1)|ovary(1)|kidney(1) 8 all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155) Breast(118;0.159) all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147) 0.000 0.40 505 330 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PANC0213_PANCREAS NA PANC0213_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 6 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PANC0213_PANCREAS NA PANC0213_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 21 173 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PANC0213_PANCREAS NA PANC0213_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 37 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 5 132 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.16 1310 255 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 288 60 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.27 143 53 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 215 362 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 77 157 ZNF323 64288 broad.mit.edu 37 6 28294200 28294201 + Frame_Shift_Ins INS - T T PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr6:28294200_28294201insT uc003nla.2 - 4 1363_1364 c.963_964insA c.(961-966)AAACCAfs p.K321fs ZNF323_uc003nld.2_Frame_Shift_Ins_p.K321fs|ZNF323_uc010jra.2_Frame_Shift_Ins_p.K321fs|ZNF323_uc003nlb.2_Frame_Shift_Ins_p.K162fs|ZNF323_uc010jrb.2_Frame_Shift_Ins_p.K162fs|ZNF323_uc003nlc.2_Frame_Shift_Ins_p.K321fs NM_001135216 NP_001128688 Q96LW9 ZN323_HUMAN zinc finger protein 323 321_322 viral reproduction nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1)|skin(1) 2 CATTCATATGGTTTTTCCCCTG 0.500 0.33 32 16 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.87 2 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 4 49 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 604 65 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 620 229 CNTN5 53942 broad.mit.edu 37 11 99715627 99715629 + In_Frame_Del DEL TAT - - PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr11:99715627_99715629delTAT uc001pga.2 + 5 660_662 c.321_323delTAT c.(319-324)GATATT>GAT p.I109del CNTN5_uc009ywv.1_In_Frame_Del_p.I109del|CNTN5_uc001pfz.2_In_Frame_Del_p.I109del|CNTN5_uc001pgb.2_In_Frame_Del_p.I35del NM_014361 NP_055176 O94779 CNTN5_HUMAN contactin 5 isoform long 109 Ig-like C2-type 1. cell adhesion anchored to membrane|plasma membrane protein binding skin(3)|ovary(2)|pancreas(2)|breast(1) 8 all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219) BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196) AACCAGATGATATTATTTTTCCA 0.355 0.41 565 399 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.51 19 20 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 26 329 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 57 151 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 152 489 BID 637 broad.mit.edu 37 22 18222255 18222256 + Splice_Site INS - T T PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr22:18222255_18222256insT uc002znd.1 - 4 394 c.224_splice c.e4-1 p.D75_splice BID_uc002znc.1_Splice_Site_p.D121_splice|BID_uc002zne.1_Splice_Site|BID_uc010gra.1_Splice_Site|BID_uc002znf.1_Splice_Site|BID_uc010grb.1_Splice_Site_p.D75_splice|BID_uc010grc.1_Splice_Site NM_001196 NP_001187 P55957 BID_HUMAN BH3 interacting domain death agonist isoform 2 activation of pro-apoptotic gene products|establishment of protein localization in membrane|induction of apoptosis by intracellular signals|induction of apoptosis via death domain receptors|neuron apoptosis|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria|release of cytochrome c from mitochondria cytosol|membrane fraction|mitochondrial outer membrane death receptor binding 0 all_epithelial(15;0.198) Lung(27;0.0419) CTTTCAGAATCTGTGTTCAGGC 0.599 0.38 241 147 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PANC0327_PANCREAS NA PANC0327_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 35 625 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 3 66 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.22 112 31 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 156 212 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 13 35 APC 324 broad.mit.edu 37 5 112175951 112175952 + Frame_Shift_Ins INS - A A PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr5:112175951_112175952insA uc010jby.2 + 16 5040_5041 c.4660_4661insA c.(4660-4662)GAAfs p.E1554fs APC_uc011cvt.1_Frame_Shift_Ins_p.E1536fs|APC_uc003kpz.3_Frame_Shift_Ins_p.E1554fs|APC_uc003kpy.3_Frame_Shift_Ins_p.E1554fs|APC_uc010jbz.2_Frame_Shift_Ins_p.E1271fs|APC_uc010jca.2_Frame_Shift_Ins_p.E854fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1554 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.T1556fs*3(35)|p.E1554fs*5(2)|p.E1554*(2)|p.?(1)|p.T1556fs*9(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1554fs*11(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GAAAGAGGCAGAAAAAACTATT 0.342 0.82 2 9 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.14 65 11 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 2 12 MLL3 58508 broad.mit.edu 37 7 151962192 151962193 + Frame_Shift_Del DEL TC - - PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr7:151962192_151962193delTC uc003wla.2 - 8 1333_1334 c.1114_1115delGA c.(1114-1116)GATfs p.D372fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 372 PHD-type 1.|RING-type. intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) AACCGCTATATCCAGGCACATT 0.450 0.11 649 83 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.45 6 5 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 51 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.23 48 14 CDKN2A 1029 broad.mit.edu 37 9 21974695 21974696 + Frame_Shift_Ins INS - T T PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr9:21974695_21974696insT uc003zpk.2 - 1 343_344 c.131_132insA c.(130-132)TACfs p.Y44fs MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_Frame_Shift_Ins_p.Y44fs|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Intron NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 44 ANK 2. cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.?(25)|p.Y44*(3)|p.Y44fs*1(1)|p.Y44fs*76(1)|p.V28_V51del(1)|p.G45del(1)|p.Y44S(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) GCCTCCGACCGTAACTATTCGG 0.683 0.92 10 118 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 898 369 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 7 57 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.26 26 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.78 27 93 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 32 264 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PANC0403_PANCREAS NA PANC0403_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 12 134 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 4 91 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.46 36 31 HTT 3064 broad.mit.edu 37 4 3076604 3076606 + In_Frame_Del DEL CAG - - rs10618869 PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr4:3076604_3076606delCAG uc011bvq.1 + 2 203_205 c.58_60delCAG c.(58-60)CAGdel p.Q40del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagc 0.335 0.16 58 11 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.54 18 21 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.68 108 232 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 40 86 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.65 6 11 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 19 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.76 6 19 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.33 70 34 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 30 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.11 133 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.48 525 490 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 45 450 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.42 94 68 NCOA3 8202 broad.mit.edu 37 20 46279860 46279861 + In_Frame_Ins INS - CAA CAA rs151060280 byFrequency PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr20:46279860_46279861insCAA uc002xtk.2 + 20 3991_3992 c.3786_3787insCAA c.(3784-3789)insCAA p.1276_1277insQ NCOA3_uc010ght.1_In_Frame_Ins_p.1267_1268insQ|NCOA3_uc002xtl.2_In_Frame_Ins_p.1272_1273insQ|NCOA3_uc002xtm.2_In_Frame_Ins_p.1271_1272insQ|NCOA3_uc002xtn.2_In_Frame_Ins_p.1275_1276insQ|NCOA3_uc010zyc.1_In_Frame_Ins_p.1071_1072insQ NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 1276_1277 Poly-Gln.|Acetyltransferase. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 agcagcagcagcagcaacagca 0.307 0.22 386 112 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 124 662 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PANC0504_PANCREAS NA PANC0504_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 92 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 3 38 TPO 7173 broad.mit.edu 37 2 1507747 1507748 + Frame_Shift_Ins INS - C C PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr2:1507747_1507748insC uc002qww.2 + 14 2505_2506 c.2414_2415insC c.(2413-2415)CACfs p.H805fs TPO_uc010ewj.2_RNA|TPO_uc002qwu.2_Frame_Shift_Ins_p.H748fs|TPO_uc002qwr.2_Frame_Shift_Ins_p.H805fs|TPO_uc002qwx.2_Frame_Shift_Ins_p.H748fs|TPO_uc010yio.1_Frame_Shift_Ins_p.H632fs|TPO_uc010yip.1_Intron|TPO_uc002qwy.1_Intron|TPO_uc002qwz.2_Intron NM_000547 NP_000538 P07202 PERT_HUMAN thyroid peroxidase isoform a 805 Extracellular (Potential).|EGF-like; calcium-binding (Potential). cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process cell surface|cytoplasm|integral to plasma membrane calcium ion binding|heme binding|iodide peroxidase activity p.H805L(1) ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1) 20 all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627) all_cancers(51;0.0338) all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12) Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550) 0.000 0.21 797 211 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.47 18 16 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.23 113 33 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 59 91 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.80 12 47 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.74 43 120 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.34 19 10 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.16 649 120 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 1 14 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.36 7 4 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 648 352 NCAM1 4684 broad.mit.edu 37 11 113078630 113078631 + Frame_Shift_Ins INS - A A PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr11:113078630_113078631insA uc009yyq.1 + 7 1162_1163 c.468_469insA c.(466-471)ATCAAAfs p.I156fs NCAM1_uc001pno.2_Frame_Shift_Ins_p.I156fs NM_001076682 NP_001070150 P13591 NCAM1_HUMAN neural cell adhesion molecule 1 isoform 3 274_275 Ig-like C2-type 3.|Extracellular (Potential). axon guidance|interferon-gamma-mediated signaling pathway anchored to membrane|extracellular region|Golgi membrane|integral to membrane ovary(1) 1 all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207) BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212) AGCTGACCATCAAAAAGGTGGA 0.490 0.22 223 62 DRD2 1813 broad.mit.edu 37 11 113286271 113286273 + In_Frame_Del DEL AGA - - PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr11:113286271_113286273delAGA uc001pnz.2 - 4 914_916 c.593_595delTCT c.(592-597)TTCTAC>TAC p.F198del DRD2_uc010rwv.1_In_Frame_Del_p.F197del|DRD2_uc001poa.3_In_Frame_Del_p.F198del|DRD2_uc001pob.3_In_Frame_Del_p.F198del|DRD2_uc009yyr.1_In_Frame_Del_p.F198del NM_000795 NP_000786 P14416 DRD2_HUMAN dopamine receptor D2 isoform long 198 Helical; Name=5; (By similarity). activation of phospholipase C activity by dopamine receptor signaling pathway|adenohypophysis development|adult walking behavior|arachidonic acid secretion|axonogenesis|behavioral response to cocaine|behavioral response to ethanol|branching morphogenesis of a nerve|cerebral cortex GABAergic interneuron migration|circadian regulation of gene expression|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|intracellular protein kinase cascade|negative regulation of blood pressure|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of dopamine receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|negative regulation of synaptic transmission, glutamatergic|neurological system process involved in regulation of systemic arterial blood pressure|peristalsis|phosphatidylinositol metabolic process|positive regulation of dopamine uptake|positive regulation of growth hormone secretion|positive regulation of neuroblast proliferation|prepulse inhibition|protein localization|regulation of heart rate|regulation of long-term neuronal synaptic plasticity|regulation of potassium ion transport|regulation of sodium ion transport|regulation of synaptic transmission, GABAergic|release of sequestered calcium ion into cytosol|response to amphetamine|response to drug|response to histamine|response to morphine|sensory perception of smell|synapse assembly|temperature homeostasis|visual learning integral to plasma membrane dopamine D2 receptor activity|dopamine receptor activity, coupled via Gi/Go|drug binding|potassium channel regulator activity|protein binding p.F198del(1) pancreas(1)|skin(1) 2 all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494) BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216) Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Carphenazine(DB01038)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Domperidone(DB01184)|Droperidol(DB00450)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Mesoridazine(DB00933)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Sulpiride(DB00391)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Ziprasidone(DB00246)|Zuclopenthixol(DB01624) AAGGGCACGTAGAAGGAGACGAT 0.596 0.19 112 27 CASC5 57082 broad.mit.edu 37 15 40939249 40939250 + Frame_Shift_Ins INS - CT CT PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr15:40939249_40939250insCT uc010bbs.1 + 18 6310_6311 c.6149_6150insCT c.(6148-6150)AACfs p.N2050fs CASC5_uc010bbt.1_Frame_Shift_Ins_p.N2024fs NM_170589 NP_733468 Q8NG31 CASC5_HUMAN cancer susceptibility candidate 5 isoform 1 2050 Necessary for kinetochore localization and for interaction with NSL1 and DSN1.|Potential. acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm protein binding breast(3)|central_nervous_system(1)|skin(1) 5 all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946) GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211) AAGATCGATAACTGCCTCACTG 0.302 0.35 34 18 SGK269 79834 broad.mit.edu 37 15 77472047 77472049 + In_Frame_Del DEL GGC - - PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr15:77472047_77472049delGGC uc002bcm.2 - 3 2528_2530 c.2220_2222delGCC c.(2218-2223)GAGCCT>GAT p.740_741EP>D SGK269_uc002bcn.2_In_Frame_Del_p.740_741EP>D NM_024776 NP_079052 Q9H792 PEAK1_HUMAN NKF3 kinase family member 740_741 cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading actin cytoskeleton|cytoplasm|focal adhesion ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding 0 STAD - Stomach adenocarcinoma(199;0.124) TTTGGCCACAGGCTCTTGAGTGG 0.502 0.31 348 156 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 20 192 SMAD4 4089 broad.mit.edu 37 18 48575168 48575169 + Frame_Shift_Ins INS - A A PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr18:48575168_48575169insA uc010xdp.1 + 3 900_901 c.362_363insA c.(361-363)TTAfs p.L121fs SMAD4_uc010xdo.1_RNA NM_005359 NP_005350 Q13485 SMAD4_HUMAN mothers against decapentaplegic homolog 4 121 MH1. BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway activin responsive factor complex|centrosome|cytosol I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity p.0?(35)|p.?(4)|p.C123fs*2(2) pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1) 369 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155) GCGTTTGACTTAAAATGTGATA 0.381 0.88 7 52 COL18A1 80781 broad.mit.edu 37 21 46924426 46924443 + Splice_Site DEL GGCCCCCCAGGCCCCCCA - - rs28696990;rs11276732;rs56328291 PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr21:46924426_46924443delGGCCCCCCAGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.64 161 282 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PANC0813_PANCREAS NA PANC0813_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 9 113 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PANC1_PANCREAS NA PANC1_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 10 92 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.58 25 35 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 168 34 HTT 3064 broad.mit.edu 37 4 3076604 3076609 + In_Frame_Del DEL CAGCAG - - rs10618869 PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr4:3076604_3076609delCAGCAG uc011bvq.1 + 2 203_208 c.58_63delCAGCAG c.(58-63)CAGCAGdel p.QQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagc 0.330 0.24 45 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.75 62 184 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.83 22 105 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.33 8 4 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.48 24 22 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.17 287 58 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 1 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 28 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.49 743 718 HERC2P2 400322 broad.mit.edu 37 15 23316188 23316189 + Splice_Site INS - A A PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr15:23316188_23316189insA uc001yvr.2 - 17 2494 c.2294_splice c.e17-1 p.E765_splice HERC2P2_uc010ayf.1_Splice_Site|HERC2P2_uc001yvp.3_Splice_Site RecName: Full=Putative HERC2-like protein 3; 0 GTTCGGCTTCTAAAAAAAATAA 0.416 0.46 42 36 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 15 277 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.47 17 15 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.81 24 104 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 69 377 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PANC1_PANCREAS NA PANC1_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 86 ARID1A 8289 broad.mit.edu 37 1 27023768 27023769 + Frame_Shift_Ins INS - C C PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr1:27023768_27023769insC uc001bmv.1 + 1 1247_1248 c.874_875insC c.(874-876)ACCfs p.T292fs ARID1A_uc001bmt.1_Frame_Shift_Ins_p.T292fs|ARID1A_uc001bmu.1_Frame_Shift_Ins_p.T292fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 292 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.85 42 241 PBRM1 55193 broad.mit.edu 37 3 52584639 52584639 + Frame_Shift_Del DEL C - - PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr3:52584639delC uc003des.2 - 29 4707 c.4695delG c.(4693-4695)GGGfs p.G1565fs PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.G1458fs|PBRM1_uc003der.2_Frame_Shift_Del_p.G1478fs|PBRM1_uc003det.2_Frame_Shift_Del_p.G1473fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.G1528fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.G1510fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.G1485fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.G1458fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 1565 Pro-rich. chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding p.L1565fs*>19(1) kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.29 182 73 PBRM1 55193 broad.mit.edu 37 3 52584643 52584643 + Frame_Shift_Del DEL A - - PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr3:52584643delA uc003des.2 - 29 4703 c.4691delT c.(4690-4692)TTGfs p.L1564fs PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.L1457fs|PBRM1_uc003der.2_Frame_Shift_Del_p.L1477fs|PBRM1_uc003det.2_Frame_Shift_Del_p.L1472fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.L1527fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.L1509fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.L1484fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.L1457fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 1564 Pro-rich. chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.52 123 132 ATR 545 broad.mit.edu 37 3 142266583 142266585 + In_Frame_Del DEL ATG - - PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr3:142266583_142266585delATG uc003eux.3 - 16 3461_3463 c.3339_3341delCAT c.(3337-3342)ATCATA>ATA p.1113_1114II>I NM_001184 NP_001175 Q13535 ATR_HUMAN ataxia telangiectasia and Rad3 related protein 1113_1114 cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence PML body ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1) 20 TTCAGGTGATATGATATCTCTCG 0.345 0.50 91 91 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.43 62 46 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 14 23 NOTCH4 4855 broad.mit.edu 37 6 32191689 32191691 + In_Frame_Del DEL AGT - - rs66464940 PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr6:32191689_32191691delAGT uc003obb.2 - 1 154_156 c.15_17delACT c.(13-18)TCACTG>TCG p.L16del NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.L16del NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 cagcagcagcagTGAAGGGGGCT 0.537 0.70 3 7 EPHB6 2051 broad.mit.edu 37 7 142562052 142562054 + In_Frame_Del DEL CCT - - rs67146761;rs8177142 PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr7:142562052_142562054delCCT uc011kst.1 + 7 1281_1283 c.494_496delCCT c.(493-498)CCCTCC>CCC p.S176del EPHB6_uc011ksu.1_In_Frame_Del_p.S176del|EPHB6_uc003wbs.2_5'UTR|EPHB6_uc003wbt.2_Intron|EPHB6_uc003wbu.2_5'UTR|EPHB6_uc003wbv.2_5'Flank NM_004445 NP_004436 O15197 EPHB6_HUMAN ephrin receptor EphB6 precursor 176 Extracellular (Potential).|Poly-Ser. extracellular region|integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1) 19 Melanoma(164;0.059) GAGAGCTTTCcctcctcctcctc 0.522 0.35 117 64 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 3 40 PCDH15 65217 broad.mit.edu 37 10 55912990 55912990 + Frame_Shift_Del DEL C - - PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr10:55912990delC uc001jju.1 - 14 2049 c.1654delG c.(1654-1656)GCTfs p.A552fs PCDH15_uc010qhq.1_Frame_Shift_Del_p.A557fs|PCDH15_uc010qhr.1_Frame_Shift_Del_p.A552fs|PCDH15_uc010qhs.1_Frame_Shift_Del_p.A564fs|PCDH15_uc010qht.1_Frame_Shift_Del_p.A559fs|PCDH15_uc010qhu.1_Frame_Shift_Del_p.A552fs|PCDH15_uc001jjv.1_Frame_Shift_Del_p.A530fs|PCDH15_uc010qhv.1_Frame_Shift_Del_p.A552fs|PCDH15_uc010qhw.1_Frame_Shift_Del_p.A515fs|PCDH15_uc010qhx.1_Frame_Shift_Del_p.A552fs|PCDH15_uc010qhy.1_Frame_Shift_Del_p.A557fs|PCDH15_uc010qhz.1_Frame_Shift_Del_p.A552fs|PCDH15_uc010qia.1_Frame_Shift_Del_p.A530fs|PCDH15_uc010qib.1_Frame_Shift_Del_p.A530fs|PCDH15_uc001jjw.2_Frame_Shift_Del_p.A552fs NM_033056 NP_149045 Q96QU1 PCD15_HUMAN protocadherin 15 isoform CD1-4 precursor 552 Cadherin 5.|Extracellular (Potential). equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse calcium ion binding pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2) 13 Melanoma(3;0.117)|Lung SC(717;0.238) TCTCCCTGAGCCCCAACAAGG 0.493 0.25 104 34 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 417 137 STAT3 6774 broad.mit.edu 37 17 40498670 40498671 + Frame_Shift_Ins INS - A A PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr17:40498670_40498671insA uc002hzl.1 - 3 429_430 c.189_190insT c.(187-192)GAGATTfs p.E63fs STAT3_uc002hzk.1_Frame_Shift_Ins_p.E63fs|STAT3_uc002hzm.1_Frame_Shift_Ins_p.E63fs|STAT3_uc010wgh.1_5'UTR|STAT3_uc002hzn.1_Frame_Shift_Ins_p.E63fs NM_139276 NP_644805 P40763 STAT3_HUMAN signal transducer and activator of transcription 63_64 cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis cytosol|nucleus|plasma membrane calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding ovary(1)|lung(1)|breast(1)|central_nervous_system(1) 4 all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135) BRCA - Breast invasive adenocarcinoma(366;0.139) TGCTGGTCAATCTCTCCCAGGA 0.446 0.17 76 16 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.34 31 16 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 69 242 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PATU8902_PANCREAS NA PATU8902_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 78 FAM123B 139285 broad.mit.edu 37 X 63411800 63411800 + Frame_Shift_Del DEL G - - PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chrX:63411800delG uc004dvo.2 - 2 1640 c.1367delC c.(1366-1368)CCTfs p.P456fs NM_152424 NP_689637 Q5JTC6 F123B_HUMAN family with sequence similarity 123B 456 Wnt receptor signaling pathway cytoplasm|nucleus|plasma membrane p.0?(40) kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1) 112 GTCACTCTGAGGAGTCAAAAG 0.552 0.36 21 12 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 5 94 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.74 10 29 HTT 3064 broad.mit.edu 37 4 3076604 3076609 + In_Frame_Del DEL CAGCAG - - rs10618869 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr4:3076604_3076609delCAGCAG uc011bvq.1 + 2 203_208 c.58_63delCAGCAG c.(58-63)CAGCAGdel p.QQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagc 0.330 0.24 94 29 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.51 21 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.72 77 197 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 46 118 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.13 156 24 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.73 3 8 ATXN1 6310 broad.mit.edu 37 6 16327915 16327916 + In_Frame_Ins INS - TGC TGC rs11969612 by1000genomes PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr6:16327915_16327916insTGC uc003nbt.2 - 8 1597_1598 c.626_627insGCA c.(625-627)CAT>CAGCAT p.208_209insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.208_209insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 208_209 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) gctgatgctgatgctgctgctg 0.381 0.43 93 69 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 46 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.53 725 806 CHEK1 1111 broad.mit.edu 37 11 125499300 125499300 + Frame_Shift_Del DEL T - - PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr11:125499300delT uc009zbo.2 + 5 1261 c.369delT c.(367-369)GGTfs p.G123fs CHEK1_uc010sbh.1_Frame_Shift_Del_p.G139fs|CHEK1_uc010sbi.1_Frame_Shift_Del_p.G123fs|CHEK1_uc001qcf.3_Frame_Shift_Del_p.G123fs|CHEK1_uc009zbp.2_Frame_Shift_Del_p.G123fs|CHEK1_uc001qcg.3_Frame_Shift_Del_p.G123fs|CHEK1_uc009zbq.2_Frame_Shift_Del_p.G123fs|CHEK1_uc001qci.1_RNA NM_001114122 NP_001107594 O14757 CHK1_HUMAN checkpoint kinase 1 123 Protein kinase. cellular response to mechanical stimulus|DNA repair|DNA replication|gamete generation|negative regulation of cell proliferation|reciprocal meiotic recombination|regulation of cyclin-dependent protein kinase activity|replicative senescence condensed nuclear chromosome|microtubule organizing center|nucleoplasm ATP binding|protein binding|protein serine/threonine kinase activity central_nervous_system(3)|lung(2)|skin(1) 6 all_hematologic(175;0.228) Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748) ATCTGCATGGTATTGGAATAA 0.308 0.19 308 73 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.45 11 9 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.30 109 47 C14orf4 64207 broad.mit.edu 37 14 77493648 77493650 + In_Frame_Del DEL GCG - - PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr14:77493648_77493650delGCG uc001xsy.2 - 1 1385_1387 c.486_488delCGC c.(484-489)GCCGCT>GCT p.162_163AA>A NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 162_163 Poly-Ala. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) TTCCACCgcagcggcggcggcgg 0.581 0.29 25 10 SRP14 6727 broad.mit.edu 37 15 40328564 40328575 + In_Frame_Del DEL TGCTGTTGTTGG - - rs16924521;rs8874;rs7535 by1000genomes PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr15:40328564_40328575delTGCTGTTGTTGG uc001zkq.2 - 5 442_453 c.370_381delCCAACAACAGCA c.(370-381)CCAACAACAGCAdel p.PTTA124del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 124_127 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgttgttgctgctgttgttggtgctgttgct 0.231 0.16 51 10 MEF2A 4205 broad.mit.edu 37 15 100252710 100252724 + In_Frame_Del DEL CAGCAGCAGCAGCAG - - rs72276751;rs72236998;rs72416294 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr15:100252710_100252724delCAGCAGCAGCAGCAG uc010urw.1 + 11 1617_1631 c.1258_1272delCAGCAGCAGCAGCAG c.(1258-1272)CAGCAGCAGCAGCAGdel p.QQQQQ425del MEF2A_uc010urv.1_In_Frame_Del_p.QQQQQ355del|MEF2A_uc010bos.2_In_Frame_Del_p.QQQQQ415del|MEF2A_uc002bvf.2_In_Frame_Del_p.QQQQQ417del|MEF2A_uc002bve.2_In_Frame_Del_p.QQQQQ423del|MEF2A_uc002bvg.2_In_Frame_Del_p.QQQQQ415del|MEF2A_uc002bvi.2_In_Frame_Del_p.QQQQQ415del|MEF2A_uc010bot.2_In_Frame_Del_p.QQQQQ347del NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 425_429 Gln/Pro-rich. apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) ATCGGGCTTCcagcagcagcagcagcagcagcagc 0.498 0.60 8 12 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.15 64 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 28 114 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.21 245 67 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 70 242 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 10 86 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes PATU8988S_PANCREAS NA PATU8988S_PANCREAS NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.23 203 59 FAM123B 139285 broad.mit.edu 37 X 63411800 63411800 + Frame_Shift_Del DEL G - - PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chrX:63411800delG uc004dvo.2 - 2 1640 c.1367delC c.(1366-1368)CCTfs p.P456fs NM_152424 NP_689637 Q5JTC6 F123B_HUMAN family with sequence similarity 123B 456 Wnt receptor signaling pathway cytoplasm|nucleus|plasma membrane p.0?(40) kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1) 112 GTCACTCTGAGGAGTCAAAAG 0.552 0.25 24 8 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 11 97 TTN 7273 broad.mit.edu 37 2 179612486 179612486 + Frame_Shift_Del DEL T - - PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr2:179612486delT uc002unb.2 - 46 14865 c.14641delA c.(14641-14643)ACTfs p.T4881fs TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron NM_133379 NP_596870 Q8WZ42 TITIN_HUMAN titin isoform novex-3 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GAAAAACTAGTTTCTATCATT 0.363 0.34 191 98 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.65 8 15 HTT 3064 broad.mit.edu 37 4 3076604 3076609 + In_Frame_Del DEL CAGCAG - - rs10618869 PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr4:3076604_3076609delCAGCAG uc011bvq.1 + 2 203_208 c.58_63delCAGCAG c.(58-63)CAGCAGdel p.QQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagc 0.330 0.25 103 34 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.65 12 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.74 73 209 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 40 79 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.71 4 10 ATXN1 6310 broad.mit.edu 37 6 16327915 16327916 + In_Frame_Ins INS - TGC TGC rs11969612 by1000genomes PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr6:16327915_16327916insTGC uc003nbt.2 - 8 1597_1598 c.626_627insGCA c.(625-627)CAT>CAGCAT p.208_209insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.208_209insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 208_209 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) gctgatgctgatgctgctgctg 0.381 0.39 122 78 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 2 23 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.85 3 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 44 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.10 91 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.51 761 803 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.41 13 9 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.24 127 41 C14orf4 64207 broad.mit.edu 37 14 77493648 77493650 + In_Frame_Del DEL GCG - - PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr14:77493648_77493650delGCG uc001xsy.2 - 1 1385_1387 c.486_488delCGC c.(484-489)GCCGCT>GCT p.162_163AA>A NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 162_163 Poly-Ala. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) TTCCACCgcagcggcggcggcgg 0.581 0.47 10 9 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.11 59 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 23 114 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 225 27 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 103 317 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 72 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes PATU8988T_PANCREAS NA PATU8988T_PANCREAS NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.23 172 50 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PC14_LUNG NA PC14_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 3 48 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - PC14_LUNG NA PC14_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.51 84 89 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PC14_LUNG NA PC14_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 53 45 EGFR 1956 broad.mit.edu 37 7 55242465 55242479 + In_Frame_Del DEL GGAATTAAGAGAAGC - - rs121913421;rs121913426;rs121913425;rs121913435;rs121913436;rs121913441;rs121913229 PC14_LUNG NA PC14_LUNG NA g.chr7:55242465_55242479delGGAATTAAGAGAAGC uc003tqk.2 + 19 2481_2495 c.2235_2249delGGAATTAAGAGAAGC c.(2233-2250)AAGGAATTAAGAGAAGCA>AAA p.ELREA746del EGFR_uc010kzg.1_In_Frame_Del_p.ELREA701del|EGFR_uc011kco.1_In_Frame_Del_p.ELREA693del NM_005228 NP_005219 P00533 EGFR_HUMAN epidermal growth factor receptor isoform a 746_750 Cytoplasmic (Potential).|Protein kinase. Missing (found in a lung cancer sample). activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity p.E746_A750del(1613)|p.L747_P753>S(110)|p.L747_A750>P(74)|p.E746_S752>V(67)|p.L747_T751del(62)|p.E746_T751>A(30)|p.L747_S752del(28)|p.L747_T751>P(20)|p.E746_T751del(18)|p.L747_E749del(18)|p.K745_E749del(14)|p.E746_E749del(12)|p.E746_S752del(10)|p.L747_T751>S(7)|p.L747_P753>Q(7)|p.E746_P753>VS(6)|p.E746_A750>IP(5)|p.L747_T751>Q(5)|p.E746_T751>I(5)|p.E746_T751>V(5)|p.E746_S752>A(5)|p.E746_T751>IP(5)|p.E746_A750>QP(4)|p.E746V(4)|p.E746_S752>D(4)|p.K745_A750del(4)|p.L747S(3)|p.L747_S752>Q(3)|p.A750P(3)|p.E746_T751>VA(3)|p.E746_T751>VP(3)|p.E746_A750>RP(2)|p.E746_A750>S(2)|p.E746_S752>T(2)|p.A750_E758>P(2)|p.E746_T751>Q(2)|p.E746_T751>S(2)|p.E746_A750>DP(2)|p.E746_T751>L(2)|p.E746K(2)|p.E746_P753del(2)|p.E746_S752>I(2)|p.K745_E746insVPVAIK(2)|p.E746_A750>AP(2)|p.L747_K754>ST(1)|p.E746_A750>A(1)|p.E746_T751>P(1)|p.E746del(1)|p.A750_K754del(1)|p.L747_S752>QH(1)|p.L747P(1)|p.E746_A750>VP(1)|p.L747_K754>N(1)|p.L747_R748>FP(1)|p.K745_L747del(1)|p.L747_T751>A(1)|p.E746_P753>LS(1)|p.E746_P753>VQ(1)|p.E746_T751>LS(1)|p.A750_E758del(1)|p.E746_R748del(1)|p.I744_A750>VK(1)|p.E746I(1)|p.L747_K754del(1)|p.R748I(1)|p.E746_A750>KP(1)|p.E746_A750>EP(1) lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1) 9571 all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318) GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607) Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072) TCGCTATCAAGGAATTAAGAGAAGCAACATCTCCG 0.479 0.74 10 28 TNFRSF11B 4982 broad.mit.edu 37 8 119945184 119945184 + Frame_Shift_Del DEL C - - PC14_LUNG NA PC14_LUNG NA g.chr8:119945184delC uc003yon.3 - 2 709 c.386delG c.(385-387)GGAfs p.G129fs TNFRSF11B_uc010mdc.1_RNA NM_002546 NP_002537 O00300 TR11B_HUMAN osteoprotegerin precursor 129 TNFR-Cys 3. apoptosis|skeletal system development cytokine activity|receptor activity central_nervous_system(2) 2 all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234) STAD - Stomach adenocarcinoma(47;0.00193) TTGCACCACTCCAAATCCAGG 0.473 0.18 76 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PC14_LUNG NA PC14_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 29 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 PC14_LUNG NA PC14_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.71 5 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PC14_LUNG NA PC14_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 215 80 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C PC14_LUNG NA PC14_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 23 243 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT PC14_LUNG NA PC14_LUNG NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.20 323 80 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PC14_LUNG NA PC14_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 72 352 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PC14_LUNG NA PC14_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 2 28 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PC3_PROSTATE NA PC3_PROSTATE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 3 144 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A PC3_PROSTATE NA PC3_PROSTATE NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 0.97 1 31 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes PC3_PROSTATE NA PC3_PROSTATE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.36 9 5 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 PC3_PROSTATE NA PC3_PROSTATE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.35 82 44 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PC3_PROSTATE NA PC3_PROSTATE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 149 201 NKD2 85409 broad.mit.edu 37 5 1038447 1038449 + In_Frame_Del DEL CAC - - rs3840989 PC3_PROSTATE NA PC3_PROSTATE NA g.chr5:1038447_1038449delCAC uc003jbt.1 + 10 1320_1322 c.1315_1317delCAC c.(1315-1317)CACdel p.H447del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.74 85 248 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PC3_PROSTATE NA PC3_PROSTATE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 28 85 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PC3_PROSTATE NA PC3_PROSTATE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 4 62 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PC3_PROSTATE NA PC3_PROSTATE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 489 196 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes PC3_PROSTATE NA PC3_PROSTATE NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.53 9 10 TP53 7157 broad.mit.edu 37 17 7578516 7578516 + Frame_Shift_Del DEL G - - PC3_PROSTATE NA PC3_PROSTATE NA g.chr17:7578516delG uc002gim.2 - 5 608 c.414delC c.(412-414)GCCfs p.A138fs TP53_uc002gig.1_Frame_Shift_Del_p.A138fs|TP53_uc002gih.2_Frame_Shift_Del_p.A138fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.A6fs|TP53_uc010cng.1_Frame_Shift_Del_p.A6fs|TP53_uc002gii.1_Frame_Shift_Del_p.A6fs|TP53_uc010cnh.1_Frame_Shift_Del_p.A138fs|TP53_uc010cni.1_Frame_Shift_Del_p.A138fs|TP53_uc002gij.2_Frame_Shift_Del_p.A138fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.A45fs|TP53_uc002gio.2_Frame_Shift_Del_p.A6fs|TP53_uc010vug.1_Frame_Shift_Del_p.A99fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 138 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). A -> D (in sporadic cancers; somatic mutation).|A -> T (in sporadic cancers; somatic mutation).|A -> S (in LFS; germline mutation).|A -> V (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.A138V(17)|p.A138P(13)|p.0?(7)|p.A138fs*32(5)|p.A138T(4)|p.A138fs*11(3)|p.N131fs*27(2)|p.A138fs*31(1)|p.L137_W146del10(1)|p.K139fs*4(1)|p.F134_T140>S(1)|p.V73fs*9(1)|p.L137_A138insX(1)|p.K139fs*31(1)|p.K132_A138delKMFCQLA(1)|p.A138_V143delAKTCPV(1)|p.A138del(1)|p.K139fs*11(1)|p.A138_P142delAKTCP(1)|p.C135_A138delCQLA(1)|p.Q136_K139delQLAK(1)|p.A138A(1)|p.C135_T140delCQLAKT(1)|p.K139fs*29(1)|p.A138S(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GGCAGGTCTTGGCCAGTTGGC 0.567 0.94 5 75 ID1 3397 broad.mit.edu 37 20 30193544 30193545 + Frame_Shift_Ins INS - G G rs11545371 PC3_PROSTATE NA PC3_PROSTATE NA g.chr20:30193544_30193545insG uc002wwg.1 + 1 453_454 c.354_355insG c.(352-357)CCCGGGfs p.P118fs ID1_uc002wwh.1_Frame_Shift_Ins_p.P118fs|hsa-mir-3193|MI0014238_5'Flank NM_002165 NP_002156 P41134 ID1_HUMAN inhibitor of DNA binding 1 isoform a 118_119 angiogenesis|blood vessel endothelial cell migration|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by transcription factor localization|transforming growth factor beta receptor signaling pathway cytoplasm protein binding ovary(1) 1 all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198) Epithelial(4;1.99e-05)|all cancers(5;0.000169)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264) TTGGAACCCCCGGGGGCCGAGG 0.614 0.12 60 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PC3_PROSTATE NA PC3_PROSTATE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 104 892 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PC3_PROSTATE NA PC3_PROSTATE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 16 254 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 3 26 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.14 49 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.30 76 32 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.57 23 31 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.60 4 6 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 15 PTEN 5728 broad.mit.edu 37 10 89653844 89653846 + In_Frame_Del DEL AAC - - PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:89653844_89653846delAAC uc001kfb.2 + 3 1173_1175 c.142_144delAAC c.(142-144)AACdel p.N49del NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 49 Phosphatase tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.?(4)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.N48D(1)|p.N48fs*6(1)|p.N48I(1)|p.N49T(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) CGTATACAGGAACAATATTGATG 0.286 0.97 4 119 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 144 23 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 151 28 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.68 204 427 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.85 5 29 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.74 11 32 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 203 69 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.21 30 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 55 85 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 19 37 CDK13 8621 broad.mit.edu 37 7 40134573 40134574 + Frame_Shift_Ins INS - T T PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chr7:40134573_40134574insT uc003thh.3 + 14 4815_4816 c.4533_4534insT c.(4531-4536)CCATACfs p.P1511fs CDK13_uc003thi.3_Frame_Shift_Ins_p.P1451fs|CDK13_uc003thj.2_Frame_Shift_Ins_p.P562fs|CDK13_uc003thk.2_Frame_Shift_Ins_p.P444fs NM_003718 NP_003709 Q14004 CDK13_HUMAN cell division cycle 2-like 5 isoform 1 1511_1512 alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity lung(2)|skin(2)|ovary(1) 5 GAGGGTTACCATACTGAGTATC 0.431 0.30 117 49 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.70 3 7 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.65 7 13 RIMS2 9699 broad.mit.edu 37 8 104513254 104513255 + Frame_Shift_Ins INS - G G PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chr8:104513254_104513255insG uc003ylp.2 + 1 279_280 c.140_141insG c.(139-141)CAGfs p.Q47fs NM_001100117 NP_001093587 Q9UQ26 RIMS2_HUMAN regulating synaptic membrane exocytosis 2 47 RabBD. intracellular protein transport cell junction|presynaptic membrane metal ion binding|Rab GTPase binding ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1) 15 OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229) ATGGATAGGCAGAAGAAAGAAG 0.629 0.57 61 80 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 3 83 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 344 144 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 46 114 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 24 176 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.87 13 85 RPS6KA3 6197 broad.mit.edu 37 X 20185733 20185733 + Frame_Shift_Del DEL T - - PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chrX:20185733delT uc004czu.2 - 17 1576 c.1576delA c.(1576-1578)ACCfs p.T526fs RPS6KA3_uc011mjk.1_Frame_Shift_Del_p.T496fs|RPS6KA3_uc004czv.2_Frame_Shift_Del_p.T513fs|RPS6KA3_uc011mjl.1_Frame_Shift_Del_p.T497fs|RPS6KA3_uc011mjm.1_Frame_Shift_Del_p.T498fs NM_004586 NP_004577 P51812 KS6A3_HUMAN ribosomal protein S6 kinase, 90kDa, polypeptide 526 Protein kinase 2. axon guidance|central nervous system development|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|skeletal system development|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|caspase inhibitor activity|magnesium ion binding|protein serine/threonine kinase activity central_nervous_system(4)|stomach(1)|ovary(1)|lung(1)|breast(1) 8 TATTCAACGGTTTTAGTTATA 0.353 0.52 47 51 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.85 8 45 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 258 51 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.34 98 51 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.47 162 141 SH2B2 10603 broad.mit.edu 37 7 101943874 101943879 + In_Frame_Del DEL GTCCCA - - PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chr7:101943874_101943879delGTCCCA uc011kko.1 + 2 214_219 c.169_174delGTCCCA c.(169-174)GTCCCAdel p.VP63del NM_020979 NP_066189 O14492 SH2B2_HUMAN SH2B adaptor protein 2 20_21 blood coagulation|insulin receptor signaling pathway|intracellular signal transduction cytosol|plasma membrane JAK pathway signal transduction adaptor activity|SH3/SH2 adaptor activity|signal transducer activity 0 agccgccccggtcccagtcccggtcc 0.471 0.40 6 4 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.40 6 4 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 427 82 GRAMD1B 57476 broad.mit.edu 37 11 123480598 123480599 + Frame_Shift_Ins INS - C C rs139670625 by1000genomes PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chr11:123480598_123480599insC uc001pyx.2 + 12 1653_1654 c.1324_1325insC c.(1324-1326)ACTfs p.T442fs GRAMD1B_uc001pyw.2_Frame_Shift_Ins_p.T449fs|GRAMD1B_uc010rzw.1_Frame_Shift_Ins_p.T402fs|GRAMD1B_uc010rzx.1_Frame_Shift_Ins_p.T402fs|GRAMD1B_uc009zbe.1_Frame_Shift_Ins_p.T438fs|GRAMD1B_uc001pyy.2_Frame_Shift_Ins_p.T133fs NM_020716 NP_065767 Q3KR37 GRM1B_HUMAN GRAM domain containing 1B 442 integral to membrane ovary(1) 1 Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394) GGCTCCCAAAACTGCCACTGTC 0.500 0.21 26 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 18 131 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.82 4 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 109 560 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 62 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 46 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.53 8 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.42 80 57 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.18 179 39 RASA1 5921 broad.mit.edu 37 5 86629095 86629096 + In_Frame_Ins INS - AGA AGA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chr5:86629095_86629096insAGA uc003kiw.2 + 4 958_959 c.840_841insAGA c.(838-843)insAGA p.283_284insR RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_In_Frame_Ins_p.106_107insR|RASA1_uc011ctv.1_In_Frame_Ins_p.116_117insR|RASA1_uc011ctw.1_In_Frame_Ins_p.117_118insR|RASA1_uc010jaw.2_In_Frame_Ins_p.106_107insR NM_002890 NP_002881 P20936 RASA1_HUMAN RAS p21 protein activator 1 isoform 1 283_284 SH3. cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis cytosol|intrinsic to internal side of plasma membrane glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding upper_aerodigestive_tract(3)|ovary(1)|lung(1) 5 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) CAGTAGAAGATAGAAGGCGTGT 0.302 0.41 16 11 RASA1 5921 broad.mit.edu 37 5 86674280 86674287 + Frame_Shift_Del DEL CACTGCTA - - PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chr5:86674280_86674287delCACTGCTA uc003kiw.2 + 18 2530_2537 c.2412_2419delCACTGCTA c.(2410-2421)GCCACTGCTACAfs p.A804fs RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_Frame_Shift_Del_p.A627fs|RASA1_uc011ctv.1_Frame_Shift_Del_p.A637fs|RASA1_uc011ctw.1_Frame_Shift_Del_p.A638fs|RASA1_uc010jaw.2_Frame_Shift_Del_p.A626fs NM_002890 NP_002881 P20936 RASA1_HUMAN RAS p21 protein activator 1 isoform 1 804_807 Ras-GAP. cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis cytosol|intrinsic to internal side of plasma membrane glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding p.A806D(1) upper_aerodigestive_tract(3)|ovary(1)|lung(1) 5 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) ATATGAAAGCCACTGCTACACAGTTTGT 0.341 0.30 70 30 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.80 2 8 TNFRSF10B 8795 broad.mit.edu 37 8 22885994 22885994 + Frame_Shift_Del DEL A - - PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chr8:22885994delA uc003xcu.2 - 5 891 c.598delT c.(598-600)TCCfs p.S200fs TNFRSF10B_uc003xcs.1_5'Flank|TNFRSF10B_uc003xct.2_Intron|TNFRSF10B_uc011kzq.1_Intron|TNFRSF10B_uc003xcv.2_Frame_Shift_Del_p.S98fs NM_003842 NP_003833 O14763 TR10B_HUMAN tumor necrosis factor receptor superfamily, 200 Extracellular (Potential).|TAPE. activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cell surface receptor linked signaling pathway|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|positive regulation of I-kappaB kinase/NF-kappaB cascade plasma membrane caspase activator activity|receptor activity|TRAIL binding 0 Prostate(55;0.0421)|Breast(100;0.067) Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703) CCTGGGCTGGAGGTCACCGTC 0.532 1.00 0 19 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.27 44 16 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 1 13 CDKN2A 1029 broad.mit.edu 37 9 21971202 21971203 + Frame_Shift_Ins INS - A A PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chr9:21971202_21971203insA uc003zpk.2 - 2 367_368 c.155_156insT c.(154-156)ATGfs p.M52fs MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Frame_Shift_Ins_p.H107fs NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 52 ANK 2. cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.?(14)|p.M52K(4)|p.M52I(3)|p.M52fs*68(2)|p.M52fs*2(1)|p.V28_V51del(1)|p.M52L(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) 0.000 0.95 84 1624 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 183 42 LAMA5 3911 broad.mit.edu 37 20 60928210 60928210 + Frame_Shift_Del DEL T - - PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chr20:60928210delT uc002ycq.2 - 3 615 c.548delA c.(547-549)CAGfs p.Q183fs NM_005560 NP_005551 O15230 LAMA5_HUMAN laminin alpha 5 precursor 183 Laminin N-terminal. angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex integrin binding ovary(1)|pancreas(1)|skin(1) 3 Breast(26;1.57e-08) BRCA - Breast invasive adenocarcinoma(19;4.36e-06) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) 0.000 1.00 0 24 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA PECAPJ49_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 195 450 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 25 FN1 2335 broad.mit.edu 37 2 216248175 216248175 + Frame_Shift_Del DEL G - - PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:216248175delG uc002vfa.2 - 31 5192 c.4926delC c.(4924-4926)ACCfs p.T1642fs FN1_uc002vfb.2_Frame_Shift_Del_p.T1551fs|FN1_uc002vfc.2_Frame_Shift_Del_p.T1551fs|FN1_uc002vfd.2_Frame_Shift_Del_p.T1642fs|FN1_uc002vfe.2_Frame_Shift_Del_p.T1551fs|FN1_uc002vff.2_Frame_Shift_Del_p.T1551fs|FN1_uc002vfg.2_Frame_Shift_Del_p.T1551fs|FN1_uc002vfh.2_Frame_Shift_Del_p.T1551fs|FN1_uc002vfi.2_Frame_Shift_Del_p.T1642fs|FN1_uc002vfj.2_Frame_Shift_Del_p.T1642fs|FN1_uc002vez.2_5'UTR|FN1_uc010zjp.1_Frame_Shift_Del_p.T269fs|FN1_uc010fvc.1_Frame_Shift_Del_p.T4fs|FN1_uc010fvd.1_Frame_Shift_Del_p.T4fs NM_212482 NP_997647 P02751 FINC_HUMAN fibronectin 1 isoform 1 preproprotein 1641 Fibronectin type-III 12; extra domain. acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix collagen binding|extracellular matrix structural constituent|heparin binding central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1) 13 Renal(323;0.127) Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) CCTGAACATCGGTCACTTGCA 0.473 0.48 86 79 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.48 13 12 TOPBP1 11073 broad.mit.edu 37 3 133368337 133368338 + Frame_Shift_Del DEL AA - - PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:133368337_133368338delAA uc003eps.2 - 10 1525_1526 c.1393_1394delTT c.(1393-1395)TTAfs p.L465fs NM_007027 NP_008958 Q92547 TOPB1_HUMAN topoisomerase (DNA) II binding protein 1 465 DNA repair|response to ionizing radiation microtubule organizing center|PML body|spindle pole DNA binding|protein C-terminus binding ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1) 7 CTTCTTTTTTAAAAGAGCTGCT 0.381 0.42 93 67 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.38 93 58 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 36 18 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.33 218 108 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 15 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.41 23 16 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 1 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 154 23 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 36 422 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.54 21 25 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.15 115 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 190 510 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 50 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 63 TNFRSF9 3604 broad.mit.edu 37 1 7998254 7998254 + Frame_Shift_Del DEL T - - rs9657965 byFrequency;by1000genomes PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:7998254delT uc001aot.2 - 4 473 c.345delA c.(343-345)AAAfs p.K115fs NM_001561 NP_001552 Q07011 TNR9_HUMAN tumor necrosis factor receptor superfamily, 115 Extracellular (Potential).|TNFR-Cys 3. induction of apoptosis|negative regulation of cell proliferation integral to plasma membrane binding|receptor activity large_intestine(1)|lung(1)|ovary(1)|skin(1) 4 Ovarian(185;0.0634)|all_lung(157;0.151) all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649) CAAACGTACCTTTTTTTGTCA 0.413 0.53 71 79 RBM15 64783 broad.mit.edu 37 1 110884261 110884263 + In_Frame_Del DEL AAG - - PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:110884261_110884263delAAG uc001dzl.1 + 1 2317_2319 c.2234_2236delAAG c.(2233-2238)AAAGAA>AAA p.E746del RBM15_uc001dzm.1_In_Frame_Del_p.E746del|uc001dzj.2_5'Flank NM_022768 NP_073605 Q96T37 RBM15_HUMAN RNA binding motif protein 15 746 interspecies interaction between organisms nucleus nucleotide binding|protein binding|RNA binding ovary(3) 3 all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634) BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135) CCTCTGAAAAAAGAAGACCGCTC 0.562 0.40 137 91 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.43 13 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.22 47 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 100 131 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 29 69 FBN2 2201 broad.mit.edu 37 5 127599141 127599141 + Frame_Shift_Del DEL G - - PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:127599141delG uc003kuu.2 - 63 8607 c.8168delC c.(8167-8169)CCTfs p.P2723fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 2723 EGF-like 47; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) GTAATACCCAGGGGGGCAGCC 0.592 0.12 49 7 HOXA13 3209 broad.mit.edu 37 7 27239320 27239337 + In_Frame_Del DEL GCAGCGGCAGCCGCGGCA - - rs35861510 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:27239320_27239337delGCAGCGGCAGCCGCGGCA uc003szb.1 - 1 389_406 c.360_377delTGCCGCGGCTGCCGCTGC c.(358-378)GCTGCCGCGGCTGCCGCTGCA>GCA p.120_126AAAAAAA>A uc003szc.1_5'Flank NM_000522 NP_000513 P31271 HXA13_HUMAN homeobox A13 120_126 Poly-Ala. skeletal system development nucleus sequence-specific DNA binding breast(1) 1 0.000 0.10 532 61 ARFGEF1 10565 broad.mit.edu 37 8 68128856 68128856 + Frame_Shift_Del DEL G - - rs142098461 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:68128856delG uc003xxo.1 - 33 5045 c.4655delC c.(4654-4656)CCAfs p.P1552fs ARFGEF1_uc003xxl.1_Frame_Shift_Del_p.P1006fs|ARFGEF1_uc003xxn.1_Frame_Shift_Del_p.P535fs NM_006421 NP_006412 Q9Y6D6 BIG1_HUMAN brefeldin A-inhibited guanine 1552 exocytosis|regulation of ARF protein signal transduction cytoplasm ARF guanyl-nucleotide exchange factor activity|myosin binding ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1) 8 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206) 0.000 0.13 55 8 SULF1 23213 broad.mit.edu 37 8 70488249 70488249 + Frame_Shift_Del DEL G - - PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:70488249delG uc010lza.1 + 6 934 c.217delG c.(217-219)GGGfs p.G73fs SULF1_uc003xyd.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xye.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xyf.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xyg.2_Frame_Shift_Del_p.G73fs NM_015170 NP_055985 Q8IWU6 SULF1_HUMAN sulfatase 1 precursor 73 apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway cell surface|endoplasmic reticulum|extracellular space|Golgi stack arylsulfatase activity|calcium ion binding central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1) 7 Breast(64;0.0654) Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534) TATGGAACATGGGGGGGCCAC 0.493 0.11 102 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 17 PTEN 5728 broad.mit.edu 37 10 89693010 89693011 + Splice_Site INS - GCCG GCCG PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:89693010_89693011insGCCG uc001kfb.2 + 6 1523 c.492_splice c.e6+2 p.K164_splice NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.?(8)|p.R55fs*1(4)|p.Y27fs*1(2)|p.K163_V166>NKGE(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GACAAAAAGGTAAGTTATTTTT 0.312 0.72 22 56 NLRP10 338322 broad.mit.edu 37 11 7981589 7981590 + Frame_Shift_Ins INS - T T rs144948801 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:7981589_7981590insT uc001mfv.1 - 2 1586_1587 c.1569_1570insA c.(1567-1572)AAAGACfs p.K523fs NM_176821 NP_789791 Q86W26 NAL10_HUMAN NLR family, pyrin domain containing 10 523_524 ATP binding lung(4)|ovary(2)|pancreas(1)|kidney(1)|skin(1) 9 Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189) GAGAAGCTGTCTTTTTTCGAGA 0.450 0.11 308 38 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 341 144 CASP1 834 broad.mit.edu 37 11 104901070 104901070 + Frame_Shift_Del DEL T - - PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:104901070delT uc010rve.1 - 5 631 c.614delA c.(613-615)AATfs p.N205fs CASP1_uc001pig.2_Frame_Shift_Del_p.N112fs|CASP1_uc001pik.2_Frame_Shift_Del_p.N168fs|CASP1_uc010rvf.1_Frame_Shift_Del_p.N112fs|CASP1_uc010rvg.1_Frame_Shift_Del_p.N184fs|CASP1_uc010rvh.1_Frame_Shift_Del_p.N112fs|CASP1_uc010rvi.1_Intron|CASP1_uc001pim.3_Frame_Shift_Del_p.N205fs|CASP1_uc009yxi.2_Frame_Shift_Del_p.N184fs|CASP1_uc010rvj.1_Frame_Shift_Del_p.N205fs|CASP1_uc009yxj.2_Frame_Shift_Del_p.N50fs|CASP1_uc010rvk.1_Frame_Shift_Del_p.N166fs NM_033292 NP_150634 P29466 CASP1_HUMAN caspase 1 isoform alpha precursor 205 cellular response to mechanical stimulus|cellular response to organic substance|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis|signal transduction cytosol caspase activator activity|cysteine-type endopeptidase activity|protein binding p.N205I(1) ovary(2) 2 Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047) BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482) Minocycline(DB01017)|Penicillamine(DB00859) AGCAGTGAGATTTTTTTTCAC 0.378 0.14 185 29 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.33 16 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 19 75 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 135 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 126 579 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 6 108 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 3 21 TTN 7273 broad.mit.edu 37 2 179416861 179416863 + In_Frame_Del DEL CTC - - PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179416861_179416863delCTC uc010zfg.1 - 284 83284_83286 c.83060_83062delGAG c.(83059-83064)GGAGAA>GAA p.G27687del uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.G21382del|TTN_uc010zfi.1_In_Frame_Del_p.G21315del|TTN_uc010zfj.1_In_Frame_Del_p.G21190del NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 28614 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CAAGTAATTTCTCCTCCTCCATT 0.438 0.82 97 450 TTN 7273 broad.mit.edu 37 2 179547531 179547548 + In_Frame_Del DEL TCATATTCTTCATATTCC - - PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179547531_179547548delTCATATTCTTCATATTCC uc010zfg.1 - 132 29462_29479 c.29238_29255delGGAATATGAAGAATATGA c.(29236-29256)GAGGAATATGAAGAATATGAT>GAT p.EEYEEY9746del TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Del_p.EEYEEY6407del|TTN_uc010fre.1_In_Frame_Del_p.EEYEEY593del NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10673_10678 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTCTTTATAATCATATTCTTCATATTCCTCATATTCTT 0.344 0.58 150 209 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.40 24 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 115 99 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 58 132 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.27 79 29 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 1 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 290 102 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.55 5 6 CIITA 4261 broad.mit.edu 37 16 10995956 10995964 + In_Frame_Del DEL CCTGCCCTG - - PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:10995956_10995964delCCTGCCCTG uc002dai.3 + 7 676_684 c.543_551delCCTGCCCTG c.(541-552)ACCCTGCCCTGC>ACC p.LPC182del CIITA_uc002daj.3_In_Frame_Del_p.LPC183del|CIITA_uc002dak.3_Intron|CIITA_uc002dag.2_In_Frame_Del_p.LPC182del|CIITA_uc002dah.2_Intron|CIITA_uc010bup.1_In_Frame_Del_p.LPC182del NM_000246 NP_000237 P33076 C2TA_HUMAN class II transactivator 182_184 interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent nucleus activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding central_nervous_system(1) 1 ACTGCTCCACCCTGCCCTGCCTGCCACTG 0.612 0.65 14 26 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 57 760 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.28 74 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 85 375 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 86 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PK1_PANCREAS NA PK1_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.54 41 49 EPHA10 284656 broad.mit.edu 37 1 38200929 38200931 + In_Frame_Del DEL CTT - - PK1_PANCREAS NA PK1_PANCREAS NA g.chr1:38200929_38200931delCTT uc009vvi.2 - 6 1575_1577 c.1489_1491delAAG c.(1489-1491)AAGdel p.K497del EPHA10_uc001cbu.2_RNA|EPHA10_uc001cbv.1_RNA NM_001099439 NP_001092909 Q5JZY3 EPHAA_HUMAN EPH receptor A10 isofom 3 497 Fibronectin type-III 2.|Extracellular (Potential). extracellular region|integral to membrane|integral to plasma membrane ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity breast(4)|stomach(3)|lung(1) 8 Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197) Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) ACGCACTCACCTTCTCGTAGTAT 0.645 0.33 10 5 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - PK1_PANCREAS NA PK1_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 628 128 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes PK1_PANCREAS NA PK1_PANCREAS NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.46 15 13 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 PK1_PANCREAS NA PK1_PANCREAS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.51 55 58 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A PK1_PANCREAS NA PK1_PANCREAS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 131 35 HTT 3064 broad.mit.edu 37 4 3076604 3076606 + In_Frame_Del DEL CAG - - rs10618869 PK1_PANCREAS NA PK1_PANCREAS NA g.chr4:3076604_3076606delCAG uc011bvq.1 + 2 203_205 c.58_60delCAG c.(58-60)CAGdel p.Q40del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagc 0.335 0.11 110 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PK1_PANCREAS NA PK1_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.73 135 359 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PK1_PANCREAS NA PK1_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.82 38 171 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes PK1_PANCREAS NA PK1_PANCREAS NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.71 6 15 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 PK1_PANCREAS NA PK1_PANCREAS NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.41 44 31 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 PK1_PANCREAS NA PK1_PANCREAS NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.15 277 49 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes PK1_PANCREAS NA PK1_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.85 6 33 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - PK1_PANCREAS NA PK1_PANCREAS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.41 16 11 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 PK1_PANCREAS NA PK1_PANCREAS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.39 90 57 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PK1_PANCREAS NA PK1_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.99 1 93 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency PK1_PANCREAS NA PK1_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.31 88 40 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 PK1_PANCREAS NA PK1_PANCREAS NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.50 10 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PK1_PANCREAS NA PK1_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.44 1143 914 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 PK1_PANCREAS NA PK1_PANCREAS NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.23 30 9 C14orf4 64207 broad.mit.edu 37 14 77493648 77493650 + In_Frame_Del DEL GCG - - PK1_PANCREAS NA PK1_PANCREAS NA g.chr14:77493648_77493650delGCG uc001xsy.2 - 1 1385_1387 c.486_488delCGC c.(484-489)GCCGCT>GCT p.162_163AA>A NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 162_163 Poly-Ala. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) TTCCACCgcagcggcggcggcgg 0.581 0.36 7 4 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C PK1_PANCREAS NA PK1_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 103 1106 MPRIP 23164 broad.mit.edu 37 17 17039562 17039567 + In_Frame_Del DEL CAGCAG - - rs148686165;rs113250356 PK1_PANCREAS NA PK1_PANCREAS NA g.chr17:17039562_17039567delCAGCAG uc002gqu.1 + 6 590_595 c.534_539delCAGCAG c.(532-540)ACCAGCAGC>ACC p.SS187del MPRIP_uc002gqv.1_In_Frame_Del_p.SS187del|MPRIP_uc002gqw.1_5'UTR NM_201274 NP_958431 Q6WCQ1 MPRIP_HUMAN myosin phosphatase-Rho interacting protein 187_188 Ser-rich.|Interaction with F-actin (By similarity). Missing (in Ref. 2; BAD89507 and 6; AAH09982). cytoplasm|cytoskeleton actin binding 0 TGGCTGTTACcagcagcagcagcagc 0.490 0.42 7 5 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PK1_PANCREAS NA PK1_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.41 250 174 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 PK1_PANCREAS NA PK1_PANCREAS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.25 144 47 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PK1_PANCREAS NA PK1_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 69 170 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PK1_PANCREAS NA PK1_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 9 165 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PK45H_PANCREAS NA PK45H_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 42 MTCP1NB 100272147 broad.mit.edu 37 X 154290143 154290144 + Frame_Shift_Ins INS - G G PK45H_PANCREAS NA PK45H_PANCREAS NA g.chrX:154290143_154290144insG uc004fmy.2 - 3 770_771 c.181_182insC c.(181-183)CTAfs p.L61fs NM_001018024 NP_001018024 P56277 MTCNB_HUMAN mature T-cell proliferation 1 neighbor 61 cell proliferation mitochondrion lung(1) 1 CTTCCGTGTTAGGTTTTCTTCC 0.436 0.11 296 38 SPEN 23013 broad.mit.edu 37 1 16262091 16262093 + In_Frame_Del DEL CTC - - PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr1:16262091_16262093delCTC uc001axk.1 + 11 9560_9562 c.9356_9358delCTC c.(9355-9360)TCTCCT>TCT p.P3120del SPEN_uc010obp.1_In_Frame_Del_p.P3079del NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 3120 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) GCGCTTCACTCTCCTCGGGCTCC 0.655 0.86 33 195 FN1 2335 broad.mit.edu 37 2 216245789 216245790 + Frame_Shift_Ins INS - A A PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr2:216245789_216245790insA uc002vfa.2 - 33 5444_5445 c.5178_5179insT c.(5176-5181)CCTAAAfs p.P1726fs FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Frame_Shift_Ins_p.P1726fs|FN1_uc002vfe.2_Frame_Shift_Ins_p.P1635fs|FN1_uc002vff.2_Frame_Shift_Ins_p.P1635fs|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Frame_Shift_Ins_p.P1726fs|FN1_uc002vfj.2_Intron|FN1_uc002vez.2_5'UTR|FN1_uc010zjp.1_Intron|FN1_uc002vfk.1_5'Flank|FN1_uc010fva.1_5'Flank|FN1_uc010fvb.1_5'Flank|FN1_uc010fvc.1_Frame_Shift_Ins_p.P88fs|FN1_uc010fvd.1_Intron NM_212482 NP_997647 P02751 FINC_HUMAN fibronectin 1 isoform 1 preproprotein 1725_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix collagen binding|extracellular matrix structural constituent|heparin binding central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1) 13 Renal(323;0.127) Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) GCCAGTCCTTTAGGGCGATCAA 0.431 0.96 7 157 TPRXL 348825 broad.mit.edu 37 3 14105883 14105885 + In_Frame_Del DEL CAG - - rs113575909 PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr3:14105883_14105885delCAG uc011avd.1 + 3 662_664 c.207_209delCAG c.(205-210)CCCAGC>CCC p.S73del TPRXL_uc003byh.1_In_Frame_Del_p.S73del|TPRXL_uc003byg.2_In_Frame_Del_p.S73del NR_002223 RecName: Full=Putative protein TPRXL; 0 gcagcagccccagcagcagcagc 0.000 0.36 7 4 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.37 31 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 103 124 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.34 85 44 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.50 6 6 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.35 24 13 SRPK2 6733 broad.mit.edu 37 7 104758331 104758332 + Frame_Shift_Ins INS - G G PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr7:104758331_104758332insG uc003vct.2 - 15 2207_2208 c.2020_2021insC c.(2020-2022)CGAfs p.R674fs SRPK2_uc003vcu.2_Frame_Shift_Ins_p.R674fs|SRPK2_uc003vcv.2_Frame_Shift_Ins_p.R685fs|uc003vcr.1_5'Flank|SRPK2_uc003vcs.1_RNA NM_182691 NP_872633 P78362 SRPK2_HUMAN serine/arginine-rich protein-specific kinase 2 674 Protein kinase. angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly cytoplasm|nucleolus 14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1) 6 AGCTGAGGCTCGTTTTTCTGGA 0.446 0.10 189 21 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 2 14 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.58 13 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 4 46 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.31 25 11 MYST4 23522 broad.mit.edu 37 10 76788480 76788481 + Frame_Shift_Ins INS - C C PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr10:76788480_76788481insC uc001jwn.1 + 18 4391_4392 c.3898_3899insC c.(3898-3900)ACCfs p.T1300fs MYST4_uc001jwo.1_Frame_Shift_Ins_p.T1008fs|MYST4_uc001jwp.1_Frame_Shift_Ins_p.T1117fs NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1300 histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) AGAAGGAAAAACCAGCCCCAGT 0.510 0.13 183 28 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 589 322 ATN1 1822 broad.mit.edu 37 12 7045892 7045903 + In_Frame_Del DEL CAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448 byFrequency;byFrequency;by1000genomes;byFrequency PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr12:7045892_7045903delCAGCAGCAGCAG uc001qrw.1 + 5 1699_1710 c.1462_1473delCAGCAGCAGCAG c.(1462-1473)CAGCAGCAGCAGdel p.QQQQ496del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQ496del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 496_499 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagc 0.467 0.24 47 15 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.48 33 30 DACH1 1602 broad.mit.edu 37 13 72440443 72440444 + In_Frame_Ins INS - CTGCTG CTGCTG PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr13:72440443_72440444insCTGCTG uc010thn.1 - 2 881_882 c.458_459insCAGCAG c.(457-459)AGT>AGCAGCAGT p.153_153S>SSS DACH1_uc010tho.1_In_Frame_Ins_p.153_153S>SSS|DACH1_uc010thp.1_In_Frame_Ins_p.153_153S>SSS NM_080759 NP_542937 Q9UI36 DACH1_HUMAN dachshund homolog 1 isoform a 153 Poly-Ser. multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus DNA binding|nucleotide binding|protein binding breast(1) 1 Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198) GBM - Glioblastoma multiforme(99;0.00032) tgctgctactactgctgctgct 0.292 0.45 51 42 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.17 95 20 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 5 39 CDK12 51755 broad.mit.edu 37 17 37618904 37618908 + Frame_Shift_Del DEL CACAA - - PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr17:37618904_37618908delCACAA uc010cvv.2 + 1 1166_1170 c.580_584delCACAA c.(580-585)CACAAAfs p.H194fs CDK12_uc010wef.1_Frame_Shift_Del_p.H194fs|CDK12_uc002hrw.3_Frame_Shift_Del_p.H194fs NM_016507 NP_057591 Q9NYV4 CDK12_HUMAN Cdc2-related kinase, arginine/serine-rich 194_195 mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1) 19 GAAGTCTGGGCACAAAGACCGGAGT 0.517 0.41 64 44 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.41 83 58 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 54 280 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PK45H_PANCREAS NA PK45H_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 7 102 FAM48B1 100130302 broad.mit.edu 37 X 24382374 24382382 + In_Frame_Del DEL TGCTGCTGC - - rs10560780 PK59_PANCREAS NA PK59_PANCREAS NA g.chrX:24382374_24382382delTGCTGCTGC uc011mjx.1 + 1 1497_1505 c.1497_1505delTGCTGCTGC c.(1495-1506)ATTGCTGCTGCT>ATT p.AAA515del NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 ctgctgctattgctgctgctgctgctgct 0.196 0.24 25 8 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - PK59_PANCREAS NA PK59_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.61 116 184 TGFBR2 7048 broad.mit.edu 37 3 30691871 30691872 + Frame_Shift_Ins INS - A A PK59_PANCREAS NA PK59_PANCREAS NA g.chr3:30691871_30691872insA uc003ceo.2 + 3 755_756 c.373_374insA c.(373-375)GAAfs p.E125fs TGFBR2_uc003cen.2_Frame_Shift_Ins_p.E150fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 125 Extracellular (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 CATTATGAAGGAAAAAAAAAAG 0.421 0.66 69 132 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 PK59_PANCREAS NA PK59_PANCREAS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.35 13 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PK59_PANCREAS NA PK59_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 45 40 PHF3 23469 broad.mit.edu 37 6 64422045 64422047 + In_Frame_Del DEL AAG - - PK59_PANCREAS NA PK59_PANCREAS NA g.chr6:64422045_64422047delAAG uc003pep.1 + 15 4587_4589 c.4561_4563delAAG c.(4561-4563)AAGdel p.K1521del PHF3_uc003pen.2_In_Frame_Del_p.K1433del|PHF3_uc011dxs.1_In_Frame_Del_p.K790del NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 1521 multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) TGGTGAAAACAAGGAGATAAAAG 0.335 0.58 33 46 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes PK59_PANCREAS NA PK59_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 24 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 PK59_PANCREAS NA PK59_PANCREAS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.36 35 20 DEPDC6 64798 broad.mit.edu 37 8 121019081 121019082 + Frame_Shift_Ins INS - C C rs141805893 PK59_PANCREAS NA PK59_PANCREAS NA g.chr8:121019081_121019082insC uc003yow.3 + 7 1150_1151 c.963_964insC c.(961-966)ACTCCCfs p.T321fs DEPDC6_uc011lid.1_Frame_Shift_Ins_p.T220fs NM_022783 NP_073620 Q8TB45 DPTOR_HUMAN DEP domain containing 6 321_322 intracellular signal transduction|negative regulation of cell size|negative regulation of protein kinase activity|negative regulation of TOR signaling cascade|regulation of apoptosis intracellular protein binding 0 Lung NSC(37;9.35e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) STAD - Stomach adenocarcinoma(47;0.00185) 0.000 0.11 765 96 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PK59_PANCREAS NA PK59_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 30 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PK59_PANCREAS NA PK59_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 354 148 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 PK59_PANCREAS NA PK59_PANCREAS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.28 21 8 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C PK59_PANCREAS NA PK59_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 22 251 ILVBL 10994 broad.mit.edu 37 19 15226818 15226819 + Frame_Shift_Ins INS - C C PK59_PANCREAS NA PK59_PANCREAS NA g.chr19:15226818_15226819insC uc002nam.2 - 13 1656_1657 c.1535_1536insG c.(1534-1536)GATfs p.D512fs ILVBL_uc010xof.1_Frame_Shift_Ins_p.D153fs|ILVBL_uc010dzw.2_Frame_Shift_Ins_p.D405fs NM_006844 NP_006835 A1L0T0 ILVBL_HUMAN ilvB (bacterial acetolactate synthase)-like 512 Thiamine pyrophosphate binding (By similarity). integral to membrane magnesium ion binding|thiamine pyrophosphate binding|transferase activity ovary(2) 2 0.000 0.91 1 10 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PK59_PANCREAS NA PK59_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 153 443 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PK59_PANCREAS NA PK59_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 6 78 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 3 29 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.33 10 5 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.38 13 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 78 136 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.45 42 34 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.42 52 38 C6orf97 80129 broad.mit.edu 37 6 151907077 151907077 + Frame_Shift_Del DEL G - - PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:151907077delG uc003qol.2 + 7 1235 c.1146delG c.(1144-1146)AAGfs p.K382fs NM_025059 NP_079335 Q8IYT3 CF097_HUMAN hypothetical protein LOC80129 382 Potential. 0 Ovarian(120;0.126) BRCA - Breast invasive adenocarcinoma(37;0.111) OV - Ovarian serous cystadenocarcinoma(155;1.48e-10) AGTTGGGAAAGGAGTCTGGGT 0.483 0.56 48 60 EZH2 2146 broad.mit.edu 37 7 148506170 148506171 + Frame_Shift_Ins INS - A A PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:148506170_148506171insA uc003wfd.1 - 19 2338_2339 c.2172_2173insT c.(2170-2175)TTTGATfs p.F724fs EZH2_uc011kug.1_Frame_Shift_Ins_p.F673fs|EZH2_uc003wfb.1_Frame_Shift_Ins_p.F729fs|EZH2_uc003wfc.1_Frame_Shift_Ins_p.F685fs|EZH2_uc011kuh.1_Frame_Shift_Ins_p.F715fs NM_004456 NP_004447 Q15910 EZH2_HUMAN enhancer of zeste 2 isoform a 724_725 SET. negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent ESC/E(Z) complex DNA binding|histone-lysine N-methyltransferase activity|protein binding p.D730fs*1(2) haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1) 183 Melanoma(164;0.15) OV - Ovarian serous cystadenocarcinoma(82;0.00239) 0.000 0.39 54 34 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 2 26 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.56 174 224 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.35 11 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 302 104 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.81 5 21 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.11 125 15 TP53 7157 broad.mit.edu 37 17 7579580 7579580 + Frame_Shift_Del DEL G - - PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:7579580delG uc002gim.2 - 4 301 c.107delC c.(106-108)CCGfs p.P36fs TP53_uc002gig.1_Frame_Shift_Del_p.P36fs|TP53_uc002gih.2_Frame_Shift_Del_p.P36fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.P36fs|TP53_uc010cni.1_Frame_Shift_Del_p.P36fs|TP53_uc002gij.2_Frame_Shift_Del_p.P36fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_5'UTR|TP53_uc010cnk.1_Frame_Shift_Del_p.P51fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 36 Transcription activation (acidic).|Interaction with HRMT1L2. P -> L (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.?(1)|p.S33fs*23(1)|p.P36fs*7(1)|p.P13fs*18(1)|p.S33fs*6(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) TGCTTGGGACGGCAAGGGGGA 0.398 0.95 1 19 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.64 36 64 RIPK4 54101 broad.mit.edu 37 21 43176840 43176847 + Frame_Shift_Del DEL GCTTTTCC - - rs138948162 byFrequency PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:43176840_43176847delGCTTTTCC uc002yzn.1 - 2 360_367 c.312_319delGGAAAAGC c.(310-321)CTGGAAAAGCTGfs p.L104fs NM_020639 NP_065690 P57078 RIPK4_HUMAN ankyrin repeat domain 3 104_107 cytoplasm|nucleus ATP binding|protein serine/threonine kinase activity ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1) 7 GAAGCCAGCAGCTTTTCCAGGGAGCCCG 0.591 0.35 66 36 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 109 294 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 90 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 PSN1_PANCREAS NA PSN1_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 4 52 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 423 118 BOK 666 broad.mit.edu 37 2 242509672 242509672 + Frame_Shift_Del DEL T - - PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr2:242509672delT uc002wbq.2 + 4 728 c.482delT c.(481-483)CTGfs p.L161fs BOK_uc002wbr.2_5'Flank NM_032515 NP_115904 Q9UMX3 BOK_HUMAN BCL2-related ovarian killer 161 activation of caspase activity|cell proliferation|signal transduction by p53 class mediator resulting in induction of apoptosis mitochondrial membrane|nucleus ovary(1) 1 all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;2.04e-33)|all cancers(36;7.87e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.52e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.64e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0835) 0.000 0.43 282 209 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.44 25 20 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.13 62 9 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.44 15 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 71 127 NIPBL 25836 broad.mit.edu 37 5 36985082 36985083 + Frame_Shift_Ins INS - A A PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr5:36985082_36985083insA uc003jkl.3 + 10 2299_2300 c.1800_1801insA c.(1798-1803)CCTAAAfs p.P600fs NIPBL_uc003jkk.3_Frame_Shift_Ins_p.P600fs|NIPBL_uc003jkm.1_Frame_Shift_Ins_p.P479fs NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 600_601 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) CTGAGACACCTAAAAAAAAGTC 0.356 0.16 42 8 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.60 38 57 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 1 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 55 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 923 442 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.54 28 33 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 100 60 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 52 275 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 PSN1_PANCREAS NA PSN1_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 77 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 QGP1_PANCREAS NA QGP1_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 41 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.14 393 62 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 58 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.43 54 41 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.78 15 53 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.65 67 125 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.79 7 26 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - AA AA rs34108497;rs146125714 QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr8:62550924_62550925insAA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.57 10 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.52 133 145 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 262 80 SIK2 23235 broad.mit.edu 37 11 111571666 111571667 + Frame_Shift_Ins INS - G G QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr11:111571666_111571667insG uc001plt.2 + 5 653_654 c.535_536insG c.(535-537)AGCfs p.S179fs NM_015191 NP_056006 Q9H0K1 SIK2_HUMAN SNF1-like kinase 2 179 Protein kinase. intracellular protein kinase cascade|regulation of insulin receptor signaling pathway Golgi apparatus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|skin(1) 3 ATGGTGTGGCAGCCCCCCTTAT 0.431 0.10 160 17 KTN1 3895 broad.mit.edu 37 14 56084768 56084770 + In_Frame_Del DEL GAG - - QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr14:56084768_56084770delGAG uc001xcb.2 + 5 1050_1052 c.748_750delGAG c.(748-750)GAGdel p.E250del KTN1_uc001xce.2_In_Frame_Del_p.E250del|KTN1_uc001xcc.2_In_Frame_Del_p.E250del|KTN1_uc001xcd.2_In_Frame_Del_p.E250del|KTN1_uc010trb.1_In_Frame_Del_p.E250del|KTN1_uc001xcf.1_In_Frame_Del_p.E250del NM_182926 NP_891556 Q86UP2 KTN1_HUMAN kinectin 1 isoform a 250 Lumenal (Potential). microtubule-based movement endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction breast(3)|ovary(2)|lung(1)|central_nervous_system(1) 7 AGATAAGAGAGAGGTTATTGATT 0.369 0.32 65 31 TP53 7157 broad.mit.edu 37 17 7579394 7579394 + Frame_Shift_Del DEL G - - QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr17:7579394delG uc002gim.2 - 4 487 c.293delC c.(292-294)CCTfs p.P98fs TP53_uc002gig.1_Frame_Shift_Del_p.P98fs|TP53_uc002gih.2_Frame_Shift_Del_p.P98fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.P98fs|TP53_uc010cni.1_Frame_Shift_Del_p.P98fs|TP53_uc002gij.2_Frame_Shift_Del_p.P98fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.P59fs|TP53_uc010cnk.1_Frame_Shift_Del_p.P113fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 98 Interaction with WWOX. P -> L (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.P98S(4)|p.S99fs*48(3)|p.G59fs*23(3)|p.P98L(2)|p.V73fs*9(1)|p.W91fs*13(1)|p.P13fs*18(1)|p.S33fs*23(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.61 473 747 TP53 7157 broad.mit.edu 37 17 7579397 7579397 + Frame_Shift_Del DEL A - - QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr17:7579397delA uc002gim.2 - 4 484 c.290delT c.(289-291)GTCfs p.V97fs TP53_uc002gig.1_Frame_Shift_Del_p.V97fs|TP53_uc002gih.2_Frame_Shift_Del_p.V97fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.V97fs|TP53_uc010cni.1_Frame_Shift_Del_p.V97fs|TP53_uc002gij.2_Frame_Shift_Del_p.V97fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.V58fs|TP53_uc010cnk.1_Frame_Shift_Del_p.V112fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 97 Interaction with WWOX. V -> I (in familial cancer not matching LFS; germline mutation and in a sporadic cancer; somatic mutation).|V -> F (in a sporadic cancer; somatic mutation).|V -> A (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.G59fs*23(3)|p.V73fs*9(1)|p.S99fs*48(1)|p.V97A(1)|p.V97I(1)|p.W91fs*13(1)|p.P13fs*18(1)|p.S33fs*23(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.36 781 442 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.68 14 30 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 72 205 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 QGP1_PANCREAS NA QGP1_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 2 28 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.52 45 49 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 2 28 THRAP3 9967 broad.mit.edu 37 1 36769478 36769479 + Frame_Shift_Ins INS - G G RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:36769478_36769479insG uc001cae.3 + 12 2952_2953 c.2728_2729insG c.(2728-2730)CGGfs p.R910fs THRAP3_uc001caf.3_Frame_Shift_Ins_p.R910fs|C1orf113_uc010oia.1_5'Flank NM_005119 NP_005110 Q9Y2W1 TR150_HUMAN thyroid hormone receptor associated protein 3 910 androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter mediator complex ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding ovary(5)|lung(3)|breast(1) 9 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) GGGTCGGGGCCGGTTCATGTTC 0.594 0.10 75 8 OBSCN 84033 broad.mit.edu 37 1 228558987 228558988 + Frame_Shift_Ins INS - G G RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:228558987_228558988insG uc009xez.1 + 94 20552_20553 c.20508_20509insG c.(20506-20511)GCCGAGfs p.A6836fs OBSCN_uc001hsr.1_Frame_Shift_Ins_p.A1465fs NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 6836_6837 apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) CTGAGGAAGCCGAGGCCAGTGA 0.733 0.13 46 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 127 164 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.29 56 23 ATXN1 6310 broad.mit.edu 37 6 16327907 16327909 + In_Frame_Del DEL TGA - - rs59310777 by1000genomes RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:16327907_16327909delTGA uc003nbt.2 - 8 1604_1606 c.633_635delTCA c.(631-636)CATCAG>CAG p.H211del ATXN1_uc010jpi.2_In_Frame_Del_p.H211del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 211 Poly-Gln. H -> HQ (in Ref. 1; CAA55793). cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgctgatgctgatgct 0.384 0.30 30 13 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.28 36 14 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.81 3 13 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.30 30 13 MYC 4609 broad.mit.edu 37 8 128750602 128750607 + In_Frame_Del DEL TACCAG - - rs114570780;rs61752959 byFrequency;by1000genomes;byFrequency;by1000genomes RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:128750602_128750607delTACCAG uc003ysh.1 + 3 607_612 c.94_99delTACCAG c.(94-99)TACCAGdel p.YQ32del MYC_uc003ysi.2_In_Frame_Del_p.YQ47del NM_002467 NP_002458 P01106 MYC_HUMAN myc proto-oncogene protein 32_33 Poly-Gln. branching involved in ureteric bud morphogenesis|cell cycle arrest|cell proliferation|cellular iron ion homeostasis|positive regulation of metanephric cap mesenchymal cell proliferation|positive regulation of transcription, DNA-dependent|regulation of telomere maintenance|regulation of transcription from RNA polymerase II promoter|response to drug nucleolus|nucleoplasm E-box binding|protein binding|sequence-specific DNA binding transcription factor activity lung(3)|ovary(1)|central_nervous_system(1)|pancreas(1) 6 all_cancers(1;6.19e-134)|all_epithelial(1;1.75e-119)|all_lung(1;5.66e-51)|Breast(1;1.08e-22)|all_neural(1;4.45e-21)|Medulloblastoma(1;1.88e-20)|Colorectal(1;1.92e-09)|Lung SC(1;4.52e-07)|Ovarian(5;0.000122)|Esophageal squamous(12;0.000995)|Renal(1;0.0921)|Hepatocellular(40;0.108)|Myeloproliferative disorder(2;0.135)|Melanoma(291;0.185) Myeloproliferative disorder(644;0.0255)|Ovarian(118;0.0654)|Breast(495;0.212)|Acute lymphoblastic leukemia(644;0.22) Epithelial(1;1.63e-94)|all cancers(1;5.82e-87)|OV - Ovarian serous cystadenocarcinoma(1;2.12e-71)|BRCA - Breast invasive adenocarcinoma(1;4.3e-14)|Lung(2;0.000381)|Colorectal(2;0.0102)|LUAD - Lung adenocarcinoma(14;0.0172)|READ - Rectum adenocarcinoma(2;0.0723)|LUSC - Lung squamous cell carcinoma(258;0.151) KIRC - Kidney renal clear cell carcinoma(542;0.248) GGAGAACTTCTACCAGCAGCAGCAGC 0.617 0.14 96 16 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.90 4 35 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.34 380 199 MYST4 23522 broad.mit.edu 37 10 76788480 76788481 + Frame_Shift_Ins INS - C C RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:76788480_76788481insC uc001jwn.1 + 18 4391_4392 c.3898_3899insC c.(3898-3900)ACCfs p.T1300fs MYST4_uc001jwo.1_Frame_Shift_Ins_p.T1008fs|MYST4_uc001jwp.1_Frame_Shift_Ins_p.T1117fs NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1300 histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) AGAAGGAAAAACCAGCCCCAGT 0.510 0.12 143 20 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.62 9 15 NCAPD3 23310 broad.mit.edu 37 11 134038484 134038485 + Frame_Shift_Ins INS - C C rs80316248 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:134038484_134038485insC uc001qhd.1 - 26 3858_3859 c.3252_3253insG c.(3250-3255)CTGTTTfs p.L1084fs NCAPD3_uc010scm.1_RNA|NCAPD3_uc009zda.1_Intron|NCAPD3_uc001qhc.1_Frame_Shift_Ins_p.L34fs NM_015261 NP_056076 P42695 CNDD3_HUMAN non-SMC condensin II complex, subunit D3 1084_1085 cell division|mitotic chromosome condensation nuclear centromeric heterochromatin|nuclear condensin complex methylated histone residue binding ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1) 5 all_hematologic(175;0.127) all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227) TTCAATGAAAACAGCCGCTTCT 0.431 0.13 131 20 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.16 67 13 THAP11 57215 broad.mit.edu 37 16 67876788 67876796 + In_Frame_Del DEL CAGCAGCAA - - RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:67876788_67876796delCAGCAGCAA uc002euo.2 + 1 576_584 c.331_339delCAGCAGCAA c.(331-339)CAGCAGCAAdel p.QQQ129del CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 129_131 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) acagcagcagcagcagcaacagcagcaac 0.316 0.36 99 55 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.24 22 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 48 116 SRMS 6725 broad.mit.edu 37 20 62178723 62178724 + Frame_Shift_Ins INS - G G RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:62178723_62178724insG uc002yfi.1 - 1 134_135 c.93_94insC c.(91-96)CCCGGGfs p.P31fs NM_080823 NP_543013 Q9H3Y6 SRMS_HUMAN src-related kinase lacking C-terminal regulatory 31_32 ATP binding|non-membrane spanning protein tyrosine kinase activity stomach(1)|lung(1) 2 all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13) Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06) TCCAGGGACCCGGGGGTGCCAT 0.693 0.13 160 23 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.15 169 31 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.97 11 329 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 16 150 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RCC10RGB_KIDNEY NA RCC10RGB_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 17 XIAP 331 broad.mit.edu 37 X 123025155 123025157 + In_Frame_Del DEL GAG - - RCC10RGB_KIDNEY NA RCC10RGB_KIDNEY NA g.chrX:123025155_123025157delGAG uc010nqu.2 + 4 1171_1173 c.1045_1047delGAG c.(1045-1047)GAGdel p.E350del XIAP_uc004etx.2_In_Frame_Del_p.E350del|XIAP_uc010nqv.2_5'UTR NM_001167 NP_001158 P98170 XIAP_HUMAN baculoviral IAP repeat-containing protein 4 350 anti-apoptosis|apoptosis|induction of apoptosis by intracellular signals|response to DNA damage stimulus cytosol caspase inhibitor activity|ligase activity|protein binding|zinc ion binding ovary(1)|lung(1) 2 TCATTCACTTGAGGAGTGTCTGG 0.197 0.90 2 18 SPEN 23013 broad.mit.edu 37 1 16256165 16256165 + Frame_Shift_Del DEL A - - RCC10RGB_KIDNEY NA RCC10RGB_KIDNEY NA g.chr1:16256165delA uc001axk.1 + 11 3634 c.3430delA c.(3430-3432)AAAfs p.K1144fs SPEN_uc010obp.1_Frame_Shift_Del_p.K1103fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 1144 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) ACCTGAACGTAAATCAGGCCA 0.413 0.61 78 120 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A RCC10RGB_KIDNEY NA RCC10RGB_KIDNEY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.15 79 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RCC10RGB_KIDNEY NA RCC10RGB_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.29 47 19 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RCC10RGB_KIDNEY NA RCC10RGB_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 18 30 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 RCC10RGB_KIDNEY NA RCC10RGB_KIDNEY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.71 67 164 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RCC10RGB_KIDNEY NA RCC10RGB_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 15 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 RCC10RGB_KIDNEY NA RCC10RGB_KIDNEY NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.70 3 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RCC10RGB_KIDNEY NA RCC10RGB_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.70 13 30 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 RCC10RGB_KIDNEY NA RCC10RGB_KIDNEY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.30 123 52 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RCC10RGB_KIDNEY NA RCC10RGB_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 34 420 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RCC10RGB_KIDNEY NA RCC10RGB_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 52 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.31 45 20 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 29 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.20 189 47 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.33 8 4 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 29 54 MGC42105 167359 broad.mit.edu 37 5 43280769 43280769 + Frame_Shift_Del DEL A - - RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:43280769delA uc003jno.2 + 4 2130 c.1249delA c.(1249-1251)AAAfs p.K417fs NM_153361 NP_699192 Q8IY84 NIM1_HUMAN serine/threonine-protein kinase NIM1 417 ATP binding|magnesium ion binding|protein serine/threonine kinase activity lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1) 9 AAGAGACCTCAAAAAAGGGTC 0.403 0.32 17 8 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 6 14 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.24 101 32 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 1 21 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.37 137 79 SRP14 6727 broad.mit.edu 37 15 40328596 40328597 + In_Frame_Ins INS - TGC TGC RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:40328596_40328597insTGC uc001zkq.2 - 5 420_421 c.348_349insGCA c.(346-351)insGCA p.116_117insA SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116_117 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) gctgcggcaggtgctgctgctg 0.228 0.27 40 15 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.59 24 35 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 113 345 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 56 BIK 638 broad.mit.edu 37 22 43525245 43525253 + In_Frame_Del DEL GCTGCTGCT - - rs62637687 byFrequency RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:43525245_43525253delGCTGCTGCT uc003bdk.2 + 5 477_485 c.417_425delGCTGCTGCT c.(415-426)GCGCTGCTGCTG>GCG p.LLL140del NM_001197 NP_001188 Q13323 BIK_HUMAN BCL2-interacting killer 140_142 Leucine-zipper (Potential).|Helical; (Potential). apoptosis|induction of apoptosis|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria endomembrane system|integral to membrane 0 Ovarian(80;0.0694) tgctgctggcgctgctgctgctgctggcg 0.560 0.54 19 22 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 2 91 SPEN 23013 broad.mit.edu 37 1 16258933 16258934 + Frame_Shift_Ins INS - C C RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr1:16258933_16258934insC uc001axk.1 + 11 6402_6403 c.6198_6199insC c.(6196-6201)AAACCGfs p.K2066fs SPEN_uc010obp.1_Frame_Shift_Ins_p.K2025fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2066_2067 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) TAGAGAAAAAACCGGCCCCTGA 0.475 0.12 74 10 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.14 230 39 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.54 6 7 FAM157A 728262 broad.mit.edu 37 3 197880131 197880136 + In_Frame_Del DEL GCAGCA - - RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr3:197880131_197880136delGCAGCA uc011bup.1 + 2 210_215 c.210_215delGCAGCA c.(208-216)TGGCAGCAG>TGG p.QQ83del NM_001145248 NP_001138720 C9JC47 F157A_HUMAN family with sequence similarity 157, member A 83_84 Gln-rich. 0 ACAAGAACTGgcagcagcagcagcag 0.403 0.40 6 4 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 74 75 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 25 51 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.47 161 140 TBP 6908 broad.mit.edu 37 6 170871034 170871035 + In_Frame_Ins INS - CAA CAA RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr6:170871034_170871035insCAA uc003qxt.2 + 3 442_443 c.210_211insCAA c.(208-213)insCAA p.95_96insQ TBP_uc003qxu.2_In_Frame_Ins_p.95_96insQ|TBP_uc011ehf.1_In_Frame_Ins_p.75_76insQ|TBP_uc011ehg.1_In_Frame_Ins_p.95_96insQ NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 95_96 cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) agcagcagcagcagcaacagca 0.158 0.40 41 27 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 29 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.64 327 577 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 291 167 SIK2 23235 broad.mit.edu 37 11 111591300 111591300 + Frame_Shift_Del DEL A - - RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr11:111591300delA uc001plt.2 + 11 1712 c.1594delA c.(1594-1596)AACfs p.N532fs NM_015191 NP_056006 Q9H0K1 SIK2_HUMAN SNF1-like kinase 2 532 intracellular protein kinase cascade|regulation of insulin receptor signaling pathway Golgi apparatus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|skin(1) 3 TCTGGAAGACAACCCTTCCCT 0.502 0.22 195 54 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.36 30 17 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.55 9 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 21 184 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 5 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 122 659 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RCM1_LARGE_INTESTINE NA RCM1_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 5 65 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RDES_BONE NA RDES_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 7 79 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes RDES_BONE NA RDES_BONE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.71 6 15 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A RDES_BONE NA RDES_BONE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 133 28 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 RDES_BONE NA RDES_BONE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.47 19 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RDES_BONE NA RDES_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.72 84 218 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RDES_BONE NA RDES_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.76 31 97 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 RDES_BONE NA RDES_BONE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.11 68 8 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 RDES_BONE NA RDES_BONE NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.13 272 39 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes RDES_BONE NA RDES_BONE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.97 1 34 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 RDES_BONE NA RDES_BONE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.39 71 45 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RDES_BONE NA RDES_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 56 MYST4 23522 broad.mit.edu 37 10 76781905 76781906 + In_Frame_Ins INS - GAA GAA rs138589645;rs111976843 by1000genomes RDES_BONE NA RDES_BONE NA g.chr10:76781905_76781906insGAA uc001jwn.1 + 16 3781_3782 c.3288_3289insGAA c.(3286-3291)insGAA p.1104_1105insE MYST4_uc001jwm.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwo.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwp.1_In_Frame_Ins_p.921_922insE NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1104_1105 histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) aggaagaagaggaagaagaaga 0.203 0.15 132 23 CASP12 120329 broad.mit.edu 37 11 104761986 104761987 + Frame_Shift_Ins INS - C C rs140309344 by1000genomes RDES_BONE NA RDES_BONE NA g.chr11:104761986_104761987insC uc001pht.1 - 4 833_834 c.577_578insG c.(577-579)GATfs p.D193fs CASP12_uc001phu.1_Frame_Shift_Ins_p.D96fs|CASP12_uc009yxf.1_Frame_Shift_Ins_p.D193fs|CASP12_uc001phv.1_Intron|CASP12_uc001phw.1_Intron|CASP12_uc001phx.1_Intron NR_000035 RecName: Full=Inactive caspase-12; Short=CASP-12; 0 GATGGTGTCATCGTGAAGAACA 0.485 0.42 7 5 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C RDES_BONE NA RDES_BONE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 8 100 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RDES_BONE NA RDES_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 34 137 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 RDES_BONE NA RDES_BONE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.24 239 77 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RDES_BONE NA RDES_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 112 958 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RDES_BONE NA RDES_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 81 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 15 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.27 22 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 48 41 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.77 6 20 FBN2 2201 broad.mit.edu 37 5 127872143 127872145 + In_Frame_Del DEL AGT - - RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr5:127872143_127872145delAGT uc003kuu.2 - 2 726_728 c.287_289delACT c.(286-291)TACTGC>TGC p.Y96del FBN2_uc003kuv.2_In_Frame_Del_p.Y96del|FBN2_uc003kuw.3_In_Frame_Del_p.Y96del|FBN2_uc003kux.1_In_Frame_Del_p.Y96del NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 96 bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) 0.000 0.40 24 16 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.20 1132 291 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 16 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 206 73 SIK2 23235 broad.mit.edu 37 11 111571666 111571667 + Frame_Shift_Ins INS - G G RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr11:111571666_111571667insG uc001plt.2 + 5 653_654 c.535_536insG c.(535-537)AGCfs p.S179fs NM_015191 NP_056006 Q9H0K1 SIK2_HUMAN SNF1-like kinase 2 179 Protein kinase. intracellular protein kinase cascade|regulation of insulin receptor signaling pathway Golgi apparatus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|skin(1) 3 ATGGTGTGGCAGCCCCCCTTAT 0.431 0.24 109 34 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.45 11 9 TP53BP1 7158 broad.mit.edu 37 15 43714217 43714219 + In_Frame_Del DEL GGA - - RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr15:43714217_43714219delGGA uc001zrs.2 - 19 4067_4069 c.3919_3921delTCC c.(3919-3921)TCCdel p.S1307del TP53BP1_uc010udp.1_In_Frame_Del_p.S1307del|TP53BP1_uc001zrq.3_In_Frame_Del_p.S1312del|TP53BP1_uc001zrr.3_In_Frame_Del_p.S1312del|TP53BP1_uc010udq.1_In_Frame_Del_p.S1312del NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 1307 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) TGGATGCCTTGGAGGAGAAGGAG 0.537 0.15 47 8 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 6 70 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.67 28 56 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 121 595 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RD_SOFT_TISSUE NA RD_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 5 39 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 3 31 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.44 74 57 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 25 49 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 16 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 59 NOTCH1 4851 broad.mit.edu 37 9 139390908 139390908 + Frame_Shift_Del DEL T - - REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:139390908delT uc004chz.2 - 34 7283 c.7283delA c.(7282-7284)CACfs p.H2428fs NM_017617 NP_060087 P46531 NOTC1_HUMAN notch1 preproprotein 2428 Cytoplasmic (Potential). aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity p.L2430_G2431>CLVSR(1)|p.H2429fs*8(1) haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1) 856 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06) 0.000 0.95 16 338 NUP98 4928 broad.mit.edu 37 11 3765771 3765772 + Frame_Shift_Del DEL GT - - REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:3765771_3765772delGT uc001lyh.2 - 12 1666_1667 c.1375_1376delAC c.(1375-1377)ACTfs p.T459fs NUP98_uc001lyi.2_Frame_Shift_Del_p.T459fs|NUP98_uc001lyj.1_Frame_Shift_Del_p.T459fs|NUP98_uc001lyk.1_Frame_Shift_Del_p.T476fs NM_016320 NP_057404 P52948 NUP98_HUMAN nucleoporin 98kD isoform 1 476 Gly/Thr-rich. carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex protein binding|structural constituent of nuclear pore|transporter activity breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1) 12 Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227) BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199) 0.000 0.43 760 578 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.77 3 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 670 375 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.43 17 13 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 37 371 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.72 26 66 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.50 395 390 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 6 106 NF2 4771 broad.mit.edu 37 22 30054198 30054222 + Frame_Shift_Del DEL ATCTGAAGATAGCTCAGGACCTGGA - - REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:30054198_30054222delATCTGAAGATAGCTCAGGACCTGGA uc003age.3 + 7 1063_1087 c.620_644delATCTGAAGATAGCTCAGGACCTGGA c.(619-645)TATCTGAAGATAGCTCAGGACCTGGAGfs p.Y207fs NF2_uc003afy.3_Frame_Shift_Del_p.Y207fs|NF2_uc003afz.3_Frame_Shift_Del_p.Y124fs|NF2_uc003agf.3_Frame_Shift_Del_p.Y207fs|NF2_uc003agb.3_Frame_Shift_Del_p.Y130fs|NF2_uc003agc.3_Frame_Shift_Del_p.Y169fs|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Frame_Shift_Del_p.Y207fs|NF2_uc003aga.3_Frame_Shift_Del_p.Y165fs|NF2_uc003agh.3_Frame_Shift_Del_p.Y166fs|NF2_uc003agi.3_Frame_Shift_Del_p.Y124fs|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Frame_Shift_Del_p.Y169fs NM_000268 NP_000259 P35240 MERL_HUMAN neurofibromin 2 isoform 1 207_215 FERM. actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane cytoskeletal protein binding|protein binding p.Q212*(8)|p.A211D(2)|p.Y207fs*20(2)|p.L214fs*6(1)|p.Q212fs*8(1)|p.E215fs*4(1)|p.A211fs*17(1)|p.?(1)|p.M216fs*7(1)|p.M205_Y207del(1)|p.L208fs*26(1)|p.E204fs*18(1)|p.Y207*(1)|p.Y207fs*27(1)|p.E215*(1)|p.L208fs*1(1)|p.L127_D382del(1)|p.L140_P252del(1) meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1) 728 GAAATGGAATATCTGAAGATAGCTCAGGACCTGGAGATGTACGGT 0.493 0.21 88 23 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 4 34 CDK11B 984 broad.mit.edu 37 1 1650890 1650892 + In_Frame_Del DEL CTC - - REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:1650890_1650892delCTC uc001agv.1 - 6 341_343 c.230_232delGAG c.(229-234)GGAGAA>GAA p.G77del CDK11B_uc001ags.1_5'Flank|CDK11B_uc001agt.1_5'Flank|CDK11B_uc001aha.1_In_Frame_Del_p.G43del|CDK11B_uc001agw.1_In_Frame_Del_p.G43del|CDK11B_uc001agy.1_In_Frame_Del_p.G77del|CDK11B_uc001agx.1_In_Frame_Del_p.G77del|CDK11B_uc001agz.1_5'UTR|SLC35E2B_uc001ahh.3_Intron|SLC35E2_uc009vkm.1_Intron|CDK11A_uc009vkr.2_In_Frame_Del_p.G77del|CDK11A_uc009vks.2_In_Frame_Del_p.G77del|CDK11A_uc010nys.1_In_Frame_Del_p.G77del|CDK11A_uc010nyt.1_In_Frame_Del_p.G77del|CDK11A_uc010nyu.1_RNA|CDK11A_uc009vkt.1_In_Frame_Del_p.G77del|CDK11A_uc009vku.1_In_Frame_Del_p.G77del|CDK11A_uc009vkv.1_In_Frame_Del_p.G77del|CDK11A_uc001aht.1_In_Frame_Del_p.G77del|CDK11B_uc001ahu.1_In_Frame_Del_p.G77del|CDK11B_uc001ahv.1_In_Frame_Del_p.G77del|CDK11B_uc001ahw.1_In_Frame_Del_p.G77del NM_033486 NP_277021 P21127 CD11B_HUMAN cell division cycle 2-like 1 (PITSLRE proteins) 77 apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent cytoplasm|nucleus ATP binding|cyclin-dependent protein kinase activity|protein binding skin(1) 1 TCATCTTCTTCTCCTCTGAAATA 0.389 0.15 222 38 RPL22 6146 broad.mit.edu 37 1 6246851 6246852 + Frame_Shift_Ins INS - T T REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:6246851_6246852insT uc001amd.2 - 4 313_314 c.267_268insA c.(265-270)AAATATfs p.K89fs RPL22_uc001ame.2_Frame_Shift_Ins_p.I84fs NM_000983 NP_000974 P35268 RL22_HUMAN ribosomal protein L22 proprotein 89_90 endocrine pancreas development|translational elongation|translational termination|viral transcription cytosolic large ribosomal subunit heparin binding|RNA binding|structural constituent of ribosome 0 Ovarian(185;0.0634) all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211) Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182) TTCTTCAAATATTTTTTGGTGA 0.366 0.55 20 24 SPEN 23013 broad.mit.edu 37 1 16259480 16259480 + Frame_Shift_Del DEL C - - REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:16259480delC uc001axk.1 + 11 6949 c.6745delC c.(6745-6747)CCCfs p.P2249fs SPEN_uc010obp.1_Frame_Shift_Del_p.P2208fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2249 RID.|Interaction with MSX2 (By similarity). interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) AGATCTGCAACCCCCCGCAGG 0.557 0.46 141 119 ARID1A 8289 broad.mit.edu 37 1 27099103 27099103 + Frame_Shift_Del DEL C - - REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:27099103delC uc001bmv.1 + 13 3892 c.3519delC c.(3517-3519)ATCfs p.I1173fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.I1173fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.I1173fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.I790fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.I20fs|ARID1A_uc009vsm.1_5'Flank|ARID1A_uc009vsn.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1173 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.P1175fs*5(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) ACAGTCAGATCCCCCCATTGC 0.572 0.61 9 14 MAST2 23139 broad.mit.edu 37 1 46495173 46495173 + Frame_Shift_Del DEL C - - REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:46495173delC uc001cov.2 + 19 2537 c.2254delC c.(2254-2256)CCCfs p.P752fs MAST2_uc001cow.2_Frame_Shift_Del_p.P752fs|MAST2_uc001coy.1_Frame_Shift_Del_p.P426fs|MAST2_uc001coz.1_Frame_Shift_Del_p.P637fs|MAST2_uc001cpa.2_RNA NM_015112 NP_055927 Q6P0Q8 MAST2_HUMAN microtubule associated serine/threonine kinase 752 Protein kinase. regulation of interleukin-12 biosynthetic process|spermatid differentiation cytoplasm|cytoskeleton|plasma membrane ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity ovary(5)|lung(3)|stomach(2)|breast(1) 11 Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184) TGAGGCACTGCCCCCAGACGC 0.552 0.49 80 76 DENND4B 9909 broad.mit.edu 37 1 153907279 153907281 + In_Frame_Del DEL CTG - - REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:153907279_153907281delCTG uc001fdd.1 - 18 3129_3131 c.2728_2730delCAG c.(2728-2730)CAGdel p.Q910del uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) ACACctgctcctgctgctgctgc 0.463 0.11 62 8 BMP2K 55589 broad.mit.edu 37 4 79792125 79792136 + In_Frame_Del DEL CAGCAACAGCAA - - REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:79792125_79792136delCAGCAACAGCAA uc003hlk.2 + 11 1586_1597 c.1420_1431delCAGCAACAGCAA c.(1420-1431)CAGCAACAGCAAdel p.QQQQ482del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQQ482del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 482_485 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 acagcagcagcagcaacagcaacagcagcagc 0.193 0.19 126 29 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 37 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 82 126 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.39 31 20 JARID2 3720 broad.mit.edu 37 6 15513220 15513220 + Frame_Shift_Del DEL A - - REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:15513220delA uc003nbj.2 + 15 3454 c.3210delA c.(3208-3210)GCAfs p.A1070fs JARID2_uc011div.1_Frame_Shift_Del_p.A898fs NM_004973 NP_004964 Q92833 JARD2_HUMAN jumonji, AT rich interactive domain 2 protein 1070 central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent chromatin binding ovary(2)|lung(1)|pancreas(1) 4 Breast(50;0.0142)|Ovarian(93;0.103) all_hematologic(90;0.00612) AAGCAGAAGCAAAAAAAGAAA 0.517 0.56 34 43 DST 667 broad.mit.edu 37 6 56420302 56420302 + Frame_Shift_Del DEL T - - REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:56420302delT uc003pdf.2 - 54 8648 c.8620delA c.(8620-8622)ATGfs p.M2874fs DST_uc003pcz.3_Frame_Shift_Del_p.M2696fs|DST_uc011dxj.1_Frame_Shift_Del_p.M2725fs|DST_uc011dxk.1_Frame_Shift_Del_p.M2736fs|DST_uc003pcy.3_Frame_Shift_Del_p.M2370fs NM_001144769 NP_001138241 Q03001 DYST_HUMAN dystonin isoform 2 4782 cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1) 14 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) TCCTGCTTCATTTTTTGGGCT 0.448 0.44 191 150 MYB 4602 broad.mit.edu 37 6 135520125 135520126 + Frame_Shift_Ins INS - AGGG AGGG REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:135520125_135520126insAGGG uc003qfc.2 + 10 1482_1483 c.1283_1284insAGGG c.(1282-1284)AAAfs p.K428fs MYB_uc003qfh.2_Frame_Shift_Ins_p.K549fs|MYB_uc003qfi.2_Frame_Shift_Ins_p.K533fs|MYB_uc010kgi.2_Frame_Shift_Ins_p.K428fs|MYB_uc003qfq.2_Frame_Shift_Ins_p.K546fs|MYB_uc010kgj.2_Frame_Shift_Ins_p.K393fs|MYB_uc003qfo.2_Frame_Shift_Ins_p.K343fs|MYB_uc003qfu.2_Frame_Shift_Ins_p.K425fs|MYB_uc003qfl.2_RNA|MYB_uc003qfv.2_RNA|MYB_uc003qfz.2_RNA|MYB_uc003qfx.2_RNA|MYB_uc003qga.2_RNA|MYB_uc003qgb.2_RNA|MYB_uc010kgk.2_RNA|MYB_uc003qfd.2_RNA|MYB_uc003qfe.2_RNA|MYB_uc003qfg.2_RNA|MYB_uc003qff.2_RNA|MYB_uc003qfj.2_RNA|MYB_uc003qfm.2_RNA|MYB_uc003qfp.2_RNA|MYB_uc003qfn.2_RNA|MYB_uc003qfk.2_RNA|MYB_uc003qfr.2_RNA|MYB_uc003qfs.2_Frame_Shift_Ins_p.K54fs|MYB_uc003qft.2_RNA|MYB_uc003qfw.2_Frame_Shift_Ins_p.K240fs|MYB_uc003qfy.2_RNA|MYB_uc003qgc.2_RNA|MYB_uc003qfb.1_Frame_Shift_Ins_p.K428fs NM_005375 NP_005366 P10242 MYB_HUMAN v-myb myeloblastosis viral oncogene homolog 428 Negative regulatory domain (By similarity). blood coagulation|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of histone H3-K4 methylation|positive regulation of histone H3-K9 methylation|positive regulation of T-helper cell differentiation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear matrix DNA binding|protein binding lung(1) 1 all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221) Lung NSC(302;3.08e-05)|Ovarian(999;0.208) OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117) ATTGGTCACAAATTGACTGTTA 0.351 0.27 41 15 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 22 KCNH2 3757 broad.mit.edu 37 7 150644883 150644884 + Frame_Shift_Ins INS - C C REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:150644883_150644884insC uc003wic.2 - 12 2788_2789 c.2775_2776insG c.(2773-2778)GGGCCGfs p.G925fs KCNH2_uc003wib.2_Frame_Shift_Ins_p.G585fs|KCNH2_uc011kux.1_Frame_Shift_Ins_p.G829fs NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 925_926 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) 0.000 0.27 701 255 MLL3 58508 broad.mit.edu 37 7 151873587 151873588 + Frame_Shift_Ins INS - A A REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:151873587_151873588insA uc003wla.2 - 38 9169_9170 c.8950_8951insT c.(8950-8952)TCTfs p.S2984fs MLL3_uc003wkz.2_Frame_Shift_Ins_p.S2045fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.S493fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 2984 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) CACACCCTGAGAAAAAACATGG 0.470 0.48 132 121 PAXIP1 22976 broad.mit.edu 37 7 154760540 154760541 + In_Frame_Ins INS - TGC TGC REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:154760540_154760541insTGC uc003wlp.2 - 7 1413_1414 c.1370_1371insGCA c.(1369-1371)CAA>CAGCAA p.457_457Q>QQ PAXIP1_uc003wlq.1_In_Frame_Ins_p.423_423Q>QQ|PAXIP1_uc011kvs.1_In_Frame_Ins_p.421_421Q>QQ|PAXIP1_uc003wlr.1_In_Frame_Ins_p.366_366Q>QQ NM_007349 NP_031375 Q6ZW49 PAXI1_HUMAN PAX interacting protein 1 457 Gln-rich. DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent histone methyltransferase complex|nuclear matrix p.F457C(1) lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_neural(206;0.119) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.0296) UCEC - Uterine corpus endometrioid carcinoma (81;0.178) GCGGATGGGCTtgctgctgctg 0.203 0.21 37 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 2 41 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.58 245 345 PAX5 5079 broad.mit.edu 37 9 36882049 36882050 + Frame_Shift_Ins INS - G G rs34810717 byFrequency;by1000genomes REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:36882049_36882050insG uc003zzo.1 - 8 1411_1412 c.963_964insC c.(961-966)CCCGCTfs p.P321fs PAX5_uc011lpt.1_Frame_Shift_Ins_p.P117fs|PAX5_uc011lpu.1_Intron|PAX5_uc011lpv.1_Intron|PAX5_uc011lpw.1_Intron|PAX5_uc011lpx.1_Intron|PAX5_uc011lpy.1_Intron|PAX5_uc010mls.1_Intron|PAX5_uc011lpz.1_Frame_Shift_Ins_p.P278fs|PAX5_uc011lqa.1_Frame_Shift_Ins_p.P213fs|PAX5_uc010mlq.1_RNA|PAX5_uc011lqb.1_RNA|PAX5_uc010mlo.1_Intron|PAX5_uc010mlp.1_Frame_Shift_Ins_p.P321fs|PAX5_uc011lqc.1_Frame_Shift_Ins_p.P278fs|PAX5_uc010mlr.1_Intron NM_016734 NP_057953 Q02548 PAX5_HUMAN paired box 5 321_322 cell differentiation|humoral immune response|nervous system development|organ morphogenesis|spermatogenesis|transcription from RNA polymerase II promoter nucleus DNA binding p.?(22)|p.A322fs*19(3) PAX5/JAK2(18) haematopoietic_and_lymphoid_tissue(142)|lung(3)|central_nervous_system(2) 147 all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44) GBM - Glioblastoma multiforme(29;0.0108) CCCTGTCCAGCGGGGGGGACGT 0.639 0.29 79 33 SYK 6850 broad.mit.edu 37 9 93607788 93607789 + Frame_Shift_Ins INS - A A REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:93607788_93607789insA uc004aqz.2 + 3 695_696 c.490_491insA c.(490-492)GAAfs p.E164fs SYK_uc004aqy.2_Frame_Shift_Ins_p.E164fs|SYK_uc004ara.2_Frame_Shift_Ins_p.E164fs|SYK_uc004arb.2_Frame_Shift_Ins_p.E164fs|SYK_uc004arc.2_Frame_Shift_Ins_p.E164fs|SYK_uc011ltr.1_RNA|SYK_uc011lts.1_RNA|SYK_uc011ltt.1_RNA NM_003177 NP_003168 P43405 KSYK_HUMAN spleen tyrosine kinase isoform 1 164 cell proliferation|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|neutrophil chemotaxis|organ morphogenesis|platelet activation|protein complex assembly cytosol|T cell receptor complex ATP binding|integrin binding|non-membrane spanning protein tyrosine kinase activity lung(2)|stomach(1)|ovary(1)|skin(1) 5 CACAGCCCATGAAAAAATGCCT 0.485 0.33 76 37 CUBN 8029 broad.mit.edu 37 10 16916432 16916433 + Frame_Shift_Ins INS - G G REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:16916432_16916433insG uc001ioo.2 - 58 9228_9229 c.9176_9177insC c.(9175-9177)CCAfs p.P3059fs CUBN_uc009xjq.1_RNA|CUBN_uc009xjr.1_Frame_Shift_Ins_p.P415fs NM_001081 NP_001072 O60494 CUBN_HUMAN cubilin precursor 3059 CUB 23. cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1) 19 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) GCATATCATTTGGGTAGTCTGC 0.426 0.47 94 82 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 524 136 ZMYM2 7750 broad.mit.edu 37 13 20657066 20657067 + In_Frame_Ins INS - TGGCCC TGGCCC REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:20657066_20657067insTGGCCC uc001umr.2 + 24 4012_4013 c.3714_3715insTGGCCC c.(3712-3717)insTGGCCC p.1238_1239insWP ZMYM2_uc001ums.2_In_Frame_Ins_p.1238_1239insWP|ZMYM2_uc001umt.2_In_Frame_Ins_p.1238_1239insWP|ZMYM2_uc001umv.2_In_Frame_Ins_p.618_619insWP|ZMYM2_uc001umw.2_In_Frame_Ins_p.691_692insWP NM_003453 NP_003444 Q9UBW7 ZMYM2_HUMAN zinc finger protein 198 1238_1239 regulation of transcription, DNA-dependent|transcription, DNA-dependent PML body ubiquitin conjugating enzyme binding|zinc ion binding lung(3)|ovary(2)|prostate(1) 6 all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856) ACTTAAGACTTTCCTTTGGCAC 0.386 0.35 43 23 MTUS2 23281 broad.mit.edu 37 13 30077301 30077301 + Frame_Shift_Del DEL G - - REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:30077301delG uc001usl.3 + 14 4156 c.4098delG c.(4096-4098)TCGfs p.S1366fs MTUS2_uc001usm.3_Frame_Shift_Del_p.S335fs|MTUS2_uc010aau.2_Frame_Shift_Del_p.S245fs|MTUS2_uc010tdq.1_Frame_Shift_Del_p.S118fs NM_001033602 NP_001028774 Q5JR59 MTUS2_HUMAN hypothetical protein LOC23281 isoform a 1356 cytoplasm|microtubule microtubule binding|protein homodimerization activity 0 GCTCCTCCTCGGGGCCCTCCT 0.632 0.47 112 98 BRCA2 675 broad.mit.edu 37 13 32972893 32972893 + Frame_Shift_Del DEL A - - REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:32972893delA uc001uub.1 + 27 10470 c.10243delA c.(10243-10245)AAAfs p.K3415fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 3415 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) AATTACAACTAAAAAATATAT 0.353 0.43 38 29 ADAM10 102 broad.mit.edu 37 15 58913755 58913756 + Frame_Shift_Del DEL TA - - REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:58913755_58913756delTA uc002afd.1 - 11 1869_1870 c.1425_1426delTA c.(1423-1428)TATAGTfs p.Y475fs ADAM10_uc010bgc.1_RNA|ADAM10_uc010ugz.1_Frame_Shift_Del_p.Y174fs|ADAM10_uc002afe.1_Intron|ADAM10_uc002aff.1_Frame_Shift_Del_p.Y12fs NM_001110 NP_001101 O14672 ADA10_HUMAN ADAM metallopeptidase domain 10 precursor 475_476 Extracellular (Potential).|Disintegrin. cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding skin(2) 2 GBM - Glioblastoma multiforme(80;0.202) CACTGGTCACTATAGCCACAAT 0.401 0.42 92 68 WNK4 65266 broad.mit.edu 37 17 40936458 40936458 + Frame_Shift_Del DEL C - - REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:40936458delC uc002ibj.2 + 4 1052 c.1031delC c.(1030-1032)GCCfs p.A344fs WNK4_uc010wgx.1_Frame_Shift_Del_p.P38fs|WNK4_uc002ibk.1_Frame_Shift_Del_p.A116fs|WNK4_uc010wgy.1_5'Flank NM_032387 NP_115763 Q96J92 WNK4_HUMAN WNK lysine deficient protein kinase 4 344 Protein kinase. intracellular protein kinase cascade tight junction ATP binding|protein serine/threonine kinase activity ovary(3)|skin(3)|stomach(1) 7 Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.0749) GAATTCATGGCCCCCGAGATG 0.617 0.59 11 16 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.41 75 52 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.26 58 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 232 667 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 9 101 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 3 37 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 366 123 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.48 77 70 TPRXL 348825 broad.mit.edu 37 3 14106310 14106311 + In_Frame_Ins INS - CCAGCACCAGCAGTC CCAGCACCAGCAGTC RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr3:14106310_14106311insCCAGCACCAGCAGTC uc011avd.1 + 3 1089_1090 c.634_635insCCAGCACCAGCAGTC c.(634-636)TCC>TCCAGCACCAGCAGTCCC p.217_218insSTSSP TPRXL_uc003byh.1_In_Frame_Ins_p.217_218insSTSSP|TPRXL_uc003byg.2_In_Frame_Ins_p.217_218insSTSSP NR_002223 RecName: Full=Putative protein TPRXL; 0 cagcagcagctccagcaccagc 0.213 0.58 30 42 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 90 119 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.81 7 30 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.11 54 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.75 4 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 61 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.30 57 24 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 1011 460 PLCB2 5330 broad.mit.edu 37 15 40589039 40589041 + In_Frame_Del DEL TTC - - RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr15:40589039_40589041delTTC uc001zld.2 - 14 1693_1695 c.1392_1394delGAA c.(1390-1395)AAGAAC>AAC p.K464del PLCB2_uc010bbo.2_In_Frame_Del_p.K464del|PLCB2_uc010ucm.1_In_Frame_Del_p.K464del NM_004573 NP_004564 Q00722 PLCB2_HUMAN phospholipase C, beta 2 464 activation of phospholipase C activity|intracellular signal transduction|lipid catabolic process|phospholipid metabolic process|synaptic transmission cytosol calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity ovary(3)|breast(3)|kidney(1)|pancreas(1) 8 all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508) AGAAAACTGGTTCTTCTTGTTCT 0.591 0.38 55 33 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 10 69 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.13 892 133 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.78 103 358 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 39 346 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RERFGC1B_STOMACH NA RERFGC1B_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 98 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 6 119 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.48 874 810 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.21 78 21 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 243 62 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.50 57 58 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 196 224 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.56 159 199 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 62 124 PMS2CL 441194 broad.mit.edu 37 7 6776721 6776722 + Frame_Shift_Ins INS - T T RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr7:6776721_6776722insT uc011jxb.1 + 5 775_776 c.1_2insT c.(1-3)ATGfs p.M1fs PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 CTTAATAAAAATGCATGCAGCG 0.411 0.49 219 211 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.71 5 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 26 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.53 132 150 MASTL 84930 broad.mit.edu 37 10 27459658 27459663 + In_Frame_Del DEL AGATAG - - rs149364724 RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr10:27459658_27459663delAGATAG uc001itm.2 + 8 2409_2414 c.1770_1775delAGATAG c.(1768-1776)TCAGATAGA>TCA p.DR591del MASTL_uc001itl.2_In_Frame_Del_p.DR591del|MASTL_uc009xkw.1_In_Frame_Del_p.DR591del|MASTL_uc009xkx.1_RNA NM_032844 NP_116233 Q96GX5 GWL_HUMAN microtubule associated serine/threonine 591_592 Protein kinase. cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus centrosome|cleavage furrow|nucleus ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity stomach(1)|ovary(1)|lung(1) 3 CCTTAGATTCAGATAGAAGCATCAAA 0.345 0.59 258 365 NOTCH3 4854 broad.mit.edu 37 19 15298807 15298808 + Splice_Site INS - G G RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr19:15298807_15298808insG uc002nan.2 - 10 1569 c.1493_splice c.e10-1 p.G498_splice NOTCH3_uc002nao.1_Splice_Site_p.G498_splice NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.72 71 185 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 138 471 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RERFLCAD1_LUNG NA RERFLCAD1_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.87 25 164 MAGEB16 139604 broad.mit.edu 37 X 35820679 35820679 + Frame_Shift_Del DEL T - - RERFLCKJ_LUNG NA RERFLCKJ_LUNG NA g.chrX:35820679delT uc010ngt.1 + 2 645 c.366delT c.(364-366)AATfs p.N122fs NM_001099921 NP_001093391 A2A368 MAGBG_HUMAN melanoma antigen family B, 16 122 MAGE. lung(3)|ovary(2)|breast(1)|skin(1) 7 TTTTGGTGAATTTCATGCTGC 0.443 0.97 1 32 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RERFLCKJ_LUNG NA RERFLCKJ_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 3 24 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RERFLCKJ_LUNG NA RERFLCKJ_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.49 75 73 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RERFLCKJ_LUNG NA RERFLCKJ_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.77 21 72 RASA1 5921 broad.mit.edu 37 5 86679550 86679550 + Frame_Shift_Del DEL T - - RERFLCKJ_LUNG NA RERFLCKJ_LUNG NA g.chr5:86679550delT uc003kiw.2 + 21 2829 c.2711delT c.(2710-2712)CTCfs p.L904fs RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_Frame_Shift_Del_p.L727fs|RASA1_uc011ctv.1_Frame_Shift_Del_p.L737fs|RASA1_uc011ctw.1_Frame_Shift_Del_p.L738fs|RASA1_uc010jaw.2_Frame_Shift_Del_p.L726fs NM_002890 NP_002881 P20936 RASA1_HUMAN RAS p21 protein activator 1 isoform 1 904 Ras-GAP. cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis cytosol|intrinsic to internal side of plasma membrane glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding upper_aerodigestive_tract(3)|ovary(1)|lung(1) 5 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) TTTCTTCGACTCATCTGTCCT 0.289 0.99 1 81 AIM1 202 broad.mit.edu 37 6 106969017 106969018 + Frame_Shift_Ins INS - TGAAA TGAAA RERFLCKJ_LUNG NA RERFLCKJ_LUNG NA g.chr6:106969017_106969018insTGAAA uc003prh.2 + 2 3197_3198 c.2710_2711insTGAAA c.(2710-2712)TTCfs p.F904fs NM_001624 NP_001615 Q9Y4K1 AIM1_HUMAN absent in melanoma 1 904 sugar binding breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1) 9 Breast(9;0.0138)|all_epithelial(6;0.169) all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473) Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305) all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858) CTTAAAGGTCTTCAATTTCAAC 0.450 0.16 127 25 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - RERFLCKJ_LUNG NA RERFLCKJ_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.83 3 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RERFLCKJ_LUNG NA RERFLCKJ_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 29 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RERFLCKJ_LUNG NA RERFLCKJ_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 312 97 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RERFLCKJ_LUNG NA RERFLCKJ_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.59 27 39 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RERFLCKJ_LUNG NA RERFLCKJ_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 146 318 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RERFLCKJ_LUNG NA RERFLCKJ_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 4 119 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.62 21 35 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.50 188 190 CCNA2 890 broad.mit.edu 37 4 122743803 122743804 + Splice_Site INS - A A RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr4:122743803_122743804insA uc003iec.3 - 2 519 c.214_splice c.e2-1 p.V72_splice NM_001237 NP_001228 P20248 CCNA2_HUMAN cyclin A cell division|mitosis|mitotic cell cycle G2/M transition DNA damage checkpoint|Ras protein signal transduction|regulation of cyclin-dependent protein kinase activity cytoplasm|nucleoplasm protein kinase binding ovary(1) 1 GGGTGCAACCTAAAAAAAAATT 0.406 0.46 29 25 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 34 45 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.88 5 38 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.45 22 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 22 CHUK 1147 broad.mit.edu 37 10 101989275 101989276 + Frame_Shift_Ins INS - G G RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr10:101989275_101989276insG uc001kqp.2 - 1 69_70 c.14_15insC c.(13-15)CCGfs p.P5fs NM_001278 NP_001269 O15111 IKKA_HUMAN conserved helix-loop-helix ubiquitous kinase 5 I-kappaB phosphorylation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway CD40 receptor complex|cytosol|internal side of plasma membrane|nucleus ATP binding|identical protein binding|IkappaB kinase activity ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|breast(1) 7 Colorectal(252;0.117) Epithelial(162;2.05e-10)|all cancers(201;1.91e-08) 0.000 0.94 19 302 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 151 41 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 62 729 TP53 7157 broad.mit.edu 37 17 7578527 7578528 + Frame_Shift_Del DEL AA - - RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr17:7578527_7578528delAA uc002gim.2 - 5 596_597 c.402_403delTT c.(400-405)TTTTGCfs p.F134fs TP53_uc002gig.1_Frame_Shift_Del_p.F134fs|TP53_uc002gih.2_Frame_Shift_Del_p.F134fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.F2fs|TP53_uc010cng.1_Frame_Shift_Del_p.F2fs|TP53_uc002gii.1_Frame_Shift_Del_p.F2fs|TP53_uc010cnh.1_Frame_Shift_Del_p.F134fs|TP53_uc010cni.1_Frame_Shift_Del_p.F134fs|TP53_uc002gij.2_Frame_Shift_Del_p.F134fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.F41fs|TP53_uc002gio.2_Frame_Shift_Del_p.F2fs|TP53_uc010vug.1_Frame_Shift_Del_p.F95fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 134_135 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). C -> S (in sporadic cancers; somatic mutation).|C -> Y (in sporadic cancers; somatic mutation; decreased E6-mediated binding to E6-AP).|C -> T (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> R (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> F (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.F134L(16)|p.F134V(9)|p.0?(7)|p.F134C(6)|p.C135G(6)|p.C135R(6)|p.C135S(4)|p.C135fs*35(4)|p.F134S(3)|p.N131fs*27(2)|p.F134F(1)|p.F134_T140>S(1)|p.K132_A138delKMFCQLA(1)|p.S127_Q136del10(1)|p.C135T(1)|p.V73fs*9(1)|p.C135fs*36(1)|p.C135fs*14(1)|p.Y126fs*11(1)|p.C135_A138delCQLA(1)|p.M133fs*13(1)|p.F134fs*14(1)|p.C135_T140delCQLAKT(1)|p.F134fs*39(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GCCAGTTGGCAAAACATCTTGT 0.569 0.97 2 68 KEAP1 9817 broad.mit.edu 37 19 10610352 10610354 + In_Frame_Del DEL TGC - - RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr19:10610352_10610354delTGC uc002moq.1 - 2 512_514 c.356_358delGCA c.(355-360)GGCATG>GTG p.119_120GM>V KEAP1_uc002mor.1_In_Frame_Del_p.119_120GM>V NM_012289 NP_036421 Q14145 KEAP1_HUMAN kelch-like ECH-associated protein 1 119_120 BTB. regulation of transcription, DNA-dependent|transcription, DNA-dependent centrosome|midbody|nucleus protein binding lung(12)|breast(3)|ovary(1)|pancreas(1) 17 OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05) 0.000 0.59 490 715 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 8 26 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 119 327 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RERFLCMS_LUNG NA RERFLCMS_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.81 5 21 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 5 54 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.32 213 101 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 7 5 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.11 128 16 GRK7 131890 broad.mit.edu 37 3 141497729 141497729 + Frame_Shift_Del DEL T - - RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr3:141497729delT uc011bnd.1 + 1 687 c.603delT c.(601-603)GGTfs p.G201fs NM_139209 NP_631948 Q8WTQ7 GRK7_HUMAN G-protein-coupled receptor kinase 7 precursor 201 ATP (By similarity).|Protein kinase. visual perception membrane ATP binding|G-protein coupled receptor kinase activity|signal transducer activity lung(2)|stomach(1)|ovary(1)|skin(1) 5 GGAAAGGTGGTTTTGGGGAGG 0.468 0.45 85 69 BMP2K 55589 broad.mit.edu 37 4 79792137 79792145 + In_Frame_Del DEL CAGCAGCAG - - rs17855588 RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr4:79792137_79792145delCAGCAGCAG uc003hlk.2 + 11 1598_1606 c.1432_1440delCAGCAGCAG c.(1432-1440)CAGCAGCAGdel p.QQQ484del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQ484del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 484_486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 gcaacagcaacagcagcagcagcagcagc 0.177 0.33 22 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 56 61 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 23 36 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.40 225 150 FER 2241 broad.mit.edu 37 5 108219172 108219176 + Frame_Shift_Del DEL AGAGA - - RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr5:108219172_108219176delAGAGA uc003kop.1 + 9 1383_1387 c.999_1003delAGAGA c.(997-1005)TTAGAGAAGfs p.L333fs FER_uc011cvf.1_Intron|FER_uc011cvg.1_Frame_Shift_Del_p.L158fs NM_005246 NP_005237 P16591 FER_HUMAN fer (fps/fes related) tyrosine kinase 333_335 Potential. intracellular signal transduction|peptidyl-tyrosine phosphorylation cytoplasm|nucleus ATP binding|non-membrane spanning protein tyrosine kinase activity lung(2)|stomach(1)|ovary(1)|kidney(1) 5 all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152) OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174) TTTTGGAGTTAGAGAAGAGAATTGA 0.332 0.27 65 24 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 1 12 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.92 2 22 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 227 63 BCL11B 64919 broad.mit.edu 37 14 99640905 99640906 + Frame_Shift_Del DEL GG - - rs74649889 by1000genomes RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr14:99640905_99640906delGG uc001yga.2 - 4 2534_2535 c.2267_2268delCC c.(2266-2268)CCCfs p.P756fs BCL11B_uc001ygb.2_Frame_Shift_Del_p.P685fs NM_138576 NP_612808 Q9C0K0 BC11B_HUMAN B-cell CLL/lymphoma 11B isoform 1 756 nucleus zinc ion binding central_nervous_system(8)|large_intestine(1)|lung(1) 10 Melanoma(154;0.0866)|all_epithelial(191;0.241) COAD - Colon adenocarcinoma(157;0.103) 0.000 0.54 42 50 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 49 396 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.12 889 118 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.82 8 36 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 61 237 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RERFLCSQ1_LUNG NA RERFLCSQ1_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 61 FAM48B1 100130302 broad.mit.edu 37 X 24382373 24382374 + In_Frame_Ins INS - TGC TGC RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chrX:24382373_24382374insTGC uc011mjx.1 + 1 1496_1497 c.1496_1497insTGC c.(1495-1497)ATT>ATTGCT p.517_518insA NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 gctgctgctattgctgctgctg 0.208 0.23 48 14 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 49 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 142 36 FAM157A 728262 broad.mit.edu 37 3 197880131 197880133 + In_Frame_Del DEL GCA - - RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr3:197880131_197880133delGCA uc011bup.1 + 2 210_212 c.210_212delGCA c.(208-213)TGGCAG>TGG p.Q84del NM_001145248 NP_001138720 C9JC47 F157A_HUMAN family with sequence similarity 157, member A 84 Gln-rich. 0 ACAAGAACTGgcagcagcagcag 0.399 0.50 22 22 HTT 3064 broad.mit.edu 37 4 3076604 3076612 + In_Frame_Del DEL CAGCAGCAG - - rs10618869 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr4:3076604_3076612delCAGCAGCAG uc011bvq.1 + 2 203_211 c.58_66delCAGCAGCAG c.(58-66)CAGCAGCAGdel p.QQQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagcagc 0.325 0.25 41 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.73 48 129 ATXN1 6310 broad.mit.edu 37 6 16327915 16327916 + In_Frame_Ins INS - TGC TGC rs11969612 by1000genomes RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr6:16327915_16327916insTGC uc003nbt.2 - 8 1597_1598 c.626_627insGCA c.(625-627)CAT>CAGCAT p.208_209insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.208_209insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 208_209 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) gctgatgctgatgctgctgctg 0.381 0.38 88 55 MICA 4276 broad.mit.edu 37 6 31380161 31380162 + Splice_Site INS - CTGCTGCTGCT CTGCTGCTGCT rs72548004;rs9279200 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr6:31380161_31380162insCTGCTGCTGCT uc003ntk.1 + 6 988 c.949_splice c.e6-1 p.A317_splice MICA_uc003rxz.1_Frame_Shift_Ins_p.G180fs RecName: Full=MHC class I polypeptide-related sequence A; Short=MIC-A; Flags: Precursor; 0 Ovarian(999;0.0253) TGTTGCTGCTGGCTGCTGCTAT 0.450 1.00 0 10 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.15 281 49 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 3 32 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.53 7 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 38 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.44 158 125 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.50 475 467 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.36 18 10 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.39 75 47 NCOR2 9612 broad.mit.edu 37 12 124887058 124887059 + In_Frame_Ins INS - GCTGCT GCTGCT rs35831183;rs67031864 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr12:124887058_124887059insGCTGCT uc010tba.1 - 14 1648_1649 c.1531_1532insAGCAGC c.(1531-1533)CCC>CAGCAGCCC p.510_511insQQ NCOR2_uc010tay.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010taz.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbb.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbc.1_In_Frame_Ins_p.509_510insQQ|NCOR2_uc001ugj.1_In_Frame_Ins_p.510_511insQQ NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 510_511 cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) GCGGGGCATGGgctgctgctgc 0.312 0.27 71 26 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.19 138 32 DACH1 1602 broad.mit.edu 37 13 72440538 72440539 + In_Frame_Ins INS - GCCGCC GCCGCC RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr13:72440538_72440539insGCCGCC uc010thn.1 - 2 786_787 c.363_364insGGCGGC c.(361-366)insGGCGGC p.121_122insGG DACH1_uc010tho.1_In_Frame_Ins_p.121_122insGG|DACH1_uc010thp.1_In_Frame_Ins_p.121_122insGG NM_080759 NP_542937 Q9UI36 DACH1_HUMAN dachshund homolog 1 isoform a 121_122 multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus DNA binding|nucleotide binding|protein binding breast(1) 1 Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198) GBM - Glioblastoma multiforme(99;0.00032) ccagcgctgatgccgccgccgc 0.079 0.16 56 11 NYNRIN 57523 broad.mit.edu 37 14 24879024 24879025 + Frame_Shift_Ins INS - A A RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr14:24879024_24879025insA uc001wpf.3 + 4 2342_2343 c.2024_2025insA c.(2023-2025)TCCfs p.S675fs NM_025081 NP_079357 Q9P2P1 NYNRI_HUMAN hypothetical protein LOC57523 675 DNA integration integral to membrane DNA binding ovary(2)|central_nervous_system(1) 3 CCCAGAGTCTCCAGAGCTCCCA 0.574 0.96 15 324 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.51 26 27 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.84 28 147 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.23 307 90 BAGE2 85319 broad.mit.edu 37 21 11047597 11047598 + Splice_Site INS - A A RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr21:11047597_11047598insA uc002yit.1 - 5 660 c.452_splice c.e5-1 NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) CCCGATTGTCTAAAAAGTAAGA 0.351 0.13 1083 162 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.41 283 196 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RH18_SOFT_TISSUE NA RH18_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 7 103 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 27 TTN 7273 broad.mit.edu 37 2 179480448 179480450 + In_Frame_Del DEL AAT - - RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr2:179480448_179480450delAAT uc010zfg.1 - 207 40898_40900 c.40674_40676delATT c.(40672-40677)TTATTT>TTT p.L13558del TTN_uc010zfh.1_In_Frame_Del_p.L7253del|TTN_uc010zfi.1_In_Frame_Del_p.L7186del|TTN_uc010zfj.1_In_Frame_Del_p.L7061del NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 14485 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) ACAAACTTTAAATAAGTACTCTT 0.374 0.50 115 116 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.39 53 34 ATP13A5 344905 broad.mit.edu 37 3 193032846 193032848 + In_Frame_Del DEL GAG - - RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr3:193032846_193032848delGAG uc011bsq.1 - 18 2071_2073 c.2071_2073delCTC c.(2071-2073)CTCdel p.L691del NM_198505 NP_940907 Q4VNC0 AT135_HUMAN ATPase type 13A5 691 ATP biosynthetic process|cation transport integral to membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding ovary(5)|skin(4)|large_intestine(2) 11 all_cancers(143;1.08e-08)|Ovarian(172;0.0386) OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06) GBM - Glioblastoma multiforme(46;0.000307) TCTCCATGATGAGAAGTCCCAGA 0.369 0.29 139 58 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.72 48 126 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.57 49 64 RAD50 10111 broad.mit.edu 37 5 131915022 131915025 + Frame_Shift_Del DEL GTCA - - rs28903086 byFrequency RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr5:131915022_131915025delGTCA uc003kxi.2 + 4 766_769 c.379_382delGTCA c.(379-384)GTCAGTfs p.V127fs RAD50_uc003kxg.1_Frame_Shift_Del_p.V28fs|RAD50_uc003kxh.2_5'UTR NM_005732 NP_005723 Q92878 RAD50_HUMAN RAD50 homolog isoform 1 127_128 DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding lung(2)|ovary(1)|skin(1) 4 all_cancers(142;0.0368)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) TGGTGAAAAGGTCAGTCTGAGCTC 0.348 0.18 231 50 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.75 3 9 ATXN1 6310 broad.mit.edu 37 6 16327867 16327868 + In_Frame_Ins INS - TGC TGC RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr6:16327867_16327868insTGC uc003nbt.2 - 8 1645_1646 c.674_675insGCA c.(673-675)CAG>CAGCAG p.225_225Q>QQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_225Q>QQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) TGCTGAGGtgctgctgctgctg 0.366 0.31 102 45 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.57 18 24 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 1 21 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.13 181 27 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.49 411 402 THAP11 57215 broad.mit.edu 37 16 67876788 67876796 + In_Frame_Del DEL CAGCAGCAA - - RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr16:67876788_67876796delCAGCAGCAA uc002euo.2 + 1 576_584 c.331_339delCAGCAGCAA c.(331-339)CAGCAGCAAdel p.QQQ129del CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 129_131 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) acagcagcagcagcagcaacagcagcaac 0.316 0.80 36 144 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 39 593 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.10 161 17 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 0.80 2 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.85 33 187 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 29 194 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RH30_SOFT_TISSUE NA RH30_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 4 128 FOXO4 4303 broad.mit.edu 37 X 70316582 70316583 + Frame_Shift_Ins INS - T T RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:70316582_70316583insT uc004dys.1 + 1 557_558 c.204_205insT c.(202-207)CTGTTGfs p.L68fs FOXO4_uc010nkz.2_Frame_Shift_Ins_p.L68fs|FOXO4_uc004dyt.1_Intron NM_005938 NP_005929 P98177 FOXO4_HUMAN forkhead box O4 68_69 cell cycle arrest|cell differentiation|embryo development|G1 phase of mitotic cell cycle|insulin receptor signaling pathway|mitotic cell cycle G2/M transition DNA damage checkpoint|muscle organ development|negative regulation of angiogenesis|negative regulation of cell proliferation|negative regulation of smooth muscle cell differentiation|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding central_nervous_system(2)|prostate(1) 3 Renal(35;0.156) AGCCGATCCTGTTGCCCTCTCG 0.693 0.38 15 9 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 53 ZNF642 339559 broad.mit.edu 37 1 40961001 40961001 + Frame_Shift_Del DEL T - - RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:40961001delT uc001cfo.2 + 6 1145 c.851delT c.(850-852)ATTfs p.I284fs ZNF642_uc009vwb.2_Frame_Shift_Del_p.I284fs|ZNF642_uc010ojk.1_Frame_Shift_Del_p.I285fs NM_198494 NP_940896 Q49AA0 ZN642_HUMAN zinc finger protein 642 284 C2H2-type 1. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding 0 Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;8.81e-19) AAACAACCTATTCACCTTACT 0.343 0.41 13 9 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.48 13 12 ROBO2 6092 broad.mit.edu 37 3 77526677 77526678 + Frame_Shift_Ins INS - A A RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:77526677_77526678insA uc003dpy.3 + 3 1144_1145 c.501_502insA c.(499-504)TGGAAAfs p.W167fs ROBO2_uc003dpz.2_Frame_Shift_Ins_p.W167fs|ROBO2_uc011bgj.1_RNA|ROBO2_uc011bgk.1_Frame_Shift_Ins_p.W167fs NM_002942 NP_002933 Q9HCK4 ROBO2_HUMAN roundabout, axon guidance receptor, homolog 2 167_168 Ig-like C2-type 2.|Extracellular (Potential). apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development axolemma|cell surface|integral to membrane axon guidance receptor activity|identical protein binding lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1) 11 Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103) CCATCTACTGGAAAAAAGACAA 0.450 0.42 70 50 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.23 30 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 115 171 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 15 42 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.32 93 44 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.40 6 4 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.21 75 20 HNRNPA2B1 3181 broad.mit.edu 37 7 26232902 26232904 + In_Frame_Del DEL ACC - - RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:26232902_26232904delACC uc003sxr.3 - 10 1183_1185 c.967_969delGGT c.(967-969)GGTdel p.G323del HNRNPA2B1_uc003sxs.3_In_Frame_Del_p.G311del NM_031243 NP_112533 P22626 ROA2_HUMAN heterogeneous nuclear ribonucleoprotein A2/B1 323 Gly-rich.|Nuclear targeting sequence (By similarity). RNA transport catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm nucleotide binding|protein binding|protein binding|RNA binding|single-stranded telomeric DNA binding ovary(1)|central_nervous_system(1)|skin(1) 3 TGTTCCTGCTACCACCAAAGTTT 0.350 0.58 45 61 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 24 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 45 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.38 65 40 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 795 426 PLEKHA5 54477 broad.mit.edu 37 12 19427887 19427888 + Frame_Shift_Ins INS - G G RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:19427887_19427888insG uc001reb.2 + 10 1351_1352 c.1265_1266insG c.(1264-1266)AAGfs p.K422fs PLEKHA5_uc010sie.1_Frame_Shift_Ins_p.K428fs|PLEKHA5_uc001rea.2_Frame_Shift_Ins_p.K422fs|PLEKHA5_uc009zin.2_Frame_Shift_Ins_p.K180fs|PLEKHA5_uc010sif.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc010sig.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc010sih.1_Frame_Shift_Ins_p.K314fs|PLEKHA5_uc001rec.1_Frame_Shift_Ins_p.K110fs NM_019012 NP_061885 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A 422 1-phosphatidylinositol binding|protein binding ovary(1)|kidney(1)|skin(1) 3 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) AAAATCCAGAAGGGGAGGGGTC 0.470 0.17 48 10 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.31 20 9 FFAR2 2867 broad.mit.edu 37 19 35940696 35940697 + Frame_Shift_Ins INS - G G RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:35940696_35940697insG uc002nzg.2 + 2 160_161 c.80_81insG c.(79-81)CTGfs p.L27fs FFAR2_uc010eea.2_Frame_Shift_Ins_p.L27fs NM_005306 NP_005297 O15552 FFAR2_HUMAN free fatty acid receptor 2 27 Helical; Name=1; (Potential). integral to plasma membrane G-protein coupled receptor activity|lipid binding central_nervous_system(1) 1 all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0724) GCCAACCTCCTGGCCCTGCGGG 0.629 0.10 91 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.22 281 80 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.15 74 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 44 266 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 7 119 MN1 4330 broad.mit.edu 37 22 28194960 28194961 + In_Frame_Ins INS - TGT TGT RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:28194960_28194961insTGT uc003adj.2 - 1 2526_2527 c.1571_1572insACA c.(1570-1572)CAG>CAACAG p.524_524Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 524 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgctgctgctgttgcAGGGA 0.401 0.28 172 67 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 39 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 238 70 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.39 20 13 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 11 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 93 109 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.49 106 100 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.75 4 12 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.58 25 35 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.31 31 14 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 16 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.64 4 7 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 4 48 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.23 102 30 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.46 7 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 576 265 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.33 118 59 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.43 64 49 CLTC 1213 broad.mit.edu 37 17 57760985 57760996 + Splice_Site DEL GGTTGCCAATGT - - RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr17:57760985_57760996delGGTTGCCAATGT uc002ixq.1 + 27 4635 c.4192_splice c.e27-1 p.V1398_splice CLTC_uc002ixp.2_Splice_Site_p.V1398_splice|CLTC_uc002ixr.1_Splice_Site_p.V1402_splice NM_004859 NP_004850 Q00610 CLH1_HUMAN clathrin heavy chain 1 axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle protein binding|structural molecule activity CLTC/ALK(44)|CLTC/TFE3(2) haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1) 48 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) TCCCATTGTAGGTTGCCAATGTGGAACTATAC 0.392 0.11 89 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.59 53 75 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 51 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 64 320 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RKN_SOFT_TISSUE NA RKN_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 78 PIM2 11040 broad.mit.edu 37 X 48776091 48776092 + Frame_Shift_Ins INS - A A RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chrX:48776091_48776092insA uc004dls.2 - 1 322_323 c.20_21insT c.(19-21)CAGfs p.Q7fs NM_006875 NP_006866 Q9P1W9 PIM2_HUMAN serine/threonine protein kinase pim-2 7 anti-apoptosis|cell proliferation|male meiosis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|response to virus ATP binding|protein serine/threonine kinase activity lung(3)|stomach(1) 4 0.000 0.10 589 69 TFE3 7030 broad.mit.edu 37 X 48887952 48887952 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chrX:48887952delC uc004dmb.3 - 10 1683 c.1445delG c.(1444-1446)GGAfs p.G482fs TFE3_uc004dmc.3_Frame_Shift_Del_p.G377fs NM_006521 NP_006512 P19532 TFE3_HUMAN transcription factor E3 482 humoral immune response|positive regulation of transcription from RNA polymerase II promoter cytoplasm|nucleus sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding ASPSCR1/TFE3(161)|PRCC/TFE3(25)|SFPQ/TFE3(6)|NONO/TFE3(2)|CLTC/TFE3(2) soft_tissue(120)|kidney(76)|central_nervous_system(1) 197 CTGGGCAGGTCCCCCCCCTAC 0.647 0.60 8 12 FOXO4 4303 broad.mit.edu 37 X 70321276 70321277 + Frame_Shift_Ins INS - G G RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chrX:70321276_70321277insG uc004dys.1 + 2 1549_1550 c.1196_1197insG c.(1195-1197)CTGfs p.L399fs FOXO4_uc010nkz.2_Intron|FOXO4_uc004dyt.1_Frame_Shift_Ins_p.L344fs NM_005938 NP_005929 P98177 FOXO4_HUMAN forkhead box O4 399 cell cycle arrest|cell differentiation|embryo development|G1 phase of mitotic cell cycle|insulin receptor signaling pathway|mitotic cell cycle G2/M transition DNA damage checkpoint|muscle organ development|negative regulation of angiogenesis|negative regulation of cell proliferation|negative regulation of smooth muscle cell differentiation|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding central_nervous_system(2)|prostate(1) 3 Renal(35;0.156) CTTCTGTTGCTGGGGGGGCTTC 0.634 0.37 266 154 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 5 196 MTM1 4534 broad.mit.edu 37 X 149828155 149828155 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chrX:149828155delA uc004fef.3 + 12 1355 c.1279delA c.(1279-1281)AAAfs p.K427fs MTM1_uc011mxx.1_RNA|MTM1_uc011mxy.1_Frame_Shift_Del_p.K390fs|MTM1_uc011mxz.1_Frame_Shift_Del_p.K312fs|MTM1_uc010nte.2_Frame_Shift_Del_p.K295fs NM_000252 NP_000243 Q13496 MTM1_HUMAN myotubularin 427 Myotubularin phosphatase. endosome to lysosome transport|intermediate filament organization|mitochondrion distribution|mitochondrion morphogenesis|phosphatidylinositol dephosphorylation|protein transport|regulation of vacuole organization filopodium|late endosome|plasma membrane|ruffle intermediate filament binding|phosphatidylinositol binding|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity upper_aerodigestive_tract(1)|ovary(1)|kidney(1) 3 Acute lymphoblastic leukemia(192;6.56e-05) 0.000 0.55 45 56 F8 2157 broad.mit.edu 37 X 154158428 154158428 + Frame_Shift_Del DEL T - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chrX:154158428delT uc004fmt.2 - 14 3808 c.3637delA c.(3637-3639)ATTfs p.I1213fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1213 B. acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) TCTTCCTGAATTTTTTTTTCT 0.328 0.38 265 159 B3GALT6 126792 broad.mit.edu 37 1 1168239 1168240 + Frame_Shift_Ins INS - G G RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr1:1168239_1168240insG uc001adk.2 + 1 611_612 c.581_582insG c.(580-582)CCGfs p.P194fs SDF4_uc001adh.3_5'Flank|SDF4_uc001adi.3_5'Flank|SDF4_uc009vjv.2_5'Flank|SDF4_uc009vjw.2_5'Flank NM_080605 NP_542172 Q96L58 B3GT6_HUMAN beta-1,3-galactosyltransferase 6 194 Lumenal (Potential). glycosaminoglycan biosynthetic process|protein glycosylation Golgi cisterna membrane|Golgi medial cisterna|integral to membrane galactosylxylosylprotein 3-beta-galactosyltransferase activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.22e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199) CGCGTCAAGCCGGGGGGGCGCT 0.619 0.41 10 7 ARID1A 8289 broad.mit.edu 37 1 27097751 27097751 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr1:27097751delC uc001bmv.1 + 12 3713 c.3340delC c.(3340-3342)CCCfs p.P1114fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.P1114fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.P1114fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.P731fs|ARID1A_uc001bmx.1_5'UTR|ARID1A_uc009vsm.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1114 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) AGAAGACCCTCCCCCAGACAT 0.542 0.45 400 329 ARID1A 8289 broad.mit.edu 37 1 27105931 27105931 + Frame_Shift_Del DEL G - - rs140055856 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr1:27105931delG uc001bmv.1 + 20 5915 c.5542delG c.(5542-5544)GGGfs p.G1848fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.G1631fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.G694fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.G176fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.G90fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1848 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.G1848fs*6(3) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GCGGATTGGTGGGGGGGACAC 0.582 0.41 310 217 MAP3K6 9064 broad.mit.edu 37 1 27692875 27692875 + Frame_Shift_Del DEL G - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr1:27692875delG uc001bny.1 - 1 463 c.214delC c.(214-216)CTGfs p.L72fs MAP3K6_uc009vsw.1_Frame_Shift_Del_p.L72fs NM_004672 NP_004663 O95382 M3K6_HUMAN mitogen-activated protein kinase kinase kinase 72 activation of JUN kinase activity ATP binding|magnesium ion binding|MAP kinase kinase kinase activity breast(4)|lung(3)|ovary(1)|central_nervous_system(1) 9 all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419) 0.000 0.18 96 21 SETDB1 9869 broad.mit.edu 37 1 150933159 150933159 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr1:150933159delC uc001evu.2 + 16 2811 c.2621delC c.(2620-2622)GCCfs p.A874fs SETDB1_uc001evv.2_Frame_Shift_Del_p.A874fs|SETDB1_uc009wmg.1_Frame_Shift_Del_p.A874fs NM_001145415 NP_001138887 Q15047 SETB1_HUMAN SET domain, bifurcated 1 isoform 1 874 SET. regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|Golgi apparatus|nucleus|plasma membrane DNA binding|histone-lysine N-methyltransferase activity|protein binding|zinc ion binding ovary(2)|upper_aerodigestive_tract(1) 3 all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211) GAGAGTGATGCCCCCTGTTCC 0.488 0.47 452 397 DENND4B 9909 broad.mit.edu 37 1 153907278 153907279 + In_Frame_Ins INS - CTG CTG rs141373027 by1000genomes RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr1:153907278_153907279insCTG uc001fdd.1 - 18 3131_3132 c.2730_2731insCAG c.(2728-2733)insCAG p.910_911insQ uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910_911 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) GACACctgctcctgctgctgct 0.455 0.40 25 17 PRCC 5546 broad.mit.edu 37 1 156761536 156761536 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr1:156761536delC uc001fqa.2 + 4 1421 c.1131delC c.(1129-1131)GTCfs p.V377fs PRCC_uc001fqb.2_Intron NM_005973 NP_005964 Q92733 PRCC_HUMAN papillary renal cell carcinoma 377 cell cycle|mitotic cell cycle checkpoint nucleus protein binding PRCC/TFE3(25) kidney(25)|central_nervous_system(2) 27 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) CGGCCCTGGTCCCCCCCCAGG 0.527 0.52 10 11 HSPA6 3310 broad.mit.edu 37 1 161494744 161494745 + Frame_Shift_Ins INS - G G RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr1:161494744_161494745insG uc001gap.2 + 2 956_957 c.296_297insG c.(295-297)GAGfs p.E99fs HSPA6_uc001gaq.2_Frame_Shift_Ins_p.E99fs NM_002155 NP_002146 P17066 HSP76_HUMAN heat shock 70kDa protein 6 (HSP70B') 99 response to unfolded protein ATP binding skin(1) 1 all_cancers(52;4.89e-16)|all_hematologic(112;0.0207) BRCA - Breast invasive adenocarcinoma(70;0.00376) GTGGTGAGCGAGGGCGGCAAGC 0.629 0.48 11 10 SCYL3 57147 broad.mit.edu 37 1 169833511 169833511 + Frame_Shift_Del DEL T - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr1:169833511delT uc001ggs.2 - 9 1152 c.954delA c.(952-954)AAAfs p.K318fs SCYL3_uc010plw.1_5'UTR|SCYL3_uc001ggt.2_Frame_Shift_Del_p.K318fs|SCYL3_uc001ggu.2_RNA NM_181093 NP_851607 Q8IZE3 PACE1_HUMAN SCY1-like 3 isoform 2 318 HEAT 2. cell migration Golgi apparatus|lamellipodium ATP binding|protein binding|protein kinase activity ovary(1)|skin(1) 2 all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181) AGCATTCACCTTTTTTGGGGC 0.393 0.51 224 229 ASTN1 460 broad.mit.edu 37 1 176863804 176863805 + Frame_Shift_Ins INS - G G RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr1:176863804_176863805insG uc001glc.2 - 17 3045_3046 c.2833_2834insC c.(2833-2835)CTGfs p.L945fs ASTN1_uc001glb.1_Frame_Shift_Ins_p.L945fs|ASTN1_uc001gld.1_Frame_Shift_Ins_p.L945fs NM_004319 NP_004310 O14525 ASTN1_HUMAN astrotactin isoform 1 953 cell migration|neuron cell-cell adhesion integral to membrane ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1) 15 CACATGACACAGGGGGCAGGAC 0.594 0.48 72 67 ABL2 27 broad.mit.edu 37 1 179077445 179077445 + Frame_Shift_Del DEL G - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr1:179077445delG uc001gmj.3 - 12 3244 c.2957delC c.(2956-2958)CCAfs p.P986fs ABL2_uc010pnf.1_Frame_Shift_Del_p.P883fs|ABL2_uc010png.1_Frame_Shift_Del_p.P862fs|ABL2_uc010pnh.1_Frame_Shift_Del_p.P965fs|ABL2_uc001gmg.3_Frame_Shift_Del_p.P868fs|ABL2_uc001gmi.3_Frame_Shift_Del_p.P971fs|ABL2_uc001gmh.3_Frame_Shift_Del_p.P950fs|ABL2_uc010pne.1_Frame_Shift_Del_p.P847fs NM_007314 NP_009298 P42684 ABL2_HUMAN arg tyrosine kinase isoform b 986 Pro-rich.|Poly-Pro. axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction cytoskeleton|cytosol ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(8)|breast(3)|ovary(2)|central_nervous_system(1) 14 Adenosine triphosphate(DB00171)|Dasatinib(DB01254) CACTGGTGGTGGGGGTGGGGC 0.532 0.47 393 343 PARP1 142 broad.mit.edu 37 1 226568818 226568818 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr1:226568818delC uc001hqd.3 - 9 1422 c.1251delG c.(1249-1251)GGGfs p.G417fs NM_001618 NP_001609 P09874 PARP1_HUMAN poly (ADP-ribose) polymerase family, member 1 417 Automodification domain.|BRCT. cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter nuclear envelope|nucleolus|transcription factor complex DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding lung(3)|ovary(2)|breast(2)|skin(2)|upper_aerodigestive_tract(1) 10 Breast(184;0.133) GBM - Glioblastoma multiforme(131;0.0531) CCGTCAACTTCCCCCCGAGTT 0.488 0.44 744 594 PKDCC 91461 broad.mit.edu 37 2 42282085 42282087 + In_Frame_Del DEL TTC - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr2:42282085_42282087delTTC uc002rsg.2 + 4 1218_1220 c.1039_1041delTTC c.(1039-1041)TTCdel p.F348del NM_138370 NP_612379 Q504Y2 PKDCC_HUMAN protein kinase-like protein SgK493 348 Protein kinase. cell differentiation|embryonic digestive tract development|lung alveolus development|negative regulation of Golgi to plasma membrane protein transport|ossification|palate development|positive regulation of bone mineralization|positive regulation of chondrocyte differentiation|protein transport Golgi apparatus ATP binding|protein kinase activity breast(1) 1 CCACAGGTTTTTCTTCACATACC 0.581 0.48 324 299 MSH6 2956 broad.mit.edu 37 2 48030582 48030583 + Frame_Shift_Del DEL TA - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr2:48030582_48030583delTA uc002rwd.3 + 5 3348_3349 c.3196_3197delTA c.(3196-3198)TATfs p.Y1066fs MSH6_uc010fbj.2_Frame_Shift_Del_p.Y764fs|MSH6_uc010yoi.1_Frame_Shift_Del_p.Y936fs|MSH6_uc010yoj.1_Frame_Shift_Del_p.Y764fs NM_000179 NP_000170 P52701 MSH6_HUMAN mutS homolog 6 1066 determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes MutSalpha complex ATP binding|DNA-dependent ATPase activity|protein binding large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1) 168 Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) CCTGGCTAACTATAGTCGAGGG 0.455 0.21 758 203 GLI2 2736 broad.mit.edu 37 2 121748126 121748127 + Frame_Shift_Ins INS - C C RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr2:121748126_121748127insC uc010flp.2 + 13 4666_4667 c.4636_4637insC c.(4636-4638)ACCfs p.T1546fs GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Frame_Shift_Ins_p.T1218fs|GLI2_uc002tmu.3_Frame_Shift_Ins_p.T1201fs NM_005270 NP_005261 P10070 GLI2_HUMAN GLI-Kruppel family member GLI2 1546 axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis nucleus|nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1) 13 Renal(3;0.0496) Prostate(154;0.0623) CCGCCTCACCACCCCCCGAAAC 0.629 0.29 140 57 LRP2 4036 broad.mit.edu 37 2 169997025 169997025 + Frame_Shift_Del DEL G - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr2:169997025delG uc002ues.2 - 72 13352 c.13139delC c.(13138-13140)CCAfs p.P4380fs NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 4380 EGF-like 17.|Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) 0.000 0.31 151 68 TTN 7273 broad.mit.edu 37 2 179408625 179408625 + Frame_Shift_Del DEL T - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr2:179408625delT uc010zfg.1 - 295 88766 c.88542delA c.(88540-88542)AAAfs p.K29514fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.K23209fs|TTN_uc010zfi.1_Frame_Shift_Del_p.K23142fs|TTN_uc010zfj.1_Frame_Shift_Del_p.K23017fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 30441 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CAATTGTGTATTTTCCAGCAT 0.403 0.45 804 660 TTN 7273 broad.mit.edu 37 2 179467186 179467188 + In_Frame_Del DEL CTT - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr2:179467186_179467188delCTT uc010zfg.1 - 232 47461_47463 c.47237_47239delAAG c.(47236-47241)GAAGGT>GGT p.E15746del uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.E9441del|TTN_uc010zfi.1_In_Frame_Del_p.E9374del|TTN_uc010zfj.1_In_Frame_Del_p.E9249del NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 16673 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCAGTAGTACCTTCTTCTTGCAT 0.409 0.48 722 655 CASP8 841 broad.mit.edu 37 2 202136290 202136292 + In_Frame_Del DEL TTT - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr2:202136290_202136292delTTT uc002uxr.1 + 4 566_568 c.357_359delTTT c.(355-360)TCTTTT>TCT p.F120del CASP8_uc010ftc.1_In_Frame_Del_p.F120del|CASP8_uc002uxo.1_In_Frame_Del_p.F120del|CASP8_uc002uxp.1_In_Frame_Del_p.F152del|CASP8_uc002uxq.1_In_Frame_Del_p.F120del|CASP8_uc002uxs.1_In_Frame_Del_p.F120del|CASP8_uc002uxt.1_In_Frame_Del_p.F179del|CASP8_uc002uxu.1_RNA|CASP8_uc010ftd.1_In_Frame_Del_p.F17del|CASP8_uc002uxv.1_In_Frame_Del_p.F120del|CASP8_uc002uxw.1_In_Frame_Del_p.F120del|CASP8_uc002uxy.1_In_Frame_Del_p.F120del|CASP8_uc002uxx.1_In_Frame_Del_p.F120del|CASP8_uc010ftf.2_In_Frame_Del_p.F120del|CASP8_uc010fte.1_In_Frame_Del_p.F17del NM_033355 NP_203519 Q14790 CASP8_HUMAN caspase 8 isoform B precursor 120 DED 2. activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor centrosome|cytosol|mitochondrial outer membrane cysteine-type endopeptidase activity|protein binding|protein binding upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1) 5 AATTGAGGTCTTTTAAGTTTCTT 0.394 0.60 49 72 TGFBR2 7048 broad.mit.edu 37 3 30691872 30691873 + Frame_Shift_Del DEL AA - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr3:30691872_30691873delAA uc003ceo.2 + 3 756_757 c.374_375delAA c.(373-375)GAAfs p.E125fs TGFBR2_uc003cen.2_Frame_Shift_Del_p.E150fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 125 Extracellular (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 ATTATGAAGGAAAAAAAAAAGC 0.426 0.49 329 319 PXK 54899 broad.mit.edu 37 3 58389639 58389640 + Splice_Site INS - A A RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr3:58389639_58389640insA uc003djz.1 + 13 1329 c.1230_splice c.e13+2 p.K410_splice PXK_uc003djx.1_Splice_Site_p.K410_splice|PXK_uc003djy.1_Splice_Site_p.K393_splice|PXK_uc003dka.1_Splice_Site_p.K410_splice|PXK_uc003dkb.1_Splice_Site_p.K327_splice|PXK_uc003dkc.1_Splice_Site_p.K393_splice|PXK_uc011bfe.1_Splice_Site_p.K377_splice|PXK_uc010hnj.1_Splice_Site_p.K377_splice|PXK_uc003dkd.1_Splice_Site_p.K273_splice|PXK_uc010hnk.1_Splice_Site_p.K184_splice NM_017771 NP_060241 Q7Z7A4 PXK_HUMAN PX domain containing serine/threonine kinase cell communication|inflammatory response|negative regulation of ATPase activity|negative regulation of ion transport|regulation of synaptic transmission centrosome|cytoplasm|nucleus|plasma membrane actin binding|ATP binding|phosphatidylinositol binding|phosphatidylinositol binding|protein C-terminus binding|protein kinase activity ovary(1) 1 BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22) CAGTTTAAGGTAAAGACAATTA 0.282 0.48 400 375 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376116 + In_Frame_Del DEL TGCTGC - - rs143860374;rs62265537 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr3:113376111_113376116delTGCTGC uc003eam.2 - 7 4824_4829 c.4413_4418delGCAGCA c.(4411-4419)CAGCAGCAA>CAA p.1471_1473QQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1415_1417QQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1471_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgct 0.359 0.12 94 13 GRK7 131890 broad.mit.edu 37 3 141497291 141497292 + Frame_Shift_Ins INS - T T RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr3:141497291_141497292insT uc011bnd.1 + 1 249_250 c.165_166insT c.(163-168)AACTTCfs p.N55fs NM_139209 NP_631948 Q8WTQ7 GRK7_HUMAN G-protein-coupled receptor kinase 7 precursor 55_56 RGS. visual perception membrane ATP binding|G-protein coupled receptor kinase activity|signal transducer activity lung(2)|stomach(1)|ovary(1)|skin(1) 5 TGTCCCTGAACTTCCACAGCCT 0.673 0.73 3 8 GRK4 2868 broad.mit.edu 37 4 2986251 2986251 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr4:2986251delA uc003ggn.1 + 2 519 c.64delA c.(64-66)AAAfs p.K22fs GRK4_uc003ggo.1_Frame_Shift_Del_p.K22fs|GRK4_uc003ggp.1_Intron|GRK4_uc003ggq.1_Intron NM_182982 NP_892027 P32298 GRK4_HUMAN G protein-coupled receptor kinase 4 isoform 22 N-terminal. cell cortex ATP binding|G-protein coupled receptor kinase activity|signal transducer activity lung(1) 1 UCEC - Uterine corpus endometrioid carcinoma (64;0.168) AGGATATGGCAAAAAAAGTGG 0.383 0.62 6 10 N4BP2 55728 broad.mit.edu 37 4 40104033 40104034 + Frame_Shift_Ins INS - T T RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr4:40104033_40104034insT uc003guy.3 + 4 906_907 c.568_569insT c.(568-570)ATTfs p.I190fs N4BP2_uc010ifq.2_Frame_Shift_Ins_p.I110fs|N4BP2_uc010ifr.2_Frame_Shift_Ins_p.I110fs NM_018177 NP_060647 Q86UW6 N4BP2_HUMAN Nedd4 binding protein 2 190 cytoplasm ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding lung(3)|breast(2)|kidney(2)|ovary(1) 8 TATGACTCCCATTTTTTCTACA 0.312 0.38 86 52 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.15 142 26 CFI 3426 broad.mit.edu 37 4 110687927 110687927 + Frame_Shift_Del DEL T - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr4:110687927delT uc003hzr.3 - 2 319 c.111delA c.(109-111)AAAfs p.K37fs CFI_uc011cft.1_Frame_Shift_Del_p.K37fs|CFI_uc003hzs.3_Frame_Shift_Del_p.K37fs NM_000204 NP_000195 P05156 CFAI_HUMAN complement factor I preproprotein 37 complement activation, classical pathway|innate immune response|proteolysis extracellular space|membrane scavenger receptor activity|serine-type endopeptidase activity 0 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.000331) GGTGAGTATATTTTTTTGCTA 0.398 0.47 282 248 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 254 220 CASP3 836 broad.mit.edu 37 4 185552987 185552987 + Frame_Shift_Del DEL T - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr4:185552987delT uc003iwh.2 - 6 678 c.415delA c.(415-417)ATAfs p.I139fs CASP3_uc003iwg.2_Frame_Shift_Del_p.I139fs|CASP3_uc003iwi.2_Frame_Shift_Del_p.I139fs NM_004346 NP_004337 P42574 CASP3_HUMAN caspase 3 preproprotein 139 activation of caspase activity by cytochrome c|DNA fragmentation involved in apoptotic nuclear change|negative regulation of apoptosis|nerve growth factor receptor signaling pathway|nuclear fragmentation involved in apoptotic nuclear change|proteolysis|response to tumor necrosis factor cytosol|mitochondrion|nucleoplasm|plasma membrane cysteine-type endopeptidase activity|protein binding kidney(1) 1 all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.057)|all_hematologic(60;0.0592) all cancers(43;2.05e-27)|Epithelial(43;4.27e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.04e-11)|Colorectal(24;2e-05)|STAD - Stomach adenocarcinoma(60;2.35e-05)|GBM - Glioblastoma multiforme(59;4.94e-05)|COAD - Colon adenocarcinoma(29;0.00017)|BRCA - Breast invasive adenocarcinoma(30;0.000218)|LUSC - Lung squamous cell carcinoma(40;0.00904)|READ - Rectum adenocarcinoma(43;0.161) Melatonin(DB01065)|Minocycline(DB01017)|Simvastatin(DB00641) AAGTTTGTTATTTTTTTCAGG 0.368 0.44 417 328 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 52 95 TSSK1B 83942 broad.mit.edu 37 5 112769462 112769462 + Frame_Shift_Del DEL G - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr5:112769462delG uc003kqm.2 - 1 1267 c.1075delC c.(1075-1077)CAAfs p.Q359fs MCC_uc003kql.3_Intron NM_032028 NP_114417 Q9BXA7 TSSK1_HUMAN testis-specific serine kinase 1 359 cell differentiation|multicellular organismal development|spermatogenesis ATP binding|magnesium ion binding|protein serine/threonine kinase activity ovary(2)|skin(2)|stomach(1) 5 all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156) Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449) 0.000 0.21 316 85 AFF4 27125 broad.mit.edu 37 5 132228016 132228017 + Frame_Shift_Ins INS - T T RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr5:132228016_132228017insT uc003kyd.2 - 13 2884_2885 c.2476_2477insA c.(2476-2478)ACAfs p.T826fs AFF4_uc011cxk.1_Frame_Shift_Ins_p.T504fs|AFF4_uc003kye.1_Frame_Shift_Ins_p.T826fs NM_014423 NP_055238 Q9UHB7 AFF4_HUMAN ALL1 fused gene from 5q31 826 transcription from RNA polymerase II promoter mitochondrion|nucleolus protein binding|sequence-specific DNA binding transcription factor activity ovary(2)|kidney(2)|skin(1) 5 all_cancers(142;0.145)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GCCATGCTCTGTTTTTGGATCT 0.470 0.46 687 590 NSD1 64324 broad.mit.edu 37 5 176696691 176696691 + Frame_Shift_Del DEL T - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr5:176696691delT uc003mfr.3 + 16 5530 c.5392delT c.(5392-5394)TTTfs p.F1798fs NSD1_uc003mft.3_Frame_Shift_Del_p.F1529fs|NSD1_uc003mfs.1_Frame_Shift_Del_p.F1695fs|NSD1_uc011dfx.1_Frame_Shift_Del_p.F1446fs NM_022455 NP_071900 Q96L73 NSD1_HUMAN nuclear receptor binding SET domain protein 1 1798 PWWP 2. negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|nucleus androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding ovary(2)|kidney(1) 3 all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002) all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198) Kidney(146;0.235) CCCAGTCCTCTTTTTTGGATC 0.507 0.42 49 35 TTK 7272 broad.mit.edu 37 6 80720539 80720539 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr6:80720539delA uc003pjc.2 + 5 552 c.478delA c.(478-480)AAAfs p.K160fs TTK_uc003pjb.3_Frame_Shift_Del_p.K160fs NM_003318 NP_003309 P33981 TTK_HUMAN TTK protein kinase 160 mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation spindle ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1) 11 all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2) BRCA - Breast invasive adenocarcinoma(397;0.0321) AGGTAATGTCAAAAAAAGTAA 0.383 0.48 27 25 TTK 7272 broad.mit.edu 37 6 80751897 80751898 + Frame_Shift_Del DEL AA - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr6:80751897_80751898delAA uc003pjc.2 + 22 2626_2627 c.2552_2553delAA c.(2551-2553)GAAfs p.E851fs TTK_uc003pjb.3_Frame_Shift_Del_p.E850fs NM_003318 NP_003309 P33981 TTK_HUMAN TTK protein kinase 851 mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation spindle ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity p.R838fs*4(3) ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1) 11 all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2) BRCA - Breast invasive adenocarcinoma(397;0.0321) AAGACTTTTGAAAAAAAAAGGG 0.297 0.50 197 194 MAP3K5 4217 broad.mit.edu 37 6 136904725 136904726 + Frame_Shift_Ins INS - T T RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr6:136904725_136904726insT uc003qhc.2 - 24 3739_3740 c.3378_3379insA c.(3376-3381)CAAGTCfs p.Q1126fs MAP3K5_uc011edj.1_Frame_Shift_Ins_p.Q373fs|MAP3K5_uc011edk.1_Frame_Shift_Ins_p.Q972fs NM_005923 NP_005914 Q99683 M3K5_HUMAN mitogen-activated protein kinase kinase kinase 1126_1127 activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding ovary(2)|skin(2)|lung(1) 5 Colorectal(23;0.24) GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569) ACCACCTGGACTTGGCTAATGC 0.406 0.26 525 188 AKAP12 9590 broad.mit.edu 37 6 151673144 151673145 + Frame_Shift_Ins INS - G G rs147705121 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr6:151673144_151673145insG uc011eep.1 + 4 3858_3859 c.3618_3619insG c.(3616-3621)TCAGGGfs p.S1206fs AKAP12_uc003qoe.2_Frame_Shift_Ins_p.S1206fs|AKAP12_uc003qof.2_Frame_Shift_Ins_p.S1108fs|AKAP12_uc010kim.2_Intron|AKAP12_uc003qog.2_Frame_Shift_Ins_p.S1101fs NM_005100 NP_005091 Q02952 AKA12_HUMAN A kinase (PRKA) anchor protein 12 isoform 1 1206_1207 G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting cell cortex|cytoskeleton|plasma membrane adenylate cyclase binding|protein kinase A binding large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1) 8 Ovarian(120;0.125) BRCA - Breast invasive adenocarcinoma(37;0.175) OV - Ovarian serous cystadenocarcinoma(155;2.98e-11) GTACCCAGTCAGGGGGCACAGA 0.520 0.48 110 101 TBP 6908 broad.mit.edu 37 6 170871014 170871016 + In_Frame_Del DEL CAG - - rs72320253 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr6:170871014_170871016delCAG uc003qxt.2 + 3 422_424 c.190_192delCAG c.(190-192)CAGdel p.Q95del TBP_uc003qxu.2_In_Frame_Del_p.Q95del|TBP_uc011ehf.1_In_Frame_Del_p.Q75del|TBP_uc011ehg.1_In_Frame_Del_p.Q95del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 95 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacaacaacagcagcagcagc 0.177 0.24 50 16 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 2 16 PRKDC 5591 broad.mit.edu 37 8 48846544 48846546 + In_Frame_Del DEL AGG - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr8:48846544_48846546delAGG uc003xqi.2 - 15 1659_1661 c.1602_1604delCCT c.(1600-1605)CTCCTG>CTG p.534_535LL>L PRKDC_uc003xqj.2_In_Frame_Del_p.534_535LL>L|PRKDC_uc011ldh.1_In_Frame_Del_p.534_535LL>L NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic 534_535 cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) GTCAGAGCTCAGGAGATGTCTGA 0.424 0.23 448 137 ARFGEF1 10565 broad.mit.edu 37 8 68145151 68145154 + Frame_Shift_Del DEL CTAT - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr8:68145151_68145154delCTAT uc003xxo.1 - 23 3706_3709 c.3316_3319delATAG c.(3316-3321)ATAGCAfs p.I1106fs ARFGEF1_uc003xxl.1_Frame_Shift_Del_p.I560fs|ARFGEF1_uc003xxn.1_Frame_Shift_Del_p.I89fs NM_006421 NP_006412 Q9Y6D6 BIG1_HUMAN brefeldin A-inhibited guanine 1106_1107 exocytosis|regulation of ARF protein signal transduction cytoplasm ARF guanyl-nucleotide exchange factor activity|myosin binding ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1) 8 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206) TGAATACTTGCTATCTGTTTCCAG 0.333 0.29 670 274 VPS13B 157680 broad.mit.edu 37 8 100887781 100887781 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr8:100887781delC uc003yiv.2 + 62 12067 c.11956delC c.(11956-11958)CCCfs p.P3986fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.P3961fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 3986 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TGCAGAACCTCCCCCCTCCAC 0.468 0.19 699 168 RGS22 26166 broad.mit.edu 37 8 100975124 100975124 + Frame_Shift_Del DEL T - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr8:100975124delT uc003yjb.1 - 25 3893 c.3698delA c.(3697-3699)AAGfs p.K1233fs RGS22_uc003yja.1_Frame_Shift_Del_p.K1052fs|RGS22_uc003yjc.1_Frame_Shift_Del_p.K1221fs NM_015668 NP_056483 Q8NE09 RGS22_HUMAN regulator of G-protein signaling 22 1233 K -> KK (in Ref. 2; CAB55986). negative regulation of signal transduction cytoplasm|plasma membrane GTPase activator activity|signal transducer activity ovary(3)|skin(2)|breast(1)|central_nervous_system(1) 7 Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169) TGCAAACAACTTTTTTTCTAG 0.313 0.41 23 16 RGS22 26166 broad.mit.edu 37 8 100990176 100990176 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr8:100990176delA uc003yjb.1 - 23 3683 c.3488delT c.(3487-3489)TTGfs p.L1163fs RGS22_uc003yja.1_Frame_Shift_Del_p.L982fs|RGS22_uc003yjc.1_Frame_Shift_Del_p.L1151fs NM_015668 NP_056483 Q8NE09 RGS22_HUMAN regulator of G-protein signaling 22 1163 Potential. negative regulation of signal transduction cytoplasm|plasma membrane GTPase activator activity|signal transducer activity ovary(3)|skin(2)|breast(1)|central_nervous_system(1) 7 Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169) TAGGACTGCCAATTTTTTTTT 0.313 0.42 319 233 FBXO43 286151 broad.mit.edu 37 8 101152941 101152941 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr8:101152941delA uc003yjd.2 - 2 2254 c.1541delT c.(1540-1542)TTAfs p.L514fs FBXO43_uc003yje.2_Frame_Shift_Del_p.L480fs|FBXO43_uc010mbp.1_Frame_Shift_Del_p.L514fs NM_001029860 NP_001025031 Q4G163 FBX43_HUMAN F-box protein 43 isoform b 514 F-box. meiosis zinc ion binding kidney(1)|skin(1) 2 all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798) Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957) CAAGGACTCTAAAACCATAGC 0.328 0.48 391 359 RIMS2 9699 broad.mit.edu 37 8 104927779 104927779 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr8:104927779delA uc003yls.2 + 5 1444 c.1203delA c.(1201-1203)GTAfs p.V401fs RIMS2_uc003ylp.2_Frame_Shift_Del_p.V623fs|RIMS2_uc003ylw.2_Frame_Shift_Del_p.V431fs|RIMS2_uc003ylq.2_Frame_Shift_Del_p.V431fs|RIMS2_uc003ylr.2_Frame_Shift_Del_p.V478fs|RIMS2_uc003ylt.2_Frame_Shift_Del_p.V24fs|RIMS2_uc003ylu.1_Frame_Shift_Del_p.V14fs|RIMS2_uc003ylv.1_Frame_Shift_Del_p.V14fs NM_014677 NP_055492 Q9UQ26 RIMS2_HUMAN regulating synaptic membrane exocytosis 2 701 PDZ. intracellular protein transport cell junction|presynaptic membrane metal ion binding|Rab GTPase binding ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1) 15 OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229) TTACTAAAGTAAAAAAAGGAA 0.323 0.17 1354 278 COL14A1 7373 broad.mit.edu 37 8 121259922 121259922 + Frame_Shift_Del DEL C - - rs61738288 byFrequency;by1000genomes RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr8:121259922delC uc003yox.2 + 21 2815 c.2550delC c.(2548-2550)GACfs p.D850fs COL14A1_uc003yoy.2_Frame_Shift_Del_p.D528fs NM_021110 NP_066933 Q05707 COEA1_HUMAN collagen, type XIV, alpha 1 precursor 850 Fibronectin type-III 7. cell-cell adhesion|collagen fibril organization collagen type XIV|extracellular space collagen binding|extracellular matrix structural constituent|protein binding, bridging ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1) 12 Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503) TTACGTGGGACCCCCCATCTT 0.463 0.22 120 33 RECQL4 9401 broad.mit.edu 37 8 145738411 145738416 + In_Frame_Del DEL GGTGCA - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr8:145738411_145738416delGGTGCA uc003zdj.2 - 16 2601_2606 c.2569_2574delTGCACC c.(2569-2574)TGCACCdel p.CT857del NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 857_858 Missing. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) AGGGCGGCCTGGTGCAGGTGCAGGTG 0.665 0.21 34 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 58 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.51 374 393 DAPK1 1612 broad.mit.edu 37 9 90256961 90256962 + Frame_Shift_Ins INS - A A RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr9:90256961_90256962insA uc004apc.2 + 10 1044_1045 c.906_907insA c.(904-909)CGGAAAfs p.R302fs DAPK1_uc004ape.2_Frame_Shift_Ins_p.R302fs|DAPK1_uc004apd.2_Frame_Shift_Ins_p.R302fs|DAPK1_uc011ltg.1_Frame_Shift_Ins_p.R302fs|DAPK1_uc011lth.1_Frame_Shift_Ins_p.R39fs NM_004938 NP_004929 P53355 DAPK1_HUMAN death-associated protein kinase 1 302_303 Calmodulin-binding. apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade actin cytoskeleton|cytoplasm ATP binding|calmodulin binding|protein serine/threonine kinase activity ovary(1)|breast(1) 2 TTGCAGCCCGGAAAAAATGGAA 0.381 0.18 438 98 EHMT1 79813 broad.mit.edu 37 9 140611232 140611232 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr9:140611232delC uc011mfc.1 + 3 277 c.240delC c.(238-240)AACfs p.N80fs EHMT1_uc004coa.2_Frame_Shift_Del_p.N80fs|EHMT1_uc004cob.1_Frame_Shift_Del_p.N49fs NM_024757 NP_079033 Q9H9B1 EHMT1_HUMAN euchromatic histone-lysine N-methyltransferase 1 80 DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation chromosome|nucleus histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding breast(2)|pancreas(1) 3 all_cancers(76;0.164) OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728) 0.000 0.28 1138 441 PIP4K2A 5305 broad.mit.edu 37 10 23003122 23003123 + Frame_Shift_Ins INS - C C RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr10:23003122_23003123insC uc001irl.3 - 1 381_382 c.133_134insG c.(133-135)GTAfs p.V45fs NM_005028 NP_005019 P48426 PI42A_HUMAN phosphatidylinositol-5-phosphate 4-kinase, type 45 PIPK. 1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding ovary(1)|skin(1) 2 CGAGTGGTTTACCCCCCACATG 0.500 0.34 340 172 MYO3A 53904 broad.mit.edu 37 10 26462760 26462760 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr10:26462760delA uc001isn.2 + 30 3927 c.3567delA c.(3565-3567)CCAfs p.P1189fs MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron NM_017433 NP_059129 Q8NEV4 MYO3A_HUMAN myosin IIIA 1189 protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception cytoplasm|filamentous actin|filopodium|myosin complex actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 18 ATCAGACTCCAAAAAAAATGA 0.403 0.35 427 234 TET1 80312 broad.mit.edu 37 10 70441157 70441157 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr10:70441157delA uc001jok.3 + 9 5331 c.4826delA c.(4825-4827)GAAfs p.E1609fs NM_030625 NP_085128 Q8NFU7 TET1_HUMAN CXXC finger 6 1609 Breakpoint for translocation to form MLL- TET1 oncogene. DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding ovary(5)|lung(2)|prostate(1)|breast(1) 9 TTCCTATAGGAAAAAAACCTT 0.358 0.45 396 328 MYST4 23522 broad.mit.edu 37 10 76788653 76788654 + In_Frame_Ins INS - GAA GAA RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr10:76788653_76788654insGAA uc001jwn.1 + 18 4564_4565 c.4071_4072insGAA c.(4069-4074)insGAA p.1368_1369insE MYST4_uc001jwo.1_In_Frame_Ins_p.1076_1077insE|MYST4_uc001jwp.1_In_Frame_Ins_p.1185_1186insE NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1368_1369 Poly-Glu. histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) aagaggaggaggaggaggaaga 0.233 0.13 323 47 PIPSL 266971 broad.mit.edu 37 10 95720247 95720247 + Frame_Shift_Del DEL G - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr10:95720247delG uc009xuj.2 - 1 1426 c.907delC c.(907-909)CAAfs p.Q303fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 AGAGCCTTTTGGGGGGCTGGT 0.517 0.44 214 165 PIPSL 266971 broad.mit.edu 37 10 95720426 95720426 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr10:95720426delA uc009xuj.2 - 1 1247 c.728delT c.(727-729)TTGfs p.L243fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTCAGCATCCAAAAAAAGACC 0.483 0.42 276 202 GRK5 2869 broad.mit.edu 37 10 121086027 121086027 + Splice_Site DEL G - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr10:121086027delG uc001led.2 + 2 286 c.53_splice c.e2-1 p.G18_splice GRK5_uc009xzh.2_Splice_Site|GRK5_uc010qta.1_Splice_Site NM_005308 NP_005299 P34947 GRK5_HUMAN G protein-coupled receptor kinase 5 G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway cytoplasm|plasma membrane|soluble fraction ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity lung(2)|stomach(1) 3 Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249) all cancers(201;0.0227) CATCTCTGCAGGGGGCGGAGG 0.577 0.43 244 184 ADAM12 8038 broad.mit.edu 37 10 127843846 127843846 + Frame_Shift_Del DEL T - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr10:127843846delT uc001ljk.2 - 4 702 c.289delA c.(289-291)ACCfs p.T97fs ADAM12_uc010qul.1_Frame_Shift_Del_p.T97fs|ADAM12_uc001ljm.2_Frame_Shift_Del_p.T97fs|ADAM12_uc001ljn.2_Frame_Shift_Del_p.T97fs|ADAM12_uc001ljl.3_Frame_Shift_Del_p.T97fs NM_003474 NP_003465 O43184 ADA12_HUMAN ADAM metallopeptidase domain 12 isoform 1 97 cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis extracellular region|integral to membrane|plasma membrane metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1) 9 all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22) COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216) AGATAGTGGGTTTCCGTGAAA 0.443 0.47 226 200 TPH1 7166 broad.mit.edu 37 11 18048090 18048090 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr11:18048090delA uc001mnp.2 - 6 776 c.750delT c.(748-750)TTTfs p.F250fs TPH1_uc009yhe.2_RNA NM_004179 NP_004170 P17752 TPH1_HUMAN tryptophan hydroxylase 1 250 aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process cytosol amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity 0 L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360) GAGTGCAGTGAAAAACTCGAA 0.413 0.12 92 12 GLYAT 10249 broad.mit.edu 37 11 58477306 58477307 + Frame_Shift_Ins INS - T T RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr11:58477306_58477307insT uc001nnb.2 - 6 978_979 c.823_824insA c.(823-825)ATGfs p.M275fs NM_201648 NP_964011 Q6IB77 GLYAT_HUMAN glycine-N-acyltransferase isoform a 275 acyl-CoA metabolic process|response to toxin|xenobiotic metabolic process mitochondrial matrix glycine N-acyltransferase activity|glycine N-benzoyltransferase activity 0 Breast(21;0.0044)|all_epithelial(135;0.0157) Glycine(DB00145) TGTGTAACTCATTTTTTGCATA 0.455 0.43 645 485 ANO1 55107 broad.mit.edu 37 11 69934046 69934046 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr11:69934046delC uc001opj.2 + 2 602 c.297delC c.(295-297)CACfs p.H99fs ANO1_uc001opk.1_Frame_Shift_Del_p.H71fs|ANO1_uc001opl.1_RNA NM_018043 NP_060513 Q5XXA6 ANO1_HUMAN anoctamin 1, calcium activated chloride channel 99 Cytoplasmic (Potential). multicellular organismal development chloride channel complex|cytoplasm|plasma membrane intracellular calcium activated chloride channel activity ovary(1)|pancreas(1) 2 0.000 0.18 338 73 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 356 50 NPAT 4863 broad.mit.edu 37 11 108032696 108032696 + Frame_Shift_Del DEL T - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr11:108032696delT uc001pjz.3 - 17 3219 c.3117delA c.(3115-3117)AAAfs p.K1039fs NPAT_uc010rvv.1_Frame_Shift_Del_p.K95fs NM_002519 NP_002510 Q14207 NPAT_HUMAN nuclear protein, ataxia-telangiectasia locus 1039 Required for acceleration of G1 phase. positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle Cajal body protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity ovary(2) 2 all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116) TTTCTTCTGATTTTTTCCCAA 0.373 0.47 571 509 MLL 4297 broad.mit.edu 37 11 118344186 118344186 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr11:118344186delC uc001pta.2 + 3 2335 c.2312delC c.(2311-2313)ACCfs p.T771fs MLL_uc001ptb.2_Frame_Shift_Del_p.T771fs|MLL_uc001psz.1_Frame_Shift_Del_p.T804fs|MLL_uc001ptd.1_Intron NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 771 apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) TCACCTCTCACCCCCCCGTCT 0.453 0.43 671 502 MLL 4297 broad.mit.edu 37 11 118344494 118344495 + Frame_Shift_Del DEL AG - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr11:118344494_118344495delAG uc001pta.2 + 3 2643_2644 c.2620_2621delAG c.(2620-2622)AGAfs p.R874fs MLL_uc001ptb.2_Frame_Shift_Del_p.R874fs|MLL_uc001psz.1_Frame_Shift_Del_p.R907fs|MLL_uc001ptd.1_Intron NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 874 apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) ggacaagagtagagagagagac 0.282 0.40 127 85 ERC1 23085 broad.mit.edu 37 12 1137352 1137352 + Frame_Shift_Del DEL G - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr12:1137352delG uc001qjb.2 + 2 524 c.283delG c.(283-285)GGGfs p.G95fs ERC1_uc001qiz.2_RNA|ERC1_uc001qjc.2_Frame_Shift_Del_p.G95fs|ERC1_uc001qja.2_RNA|ERC1_uc001qjd.2_RNA|ERC1_uc001qjf.2_Frame_Shift_Del_p.G95fs NM_178040 NP_829884 Q8IUD2 RB6I2_HUMAN RAB6-interacting protein 2 isoform epsilon 95 I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport Golgi membrane|IkappaB kinase complex|presynaptic membrane leucine zipper domain binding ovary(2)|lung(2)|breast(1) 5 all_epithelial(11;0.0698)|Ovarian(42;0.107) OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567) TGGCCGTTCTGGGGGACGTCT 0.493 0.54 287 332 PHC1 1911 broad.mit.edu 37 12 9085324 9085325 + In_Frame_Ins INS - GCA GCA RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr12:9085324_9085325insGCA uc001qvd.2 + 8 1427_1428 c.1271_1272insGCA c.(1270-1272)GCG>GCGCAG p.439_440insQ PHC1_uc001qvc.1_In_Frame_Ins_p.394_395insQ|PHC1_uc010sgn.1_In_Frame_Ins_p.439_440insQ|PHC1_uc001qve.2_In_Frame_Ins_p.439_440insQ NM_004426 NP_004417 P78364 PHC1_HUMAN polyhomeotic 1-like 439_440 Poly-Gln. multicellular organismal development PcG protein complex DNA binding|zinc ion binding ovary(1)|breast(1) 2 CTCCAGTTGGCgcagcagcagc 0.455 0.21 31 8 LRP6 4040 broad.mit.edu 37 12 12303942 12303942 + Frame_Shift_Del DEL T - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr12:12303942delT uc001rah.3 - 13 2964 c.2822delA c.(2821-2823)AAGfs p.K941fs BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Frame_Shift_Del_p.K941fs NM_002336 NP_002327 O75581 LRP6_HUMAN low density lipoprotein receptor-related protein 941 Extracellular (Potential).|Beta-propeller 4. cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1) 12 Prostate(47;0.0865) GATGGCACTCTTTTGACTGAA 0.423 0.44 393 303 MLL2 8085 broad.mit.edu 37 12 49426906 49426908 + In_Frame_Del DEL TGC - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr12:49426906_49426908delTGC uc001rta.3 - 39 11580_11582 c.11580_11582delGCA c.(11578-11583)CAGCAA>CAA p.3860_3861QQ>Q NM_003482 NP_003473 O14686 MLL2_HUMAN myeloid/lymphoid or mixed-lineage leukemia 2 3860_3861 Gln-rich. chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent histone methyltransferase complex histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2) 41 gtgctgttgttgctgctgctgct 0.512 0.28 18 7 GLI1 2735 broad.mit.edu 37 12 57860075 57860075 + Frame_Shift_Del DEL G - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr12:57860075delG uc001snx.2 + 8 893 c.815delG c.(814-816)TGGfs p.W272fs GLI1_uc009zpq.2_Frame_Shift_Del_p.W144fs NM_005269 NP_005260 P08151 GLI1_HUMAN GLI family zinc finger 1 isoform 1 272 C2H2-type 2. epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter cytosol|nucleus transcription regulatory region DNA binding|zinc ion binding skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1) 15 GBM - Glioblastoma multiforme(3;3.99e-32) GTGTGCCACTGGGGGGGCTGC 0.597 0.40 619 414 IRAK3 11213 broad.mit.edu 37 12 66620514 66620515 + Frame_Shift_Ins INS - A A RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr12:66620514_66620515insA uc001sth.2 + 7 767_768 c.665_666insA c.(664-666)CCAfs p.P222fs IRAK3_uc010ssy.1_Frame_Shift_Ins_p.P161fs NM_007199 NP_009130 Q9Y616 IRAK3_HUMAN interleukin-1 receptor-associated kinase 3 222 Protein kinase. interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|negative regulation of innate immune response|negative regulation of interleukin-12 production|negative regulation of interleukin-6 production|negative regulation of macrophage cytokine production|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein catabolic process|negative regulation of protein complex disassembly|negative regulation of toll-like receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of macrophage tolerance induction|positive regulation of NF-kappaB transcription factor activity|response to exogenous dsRNA|response to lipopolysaccharide|response to peptidoglycan cytoplasm|nucleus ATP binding|magnesium ion binding|protein heterodimerization activity|protein homodimerization activity|protein serine/threonine kinase activity lung(3)|ovary(2)|breast(2)|central_nervous_system(1) 8 GBM - Glioblastoma multiforme(28;0.0203) TTTCATCACCCAAACATACTAG 0.386 0.30 1072 462 MED13L 23389 broad.mit.edu 37 12 116429108 116429108 + Frame_Shift_Del DEL T - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr12:116429108delT uc001tvw.2 - 17 3706 c.3651delA c.(3649-3651)AAAfs p.K1217fs NM_015335 NP_056150 Q71F56 MD13L_HUMAN mediator complex subunit 13-like 1217 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1) 8 all_neural(191;0.117)|Medulloblastoma(191;0.163) BRCA - Breast invasive adenocarcinoma(302;0.0407) GCTCCTGGGGTTTTTTGGTTC 0.463 0.50 334 330 HNF1A 6927 broad.mit.edu 37 12 121434367 121434367 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr12:121434367delC uc001tzg.2 + 6 1154 c.1131delC c.(1129-1131)CTCfs p.L377fs HNF1A_uc001tze.1_Frame_Shift_Del_p.L377fs|HNF1A_uc001tzf.2_Frame_Shift_Del_p.L377fs|HNF1A_uc010szn.1_Frame_Shift_Del_p.L377fs NM_000545 NP_000536 P20823 HNF1A_HUMAN hepatic nuclear factor-1-alpha 377 glucose homeostasis|glucose import|insulin secretion|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|renal glucose absorption cytoplasm|nucleus|protein complex DNA binding|protein dimerization activity|protein heterodimerization activity|protein homodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding liver(92)|large_intestine(15)|endometrium(6)|breast(2)|lung(1) 116 all_neural(191;0.0684)|Medulloblastoma(191;0.0922) GGGGCCCCCTCCCCCCTGTCA 0.667 0.22 40 11 P2RX7 5027 broad.mit.edu 37 12 121622165 121622165 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr12:121622165delC uc001tzm.2 + 13 1444 c.1348delC c.(1348-1350)CCCfs p.P450fs P2RX7_uc001tzn.2_Frame_Shift_Del_p.P360fs|P2RX7_uc001tzo.2_RNA|P2RX7_uc001tzp.2_Frame_Shift_Del_p.P161fs|P2RX7_uc001tzq.2_Frame_Shift_Del_p.P280fs NM_002562 NP_002553 Q99572 P2RX7_HUMAN purinergic receptor P2X7 450 integral to membrane ATP binding|ion channel activity|receptor activity large_intestine(2)|lung(1)|breast(1)|skin(1) 5 all_neural(191;0.0684)|Medulloblastoma(191;0.0922) CCATGACACACCCCCGATTCC 0.547 0.40 398 262 BCL7A 605 broad.mit.edu 37 12 122468673 122468673 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr12:122468673delC uc001ubp.2 + 2 297 c.160delC c.(160-162)CCCfs p.P54fs BCL7A_uc001ubo.2_Frame_Shift_Del_p.P54fs NM_001024808 NP_001019979 Q4VC05 BCL7A_HUMAN B-cell CLL/lymphoma 7A isoform b 54 negative regulation of transcription, DNA-dependent ovary(1)|lung(1) 2 all_neural(191;0.0837)|Medulloblastoma(191;0.163) OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231) TGTGACGGAGCCCAAGGTTGA 0.587 0.11 85 10 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.17 38 8 BRCA2 675 broad.mit.edu 37 13 32913837 32913837 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr13:32913837delA uc001uub.1 + 11 5572 c.5345delA c.(5344-5346)CAAfs p.Q1782fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 1782 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding p.N1784fs*7(1) ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) GTTGAAGATCAAAAAAACACT 0.318 0.44 379 299 DCLK1 9201 broad.mit.edu 37 13 36382412 36382412 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr13:36382412delC uc001uvf.2 - 14 2045 c.1812delG c.(1810-1812)GGGfs p.G604fs DCLK1_uc001uve.3_Frame_Shift_Del_p.G297fs|DCLK1_uc010teh.1_Frame_Shift_Del_p.G297fs|DCLK1_uc010abk.2_Frame_Shift_Del_p.G124fs NM_004734 NP_004725 O15075 DCLK1_HUMAN doublecortin-like kinase 1 604 Protein kinase. cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus integral to plasma membrane ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity stomach(6)|ovary(2)|skin(1) 9 Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638) AGTCCACCTGCCCCATCAAAA 0.443 0.16 500 92 NYNRIN 57523 broad.mit.edu 37 14 24885305 24885305 + Frame_Shift_Del DEL G - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr14:24885305delG uc001wpf.3 + 9 4668 c.4350delG c.(4348-4350)CAGfs p.Q1450fs NM_025081 NP_079357 Q9P2P1 NYNRI_HUMAN hypothetical protein LOC57523 1450 DNA integration integral to membrane DNA binding ovary(2)|central_nervous_system(1) 3 AGGGTGCCCAGGGGGGTGGGC 0.592 0.46 142 119 PSEN1 5663 broad.mit.edu 37 14 73637619 73637621 + In_Frame_Del DEL GAA - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr14:73637619_73637621delGAA uc001xnr.2 + 4 486_488 c.202_204delGAA c.(202-204)GAAdel p.E69del PSEN1_uc001xnv.2_In_Frame_Del_p.E65del|PSEN1_uc010ark.2_In_Frame_Del_p.E65del|PSEN1_uc001xnt.1_RNA|PSEN1_uc001xnu.2_RNA|PSEN1_uc001xnq.3_In_Frame_Del_p.E69del NM_000021 NP_000012 P49768 PSN1_HUMAN presenilin 1 isoform I-467 69 Cytoplasmic (Potential). Missing: No effect on interaction with GFAP. amyloid precursor protein catabolic process|anti-apoptosis|beta-amyloid metabolic process|cell-cell adhesion|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|smooth endoplasmic reticulum calcium ion homeostasis apical plasma membrane|axon|cell cortex|cell surface|centrosome|ciliary rootlet|dendritic shaft|endoplasmic reticulum membrane|gamma-secretase complex|Golgi membrane|growth cone|integral to plasma membrane|kinetochore|lysosomal membrane|membrane raft|mitochondrial inner membrane|neuromuscular junction|neuronal cell body|nuclear outer membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum|smooth endoplasmic reticulum|Z disc aspartic-type endopeptidase activity|beta-catenin binding|cadherin binding|calcium channel activity|PDZ domain binding breast(1)|kidney(1) 2 BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.075) GCAAGATGAGGAAGAAGATGAGG 0.542 0.54 104 123 SRP14 6727 broad.mit.edu 37 15 40328597 40328599 + In_Frame_Del DEL TGC - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr15:40328597_40328599delTGC uc001zkq.2 - 5 418_420 c.346_348delGCA c.(346-348)GCAdel p.A116del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgcggcaggtgctgctgctgct 0.227 0.27 121 45 TP53BP1 7158 broad.mit.edu 37 15 43714257 43714257 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr15:43714257delC uc001zrs.2 - 19 4029 c.3881delG c.(3880-3882)GGCfs p.G1294fs TP53BP1_uc010udp.1_Frame_Shift_Del_p.G1294fs|TP53BP1_uc001zrq.3_Frame_Shift_Del_p.G1299fs|TP53BP1_uc001zrr.3_Frame_Shift_Del_p.G1299fs|TP53BP1_uc010udq.1_Frame_Shift_Del_p.G1299fs NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 1294 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) ACCTGAGGAGCCCCCAGTCTG 0.493 0.48 100 94 ZNF423 23090 broad.mit.edu 37 16 49671855 49671855 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr16:49671855delC uc002efs.2 - 5 1506 c.1208delG c.(1207-1209)GGCfs p.G403fs ZNF423_uc010vgn.1_Frame_Shift_Del_p.G286fs NM_015069 NP_055884 Q2M1K9 ZN423_HUMAN zinc finger protein 423 403 cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus zinc ion binding ovary(1)|lung(1)|kidney(1)|pancreas(1) 4 all_cancers(37;0.0155) CTTGGTCCAGCCCTGCCCGTC 0.632 0.45 28 23 FANCA 2175 broad.mit.edu 37 16 89858927 89858928 + Frame_Shift_Del DEL CT - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr16:89858927_89858928delCT uc002fou.1 - 12 1076_1077 c.1034_1035delAG c.(1033-1035)GAGfs p.E345fs FANCA_uc010vpn.1_Frame_Shift_Del_p.E345fs NM_000135 NP_000126 O15360 FANCA_HUMAN Fanconi anemia, complementation group A isoform 345 DNA repair|protein complex assembly cytoplasm|nucleoplasm protein binding ovary(2)|breast(2)|central_nervous_system(1)|skin(1) 6 Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194) BRCA - Breast invasive adenocarcinoma(80;0.028) CAAAGCTCCACTCTCTCTGCAT 0.475 0.38 81 49 USP6 9098 broad.mit.edu 37 17 5074001 5074002 + Frame_Shift_Ins INS - GG GG rs146195872;rs139084556 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr17:5074001_5074002insGG uc002gau.1 + 36 5975_5976 c.3745_3746insGG c.(3745-3747)CGGfs p.R1249fs USP6_uc002gav.1_Frame_Shift_Ins_p.R1249fs|USP6_uc010ckz.1_Frame_Shift_Ins_p.R932fs NM_004505 NP_004496 P35125 UBP6_HUMAN ubiquitin specific protease 6 1249 protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process lysosome|plasma membrane|recycling endosome calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1) 5 AGGGCATATGCGGGGGGGCAGC 0.545 0.14 115 19 MYH4 4622 broad.mit.edu 37 17 10362680 10362680 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr17:10362680delA uc002gmn.2 - 15 1586 c.1475delT c.(1474-1476)TTCfs p.F492fs uc002gml.1_Intron NM_017533 NP_060003 Q9Y623 MYH4_HUMAN myosin, heavy polypeptide 4, skeletal muscle 492 Myosin head-like. muscle filament sliding muscle myosin complex|myosin filament|sarcomere actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle ovary(10)|skin(2)|central_nervous_system(1) 13 GTGGTGGTTGAAAAACTGTTG 0.468 0.49 312 303 NF1 4763 broad.mit.edu 37 17 29552144 29552144 + Frame_Shift_Del DEL T - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr17:29552144delT uc002hgg.2 + 17 2210 c.1877delT c.(1876-1878)CTTfs p.L626fs NF1_uc002hgh.2_Frame_Shift_Del_p.L626fs|NF1_uc010csn.1_Frame_Shift_Del_p.L486fs|NF1_uc002hgi.1_5'UTR NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 626 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) CACTTTCTCCTTTTTTACGGG 0.393 0.48 443 409 NF1 4763 broad.mit.edu 37 17 29667620 29667620 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr17:29667620delA uc002hgg.2 + 47 7352 c.7019delA c.(7018-7020)CAAfs p.Q2340fs NF1_uc002hgh.2_Frame_Shift_Del_p.Q2319fs|NF1_uc010cso.2_Frame_Shift_Del_p.Q528fs|NF1_uc010wbt.1_5'UTR|NF1_uc010wbu.1_RNA NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 2340 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) CTTCTTGAACAAAACCTGCAT 0.443 0.48 483 454 TAF15 8148 broad.mit.edu 37 17 34171886 34171886 + Frame_Shift_Del DEL G - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr17:34171886delG uc002hkd.2 + 15 1669 c.1583delG c.(1582-1584)CGGfs p.R528fs TAF15_uc002hkc.2_Frame_Shift_Del_p.R525fs NM_139215 NP_631961 Q92804 RBP56_HUMAN TBP-associated factor 15 isoform 1 528 Arg/Gly-rich.|16.|21 X approximate tandem repeats of D-R- [S,G](0,3)-G-G-Y-G-G. positive regulation of transcription, DNA-dependent cytoplasm|nucleus DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding TAF15/NR4A3(33) bone(33)|lung(1)|skin(1) 35 Ovarian(249;0.17) UCEC - Uterine corpus endometrioid carcinoma (308;0.0193) gACAGAAGCCGGGGGGGCTAT 0.348 0.41 10 7 ACACA 31 broad.mit.edu 37 17 35608932 35608932 + Frame_Shift_Del DEL T - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr17:35608932delT uc002hnm.2 - 16 2160 c.1969delA c.(1969-1971)AGGfs p.R657fs ACACA_uc002hnk.2_Frame_Shift_Del_p.R579fs|ACACA_uc002hnl.2_Frame_Shift_Del_p.R599fs|ACACA_uc002hnn.2_Frame_Shift_Del_p.R657fs|ACACA_uc002hno.2_Frame_Shift_Del_p.R694fs|ACACA_uc010cuz.2_Frame_Shift_Del_p.R657fs NM_198836 NP_942133 Q13085 ACACA_HUMAN acetyl-Coenzyme A carboxylase alpha isoform 2 657 acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process cytosol acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding large_intestine(1)|ovary(1) 2 Breast(25;0.00157)|Ovarian(249;0.15) Biotin(DB00121) AAAGCCTACCTTTCTAAGGAG 0.498 0.53 175 197 TOP2A 7153 broad.mit.edu 37 17 38562730 38562731 + Frame_Shift_Ins INS - TGCT TGCT RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr17:38562730_38562731insTGCT uc002huq.2 - 16 1984_1985 c.1858_1859insAGCA c.(1858-1860)ACAfs p.T620fs NM_001067 NP_001058 P11388 TOP2A_HUMAN DNA topoisomerase II, alpha isozyme 620 apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1) 7 Breast(137;0.00328) STAD - Stomach adenocarcinoma(5;0.00183) Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385) TTCCTTTGATGTGCTGGTGCCC 0.371 0.41 177 125 STAT3 6774 broad.mit.edu 37 17 40475061 40475063 + In_Frame_Del DEL CTT - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr17:40475061_40475063delCTT uc002hzl.1 - 20 2087_2089 c.1847_1849delAAG c.(1846-1851)GAAGGA>GGA p.E616del STAT3_uc002hzk.1_In_Frame_Del_p.E616del|STAT3_uc002hzm.1_In_Frame_Del_p.E616del|STAT3_uc010wgh.1_In_Frame_Del_p.E518del|STAT3_uc002hzn.1_In_Frame_Del_p.E616del NM_139276 NP_644805 P40763 STAT3_HUMAN signal transducer and activator of transcription 616 SH2. cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis cytosol|nucleus|plasma membrane calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding ovary(1)|lung(1)|breast(1)|central_nervous_system(1) 4 all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135) BRCA - Breast invasive adenocarcinoma(366;0.139) GTGACGCCTCCTTCTTTGCTGCT 0.562 0.47 643 567 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 1.00 0 17 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.18 74 16 RNF43 54894 broad.mit.edu 37 17 56435160 56435160 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr17:56435160delA uc002iwf.2 - 8 3933 c.1977delT c.(1975-1977)GGTfs p.G659fs RNF43_uc010wnv.1_Frame_Shift_Del_p.G618fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.G659fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.G659fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.G532fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 659 Pro-rich.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.15 312 53 RNF43 54894 broad.mit.edu 37 17 56435161 56435161 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr17:56435161delC uc002iwf.2 - 8 3932 c.1976delG c.(1975-1977)GGTfs p.G659fs RNF43_uc010wnv.1_Frame_Shift_Del_p.G618fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.G659fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.G659fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.G532fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 659 Pro-rich.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.56 79 100 NOTCH3 4854 broad.mit.edu 37 19 15289955 15289955 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr19:15289955delA uc002nan.2 - 22 3675 c.3599delT c.(3598-3600)TTGfs p.L1200fs NOTCH3_uc002nao.1_Frame_Shift_Del_p.L1148fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 1200 Extracellular (Potential).|EGF-like 30; calcium-binding (Potential). Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) CTCGCAGCGCAAACCAGTGTA 0.657 0.67 4 8 CPAMD8 27151 broad.mit.edu 37 19 17039884 17039884 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr19:17039884delC uc002nfb.2 - 24 3185 c.3153delG c.(3151-3153)GGGfs p.G1051fs NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 1004 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 TGTTCTGATGCCCCCCCAGGA 0.587 0.43 170 128 MAP3K10 4294 broad.mit.edu 37 19 40698086 40698087 + Frame_Shift_Del DEL TG - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr19:40698086_40698087delTG uc002ona.2 + 1 436_437 c.148_149delTG c.(148-150)TGTfs p.C50fs NM_002446 NP_002437 Q02779 M3K10_HUMAN mitogen-activated protein kinase kinase kinase 50 SH3. activation of JUN kinase activity|induction of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of JNK cascade|protein autophosphorylation|smoothened signaling pathway cytoplasm ATP binding|bHLH transcription factor binding|JUN kinase kinase kinase activity|protein homodimerization activity|transcription corepressor activity ovary(2)|lung(2)|skin(1)|pancreas(1) 6 0.000 0.26 550 189 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.42 65 48 JAG1 182 broad.mit.edu 37 20 10630969 10630969 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr20:10630969delC uc002wnw.2 - 9 1676 c.1160delG c.(1159-1161)GGCfs p.G387fs JAG1_uc010gcd.1_5'UTR NM_000214 NP_000205 P78504 JAG1_HUMAN jagged 1 precursor 387 Extracellular (Potential).|EGF-like 5; calcium-binding (Potential). angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation extracellular region|integral to plasma membrane calcium ion binding|growth factor activity|Notch binding|structural molecule activity lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1) 9 CTGGCAGGTGCCCCCGTGGGA 0.468 0.64 9 16 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 555 67 COL18A1 80781 broad.mit.edu 37 21 46888673 46888673 + Frame_Shift_Del DEL G - - rs76148908 by1000genomes RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr21:46888673delG uc011afs.1 + 2 1890 c.1869delG c.(1867-1869)GCGfs p.A623fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.A208fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.A388fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 623 TSP N-terminal. cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.37 514 305 COL18A1 80781 broad.mit.edu 37 21 46900749 46900749 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr21:46900749delC uc011afs.1 + 12 2854 c.2833delC c.(2833-2835)CCCfs p.P945fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.P530fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.P710fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 945 Triple-helical region 3 (COL3). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.56 465 580 COL18A1 80781 broad.mit.edu 37 21 46917558 46917559 + Frame_Shift_Ins INS - C C RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr21:46917558_46917559insC uc011afs.1 + 31 3932_3933 c.3911_3912insC c.(3910-3912)GGCfs p.G1304fs COL18A1_uc002zhg.2_Frame_Shift_Ins_p.G889fs|COL18A1_uc002zhi.2_Frame_Shift_Ins_p.G1069fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1304 Triple-helical region 7 (COL7). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.19 440 105 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 73 307 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 21 336 MED15 51586 broad.mit.edu 37 22 20918916 20918918 + In_Frame_Del DEL CAG - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr22:20918916_20918918delCAG uc002zsp.2 + 6 711_713 c.631_633delCAG c.(631-633)CAGdel p.Q218del MED15_uc002zsn.1_In_Frame_Del_p.Q137del|MED15_uc002zso.2_In_Frame_Del_p.Q147del|MED15_uc002zsq.2_In_Frame_Del_p.Q218del|MED15_uc010gso.2_In_Frame_Del_p.Q218del|MED15_uc002zsr.2_In_Frame_Del_p.Q192del|MED15_uc011ahs.1_In_Frame_Del_p.Q192del|MED15_uc011aht.1_In_Frame_Del_p.Q192del|MED15_uc002zss.2_In_Frame_Del_p.Q137del|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 218 Poly-Gln. Missing (in Ref. 4; CAG30423). regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) gcagcagctccagcagcagcagc 0.187 0.19 83 20 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.20 57 14 ZNRF3 84133 broad.mit.edu 37 22 29445208 29445209 + Frame_Shift_Del DEL GT - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr22:29445208_29445209delGT uc003aeg.2 + 8 904_905 c.739_740delGT c.(739-741)GTGfs p.V247fs ZNRF3_uc003aeh.1_Frame_Shift_Del_p.V247fs NM_032173 NP_115549 Q9ULT6 ZNRF3_HUMAN zinc and ring finger 3 347 Cytoplasmic (Potential). integral to membrane zinc ion binding ovary(1) 1 0.000 0.51 143 151 NF2 4771 broad.mit.edu 37 22 30060991 30060991 + Frame_Shift_Del DEL C - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr22:30060991delC uc003age.3 + 9 1266 c.823delC c.(823-825)CCAfs p.P275fs NF2_uc003afy.3_Frame_Shift_Del_p.P275fs|NF2_uc003afz.3_Frame_Shift_Del_p.P192fs|NF2_uc003agf.3_Frame_Shift_Del_p.P275fs|NF2_uc003agb.3_Frame_Shift_Del_p.P198fs|NF2_uc003agc.3_Frame_Shift_Del_p.P237fs|NF2_uc003agd.3_RNA|NF2_uc003agg.3_Frame_Shift_Del_p.P275fs|NF2_uc003aga.3_Frame_Shift_Del_p.P233fs|NF2_uc003agh.3_Frame_Shift_Del_p.P234fs|NF2_uc003agi.3_Frame_Shift_Del_p.P192fs|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Frame_Shift_Del_p.P237fs|NF2_uc010gvp.2_5'UTR NM_000268 NP_000259 P35240 MERL_HUMAN neurofibromin 2 isoform 1 275 FERM. actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane cytoskeletal protein binding|protein binding p.L127_D382del(1)|p.F271_L295del(1)|p.?(1) meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1) 728 TACTATTAAACCACTGGATAA 0.388 0.44 352 278 MYH9 4627 broad.mit.edu 37 22 36682803 36682805 + In_Frame_Del DEL CTT - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr22:36682803_36682805delCTT uc003apg.2 - 35 5251_5253 c.5020_5022delAAG c.(5020-5022)AAGdel p.K1674del NM_002473 NP_002464 P35579 MYH9_HUMAN myosin, heavy polypeptide 9, non-muscle 1674 Potential. actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1) 11 TGCTCTTCAGCTTCTTCTCGTTC 0.650 0.46 396 333 EP300 2033 broad.mit.edu 37 22 41522009 41522009 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr22:41522009delA uc003azl.3 + 3 1266 c.871delA c.(871-873)AAAfs p.K291fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 291 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 TGCTATGGACAAAAAGGCAGT 0.408 0.47 448 405 EP300 2033 broad.mit.edu 37 22 41566525 41566525 + Frame_Shift_Del DEL A - - RKO_LARGE_INTESTINE NA RKO_LARGE_INTESTINE NA g.chr22:41566525delA uc003azl.3 + 27 4797 c.4402delA c.(4402-4404)AAAfs p.K1468fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1468 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding p.M1470fs*3(3) haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 GGAATGGTACAAAAAAATGCT 0.473 0.45 611 504 RPS6KA3 6197 broad.mit.edu 37 X 20187558 20187560 + In_Frame_Del DEL GAA - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chrX:20187558_20187560delGAA uc004czu.2 - 16 1403_1405 c.1403_1405delTTC c.(1402-1407)CTTCGT>CGT p.L468del RPS6KA3_uc011mjk.1_In_Frame_Del_p.L438del|RPS6KA3_uc004czv.2_In_Frame_Del_p.L455del|RPS6KA3_uc011mjl.1_In_Frame_Del_p.L439del|RPS6KA3_uc011mjm.1_In_Frame_Del_p.L440del NM_004586 NP_004577 P51812 KS6A3_HUMAN ribosomal protein S6 kinase, 90kDa, polypeptide 468 Protein kinase 2. axon guidance|central nervous system development|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|skeletal system development|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|caspase inhibitor activity|magnesium ion binding|protein serine/threonine kinase activity central_nervous_system(4)|stomach(1)|ovary(1)|lung(1)|breast(1) 8 TGTCCATAACGAAGAAGAATTTC 0.315 0.32 63 30 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 59 F8 2157 broad.mit.edu 37 X 154157686 154157686 + Frame_Shift_Del DEL T - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chrX:154157686delT uc004fmt.2 - 14 4550 c.4379delA c.(4378-4380)AATfs p.N1460fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1460 B. N -> K (in HEMA). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AGAAAGGTTATTTTTTTTGGC 0.413 0.38 194 119 RPL22 6146 broad.mit.edu 37 1 6257785 6257786 + Frame_Shift_Del DEL TT - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr1:6257785_6257786delTT uc001amd.2 - 2 89_90 c.43_44delAA c.(43-45)AAGfs p.K15fs RPL22_uc001ame.2_Frame_Shift_Del_p.K15fs NM_000983 NP_000974 P35268 RL22_HUMAN ribosomal protein L22 proprotein 15 endocrine pancreas development|translational elongation|translational termination|viral transcription cytosolic large ribosomal subunit heparin binding|RNA binding|structural constituent of ribosome 0 Ovarian(185;0.0634) all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211) Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182) AACTTGCTTCTTTTTTTTGCCC 0.396 0.48 100 94 TNFRSF9 3604 broad.mit.edu 37 1 7998254 7998254 + Frame_Shift_Del DEL T - - rs9657965 byFrequency;by1000genomes RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr1:7998254delT uc001aot.2 - 4 473 c.345delA c.(343-345)AAAfs p.K115fs NM_001561 NP_001552 Q07011 TNR9_HUMAN tumor necrosis factor receptor superfamily, 115 Extracellular (Potential).|TNFR-Cys 3. induction of apoptosis|negative regulation of cell proliferation integral to plasma membrane binding|receptor activity large_intestine(1)|lung(1)|ovary(1)|skin(1) 4 Ovarian(185;0.0634)|all_lung(157;0.151) all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649) CAAACGTACCTTTTTTTGTCA 0.413 0.55 34 42 SPEN 23013 broad.mit.edu 37 1 16259043 16259043 + Frame_Shift_Del DEL G - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr1:16259043delG uc001axk.1 + 11 6512 c.6308delG c.(6307-6309)AGGfs p.R2103fs SPEN_uc010obp.1_Frame_Shift_Del_p.R2062fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2103 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) GTCAGTCCCAGGGGGGCTGCA 0.512 0.49 56 53 ARID1A 8289 broad.mit.edu 37 1 27087373 27087373 + Frame_Shift_Del DEL C - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr1:27087373delC uc001bmv.1 + 5 2320 c.1947delC c.(1945-1947)CTCfs p.L649fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.L649fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.L649fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.L266fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 649 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) TAGATGACCTCCCCATGGGGA 0.428 0.50 111 109 JAK1 3716 broad.mit.edu 37 1 65305357 65305357 + Frame_Shift_Del DEL T - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr1:65305357delT uc001dbu.1 - 20 3020 c.2771delA c.(2770-2772)AAGfs p.K924fs JAK1_uc009wam.1_Frame_Shift_Del_p.K912fs|JAK1_uc009wal.1_Frame_Shift_Del_p.K101fs NM_002227 NP_002218 P23458 JAK1_HUMAN janus kinase 1 924 Protein kinase 2. interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway cytoskeleton|cytosol|endomembrane system|membrane|nucleus ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1) 61 BRCA - Breast invasive adenocarcinoma(111;0.0485) CTCGATTTCCTTTTTCAGATC 0.473 0.47 107 95 TPM3 7170 broad.mit.edu 37 1 154145644 154145644 + Frame_Shift_Del DEL T - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr1:154145644delT uc001fec.1 - 4 526 c.411delA c.(409-411)AAAfs p.K137fs TPM3_uc001fdx.1_5'Flank|TPM3_uc010pei.1_Frame_Shift_Del_p.K10fs|TPM3_uc001fdy.1_Frame_Shift_Del_p.K100fs|TPM3_uc001fdz.1_Frame_Shift_Del_p.K100fs|TPM3_uc001fea.1_Frame_Shift_Del_p.K100fs|TPM3_uc001feb.1_Frame_Shift_Del_p.K100fs|TPM3_uc010pej.1_Frame_Shift_Del_p.K33fs|TPM3_uc009wor.2_Intron|TPM3_uc001fed.1_Frame_Shift_Del_p.K100fs NM_152263 NP_689476 P06753 TPM3_HUMAN tropomyosin 3 isoform 1 136 By similarity. cellular component movement|muscle filament sliding|regulation of muscle contraction cytosol|muscle thin filament tropomyosin|stress fiber actin binding TPM3/ALK(33) haematopoietic_and_lymphoid_tissue(22)|soft_tissue(11)|skin(1) 34 all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128) TTTCTTCATCTTTTAAGGCCC 0.448 0.43 152 113 NTRK1 4914 broad.mit.edu 37 1 156848967 156848968 + Frame_Shift_Ins INS - C C rs80356676 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr1:156848967_156848968insC uc001fqh.1 + 15 1915_1916 c.1859_1860insC c.(1858-1860)GGCfs p.G620fs NTRK1_uc001fqf.1_Frame_Shift_Ins_p.G584fs|NTRK1_uc009wsi.1_Frame_Shift_Ins_p.G319fs|NTRK1_uc001fqi.1_Frame_Shift_Ins_p.G614fs|NTRK1_uc009wsk.1_Frame_Shift_Ins_p.G617fs NM_002529 NP_002520 P04629 NTRK1_HUMAN neurotrophic tyrosine kinase, receptor, type 1 620 Cytoplasmic (Potential).|Protein kinase. activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction endosome|integral to plasma membrane ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity lung(9)|ovary(6)|stomach(1)|central_nervous_system(1) 17 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) Imatinib(DB00619) GTGGCTCCAGGCCCCCTGGGTC 0.634 0.41 47 33 CABC1 56997 broad.mit.edu 37 1 227170395 227170395 + Frame_Shift_Del DEL C - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr1:227170395delC uc001hqm.1 + 12 4289 c.870delC c.(868-870)AACfs p.N290fs CABC1_uc001hqn.1_Frame_Shift_Del_p.N290fs|CABC1_uc009xeq.1_Frame_Shift_Del_p.N238fs|CABC1_uc010pvq.1_Frame_Shift_Del_p.N11fs|CABC1_uc010pvr.1_Frame_Shift_Del_p.N11fs|CABC1_uc001hqo.1_Frame_Shift_Del_p.N11fs|CABC1_uc009xer.1_5'Flank NM_020247 NP_064632 Q8NI60 ADCK3_HUMAN chaperone, ABC1 activity of bc1 complex like 290 cell death mitochondrion ATP binding|protein serine/threonine kinase activity 0 Prostate(94;0.0771) CCTTTATCAACCCCCACCTGG 0.607 0.31 33 15 ROCK2 9475 broad.mit.edu 37 2 11347937 11347937 + Frame_Shift_Del DEL T - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr2:11347937delT uc002rbd.1 - 20 2913 c.2464delA c.(2464-2466)ATGfs p.M822fs NM_004850 NP_004841 O75116 ROCK2_HUMAN Rho-associated, coiled-coil containing protein 822 Potential. axon guidance|cytokinesis|intracellular signal transduction cytosol|plasma membrane ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity stomach(2)|skin(2) 4 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162) TTTTCTGACATTTTTAGTGTG 0.338 0.43 129 99 NRBP1 29959 broad.mit.edu 37 2 27663753 27663754 + Frame_Shift_Ins INS - C C RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr2:27663753_27663754insC uc002rko.2 + 15 2107_2108 c.1275_1276insC c.(1273-1278)GTGCCCfs p.V425fs NRBP1_uc002rkq.2_Frame_Shift_Ins_p.V424fs|NRBP1_uc002rkp.2_Frame_Shift_Ins_p.V425fs|NRBP1_uc002rkr.2_Frame_Shift_Ins_p.V216fs|KRTCAP3_uc002rks.2_5'Flank|KRTCAP3_uc010ylr.1_5'Flank|KRTCAP3_uc002rkt.2_5'Flank NM_013392 NP_037524 Q9UHY1 NRBP_HUMAN nuclear receptor binding protein 425_426 ER to Golgi vesicle-mediated transport|gene expression|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor cell cortex|endomembrane system|lamellipodium|membrane|nucleoplasm ATP binding|protein homodimerization activity|protein kinase activity ovary(2)|lung(1) 3 Acute lymphoblastic leukemia(172;0.155) CACCTGTCGTGCCCCCCTCTGT 0.599 0.47 8 7 BCL11A 53335 broad.mit.edu 37 2 60689254 60689254 + Frame_Shift_Del DEL G - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr2:60689254delG uc002sae.1 - 4 1021 c.793delC c.(793-795)CTGfs p.L265fs BCL11A_uc002sab.2_Frame_Shift_Del_p.L265fs|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Frame_Shift_Del_p.L231fs|BCL11A_uc002sad.1_Frame_Shift_Del_p.L113fs|BCL11A_uc002saf.1_Frame_Shift_Del_p.L231fs NM_022893 NP_075044 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A isoform 1 265 Pro-rich. negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|cytoplasm|nucleus|nucleus nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding central_nervous_system(6)|breast(3)|ovary(2)|skin(2) 13 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) GGACTAAACAGGGGGGGAGTG 0.582 0.31 9 4 LRP2 4036 broad.mit.edu 37 2 169997025 169997025 + Frame_Shift_Del DEL G - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr2:169997025delG uc002ues.2 - 72 13352 c.13139delC c.(13138-13140)CCAfs p.P4380fs NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 4380 EGF-like 17.|Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) 0.000 0.48 117 107 LRP2 4036 broad.mit.edu 37 2 170088332 170088332 + Frame_Shift_Del DEL A - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr2:170088332delA uc002ues.2 - 31 5332 c.5119delT c.(5119-5121)TCCfs p.S1707fs NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 1707 EGF-like 7.|Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) CTGCAGCGGGAAAAGGCACAT 0.473 0.36 49 28 ITGAV 3685 broad.mit.edu 37 2 187511448 187511448 + Frame_Shift_Del DEL A - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr2:187511448delA uc002upq.2 + 13 1471 c.1195delA c.(1195-1197)AAAfs p.K399fs ITGAV_uc010frs.2_Frame_Shift_Del_p.K363fs|ITGAV_uc010zfv.1_Frame_Shift_Del_p.K353fs NM_002210 NP_002201 P06756 ITAV_HUMAN integrin alpha-V isoform 1 precursor 399 FG-GAP 6.|Extracellular (Potential). angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance integrin complex receptor activity|transforming growth factor beta binding ovary(2)|kidney(1)|skin(1) 4 OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189) STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108) GGGTGAAGATAAAAAAGGAAT 0.323 0.44 43 34 CASP8 841 broad.mit.edu 37 2 202149799 202149799 + Frame_Shift_Del DEL T - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr2:202149799delT uc002uxr.1 + 9 1272 c.1063delT c.(1063-1065)TTTfs p.F355fs CASP8_uc002uxp.1_Frame_Shift_Del_p.F372fs|CASP8_uc002uxq.1_Frame_Shift_Del_p.F340fs|CASP8_uc002uxt.1_Frame_Shift_Del_p.F414fs|CASP8_uc002uxu.1_RNA|CASP8_uc002uxw.1_Frame_Shift_Del_p.F340fs|CASP8_uc002uxy.1_Intron|CASP8_uc002uxx.1_Intron|CASP8_uc010ftf.2_Frame_Shift_Del_p.F271fs NM_033355 NP_203519 Q14790 CASP8_HUMAN caspase 8 isoform B precursor 355 activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor centrosome|cytosol|mitochondrial outer membrane cysteine-type endopeptidase activity|protein binding|protein binding p.S355F(1) upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1) 5 ACCCAAAGTGTTTTTTATTCA 0.453 0.47 116 102 ACVR2B 93 broad.mit.edu 37 3 38519754 38519754 + Frame_Shift_Del DEL C - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr3:38519754delC uc003cif.2 + 4 517 c.493delC c.(493-495)CCCfs p.P165fs ACVR2B_uc003cig.2_5'UTR NM_001106 NP_001097 Q13705 AVR2B_HUMAN activin A receptor, type IIB precursor 165 Cytoplasmic (Potential). activin receptor signaling pathway|anterior/posterior pattern formation|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|regulation of transcription, DNA-dependent cell surface|cytoplasm|integral to plasma membrane activin receptor activity|ATP binding|growth factor binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity lung(1) 1 Medulloblastoma(35;0.163) KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071) GCATCGCAAGCCCCCCTACGG 0.617 0.39 71 46 FLNB 2317 broad.mit.edu 37 3 58107010 58107010 + Frame_Shift_Del DEL G - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr3:58107010delG uc003djj.2 + 20 3071 c.2906delG c.(2905-2907)AGGfs p.R969fs FLNB_uc010hne.2_Frame_Shift_Del_p.R969fs|FLNB_uc003djk.2_Frame_Shift_Del_p.R969fs|FLNB_uc010hnf.2_Frame_Shift_Del_p.R969fs|FLNB_uc003djl.2_Frame_Shift_Del_p.R800fs|FLNB_uc003djm.2_Frame_Shift_Del_p.R800fs NM_001457 NP_001448 O75369 FLNB_HUMAN filamin B isoform 2 969 Filamin 8. actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction cell cortex|integral to membrane|nucleus|sarcomere actin binding breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1) 19 BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898) 0.000 0.49 535 514 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.36 14 8 GMPS 8833 broad.mit.edu 37 3 155628544 155628544 + Frame_Shift_Del DEL A - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr3:155628544delA uc003faq.2 + 6 925 c.590delA c.(589-591)GAAfs p.E197fs GMPS_uc011bom.1_Frame_Shift_Del_p.E98fs NM_003875 NP_003866 P49915 GUAA_HUMAN guanine monophosphate synthetase 197 Glutamine amidotransferase type-1. glutamine metabolic process|purine base biosynthetic process cytosol ATP binding|GMP synthase (glutamine-hydrolyzing) activity|GMP synthase activity ovary(2)|lung(1) 3 Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114) L-Glutamic Acid(DB00142)|L-Glutamine(DB00130) GGCCTTACAGAAAATGGAAAA 0.358 0.46 49 41 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.14 90 15 BMP2K 55589 broad.mit.edu 37 4 79792103 79792104 + In_Frame_Ins INS - CAA CAA rs141745080 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr4:79792103_79792104insCAA uc003hlk.2 + 11 1564_1565 c.1398_1399insCAA c.(1396-1401)insCAA p.486_487insQ BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Ins_p.486_487insQ|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486_487 Gln/His-rich. nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 agcagcagcagcagcaacagca 0.213 0.10 74 8 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.13 48 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 93 84 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.30 44 19 TSSK1B 83942 broad.mit.edu 37 5 112769462 112769462 + Frame_Shift_Del DEL G - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr5:112769462delG uc003kqm.2 - 1 1267 c.1075delC c.(1075-1077)CAAfs p.Q359fs MCC_uc003kql.3_Intron NM_032028 NP_114417 Q9BXA7 TSSK1_HUMAN testis-specific serine kinase 1 359 cell differentiation|multicellular organismal development|spermatogenesis ATP binding|magnesium ion binding|protein serine/threonine kinase activity ovary(2)|skin(2)|stomach(1) 5 all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156) Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449) 0.000 0.25 428 139 DST 667 broad.mit.edu 37 6 56362694 56362695 + Frame_Shift_Ins INS - T T RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr6:56362694_56362695insT uc003pdf.2 - 75 13724_13725 c.13696_13697insA c.(13696-13698)ACAfs p.T4566fs DST_uc003pcz.3_Frame_Shift_Ins_p.T4388fs|DST_uc011dxj.1_Frame_Shift_Ins_p.T4417fs|DST_uc011dxk.1_Frame_Shift_Ins_p.T4428fs|DST_uc003pcy.3_Frame_Shift_Ins_p.T4062fs NM_001144769 NP_001138241 Q03001 DYST_HUMAN dystonin isoform 2 6474 Spectrin 15. cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1) 14 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) CCTTTGTTCTGTTTTTTCCAAA 0.391 0.45 86 69 MLLT4 4301 broad.mit.edu 37 6 168366691 168366692 + In_Frame_Ins INS - GAG GAG RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr6:168366691_168366692insGAG uc003qwd.2 + 32 5374_5375 c.5232_5233insGAG c.(5230-5235)insGAG p.1750_1751insE NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 1740_1741 adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) 0.000 0.36 415 229 GLI3 2737 broad.mit.edu 37 7 42005573 42005573 + Frame_Shift_Del DEL G - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr7:42005573delG uc011kbh.1 - 15 3189 c.3098delC c.(3097-3099)CCGfs p.P1033fs GLI3_uc011kbg.1_Frame_Shift_Del_p.P974fs NM_000168 NP_000159 P10071 GLI3_HUMAN GLI-Kruppel family member GLI3 1033 negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis cilium|cytosol|nucleolus beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1) 19 0.000 0.41 1060 748 BRAF 673 broad.mit.edu 37 7 140482927 140482927 + Frame_Shift_Del DEL G - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr7:140482927delG uc003vwc.3 - 10 1269 c.1208delC c.(1207-1209)CCTfs p.P403fs NM_004333 NP_004324 P15056 BRAF_HUMAN B-Raf 403 activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission cytosol|nucleus|plasma membrane ATP binding|metal ion binding KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2) thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1) 18290 Melanoma(164;0.00956) Sorafenib(DB00398) TAATGAGGCAGGGGGGGTAGC 0.428 0.36 109 62 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 10 NOS3 4846 broad.mit.edu 37 7 150698398 150698398 + Frame_Shift_Del DEL G - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr7:150698398delG uc003wif.2 + 11 1609 c.1313delG c.(1312-1314)AGGfs p.R438fs NOS3_uc011kuy.1_Frame_Shift_Del_p.R232fs|NOS3_uc011kuz.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kva.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kvb.1_Frame_Shift_Del_p.R438fs NM_000603 NP_000594 P29474 NOS3_HUMAN nitric oxide synthase 3 isoform 1 438 Interaction with NOSIP. anti-apoptosis|arginine catabolic process|blood vessel remodeling|endothelial cell migration|mitochondrion organization|negative regulation of muscle hyperplasia|negative regulation of platelet activation|nitric oxide biosynthetic process|platelet activation|positive regulation of angiogenesis|positive regulation of guanylate cyclase activity|positive regulation of vasodilation|regulation of blood vessel size|regulation of nitric-oxide synthase activity|regulation of systemic arterial blood pressure by endothelin|response to fluid shear stress|response to heat|smooth muscle hyperplasia caveola|cytoskeleton|cytosol|Golgi membrane actin monomer binding|arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding central_nervous_system(5)|large_intestine(2)|skin(1) 8 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) L-Arginine(DB00125)|L-Citrulline(DB00155)|Rosuvastatin(DB01098)|Tetrahydrobiopterin(DB00360) CAGAAGGCCAGGGGGGGCTGC 0.617 0.35 13 7 PRKDC 5591 broad.mit.edu 37 8 48701554 48701555 + Frame_Shift_Ins INS - T T RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr8:48701554_48701555insT uc003xqi.2 - 77 10871_10872 c.10814_10815insA c.(10813-10815)AACfs p.N3605fs PRKDC_uc003xqj.2_Frame_Shift_Ins_p.N3605fs|PRKDC_uc011ldh.1_Intron NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic 3605 cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) TTTTTTCAATGTTTTTTTTATT 0.401 0.24 218 67 SULF1 23213 broad.mit.edu 37 8 70488249 70488249 + Frame_Shift_Del DEL G - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr8:70488249delG uc010lza.1 + 6 934 c.217delG c.(217-219)GGGfs p.G73fs SULF1_uc003xyd.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xye.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xyf.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xyg.2_Frame_Shift_Del_p.G73fs NM_015170 NP_055985 Q8IWU6 SULF1_HUMAN sulfatase 1 precursor 73 apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway cell surface|endoplasmic reticulum|extracellular space|Golgi stack arylsulfatase activity|calcium ion binding central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1) 7 Breast(64;0.0654) Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534) TATGGAACATGGGGGGGCCAC 0.493 0.28 86 33 POU5F1B 5462 broad.mit.edu 37 8 128428152 128428153 + Frame_Shift_Ins INS - A A RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr8:128428152_128428153insA uc003ysf.2 + 1 296_297 c.41_42insA c.(40-42)CCTfs p.P14fs uc003ysc.1_Intron|uc003ysd.1_Intron|LOC727677_uc003yse.1_Intron NM_001159542 NP_001153014 Q06416 P5F1B_HUMAN POU class 5 homeobox 1B 14 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 TTCTCGCCCCCTCCAGGCGGTG 0.639 0.31 11 5 HSF1 3297 broad.mit.edu 37 8 145537675 145537675 + Frame_Shift_Del DEL C - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr8:145537675delC uc003zbt.3 + 12 1512 c.1342delC c.(1342-1344)CCCfs p.P448fs HSF1_uc003zbu.3_RNA NM_005526 NP_005517 Q00613 HSF1_HUMAN heat shock transcription factor 1 448 Transactivation domain. cytoplasm protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055) 0.000 0.30 38 16 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.29 418 167 MLLT3 4300 broad.mit.edu 37 9 20414311 20414313 + In_Frame_Del DEL CTG - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr9:20414311_20414313delCTG uc003zoe.2 - 5 790_792 c.531_533delCAG c.(529-534)AGCAGT>AGT p.177_178SS>S MLLT3_uc011lne.1_In_Frame_Del_p.145_146SS>S|MLLT3_uc011lnf.1_In_Frame_Del_p.174_175SS>S|MLLT3_uc003zof.2_5'UTR NM_004529 NP_004520 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia 177_178 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding lung(2)|ovary(1) 3 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) gctgctgctactgctgctgctgc 0.143 0.10 128 15 PTENP1 11191 broad.mit.edu 37 9 33675850 33675850 + Frame_Shift_Del DEL T - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr9:33675850delT uc003zth.3 - 1 1569 c.698delA c.(697-699)AAGfs p.K233fs NR_023917 SubName: Full=Phosphatase and tensin homolog 2; Flags: Fragment; 0 CATTTTGTCCTTTTTTAGCAT 0.378 0.48 135 123 PAPPA 5069 broad.mit.edu 37 9 118949931 118949932 + Frame_Shift_Ins INS - C C RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr9:118949931_118949932insC uc004bjn.2 + 2 1295_1296 c.914_915insC c.(913-915)AGCfs p.S305fs PAPPA_uc011lxp.1_Frame_Shift_Ins_p.S98fs|PAPPA_uc011lxq.1_Frame_Shift_Ins_p.S98fs NM_002581 NP_002572 Q13219 PAPP1_HUMAN pregnancy-associated plasma protein A 305 Metalloprotease. cell differentiation|female pregnancy cytoplasm|extracellular region|membrane metalloendopeptidase activity|zinc ion binding ovary(4)|skin(4)|pancreas(1) 9 GATGGCAGCAGCCCCAAAGTGG 0.564 0.34 21 11 PIP4K2A 5305 broad.mit.edu 37 10 22828937 22828937 + Frame_Shift_Del DEL T - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr10:22828937delT uc001irl.3 - 9 1351 c.1103delA c.(1102-1104)AAGfs p.K368fs PIP4K2A_uc010qcu.1_Frame_Shift_Del_p.K228fs NM_005028 NP_005019 P48426 PI42A_HUMAN phosphatidylinositol-5-phosphate 4-kinase, type 368 PIPK. 1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding ovary(1)|skin(1) 2 GGCAGCTTTCTTTTTTGCATC 0.348 0.45 132 106 PDCD11 22984 broad.mit.edu 37 10 105158207 105158207 + Frame_Shift_Del DEL C - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr10:105158207delC uc001kwy.1 + 2 111 c.24delC c.(22-24)TTCfs p.F8fs USMG5_uc001kww.1_5'Flank|USMG5_uc001kwx.1_5'Flank NM_014976 NP_055791 Q14690 RRP5_HUMAN programmed cell death 11 8 mRNA processing|rRNA processing nucleolus RNA binding|transcription factor binding ovary(2)|breast(2)|skin(2)|central_nervous_system(1) 7 Colorectal(252;0.0747)|Breast(234;0.128) Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208) AAGAAAGCTTCCCCCGAGGAG 0.413 0.47 74 65 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 314 68 ATM 472 broad.mit.edu 37 11 108172510 108172510 + Frame_Shift_Del DEL A - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr11:108172510delA uc001pkb.1 + 35 5698 c.5313delA c.(5311-5313)AGAfs p.R1771fs ATM_uc009yxr.1_Frame_Shift_Del_p.R1771fs|ATM_uc001pke.1_Frame_Shift_Del_p.R423fs|ATM_uc001pkg.1_Frame_Shift_Del_p.R128fs|ATM_uc009yxt.1_5'Flank NM_000051 NP_000042 Q13315 ATM_HUMAN ataxia telangiectasia mutated isoform 1 1771 cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence cytoplasmic membrane-bounded vesicle|nucleoplasm 1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1) 240 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147) GAACATCAAGAAAAAAGGTCT 0.343 0.41 69 48 CDKN1B 1027 broad.mit.edu 37 12 12870842 12870842 + Frame_Shift_Del DEL C - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr12:12870842delC uc001rat.2 + 1 541 c.69delC c.(67-69)CACfs p.H23fs NM_004064 NP_004055 P46527 CDN1B_HUMAN cyclin-dependent kinase inhibitor 1B 23 autophagic cell death|cell cycle arrest|cellular response to lithium ion|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of transcription, DNA-dependent|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process|S phase of mitotic cell cycle cytosol|endosome|nucleoplasm cyclin-dependent protein kinase inhibitor activity|protein phosphatase binding|transforming growth factor beta receptor, cytoplasmic mediator activity ovary(1)|lung(1) 2 Prostate(47;0.0322)|all_epithelial(100;0.159) BRCA - Breast invasive adenocarcinoma(232;0.0336) AGGCGGAGCACCCCAAGCCCT 0.637 0.46 34 29 GRIN2B 2904 broad.mit.edu 37 12 14019044 14019044 + Frame_Shift_Del DEL G - - rs77738206 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr12:14019044delG uc001rbt.2 - 2 278 c.99delC c.(97-99)CCCfs p.P33fs NM_000834 NP_000825 Q13224 NMDE2_HUMAN N-methyl-D-aspartate receptor subunit 2B 33 Extracellular (Potential). response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding central_nervous_system(4)|ovary(3)|skin(3)|lung(2) 12 Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043) 0.000 0.55 318 389 MLL2 8085 broad.mit.edu 37 12 49426729 49426730 + In_Frame_Ins INS - GCT GCT RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr12:49426729_49426730insGCT uc001rta.3 - 39 11758_11759 c.11758_11759insAGC c.(11758-11760)CTA>CAGCTA p.3919_3920insQ NM_003482 NP_003473 O14686 MLL2_HUMAN myeloid/lymphoid or mixed-lineage leukemia 2 3919_3920 Potential.|Gln-rich. chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent histone methyltransferase complex histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2) 41 ttgctgttgtagctgctgctgc 0.124 0.17 64 13 LRP1 4035 broad.mit.edu 37 12 57603940 57603940 + Frame_Shift_Del DEL C - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr12:57603940delC uc001snd.2 + 81 13034 c.12568delC c.(12568-12570)CCCfs p.P4190fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 4190 Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CTCTCCAACGCCCCCCCCAGA 0.637 0.46 21 18 GLI1 2735 broad.mit.edu 37 12 57860075 57860075 + Frame_Shift_Del DEL G - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr12:57860075delG uc001snx.2 + 8 893 c.815delG c.(814-816)TGGfs p.W272fs GLI1_uc009zpq.2_Frame_Shift_Del_p.W144fs NM_005269 NP_005260 P08151 GLI1_HUMAN GLI family zinc finger 1 isoform 1 272 C2H2-type 2. epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter cytosol|nucleus transcription regulatory region DNA binding|zinc ion binding skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1) 15 GBM - Glioblastoma multiforme(3;3.99e-32) GTGTGCCACTGGGGGGGCTGC 0.597 0.44 181 145 BRCA2 675 broad.mit.edu 37 13 32912770 32912771 + Frame_Shift_Ins INS - T T RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr13:32912770_32912771insT uc001uub.1 + 11 4505_4506 c.4278_4279insT c.(4276-4281)ACATTTfs p.T1426fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 1426_1427 BRCA2 3. cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) CTTCTGATACATTTTTTCAGAC 0.312 0.47 93 84 BRCA2 675 broad.mit.edu 37 13 32913952 32913953 + Frame_Shift_Ins INS - A A RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr13:32913952_32913953insA uc001uub.1 + 11 5687_5688 c.5460_5461insA c.(5458-5463)TGCAAAfs p.C1820fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 1820_1821 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) CTTCACCCTGCAAAAATAAAAA 0.356 0.43 117 90 FOXO1 2308 broad.mit.edu 37 13 41239932 41239933 + Frame_Shift_Ins INS - G G RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr13:41239932_41239933insG uc001uxl.3 - 1 802_803 c.417_418insC c.(415-420)CCCGCCfs p.P139fs NM_002015 NP_002006 Q12778 FOXO1_HUMAN forkhead box O1 139_140 anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding PAX3/FOXO1(749)|PAX7/FOXO1(197) soft_tissue(946)|lung(1)|central_nervous_system(1) 948 Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194) all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815) 0.000 0.45 232 188 MKRN3 7681 broad.mit.edu 37 15 23811405 23811405 + Frame_Shift_Del DEL C - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr15:23811405delC uc001ywh.3 + 1 952 c.476delC c.(475-477)GCCfs p.A159fs MKRN3_uc001ywi.2_Intron|MKRN3_uc010ayi.1_Frame_Shift_Del_p.A159fs NM_005664 NP_005655 Q13064 MKRN3_HUMAN makorin ring finger protein 3 159 ribonucleoprotein complex ligase activity|nucleic acid binding|zinc ion binding lung(6)|large_intestine(2)|ovary(2) 10 all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14) all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012) GTGGCGGAAGCCCCCCCGGCT 0.642 0.34 25 13 C15orf2 23742 broad.mit.edu 37 15 24921326 24921326 + Frame_Shift_Del DEL C - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr15:24921326delC uc001ywo.2 + 1 786 c.312delC c.(310-312)AACfs p.N104fs NM_018958 NP_061831 Q9NZP6 CO002_HUMAN hypothetical protein LOC23742 104 cell differentiation|multicellular organismal development|spermatogenesis ovary(2)|large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1) 8 all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086) all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229) CTGCTCGGAACCCCCCGAGGT 0.677 0.36 14 8 PHF23 79142 broad.mit.edu 37 17 7139932 7139932 + Frame_Shift_Del DEL C - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr17:7139932delC uc002gfa.2 - 4 541 c.314delG c.(313-315)GGTfs p.G105fs DVL2_uc002gez.1_5'Flank|DVL2_uc010vtr.1_5'Flank|DVL2_uc010clz.1_5'Flank|PHF23_uc010vtt.1_Intron|PHF23_uc010cma.2_5'UTR NM_024297 NP_077273 Q9BUL5 PHF23_HUMAN PHD finger protein 23 105 zinc ion binding 0 0.000 0.44 130 104 TP53 7157 broad.mit.edu 37 17 7578195 7578197 + In_Frame_Del DEL CAC - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr17:7578195_7578197delCAC uc002gim.2 - 6 846_848 c.652_654delGTG c.(652-654)GTGdel p.V218del TP53_uc002gig.1_In_Frame_Del_p.V218del|TP53_uc002gih.2_In_Frame_Del_p.V218del|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_In_Frame_Del_p.V86del|TP53_uc010cng.1_In_Frame_Del_p.V86del|TP53_uc002gii.1_In_Frame_Del_p.V86del|TP53_uc010cnh.1_In_Frame_Del_p.V218del|TP53_uc010cni.1_In_Frame_Del_p.V218del|TP53_uc002gij.2_In_Frame_Del_p.V218del|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_In_Frame_Del_p.V125del|TP53_uc002gio.2_In_Frame_Del_p.V86del|TP53_uc010vug.1_In_Frame_Del_p.V179del NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 218 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). V -> A (in sporadic cancers; somatic mutation).|V -> M (in sporadic cancers; somatic mutation).|V -> G (in sporadic cancers; somatic mutation).|V -> L (in sporadic cancers; somatic mutation).|V -> E (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.V218E(8)|p.V218M(7)|p.0?(7)|p.V218G(5)|p.V218del(5)|p.V218A(3)|p.K164_P219del(1)|p.S215fs*27(1)|p.S215fs*29(1)|p.V218_P219insX(1)|p.V218_Y220delVPY(1)|p.V216_Y220delVVVPY(1)|p.D208fs*1(1)|p.V216fs*28(1)|p.?(1)|p.V218L(1)|p.V218_E221delVPYE(1)|p.V218V(1)|p.V218fs*26(1)|p.S215_V218>R(1)|p.T211fs*28(1)|p.V218_E224delVPYEPPE(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GCTCATAGGGCACCACCACACTA 0.552 0.40 78 52 COL1A1 1277 broad.mit.edu 37 17 48264275 48264275 + Frame_Shift_Del DEL G - - rs146016027 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr17:48264275delG uc002iqm.2 - 48 3666 c.3540delC c.(3538-3540)CCCfs p.P1180fs NM_000088 NP_000079 P02452 CO1A1_HUMAN alpha 1 type I collagen preproprotein 1180 Triple-helical region. axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception collagen type I|extracellular space|plasma membrane identical protein binding|platelet-derived growth factor binding COL1A1/PDGFB(372) soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1) 382 Collagenase(DB00048)|Palifermin(DB00039) CAGGAGGGCCGGGGGGACCCT 0.642 0.33 26 13 ITGB4 3691 broad.mit.edu 37 17 73746261 73746261 + Frame_Shift_Del DEL C - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr17:73746261delC uc002jpg.2 + 28 3573 c.3386delC c.(3385-3387)GCCfs p.A1129fs ITGB4_uc002jph.2_Frame_Shift_Del_p.A1129fs|ITGB4_uc002jpi.3_Frame_Shift_Del_p.A1129fs|ITGB4_uc002jpj.2_Frame_Shift_Del_p.A1129fs NM_000213 NP_000204 P16144 ITB4_HUMAN integrin beta 4 isoform 1 precursor 1129 Fibronectin type-III 1.|Cytoplasmic (Potential). cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding cell leading edge|cell surface|hemidesmosome|integrin complex protein binding|receptor activity lung(4) 4 all_cancers(13;1.5e-07) all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154) GACCTGGGCGCCCCGCAGAAC 0.627 0.32 34 16 FASN 2194 broad.mit.edu 37 17 80043423 80043423 + Frame_Shift_Del DEL G - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr17:80043423delG uc002kdu.2 - 23 4174 c.4057delC c.(4057-4059)CTCfs p.L1353fs FASN_uc002kdw.1_Frame_Shift_Del_p.L569fs NM_004104 NP_004095 P49327 FAS_HUMAN fatty acid synthase 1353 LGDI -> SGH (in Ref. 2; AAA73576). energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process cytosol|Golgi apparatus|melanosome|plasma membrane 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding central_nervous_system(1) 1 all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246) OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237) Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339) ATGTCCCCGAGGGGGTGCCCC 0.706 0.31 9 4 SMAD7 4092 broad.mit.edu 37 18 46474795 46474795 + Frame_Shift_Del DEL G - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr18:46474795delG uc002ldg.2 - 2 913 c.626delC c.(625-627)CCTfs p.P209fs SMAD7_uc010xde.1_5'UTR NM_005904 NP_005895 O15105 SMAD7_HUMAN SMAD family member 7 209 Poly-Pro.|PY-motif.|Important for interaction with SMURF2. Missing: Diminishes interaction with SMURF2. adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding 0 Colorectal(1;0.0518) GGAGTAAGGAGGGGGGGGAGA 0.388 0.87 8 55 ELAVL1 1994 broad.mit.edu 37 19 8046013 8046014 + Frame_Shift_Ins INS - CT CT RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr19:8046013_8046014insCT uc002mjb.2 - 3 396_397 c.229_230insAG c.(229-231)GCGfs p.A77fs NM_001419 NP_001410 Q15717 ELAV1_HUMAN ELAV-like 1 77 RRM 1. 3'-UTR-mediated mRNA stabilization|multicellular organismal development cytoplasm|nucleoplasm identical protein binding|mRNA binding|nucleotide binding 0 CGTGTTGATCGCTCTCTCTGCA 0.530 0.46 151 130 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.48 33 30 LMTK3 114783 broad.mit.edu 37 19 49002846 49002846 + Frame_Shift_Del DEL C - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr19:49002846delC uc002pjk.2 - 12 1567 c.1567delG c.(1567-1569)GCAfs p.A523fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.27 209 78 COL18A1 80781 broad.mit.edu 37 21 46917559 46917559 + Frame_Shift_Del DEL C - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr21:46917559delC uc011afs.1 + 31 3933 c.3912delC c.(3910-3912)GGCfs p.G1304fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.G889fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.G1069fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1304 Triple-helical region 7 (COL7). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.42 455 325 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 141 347 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.99 1 69 XBP1 7494 broad.mit.edu 37 22 29191458 29191460 + In_Frame_Del DEL ACC - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr22:29191458_29191460delACC uc011akl.1 - 6 882_884 c.834_836delGGT c.(832-837)GTGGTA>GTA p.278_279VV>V XBP1_uc003aec.2_In_Frame_Del_p.99_100VV>V|XBP1_uc003aed.2_3'UTR|XBP1_uc003aef.2_In_Frame_Del_p.99_100VV>V NM_001079539 NP_001073007 P17861 XBP1_HUMAN X-box binding protein 1 isoform XBP1(S) Error:Variant_position_missing_in_P17861_after_alignment immune response nucleus protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity breast(1) 1 0.000 0.45 128 104 NF2 4771 broad.mit.edu 37 22 30050708 30050708 + Frame_Shift_Del DEL A - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr22:30050708delA uc003age.3 + 5 953 c.510delA c.(508-510)CCAfs p.P170fs NF2_uc003afy.3_Frame_Shift_Del_p.P170fs|NF2_uc003afz.3_Frame_Shift_Del_p.P87fs|NF2_uc003agf.3_Frame_Shift_Del_p.P170fs|NF2_uc003agb.3_Frame_Shift_Del_p.P93fs|NF2_uc003agc.3_Frame_Shift_Del_p.P132fs|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Frame_Shift_Del_p.P170fs|NF2_uc003aga.3_Frame_Shift_Del_p.P128fs|NF2_uc003agh.3_Frame_Shift_Del_p.P129fs|NF2_uc003agi.3_Frame_Shift_Del_p.P87fs|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Frame_Shift_Del_p.P132fs NM_000268 NP_000259 P35240 MERL_HUMAN neurofibromin 2 isoform 1 170 FERM. actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane cytoskeletal protein binding|protein binding p.L127_D382del(1)|p.P170fs*4(1)|p.L140_P252del(1)|p.?(1)|p.P170fs*29(1) meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1) 728 AATTGCTTCCAAAAAGGGTAA 0.423 0.44 69 55 TNRC6B 23112 broad.mit.edu 37 22 40662480 40662480 + Frame_Shift_Del DEL G - - RL952_ENDOMETRIUM NA RL952_ENDOMETRIUM NA g.chr22:40662480delG uc011aor.1 + 5 2457 c.2246delG c.(2245-2247)TGGfs p.W749fs TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Frame_Shift_Del_p.W749fs|TNRC6B_uc003ayo.2_Frame_Shift_Del_p.W553fs NM_001162501 NP_001155973 Q9UPQ9 TNR6B_HUMAN trinucleotide repeat containing 6B isoform 1 749 gene silencing by RNA|regulation of translation cytoplasmic mRNA processing body nucleotide binding|RNA binding 0 AAGAATGGTTGGGGGGAGGAA 0.512 0.39 53 34 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 47 ATP13A5 344905 broad.mit.edu 37 3 193044800 193044800 + Frame_Shift_Del DEL G - - RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:193044800delG uc011bsq.1 - 13 1508 c.1508delC c.(1507-1509)CCTfs p.P503fs NM_198505 NP_940907 Q4VNC0 AT135_HUMAN ATPase type 13A5 503 ATP biosynthetic process|cation transport integral to membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding ovary(5)|skin(4)|large_intestine(2) 11 all_cancers(143;1.08e-08)|Ovarian(172;0.0386) OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06) GBM - Glioblastoma multiforme(46;0.000307) GTCAGCAGTAGGGACAGTCCC 0.408 0.45 47 38 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 81 99 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 20 47 MLL3 58508 broad.mit.edu 37 7 151945444 151945445 + Frame_Shift_Del DEL AC - - RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:151945444_151945445delAC uc003wla.2 - 14 2293_2294 c.2074_2075delGT c.(2074-2076)GTCfs p.V692fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 692 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TGGAAGAGTGACAGATTCCATG 0.426 0.64 220 397 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.38 507 313 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 279 80 NOVA1 4857 broad.mit.edu 37 14 27066541 27066542 + Frame_Shift_Ins INS - G G RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:27066541_27066542insG uc001wpy.2 - 1 419_420 c.101_102insC c.(100-102)CCTfs p.P34fs NOVA1_uc001wpz.2_Frame_Shift_Ins_p.P34fs|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_Frame_Shift_Ins_p.P34fs NM_002515 NP_002506 P51513 NOVA1_HUMAN neuro-oncological ventral antigen 1 isoform 1 34 Bipartite nuclear localization signal (Potential). locomotory behavior|RNA splicing|synaptic transmission nucleus RNA binding skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1) 5 GBM - Glioblastoma multiforme(265;0.0135) 0.000 0.40 649 438 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 11 146 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.45 16 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 80 499 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 57 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RMUGS_OVARY NA RMUGS_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 6 77 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 RMUGS_OVARY NA RMUGS_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 27 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RMUGS_OVARY NA RMUGS_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 131 174 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes RMUGS_OVARY NA RMUGS_OVARY NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.47 140 123 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 RMUGS_OVARY NA RMUGS_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.77 75 257 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RMUGS_OVARY NA RMUGS_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 3 42 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency RMUGS_OVARY NA RMUGS_OVARY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.17 72 15 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 RMUGS_OVARY NA RMUGS_OVARY NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.47 9 8 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 RMUGS_OVARY NA RMUGS_OVARY NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.59 24 34 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C RMUGS_OVARY NA RMUGS_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 3 29 GAS7 8522 broad.mit.edu 37 17 10101576 10101578 + In_Frame_Del DEL CTT - - RMUGS_OVARY NA RMUGS_OVARY NA g.chr17:10101576_10101578delCTT uc002gmg.1 - 1 291_293 c.130_132delAAG c.(130-132)AAGdel p.K44del NM_201433 NP_958839 O60861 GAS7_HUMAN growth arrest-specific 7 isoform c 44 SH3. cell cycle arrest cytoplasm sequence-specific DNA binding transcription factor activity lung(1)|pancreas(1) 2 GCCCGTCCTCCTTCTCGCCTTCC 0.734 0.92 3 35 TRIM37 4591 broad.mit.edu 37 17 57093049 57093049 + Frame_Shift_Del DEL A - - RMUGS_OVARY NA RMUGS_OVARY NA g.chr17:57093049delA uc002iwy.3 - 21 2942 c.2498delT c.(2497-2499)TTGfs p.L833fs TRIM37_uc002iwz.3_Frame_Shift_Del_p.L833fs|TRIM37_uc002ixa.3_Frame_Shift_Del_p.L711fs|TRIM37_uc010woc.1_Frame_Shift_Del_p.L799fs NM_001005207 NP_001005207 O94972 TRI37_HUMAN tripartite motif-containing 37 protein 833 perinuclear region of cytoplasm|peroxisome ligase activity|protein binding|zinc ion binding lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1) 7 Medulloblastoma(34;0.0922)|all_neural(34;0.101) ATCTGAATCCAAAGCTTTACA 0.468 0.48 59 55 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RMUGS_OVARY NA RMUGS_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.52 179 192 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RMUGS_OVARY NA RMUGS_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 27 263 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RMUGS_OVARY NA RMUGS_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 134 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 29 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.50 11 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 76 135 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 29 47 MSH5 4439 broad.mit.edu 37 6 31727933 31727934 + Frame_Shift_Ins INS - G G rs28405564 RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:31727933_31727934insG uc003nwv.1 + 19 1831_1832 c.1752_1753insG c.(1750-1755)AAAGGGfs p.K584fs MSH5_uc003nwt.1_Frame_Shift_Ins_p.K601fs|MSH5_uc003nwu.1_Frame_Shift_Ins_p.K584fs|MSH5_uc003nww.1_Frame_Shift_Ins_p.K584fs|MSH5_uc003nwx.1_Frame_Shift_Ins_p.K601fs|MSH5_uc011dof.1_Frame_Shift_Ins_p.K283fs|MSH5_uc003nwy.1_Frame_Shift_Ins_p.K258fs|MSH5_uc003nwz.3_RNA|C6orf26_uc003nxa.3_5'Flank NM_172166 NP_751898 O43196 MSH5_HUMAN mutS homolog 5 isoform c 584_585 chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination synaptonemal complex ATP binding|DNA-dependent ATPase activity|mismatched DNA binding ovary(2)|breast(1) 3 GTGGGGACAAAGGGAGGGTCAA 0.574 0.13 93 14 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.42 31 22 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 25 PTENP1 11191 broad.mit.edu 37 9 33676095 33676096 + Frame_Shift_Del DEL AT - - RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:33676095_33676096delAT uc003zth.3 - 1 1323_1324 c.452_453delAT c.(451-453)CATfs p.H151fs NR_023917 SubName: Full=Phosphatase and tensin homolog 2; Flags: Fragment; 0 TATAATCCACATGATTCTTTAC 0.426 0.48 146 134 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 347 178 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.34 53 27 NCOA3 8202 broad.mit.edu 37 20 46279815 46279817 + In_Frame_Del DEL GCA - - rs3830810 RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:46279815_46279817delGCA uc002xtk.2 + 20 3946_3948 c.3741_3743delGCA c.(3739-3744)ATGCAG>ATG p.Q1276del NCOA3_uc010ght.1_In_Frame_Del_p.Q1267del|NCOA3_uc002xtl.2_In_Frame_Del_p.Q1272del|NCOA3_uc002xtm.2_In_Frame_Del_p.Q1271del|NCOA3_uc002xtn.2_In_Frame_Del_p.Q1275del|NCOA3_uc010zyc.1_In_Frame_Del_p.Q1071del NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 1276 Poly-Gln.|Acetyltransferase. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 CTATGATGATgcagcagcagcag 0.286 0.11 91 11 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.33 72 35 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 57 474 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 5 63 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.84 4 21 TTN 7273 broad.mit.edu 37 2 179605519 179605519 + Frame_Shift_Del DEL A - - RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179605519delA uc010zfh.1 - 46 12152 c.11928delT c.(11926-11928)TCTfs p.S3976fs TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Frame_Shift_Del_p.S3909fs|TTN_uc010zfj.1_Frame_Shift_Del_p.S3784fs|TTN_uc002umz.1_Intron NM_133437 NP_597681 Q8WZ42 TITIN_HUMAN titin isoform novex-2 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GTAGGTTGGGAGATGGTTCCT 0.453 0.20 74 19 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 68 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.29 34 14 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 26 41 PIP5K1P1 206426 broad.mit.edu 37 6 7988220 7988221 + In_Frame_Ins INS - AAC AAC RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:7988220_7988221insAAC uc003mxx.3 + 1 1886_1887 c.1451_1452insAAC c.(1450-1452)ATA>ATAACA p.484_485insT TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 TCACAAGTGATAAAGGTGCAAG 0.480 0.47 80 72 PIP5K1P1 206426 broad.mit.edu 37 6 7988269 7988275 + Frame_Shift_Del DEL ACCTCAG - - RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:7988269_7988275delACCTCAG uc003mxx.3 + 1 1935_1941 c.1500_1506delACCTCAG c.(1498-1506)TTACCTCAGfs p.L500fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CTGATGTTTTACCTCAGACCTCAGAAT 0.454 0.36 62 35 NUP153 9972 broad.mit.edu 37 6 17633077 17633078 + Splice_Site INS - A A rs36027788;rs147103527 RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:17633077_17633078insA uc003ncd.1 - 17 2665 c.2465_splice c.e17-1 p.G822_splice NUP153_uc011dje.1_Splice_Site_p.G853_splice|NUP153_uc010jpl.1_Splice_Site_p.G780_splice NM_005124 NP_005115 P49790 NU153_HUMAN nucleoporin 153kDa carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm DNA binding|protein binding|transporter activity|zinc ion binding lung(4)|ovary(2)|breast(2)|skin(1) 9 Breast(50;0.0259)|Ovarian(93;0.0584) all_hematologic(90;0.125) all cancers(50;0.0981)|Epithelial(50;0.112) CTGAACTTCCTAAAAAAAAAAA 0.406 0.20 60 15 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.95 1 20 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.15 100 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 71 313 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 1 25 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 36 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.31 20 9 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.53 17 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 38 62 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 14 20 NR3C1 2908 broad.mit.edu 37 5 142678327 142678329 + In_Frame_Del DEL AGG - - rs61753497 RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:142678327_142678329delAGG uc003lmz.2 - 6 2288_2290 c.1796_1798delCCT c.(1795-1800)TCCTGG>TGG p.S599del NR3C1_uc003lmy.2_In_Frame_Del_p.S600del|NR3C1_uc003lna.2_In_Frame_Del_p.S599del|NR3C1_uc003lnb.2_In_Frame_Del_p.S599del|NR3C1_uc011dbk.1_In_Frame_Del_p.S202del|NR3C1_uc003lnc.2_In_Frame_Del_p.S599del|NR3C1_uc003lnd.2_In_Frame_Del_p.S599del|NR3C1_uc003lne.2_In_Frame_Del_p.S599del|NR3C1_uc003lnf.2_In_Frame_Del_p.S600del NM_000176 NP_000167 P04150 GCR_HUMAN glucocorticoid receptor isoform alpha 599 Steroid-binding. chromatin modification|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus|transcription from RNA polymerase II promoter mitochondrial matrix|nucleoplasm glucocorticoid receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding ovary(2) 2 Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361) KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176) Amcinonide(DB00288)|Betamethasone(DB00443)|Budesonide(DB01222)|Dexamethasone(DB01234)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluticasone Propionate(DB00588)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol Etabonate(DB00873)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Prednisone(DB00635) AGAAACATCCAGGAGTACTGCAG 0.409 0.26 28 10 ATXN1 6310 broad.mit.edu 37 6 16327915 16327916 + In_Frame_Ins INS - TGC TGC rs11969612 by1000genomes RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:16327915_16327916insTGC uc003nbt.2 - 8 1597_1598 c.626_627insGCA c.(625-627)CAT>CAGCAT p.208_209insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.208_209insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 208_209 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) gctgatgctgatgctgctgctg 0.381 0.17 33 7 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.42 18 13 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.60 52 79 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 25 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 461 52 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.37 272 157 TRIM29 23650 broad.mit.edu 37 11 120008680 120008681 + Frame_Shift_Ins INS - T T RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:120008680_120008681insT uc001pwz.2 - 1 183_184 c.59_60insA c.(58-60)CGGfs p.R20fs TRIM29_uc001pxa.2_RNA NM_012101 NP_036233 Q14134 TRI29_HUMAN tripartite motif protein TRIM29 20 transcription from RNA polymerase II promoter cytoplasm protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1)|breast(1)|kidney(1)|skin(1) 4 Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;5.37e-06) 0.000 1.00 0 10 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.30 62 26 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.46 57 49 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 268 586 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 4 48 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.40 6 4 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.27 19 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.42 105 77 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 21 40 HDAC2 3066 broad.mit.edu 37 6 114264518 114264518 + Frame_Shift_Del DEL T - - RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:114264518delT uc003pwd.1 - 12 1657 c.1657delA c.(1657-1659)ACAfs p.T553fs HDAC2_uc003pwc.1_Frame_Shift_Del_p.T429fs|HDAC2_uc003pwe.1_Frame_Shift_Del_p.T429fs NM_001527 NP_001518 Q92769 HDAC2_HUMAN histone deacetylase 2 459 blood coagulation|dendrite development|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|maintenance of chromatin silencing|negative regulation of apoptosis|negative regulation of cell cycle|negative regulation of neuron projection development|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of proteolysis|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter cytoplasm|ESC/E(Z) complex|NuRD complex|Sin3 complex chromatin binding|enzyme binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|sequence-specific DNA binding|transcription factor binding skin(2)|ovary(1)|central_nervous_system(1) 4 all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24) all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832) Vorinostat(DB02546) ATCTGACCTGtttttttgtcc 0.254 0.46 82 71 WWP1 11059 broad.mit.edu 37 8 87460443 87460443 + Frame_Shift_Del DEL A - - RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:87460443delA uc003ydt.2 + 19 2345 c.2065delA c.(2065-2067)AAAfs p.K689fs WWP1_uc010mai.2_Frame_Shift_Del_p.K465fs NM_007013 NP_008944 Q9H0M0 WWP1_HUMAN WW domain containing E3 ubiquitin protein ligase 689 HECT. central nervous system development|entry of virus into host cell|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|signal transduction cytoplasm|nucleus|plasma membrane|ubiquitin ligase complex protein binding|ubiquitin-protein ligase activity lung(1)|liver(1) 2 0.000 0.41 111 77 CSMD3 114788 broad.mit.edu 37 8 113421253 113421254 + Frame_Shift_Ins INS - A A RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:113421253_113421254insA uc003ynu.2 - 33 5562_5563 c.5403_5404insT c.(5401-5406)TTTGGCfs p.F1801fs CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Frame_Shift_Ins_p.F1761fs|CSMD3_uc011lhx.1_Frame_Shift_Ins_p.F1697fs NM_198123 NP_937756 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 isoform 1 1801_1802 Extracellular (Potential).|CUB 10. integral to membrane|plasma membrane ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1) 63 ACAAACTGGCCAAACACCACTG 0.426 0.19 30 7 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 184 42 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.53 7 8 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.14 101 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 4 59 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 62 408 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 61 KDM6A 7403 broad.mit.edu 37 X 44942835 44942835 + Frame_Shift_Del DEL C - - RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chrX:44942835delC uc004dge.3 + 23 3790 c.3415delC c.(3415-3417)CCAfs p.P1139fs KDM6A_uc011mkz.1_Frame_Shift_Del_p.P1191fs|KDM6A_uc011mla.1_Frame_Shift_Del_p.P1094fs|KDM6A_uc011mlb.1_Frame_Shift_Del_p.P1146fs|KDM6A_uc011mlc.1_Frame_Shift_Del_p.P843fs|KDM6A_uc011mld.1_Frame_Shift_Del_p.P778fs NM_021140 NP_066963 O15550 KDM6A_HUMAN ubiquitously transcribed tetratricopeptide 1139 JmjC. histone H3-K4 methylation metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen p.P1139fs*19(1) kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2) 84 CATGAAAGTTCCAGGGAGCAG 0.378 0.47 73 66 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.73 18 49 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 249 77 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.62 5 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 45 75 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 14 36 CDKN1A 1026 broad.mit.edu 37 6 36651907 36651908 + Frame_Shift_Ins INS - G G RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr6:36651907_36651908insG uc003omm.3 + 2 151_152 c.29_30insG c.(28-30)CAGfs p.Q10fs CDKN1A_uc011dtq.1_Frame_Shift_Ins_p.Q44fs|CDKN1A_uc003oml.2_Frame_Shift_Ins_p.Q10fs|CDKN1A_uc003omn.2_Frame_Shift_Ins_p.Q10fs NM_000389 NP_000380 P38936 CDN1A_HUMAN cyclin-dependent kinase inhibitor 1A 10 cell cycle arrest|cellular response to extracellular stimulus|cellular response to ionizing radiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|induction of apoptosis by intracellular signals|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of fibroblast proliferation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|S phase of mitotic cell cycle|stress-induced premature senescence cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleoplasm|PCNA-p21 complex cyclin-dependent protein kinase activating kinase activity|cyclin-dependent protein kinase inhibitor activity|metal ion binding ovary(1)|breast(1) 2 GATGTCCGTCAGAACCCATGCG 0.644 0.98 2 121 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.71 4 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.44 18 14 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 51 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.28 464 178 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 740 289 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.33 30 15 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.83 4 20 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 44 139 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 52 669 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RT112_URINARY_TRACT NA RT112_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 8 99 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 RVH421_SKIN NA RVH421_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 36 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes RVH421_SKIN NA RVH421_SKIN NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.42 11 8 TPRXL 348825 broad.mit.edu 37 3 14106317 14106318 + In_Frame_Ins INS - CAGCAGTCCCAGCAC CAGCAGTCCCAGCAC RVH421_SKIN NA RVH421_SKIN NA g.chr3:14106317_14106318insCAGCAGTCCCAGCAC uc011avd.1 + 3 1096_1097 c.641_642insCAGCAGTCCCAGCAC c.(640-642)ACC>ACCAGCAGTCCCAGCACC p.214_214T>TSSPST TPRXL_uc003byh.1_In_Frame_Ins_p.214_214T>TSSPST|TPRXL_uc003byg.2_In_Frame_Ins_p.214_214T>TSSPST NR_002223 RecName: Full=Putative protein TPRXL; 0 agctccagcaccagcagtccca 0.233 0.50 5 5 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 RVH421_SKIN NA RVH421_SKIN NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.48 12 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 RVH421_SKIN NA RVH421_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.75 64 192 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 RVH421_SKIN NA RVH421_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.40 75 49 MSH3 4437 broad.mit.edu 37 5 79950696 79950697 + In_Frame_Ins INS - GCTGCAGCG GCTGCAGCG RVH421_SKIN NA RVH421_SKIN NA g.chr5:79950696_79950697insGCTGCAGCG uc003kgz.2 + 1 403_404 c.150_151insGCTGCAGCG c.(148-153)insGCTGCAGCG p.62_63insAAA DHFR_uc011ctl.1_5'UTR|DHFR_uc011ctm.1_5'UTR|DHFR_uc010jap.1_RNA|DHFR_uc003kgx.1_In_Frame_Ins_p.20_20A>AAAA|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 62_63 Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) TGGACCCTGGCGCTgcagcggc 0.554 0.17 33 7 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 RVH421_SKIN NA RVH421_SKIN NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.68 46 98 ATXN1 6310 broad.mit.edu 37 6 16327907 16327909 + In_Frame_Del DEL TGA - - rs59310777 by1000genomes RVH421_SKIN NA RVH421_SKIN NA g.chr6:16327907_16327909delTGA uc003nbt.2 - 8 1604_1606 c.633_635delTCA c.(631-636)CATCAG>CAG p.H211del ATXN1_uc010jpi.2_In_Frame_Del_p.H211del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 211 Poly-Gln. H -> HQ (in Ref. 1; CAA55793). cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgctgatgctgatgct 0.384 0.10 187 20 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes RVH421_SKIN NA RVH421_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 RVH421_SKIN NA RVH421_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 37 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 RVH421_SKIN NA RVH421_SKIN NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.38 8 5 ACACB 32 broad.mit.edu 37 12 109609689 109609708 + Frame_Shift_Del DEL TGTGGACATTGCCAAGAGAA - - RVH421_SKIN NA RVH421_SKIN NA g.chr12:109609689_109609708delTGTGGACATTGCCAAGAGAA uc001tob.2 + 5 1124_1143 c.1005_1024delTGTGGACATTGCCAAGAGAA c.(1003-1026)ATTGTGGACATTGCCAAGAGAATCfs p.I335fs ACACB_uc001toc.2_Frame_Shift_Del_p.I335fs NM_001093 NP_001084 O00763 ACACB_HUMAN acetyl-Coenzyme A carboxylase beta 335_342 Biotin carboxylation. acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation cytosol|endomembrane system|Golgi apparatus|membrane acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1) 8 Biotin(DB00121) TGGAGCTGATTGTGGACATTGCCAAGAGAATCCCCGTGCA 0.532 0.12 99 14 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency RVH421_SKIN NA RVH421_SKIN NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.24 89 28 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C RVH421_SKIN NA RVH421_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 33 270 TP53 7157 broad.mit.edu 37 17 7579533 7579533 + Frame_Shift_Del DEL G - - RVH421_SKIN NA RVH421_SKIN NA g.chr17:7579533delG uc002gim.2 - 4 348 c.154delC c.(154-156)CAAfs p.Q52fs TP53_uc002gig.1_Frame_Shift_Del_p.Q52fs|TP53_uc002gih.2_Frame_Shift_Del_p.Q52fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.Q52fs|TP53_uc010cni.1_Frame_Shift_Del_p.Q52fs|TP53_uc002gij.2_Frame_Shift_Del_p.Q52fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.Q13fs|TP53_uc010cnk.1_Frame_Shift_Del_p.Q67fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 52 TADII.|Interaction with HRMT1L2. Q -> H (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.Q52*(6)|p.Q52>P*(1)|p.Q52H(1)|p.E51fs*59(1)|p.I50fs*4(1)|p.D48fs*55(1)|p.Q52fs*67(1)|p.Q52fs*6(1)|p.E51_Q52insX(1)|p.P13fs*18(1)|p.S33fs*23(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.22 1333 377 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 RVH421_SKIN NA RVH421_SKIN NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.30 32 14 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 RVH421_SKIN NA RVH421_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.54 67 79 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 RVH421_SKIN NA RVH421_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 97 543 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 RVH421_SKIN NA RVH421_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 107 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 S117_SOFT_TISSUE NA S117_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 2 97 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 S117_SOFT_TISSUE NA S117_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.33 68 33 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 S117_SOFT_TISSUE NA S117_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 36 69 FOXP2 93986 broad.mit.edu 37 7 114269956 114269961 + In_Frame_Del DEL CAACAA - - S117_SOFT_TISSUE NA S117_SOFT_TISSUE NA g.chr7:114269956_114269961delCAACAA uc003vhb.2 + 5 867_872 c.493_498delCAACAA c.(493-498)CAACAAdel p.QQ189del FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_In_Frame_Del_p.QQ214del|FOXP2_uc003vha.2_In_Frame_Del_p.QQ97del|FOXP2_uc011kmu.1_In_Frame_Del_p.QQ206del|FOXP2_uc011kmv.1_In_Frame_Del_p.QQ189del|FOXP2_uc010ljz.1_In_Frame_Del_p.QQ97del|FOXP2_uc003vgt.1_RNA|FOXP2_uc003vgv.1_In_Frame_Del_p.QQ189del|FOXP2_uc003vgx.2_In_Frame_Del_p.QQ189del|FOXP2_uc003vhd.2_In_Frame_Del_p.QQ189del|FOXP2_uc003vhc.2_In_Frame_Del_p.QQ214del NM_014491 NP_055306 O15409 FOXP2_HUMAN forkhead box P2 isoform I 189_190 Gln-rich. camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning cytoplasm|transcription factor complex chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1) 8 acaacagcagcaacaacagcagcagc 0.165 0.12 49 7 EPHB6 2051 broad.mit.edu 37 7 142562052 142562054 + In_Frame_Del DEL CCT - - rs67146761;rs8177142 S117_SOFT_TISSUE NA S117_SOFT_TISSUE NA g.chr7:142562052_142562054delCCT uc011kst.1 + 7 1281_1283 c.494_496delCCT c.(493-498)CCCTCC>CCC p.S176del EPHB6_uc011ksu.1_In_Frame_Del_p.S176del|EPHB6_uc003wbs.2_5'UTR|EPHB6_uc003wbt.2_Intron|EPHB6_uc003wbu.2_5'UTR|EPHB6_uc003wbv.2_5'Flank NM_004445 NP_004436 O15197 EPHB6_HUMAN ephrin receptor EphB6 precursor 176 Extracellular (Potential).|Poly-Ser. extracellular region|integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1) 19 Melanoma(164;0.059) GAGAGCTTTCcctcctcctcctc 0.522 0.53 89 102 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency S117_SOFT_TISSUE NA S117_SOFT_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.67 422 863 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 S117_SOFT_TISSUE NA S117_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 149 30 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 S117_SOFT_TISSUE NA S117_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 6 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 S117_SOFT_TISSUE NA S117_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 34 226 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 S117_SOFT_TISSUE NA S117_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 7 71 SHROOM4 57477 broad.mit.edu 37 X 50350758 50350759 + In_Frame_Ins INS - TGCTGCTGCTGT TGCTGCTGCTGT SBC5_LUNG NA SBC5_LUNG NA g.chrX:50350758_50350759insTGCTGCTGCTGT uc004dpe.2 - 6 3409_3410 c.3383_3384insACAGCAGCAGCA c.(3382-3384)CAG>CAACAGCAGCAGCAG p.1128_1128Q>QQQQQ SHROOM4_uc004dpd.3_RNA NM_020717 NP_065768 Q9ULL8 SHRM4_HUMAN shroom family member 4 1128 Gln-rich. actin filament organization|brain development|cell morphogenesis|cognition apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus actin filament binding upper_aerodigestive_tract(1) 1 Ovarian(276;0.236) cctgttgcttctgctgctgctg 0.252 0.42 11 8 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SBC5_LUNG NA SBC5_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 11 104 PTPRU 10076 broad.mit.edu 37 1 29652166 29652167 + Frame_Shift_Ins INS - AA AA SBC5_LUNG NA SBC5_LUNG NA g.chr1:29652166_29652167insAA uc001bru.2 + 31 4444_4445 c.4334_4335insAA c.(4333-4335)TCAfs p.S1445fs PTPRU_uc001brv.2_Frame_Shift_Ins_p.S1441fs|PTPRU_uc001brw.2_Frame_Shift_Ins_p.S1435fs|PTPRU_uc009vtq.2_Frame_Shift_Ins_p.S1439fs|PTPRU_uc009vtr.2_Frame_Shift_Ins_p.S1432fs|PTPRU_uc001brx.2_Frame_Shift_Ins_p.S171fs NM_005704 NP_005695 Q92729 PTPRU_HUMAN protein tyrosine phosphatase, receptor type, U 1445 Cytoplasmic (Potential). canonical Wnt receptor signaling pathway|cell differentiation|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transmembrane receptor protein tyrosine phosphatase signaling pathway cell-cell junction|integral to plasma membrane beta-catenin binding|transmembrane receptor protein tyrosine phosphatase activity large_intestine(3)|ovary(1)|kidney(1)|central_nervous_system(1)|skin(1) 7 Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123) Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871) GGGCTGGAGTCAAGATAGCGGG 0.609 0.27 53 20 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SBC5_LUNG NA SBC5_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.33 1248 627 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A SBC5_LUNG NA SBC5_LUNG NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 1.00 0 10 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SBC5_LUNG NA SBC5_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.21 62 16 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SBC5_LUNG NA SBC5_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 112 30 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SBC5_LUNG NA SBC5_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.31 153 69 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SBC5_LUNG NA SBC5_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 59 98 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SBC5_LUNG NA SBC5_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.23 51 15 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SBC5_LUNG NA SBC5_LUNG NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.73 3 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SBC5_LUNG NA SBC5_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 3 19 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SBC5_LUNG NA SBC5_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.62 8 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SBC5_LUNG NA SBC5_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.54 216 256 CDKN2A 1029 broad.mit.edu 37 9 21971093 21971113 + In_Frame_Del DEL CCTCCCGGGCAGCGTCGTGCA - - rs137854597;rs121913384;rs11552822;rs34968276;rs121913385 SBC5_LUNG NA SBC5_LUNG NA g.chr9:21971093_21971113delCCTCCCGGGCAGCGTCGTGCA uc003zpk.2 - 2 457_477 c.245_265delTGCACGACGCTGCCCGGGAGG c.(244-267)GTGCACGACGCTGCCCGGGAGGGC>GGC p.VHDAARE82del MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_In_Frame_Del_p.ARRCPGG138del NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 82_88 ANK 3. E -> D (in a biliary tract tumor). cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.H83Y(27)|p.E88*(13)|p.?(13)|p.D84Y(9)|p.E88E(6)|p.D84V(4)|p.G89S(4)|p.E88K(3)|p.D84N(3)|p.D84fs*63(2)|p.D84H(2)|p.E88D(2)|p.H83P(2)|p.D84G(2)|p.V82M(2)|p.H83fs*2(2)|p.T79fs*37(1)|p.V82_G89>G(1)|p.V82L(1)|p.R80fs*34(1)|p.A86V(1)|p.E88A(1)|p.H83N(1)|p.E88G(1)|p.A138V(1)|p.V82fs*62(1)|p.A68fs*3(1)|p.E88V(1)|p.H83Q(1)|p.P81_A85del(1)|p.V82fs*44(1)|p.V82V(1)|p.V82_E88del(1)|p.D84_F90del(1)|p.D84fs*36(1)|p.R137fs*48(1)|p.D84D(1)|p.A86fs*34(1)|p.A85T(1)|p.A85P(1)|p.E87K(1)|p.R87L(1)|p.D84fs*0(1)|p.E61_L94del(1)|p.R87Q(1)|p.R87W(1)|p.H83R(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) 0.000 0.11 280 36 TGFBR1 7046 broad.mit.edu 37 9 101867563 101867564 + Frame_Shift_Ins INS - T T SBC5_LUNG NA SBC5_LUNG NA g.chr9:101867563_101867564insT uc004azc.2 + 1 152_153 c.76_77insT c.(76-78)GCGfs p.A26fs TGFBR1_uc004azd.2_Frame_Shift_Ins_p.A26fs NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.24 25 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SBC5_LUNG NA SBC5_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 273 32 NEK3 4752 broad.mit.edu 37 13 52725278 52725279 + Splice_Site INS - A A SBC5_LUNG NA SBC5_LUNG NA g.chr13:52725278_52725279insA uc001vgi.2 - 7 783 c.548_splice c.e7+1 p.S183_splice NEK3_uc001vgg.2_Splice_Site_p.S177_splice|NEK3_uc001vgh.2_Splice_Site_p.S204_splice|NEK3_uc010tgx.1_Splice_Site|NEK3_uc010tgy.1_Splice_Site_p.S183_splice NM_152720 NP_689933 P51956 NEK3_HUMAN NIMA-related kinase 3 isoform a cell division|mitosis nucleus ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173) GBM - Glioblastoma multiforme(99;2.81e-08) ATGCAGCACTCACCTTTTATTG 0.421 0.44 314 247 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SBC5_LUNG NA SBC5_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 90 642 ACACA 31 broad.mit.edu 37 17 35601647 35601647 + Frame_Shift_Del DEL C - - SBC5_LUNG NA SBC5_LUNG NA g.chr17:35601647delC uc002hnm.2 - 21 2679 c.2488delG c.(2488-2490)GAAfs p.E830fs ACACA_uc002hnk.2_Frame_Shift_Del_p.E752fs|ACACA_uc002hnl.2_Frame_Shift_Del_p.E772fs|ACACA_uc002hnn.2_Frame_Shift_Del_p.E830fs|ACACA_uc002hno.2_Frame_Shift_Del_p.E867fs|ACACA_uc010cuz.2_Frame_Shift_Del_p.E830fs NM_198836 NP_942133 Q13085 ACACA_HUMAN acetyl-Coenzyme A carboxylase alpha isoform 2 830 acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process cytosol acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding large_intestine(1)|ovary(1) 2 Breast(25;0.00157)|Ovarian(249;0.15) Biotin(DB00121) GTGTGAAGTTCAGCCTGTCAA 0.448 0.23 775 229 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - SBC5_LUNG NA SBC5_LUNG NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 0.85 4 23 SMARCA4 6597 broad.mit.edu 37 19 11144148 11144149 + Frame_Shift_Del DEL GC - - SBC5_LUNG NA SBC5_LUNG NA g.chr19:11144148_11144149delGC uc002mqf.3 + 26 4013_4014 c.3729_3730delGC c.(3727-3732)CGGCGCfs p.R1243fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.R1243fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.R1243fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.R1243fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.R1243fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.R1243fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.R1243fs|SMARCA4_uc010dxt.1_Frame_Shift_Del_p.R463fs|SMARCA4_uc002mqh.3_Frame_Shift_Del_p.R366fs|SMARCA4_uc002mqi.1_Frame_Shift_Del_p.R446fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 1243_1244 Helicase C-terminal. chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.A1245fs*13(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) GCCATGAGCGGCGCGCCTTCCT 0.639 0.88 10 71 NOTCH3 4854 broad.mit.edu 37 19 15288536 15288536 + Frame_Shift_Del DEL G - - SBC5_LUNG NA SBC5_LUNG NA g.chr19:15288536delG uc002nan.2 - 24 4279 c.4203delC c.(4201-4203)TGCfs p.C1401fs NOTCH3_uc002nao.1_Frame_Shift_Del_p.C1349fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 1401 Extracellular (Potential).|LNR 1. Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.13 145 22 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SBC5_LUNG NA SBC5_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.66 104 206 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SBC5_LUNG NA SBC5_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 30 219 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 50 TGFBR2 7048 broad.mit.edu 37 3 30691871 30691872 + Frame_Shift_Ins INS - A A SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr3:30691871_30691872insA uc003ceo.2 + 3 755_756 c.373_374insA c.(373-375)GAAfs p.E125fs TGFBR2_uc003cen.2_Frame_Shift_Ins_p.E150fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 125 Extracellular (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 CATTATGAAGGAAAAAAAAAAG 0.421 0.67 23 46 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.34 21 11 BMP2K 55589 broad.mit.edu 37 4 79792082 79792083 + In_Frame_Ins INS - CAG CAG rs5859654;rs35071794 SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr4:79792082_79792083insCAG uc003hlk.2 + 11 1543_1544 c.1377_1378insCAG c.(1375-1380)insCAG p.486_487insQ BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Ins_p.486_487insQ|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486_487 Gln/His-rich. nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 GTCATCCTCACcagcagcagca 0.262 0.19 136 31 MAML3 55534 broad.mit.edu 37 4 140641185 140641186 + Frame_Shift_Ins INS - G G SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr4:140641185_140641186insG uc003ihz.1 - 7 3445_3446 c.2693_2694insC c.(2692-2694)CCTfs p.P898fs MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_Frame_Shift_Ins_p.P366fs NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 899 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) GCCCAGAGGCAGGTTGCCTCGG 0.530 0.10 375 41 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 74 126 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 23 62 ATXN1 6310 broad.mit.edu 37 6 16327915 16327916 + In_Frame_Ins INS - TGC TGC rs11969612 by1000genomes SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr6:16327915_16327916insTGC uc003nbt.2 - 8 1597_1598 c.626_627insGCA c.(625-627)CAT>CAGCAT p.208_209insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.208_209insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 208_209 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) gctgatgctgatgctgctgctg 0.381 0.16 69 13 MSH5 4439 broad.mit.edu 37 6 31727933 31727934 + Frame_Shift_Ins INS - G G rs28405564 SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr6:31727933_31727934insG uc003nwv.1 + 19 1831_1832 c.1752_1753insG c.(1750-1755)AAAGGGfs p.K584fs MSH5_uc003nwt.1_Frame_Shift_Ins_p.K601fs|MSH5_uc003nwu.1_Frame_Shift_Ins_p.K584fs|MSH5_uc003nww.1_Frame_Shift_Ins_p.K584fs|MSH5_uc003nwx.1_Frame_Shift_Ins_p.K601fs|MSH5_uc011dof.1_Frame_Shift_Ins_p.K283fs|MSH5_uc003nwy.1_Frame_Shift_Ins_p.K258fs|MSH5_uc003nwz.3_RNA|C6orf26_uc003nxa.3_5'Flank NM_172166 NP_751898 O43196 MSH5_HUMAN mutS homolog 5 isoform c 584_585 chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination synaptonemal complex ATP binding|DNA-dependent ATPase activity|mismatched DNA binding ovary(2)|breast(1) 3 GTGGGGACAAAGGGAGGGTCAA 0.574 0.11 72 9 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.40 25 17 ARID1B 57492 broad.mit.edu 37 6 157099402 157099403 + In_Frame_Ins INS - CAG CAG SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr6:157099402_157099403insCAG uc003qqn.2 + 1 317_318 c.165_166insCAG c.(163-168)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) TAAACCAGTTCcagcagcagca 0.124 0.16 87 17 MLLT4 4301 broad.mit.edu 37 6 168351928 168351928 + Frame_Shift_Del DEL A - - SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr6:168351928delA uc003qwd.2 + 29 4012 c.3870delA c.(3868-3870)CGAfs p.R1290fs MLLT4_uc003qwb.1_Frame_Shift_Del_p.R1275fs|MLLT4_uc003qwc.1_Frame_Shift_Del_p.R1291fs|MLLT4_uc003qwg.1_Frame_Shift_Del_p.R600fs NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 1291 adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) AGCGGCATCGAATAGAGGCAG 0.423 0.39 54 35 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.47 10 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 5 58 SMARCA2 6595 broad.mit.edu 37 9 2039774 2039776 + In_Frame_Del DEL CAA - - rs13296987 byFrequency SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr9:2039774_2039776delCAA uc003zhc.2 + 4 763_765 c.664_666delCAA c.(664-666)CAAdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) acagcagcagcaacagcagcagc 0.266 0.53 46 51 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.33 568 279 CDKN2A 1029 broad.mit.edu 37 9 21971124 21971125 + Frame_Shift_Del DEL GA - - SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr9:21971124_21971125delGA uc003zpk.2 - 2 445_446 c.233_234delTC c.(232-234)CTCfs p.L78fs MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Frame_Shift_Del_p.S133fs NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 78 ANK 3. cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.L78fs*41(17)|p.?(13)|p.E61_L94del(1)|p.L78fs*68(1)|p.A76fs*64(1)|p.T79fs*41(1)|p.L65fs*38(1)|p.L78fs*67(1)|p.A68fs*3(1)|p.L78H(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) 0.000 0.60 151 226 MELK 9833 broad.mit.edu 37 9 36589578 36589579 + Frame_Shift_Ins INS - T T SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr9:36589578_36589579insT uc003zzn.2 + 4 328_329 c.190_191insT c.(190-192)CTGfs p.L64fs MELK_uc011lpm.1_5'UTR|MELK_uc011lpn.1_Frame_Shift_Ins_p.L64fs|MELK_uc011lpo.1_5'UTR|MELK_uc010mll.2_Frame_Shift_Ins_p.L32fs|MELK_uc011lpp.1_Frame_Shift_Ins_p.L64fs|MELK_uc010mlm.2_Intron|MELK_uc011lpq.1_5'UTR|MELK_uc011lpr.1_Frame_Shift_Ins_p.L64fs|MELK_uc011lps.1_Frame_Shift_Ins_p.L32fs NM_014791 NP_055606 Q14680 MELK_HUMAN maternal embryonic leucine zipper kinase 64 Protein kinase. cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1) 6 Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06) STAD - Stomach adenocarcinoma(86;0.228) CTTGAAGAACCTGAGACATCAG 0.406 0.48 60 55 SLC3A2 6520 broad.mit.edu 37 11 62638220 62638221 + Frame_Shift_Ins INS - G G SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr11:62638220_62638221insG uc001nwd.2 + 2 340_341 c.116_117insG c.(115-117)TTGfs p.L39fs SLC3A2_uc001nwb.2_Frame_Shift_Ins_p.L39fs|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c 39 blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.32 69 33 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.90 4 38 ADRBK1 156 broad.mit.edu 37 11 67052434 67052435 + Frame_Shift_Ins INS - G G SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr11:67052434_67052435insG uc009yrn.1 + 19 2037_2038 c.1771_1772insG c.(1771-1773)CGGfs p.R591fs ADRBK1_uc009yrm.1_Intron NM_001619 NP_001610 P25098 ARBK1_HUMAN beta-adrenergic receptor kinase 1 591 PH. activation of phospholipase C activity|cardiac muscle contraction|desensitization of G-protein coupled receptor protein signaling pathway|muscarinic acetylcholine receptor signaling pathway|negative regulation of striated muscle contraction|negative regulation of the force of heart contraction by chemical signal|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of catecholamine secretion|tachykinin receptor signaling pathway cytosol|soluble fraction alpha-2A adrenergic receptor binding|ATP binding|beta-adrenergic receptor kinase activity|Edg-2 lysophosphatidic acid receptor binding|G-protein coupled receptor kinase activity|signal transducer activity large_intestine(1) 1 BRCA - Breast invasive adenocarcinoma(15;2.26e-06) Adenosine triphosphate(DB00171) CCTCGAGTGGCGGGGCGAGGGC 0.688 0.16 98 18 ATN1 1822 broad.mit.edu 37 12 7045885 7045886 + In_Frame_Ins INS - CAG CAG SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr12:7045885_7045886insCAG uc001qrw.1 + 5 1692_1693 c.1455_1456insCAG c.(1453-1458)insCAG p.502_503insQ ATN1_uc001qrx.1_In_Frame_Ins_p.502_503insQ|ATN1_uc001qry.1_In_Frame_Ins_p.486_487insQ NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502_503 cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 ACCACcagcaacagcaacagca 0.441 0.37 80 47 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.52 68 73 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.56 64 80 SMAD7 4092 broad.mit.edu 37 18 46476544 46476561 + In_Frame_Del DEL GCGCCGGCGCCCGCGGCT - - SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr18:46476544_46476561delGCGCCGGCGCCCGCGGCT uc002ldg.2 - 1 521_538 c.234_251delAGCCGCGGGCGCCGGCGC c.(232-252)CCAGCCGCGGGCGCCGGCGCG>CCG p.AAGAGA79del SMAD7_uc010xde.1_5'Flank NM_005904 NP_005895 O15105 SMAD7_HUMAN SMAD family member 7 79_84 MH1. adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding 0 Colorectal(1;0.0518) 0.000 0.24 744 234 FFAR2 2867 broad.mit.edu 37 19 35940696 35940697 + Frame_Shift_Ins INS - G G SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr19:35940696_35940697insG uc002nzg.2 + 2 160_161 c.80_81insG c.(79-81)CTGfs p.L27fs FFAR2_uc010eea.2_Frame_Shift_Ins_p.L27fs NM_005306 NP_005297 O15552 FFAR2_HUMAN free fatty acid receptor 2 27 Helical; Name=1; (Potential). integral to plasma membrane G-protein coupled receptor activity|lipid binding central_nervous_system(1) 1 all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0724) GCCAACCTCCTGGCCCTGCGGG 0.629 0.12 80 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 50 145 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 56 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SCABER_URINARY_TRACT NA SCABER_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 33 359 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SCC15_UPPER_AERODIGESTIVE_TRACT NA SCC15_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 48 ZAK 51776 broad.mit.edu 37 2 174128577 174128579 + In_Frame_Del DEL ATT - - SCC15_UPPER_AERODIGESTIVE_TRACT NA SCC15_UPPER_AERODIGESTIVE_TRACT NA g.chr2:174128577_174128579delATT uc002uhz.2 + 19 1856_1858 c.1656_1658delATT c.(1654-1659)ACATTA>ACA p.L553del uc002uib.2_Intron NM_016653 NP_057737 Q9NYL2 MLTK_HUMAN MLK-related kinase isoform 1 553 activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation cytoplasm|nucleus ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding lung(3)|stomach(1)|ovary(1)|skin(1) 6 OV - Ovarian serous cystadenocarcinoma(117;0.176) CCATTCAGACATTATTCACCAAT 0.409 0.57 57 76 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SCC15_UPPER_AERODIGESTIVE_TRACT NA SCC15_UPPER_AERODIGESTIVE_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.42 7 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SCC15_UPPER_AERODIGESTIVE_TRACT NA SCC15_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 74 87 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SCC15_UPPER_AERODIGESTIVE_TRACT NA SCC15_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 140 278 CYP3A4 1576 broad.mit.edu 37 7 99355806 99355807 + Frame_Shift_Ins INS - T T rs67666821 SCC15_UPPER_AERODIGESTIVE_TRACT NA SCC15_UPPER_AERODIGESTIVE_TRACT NA g.chr7:99355806_99355807insT uc003urv.1 - 13 1565_1566 c.1461_1462insA c.(1459-1464)AAACCCfs p.K487fs CYP3A4_uc003urw.1_Frame_Shift_Ins_p.K486fs|CYP3A4_uc011kiz.1_Frame_Shift_Ins_p.K446fs|CYP3A4_uc011kja.1_Frame_Shift_Ins_p.K438fs|CYP3A4_uc011kjb.1_Frame_Shift_Ins_p.K337fs NM_017460 NP_059488 P08684 CP3A4_HUMAN cytochrome P450, family 3, subfamily A, 487_488 alkaloid catabolic process|androgen metabolic process|exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid catabolic process|xenobiotic metabolic process cell surface|endoplasmic reticulum membrane|integral to membrane|microsome albendazole monooxygenase activity|caffeine oxidase activity|electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding|quinine 3-monooxygenase activity|steroid binding|taurochenodeoxycholate 6alpha-hydroxylase activity|testosterone 6-beta-hydroxylase activity|vitamin D 24-hydroxylase activity|vitamin D3 25-hydroxylase activity central_nervous_system(3)|ovary(1) 4 Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228) Albendazole(DB00518)|Alclometasone(DB00240)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Aliskiren(DB01258)|Almotriptan(DB00918)|Alosetron(DB00969)|Alprazolam(DB00404)|Amlodipine(DB00381)|Amprenavir(DB00701)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Benazepril(DB00542)|Bepridil(DB01244)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bortezomib(DB00188)|Bosentan(DB00559)|Bromocriptine(DB01200)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Buspirone(DB00490)|Busulfan(DB01008)|Carbamazepine(DB00564)|Cevimeline(DB00185)|Chlorpheniramine(DB01114)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cinacalcet(DB01012)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clindamycin(DB01190)|Clofibrate(DB00636)|Clonazepam(DB01068)|Clopidogrel(DB00758)|Cocaine(DB00907)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cyproterone(DB04839)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Delavirdine(DB00705)|Desogestrel(DB00304)|Dexamethasone(DB01234)|Diazepam(DB00829)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dofetilide(DB00204)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Doxorubicin(DB00997)|Drospirenone(DB01395)|Dutasteride(DB01126)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Epirubicin(DB00445)|Eplerenone(DB00700)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Exemestane(DB00990)|Felodipine(DB01023)|Fentanyl(DB00813)|Fexofenadine(DB00950)|Finasteride(DB01216)|Fluconazole(DB00196)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Fosamprenavir(DB01319)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Granisetron(DB00889)|Grepafloxacin(DB00365)|Halofantrine(DB01218)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Imatinib(DB00619)|Indinavir(DB00224)|Ipratropium(DB00332)|Irinotecan(DB00762)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levomethadyl Acetate(DB01227)|Levothyroxine(DB00451)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Maraviroc(DB04835)|Marinol(DB00470)|Mebendazole(DB00643)|Medroxyprogesterone(DB00603)|Methadone(DB00333)|Methylprednisolone(DB00959)|Metyrapone(DB01011)|Mibefradil(DB01388)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirtazapine(DB00370)|Modafinil(DB00745)|Mometasone(DB00764)|Montelukast(DB00471)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norgestrel(DB00506)|Nystatin(DB00646)|Ondansetron(DB00904)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paricalcitol(DB00910)|Phenmetrazine(DB00830)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prednisolone(DB00860)|Prednisone(DB00635)|Prochlorperazine(DB00433)|Quetiapine(DB01224)|Quinapril(DB00881)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranolazine(DB00243)|Reboxetine(DB00234)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampin(DB01045)|Rimonabant(DB06155)|Ritonavir(DB00503)|Rofecoxib(DB00533)|Roxithromycin(DB00778)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sertindole(DB06144)|Sibutramine(DB01105)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Terconazole(DB00251)|Terfenadine(DB00342)|Testosterone(DB00624)|Tiagabine(DB00906)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tiotropium(DB01409)|Tipranavir(DB00932)|Toremifene(DB00539)|Triazolam(DB00897)|Trimetrexate(DB01157)|Troglitazone(DB00197)|Valdecoxib(DB00580)|Vardenafil(DB00862)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Voriconazole(DB00582)|Zaleplon(DB00962)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909) AGAACAACGGGTTTTTCTGGTT 0.401 0.55 65 80 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SCC15_UPPER_AERODIGESTIVE_TRACT NA SCC15_UPPER_AERODIGESTIVE_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.66 39 76 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SCC15_UPPER_AERODIGESTIVE_TRACT NA SCC15_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 182 59 NCAPD3 23310 broad.mit.edu 37 11 134037889 134037892 + Splice_Site DEL ACTT - - SCC15_UPPER_AERODIGESTIVE_TRACT NA SCC15_UPPER_AERODIGESTIVE_TRACT NA g.chr11:134037889_134037892delACTT uc001qhd.1 - 27 4179 c.3573_splice c.e27+1 p.Q1191_splice NCAPD3_uc010scm.1_Splice_Site|NCAPD3_uc009zda.1_Splice_Site|NCAPD3_uc001qhc.1_Splice_Site_p.Q141_splice NM_015261 NP_056076 P42695 CNDD3_HUMAN non-SMC condensin II complex, subunit D3 cell division|mitotic chromosome condensation nuclear centromeric heterochromatin|nuclear condensin complex methylated histone residue binding ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1) 5 all_hematologic(175;0.127) all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227) CAACACACTCACTTGTGAGATGAG 0.485 0.98 4 166 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SCC15_UPPER_AERODIGESTIVE_TRACT NA SCC15_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 73 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 11 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 169 55 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.34 31 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 51 41 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 3 9 SMARCA2 6595 broad.mit.edu 37 9 2039806 2039807 + In_Frame_Ins INS - CAA CAA SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr9:2039806_2039807insCAA uc003zhc.2 + 4 795_796 c.696_697insCAA c.(694-699)insCAA p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.31 475 215 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.56 24 31 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 88 30 GRAMD1B 57476 broad.mit.edu 37 11 123480598 123480599 + Frame_Shift_Ins INS - C C rs139670625 by1000genomes SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr11:123480598_123480599insC uc001pyx.2 + 12 1653_1654 c.1324_1325insC c.(1324-1326)ACTfs p.T442fs GRAMD1B_uc001pyw.2_Frame_Shift_Ins_p.T449fs|GRAMD1B_uc010rzw.1_Frame_Shift_Ins_p.T402fs|GRAMD1B_uc010rzx.1_Frame_Shift_Ins_p.T402fs|GRAMD1B_uc009zbe.1_Frame_Shift_Ins_p.T438fs|GRAMD1B_uc001pyy.2_Frame_Shift_Ins_p.T133fs NM_020716 NP_065767 Q3KR37 GRM1B_HUMAN GRAM domain containing 1B 442 integral to membrane ovary(1) 1 Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394) GGCTCCCAAAACTGCCACTGTC 0.500 0.26 31 11 THAP11 57215 broad.mit.edu 37 16 67876788 67876796 + In_Frame_Del DEL CAGCAGCAA - - SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr16:67876788_67876796delCAGCAGCAA uc002euo.2 + 1 576_584 c.331_339delCAGCAGCAA c.(331-339)CAGCAGCAAdel p.QQQ129del CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 129_131 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) acagcagcagcagcagcaacagcagcaac 0.316 0.32 38 18 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 14 112 TP53 7157 broad.mit.edu 37 17 7578222 7578223 + Frame_Shift_Del DEL TC - - SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr17:7578222_7578223delTC uc002gim.2 - 6 820_821 c.626_627delGA c.(625-627)AGAfs p.R209fs TP53_uc002gig.1_Frame_Shift_Del_p.R209fs|TP53_uc002gih.2_Frame_Shift_Del_p.R209fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.R77fs|TP53_uc010cng.1_Frame_Shift_Del_p.R77fs|TP53_uc002gii.1_Frame_Shift_Del_p.R77fs|TP53_uc010cnh.1_Frame_Shift_Del_p.R209fs|TP53_uc010cni.1_Frame_Shift_Del_p.R209fs|TP53_uc002gij.2_Frame_Shift_Del_p.R209fs|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Frame_Shift_Del_p.R116fs|TP53_uc002gio.2_Frame_Shift_Del_p.R77fs|TP53_uc010vug.1_Frame_Shift_Del_p.R170fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 209 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). R -> I (in sporadic cancers; somatic mutation).|R -> S (in a sporadic cancer; somatic mutation).|R -> T (in sporadic cancers; somatic mutation).|R -> K (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.R209fs*6(31)|p.R209*(9)|p.0?(7)|p.R209T(3)|p.R209K(3)|p.R209fs*35(2)|p.D207fs*6(2)|p.R209fs*38(2)|p.K164_P219del(1)|p.E204_N210delEYLDDRN(1)|p.R209fs*36(1)|p.D207_R213delDDRNTFR(1)|p.D208_V216delDRNTFRHSV(1)|p.D208fs*1(1)|p.N210fs*7(1)|p.R209R(1)|p.R209S(1)|p.R209I(1)|p.R209_R213delRNTFR(1)|p.D207_V216del10(1)|p.R209fs*7(1)|p.R209fs*5(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GAAAAGTGTTTCTGTCATCCAA 0.535 0.99 1 88 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 28 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 43 399 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SCC25_UPPER_AERODIGESTIVE_TRACT NA SCC25_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 31 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.87 9 59 PDE4DIP 9659 broad.mit.edu 37 1 144863410 144863411 + Frame_Shift_Del DEL TG - - SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144863410_144863411delTG uc001elw.3 - 37 6283_6284 c.5992_5993delCA c.(5992-5994)CAGfs p.Q1998fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.Q1892fs|PDE4DIP_uc001elv.3_Frame_Shift_Del_p.Q1005fs|PDE4DIP_uc001ema.2_3'UTR NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 1998 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) CTCTTCACACTGTTGCTGCAGG 0.525 0.14 564 94 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.22 225 63 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 91 130 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 22 62 NSD1 64324 broad.mit.edu 37 5 176637654 176637654 + Frame_Shift_Del DEL T - - SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr5:176637654delT uc003mfr.3 + 5 2392 c.2254delT c.(2254-2256)TCTfs p.S752fs NSD1_uc003mft.3_Frame_Shift_Del_p.S483fs|NSD1_uc003mfs.1_Frame_Shift_Del_p.S649fs|NSD1_uc011dfx.1_Frame_Shift_Del_p.S400fs NM_022455 NP_071900 Q96L73 NSD1_HUMAN nuclear receptor binding SET domain protein 1 752 negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|nucleus androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding ovary(2)|kidney(1) 3 all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002) all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198) Kidney(146;0.235) TGATGCTCTCTCTCCAAAATT 0.438 0.99 2 317 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.43 8 6 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 1 11 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.11 588 70 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.71 9 22 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 250 87 FSCB 84075 broad.mit.edu 37 14 44975072 44975122 + In_Frame_Del DEL TTCAGCTGGTGGAGGCAGAATTTCAGCAGGAGGCTCTTCTGAAGGGGACTC - - rs35931814;rs143087159;rs148228869;rs17857204 byFrequency SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr14:44975072_44975122delTTCAGCTGGTGGAGGCAGAATTTCAGCAGGAGGCTCTTCTGAAGGGGACTC uc001wvn.2 - 1 1378_1428 c.1069_1119delGAGTCCCCTTCAGAAGAGCCTCCTGCTGAAATTCTGCCTCCACCAGCTGAA c.(1069-1119)GAGTCCCCTTCAGAAGAGCCTCCTGCTGAAATTCTGCCTCCACCAGCTGAAdel p.ESPSEEPPAEILPPPAE357del NM_032135 NP_115511 Q5H9T9 FSCB_HUMAN fibrous sheath CABYR binding protein 357_373 Pro-rich. cilium lung(3)|breast(3)|ovary(2)|central_nervous_system(1) 9 GBM - Glioblastoma multiforme(112;0.128) AAGGAGACTTTTCAGCTGGTGGAGGCAGAATTTCAGCAGGAGGCTCTTCTGAAGGGGACTCTTCAGCTGAT 0.514 0.63 81 138 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 11 75 MINK1 50488 broad.mit.edu 37 17 4793026 4793027 + In_Frame_Ins INS - AGGAGGAGCGGCGGC AGGAGGAGCGGCGGC SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr17:4793026_4793027insAGGAGGAGCGGCGGC uc010vsl.1 + 13 1511_1512 c.1315_1316insAGGAGGAGCGGCGGC c.(1315-1317)GAG>GAGGAGGAGCGGCGGCAG p.444_445insEERRQ MINK1_uc010vsk.1_In_Frame_Ins_p.444_445insEERRQ|MINK1_uc010vsm.1_In_Frame_Ins_p.444_445insEERRQ|MINK1_uc010vsn.1_In_Frame_Ins_p.444_445insEERRQ|MINK1_uc010vso.1_In_Frame_Ins_p.389_390insEERRQ|MINK1_uc010vsp.1_5'UTR NM_153827 NP_722549 Q8N4C8 MINK1_HUMAN misshapen-like kinase 1 isoform 3 444_445 JNK cascade cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)|skin(1) 6 0.000 0.38 398 240 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.25 46 15 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.21 84 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 87 400 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SCC4_UPPER_AERODIGESTIVE_TRACT NA SCC4_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 79 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SCLC21H_LUNG NA SCLC21H_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.70 10 23 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.35 222 120 CAMKV 79012 broad.mit.edu 37 3 49897114 49897114 + Frame_Shift_Del DEL G - - SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr3:49897114delG uc003cxt.1 - 11 1336 c.1143delC c.(1141-1143)CCCfs p.P381fs CAMKV_uc011bcy.1_Frame_Shift_Del_p.P306fs|CAMKV_uc003cxv.1_Frame_Shift_Del_p.P353fs|CAMKV_uc003cxw.1_Frame_Shift_Del_p.P213fs|CAMKV_uc003cxx.1_Frame_Shift_Del_p.P213fs|CAMKV_uc003cxu.2_Intron|CAMKV_uc011bcz.1_Intron|CAMKV_uc011bda.1_Intron NM_024046 NP_076951 Q8NCB2 CAMKV_HUMAN CaM kinase-like vesicle-associated 381 Ala-rich. cytoplasmic vesicle membrane|plasma membrane ATP binding|protein serine/threonine kinase activity ovary(2)|lung(2)|large_intestine(2)|central_nervous_system(1) 7 BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621) TACGGTCTGCGGGGGCCACAT 0.642 0.89 4 33 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.26 31 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 67 98 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.79 26 97 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.82 2 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 252 114 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.60 18 27 KIAA1409 57578 broad.mit.edu 37 14 94063826 94063826 + Frame_Shift_Del DEL C - - SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr14:94063826delC uc001ybv.1 + 21 2864 c.2781delC c.(2779-2781)AACfs p.N927fs KIAA1409_uc001ybs.1_Frame_Shift_Del_p.N927fs NM_020818 NP_065869 Q9P2D8 UNC79_HUMAN hypothetical protein LOC57578 1104 integral to membrane ovary(10)|skin(4)|large_intestine(3) 17 all_cancers(154;0.0354)|all_epithelial(191;0.216) Epithelial(152;0.188) AGGATGTCAACCCCGCAGTGG 0.507 0.44 82 64 LTK 4058 broad.mit.edu 37 15 41804422 41804422 + Frame_Shift_Del DEL T - - SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr15:41804422delT uc001zoa.3 - 4 579 c.401delA c.(400-402)AACfs p.N134fs LTK_uc001zob.3_Frame_Shift_Del_p.N134fs|LTK_uc010ucx.1_Frame_Shift_Del_p.N134fs|LTK_uc010bcg.2_Intron NM_002344 NP_002335 P29376 LTK_HUMAN leukocyte receptor tyrosine kinase isoform 1 134 Extracellular (Potential). apoptosis|cell proliferation|phosphatidylinositol 3-kinase cascade|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane|soluble fraction ATP binding|transmembrane receptor protein tyrosine kinase activity lung(6)|central_nervous_system(1) 7 all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172) OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113) CGACAGGTGGTTCTTGGCGCC 0.692 0.46 29 25 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 25 210 BRCA1 672 broad.mit.edu 37 17 41245670 41245671 + Frame_Shift_Ins INS - ACTA ACTA rs8176154 SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr17:41245670_41245671insACTA uc002icq.2 - 10 2109_2110 c.1877_1878insTAGT c.(1876-1878)GTAfs p.V626fs BRCA1_uc010whp.1_Intron|BRCA1_uc010whl.1_Intron|BRCA1_uc010whm.1_Intron|BRCA1_uc002icp.3_Frame_Shift_Ins_p.V555fs|BRCA1_uc002icu.2_Intron|BRCA1_uc010cyx.2_Frame_Shift_Ins_p.V579fs|BRCA1_uc002ict.2_Frame_Shift_Ins_p.V626fs|BRCA1_uc010whn.1_Intron|BRCA1_uc010who.1_Intron|BRCA1_uc010whq.1_Intron|BRCA1_uc002idc.1_Intron|BRCA1_uc010whr.1_Intron|BRCA1_uc002idd.2_Frame_Shift_Ins_p.V626fs|BRCA1_uc002ide.1_Frame_Shift_Ins_p.V457fs|BRCA1_uc010cyy.1_Frame_Shift_Ins_p.V626fs|BRCA1_uc010whs.1_Frame_Shift_Ins_p.V626fs|BRCA1_uc010cyz.2_Frame_Shift_Ins_p.V579fs|BRCA1_uc010cza.2_Frame_Shift_Ins_p.V600fs|BRCA1_uc010wht.1_Frame_Shift_Ins_p.V330fs NM_007294 NP_009225 P38398 BRCA1_HUMAN breast cancer 1, early onset isoform 1 626 androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding ovary(24)|breast(21)|lung(4)|central_nervous_system(1)|endometrium(1)|urinary_tract(1) 52 Breast(137;0.000717) BRCA - Breast invasive adenocarcinoma(366;0.126) TTCTACTGACTACTAGTTCAAG 0.361 0.39 319 207 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 56 322 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SCLC21H_LUNG NA SCLC21H_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 75 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 56 MAST2 23139 broad.mit.edu 37 1 46463406 46463406 + Frame_Shift_Del DEL T - - SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:46463406delT uc001cov.2 + 6 886 c.603delT c.(601-603)CCTfs p.P201fs MAST2_uc001cow.2_Frame_Shift_Del_p.P201fs|MAST2_uc001cox.1_Frame_Shift_Del_p.P58fs|MAST2_uc001coy.1_5'UTR|MAST2_uc001coz.1_Frame_Shift_Del_p.P86fs|MAST2_uc009vya.2_Frame_Shift_Del_p.P116fs NM_015112 NP_055927 Q6P0Q8 MAST2_HUMAN microtubule associated serine/threonine kinase 201 regulation of interleukin-12 biosynthetic process|spermatid differentiation cytoplasm|cytoskeleton|plasma membrane ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity ovary(5)|lung(3)|stomach(2)|breast(1) 11 Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184) GTAACAGTCCTTTGGACAGCC 0.488 0.40 113 74 ROBO2 6092 broad.mit.edu 37 3 77638021 77638022 + Frame_Shift_Ins INS - T T SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:77638021_77638022insT uc003dpy.3 + 17 3263_3264 c.2620_2621insT c.(2620-2622)ATGfs p.M874fs ROBO2_uc003dpz.2_Frame_Shift_Ins_p.M878fs|ROBO2_uc011bgj.1_RNA|ROBO2_uc011bgk.1_Frame_Shift_Ins_p.M878fs|ROBO2_uc003dqa.2_Frame_Shift_Ins_p.M1fs NM_002942 NP_002933 Q9HCK4 ROBO2_HUMAN roundabout, axon guidance receptor, homolog 2 874 Helical; (Potential). apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development axolemma|cell surface|integral to membrane axon guidance receptor activity|identical protein binding lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1) 11 Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103) GGTAATTCTGATGGGTTTTAGC 0.411 0.44 59 47 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.37 19 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 101 133 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 30 18 RAD50 10111 broad.mit.edu 37 5 131915178 131915179 + Frame_Shift_Ins INS - T T SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:131915178_131915179insT uc003kxi.2 + 4 922_923 c.535_536insT c.(535-537)ATTfs p.I179fs RAD50_uc003kxg.1_Frame_Shift_Ins_p.I80fs|RAD50_uc003kxh.2_Frame_Shift_Ins_p.I40fs NM_005732 NP_005723 Q92878 RAD50_HUMAN RAD50 homolog isoform 1 179 DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding lung(2)|ovary(1)|skin(1) 4 all_cancers(142;0.0368)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GTTTGATGAGATTTTTTCAGCA 0.332 0.53 37 41 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.83 3 15 MLL3 58508 broad.mit.edu 37 7 151845524 151845524 + Frame_Shift_Del DEL A - - SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:151845524delA uc003wla.2 - 52 13707 c.13488delT c.(13486-13488)TTTfs p.F4496fs MLL3_uc003wkz.2_Frame_Shift_Del_p.F3614fs|MLL3_uc003wkx.2_Frame_Shift_Del_p.F654fs|MLL3_uc003wky.2_Frame_Shift_Del_p.F2060fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 4496 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTTTGTCCTTAAAAAACATGC 0.433 0.42 113 83 MLL3 58508 broad.mit.edu 37 7 151874147 151874148 + Frame_Shift_Ins INS - T T SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:151874147_151874148insT uc003wla.2 - 38 8609_8610 c.8390_8391insA c.(8389-8391)AAGfs p.K2797fs MLL3_uc003wkz.2_Frame_Shift_Ins_p.K1858fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.K306fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 2797 K -> R (in Ref. 1; AAK00583). intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding p.K2797fs*26(18) large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTTCTTGTTCCTTTTTTTTTGG 0.347 0.35 85 46 ARHGEF10 9639 broad.mit.edu 37 8 1828284 1828285 + Frame_Shift_Ins INS - G G SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:1828284_1828285insG uc003wpr.2 + 9 1092_1093 c.914_915insG c.(913-915)GTGfs p.V305fs ARHGEF10_uc003wpq.1_Frame_Shift_Ins_p.V330fs|ARHGEF10_uc003wps.2_Intron|ARHGEF10_uc003wpt.2_Intron|ARHGEF10_uc003wpv.2_Intron|ARHGEF10_uc010lre.2_5'Flank NM_014629 NP_055444 O15013 ARHGA_HUMAN Rho guanine nucleotide exchange factor 10 330 Potential. centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis centrosome|cytosol|soluble fraction kinesin binding|Rho guanyl-nucleotide exchange factor activity large_intestine(1) 1 Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834) COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718) GCAAGCACGGTGGGCGTGGTGG 0.510 0.39 100 63 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 41 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.67 5 10 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.47 9 8 SRP14 6727 broad.mit.edu 37 15 40328596 40328597 + In_Frame_Ins INS - TGC TGC SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:40328596_40328597insTGC uc001zkq.2 - 5 420_421 c.348_349insGCA c.(346-351)insGCA p.116_117insA SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116_117 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) gctgcggcaggtgctgctgctg 0.228 0.19 103 24 MGA 23269 broad.mit.edu 37 15 42058964 42058964 + Frame_Shift_Del DEL A - - SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:42058964delA uc010ucy.1 + 24 8865 c.8684delA c.(8683-8685)GACfs p.D2895fs MGA_uc010ucz.1_Frame_Shift_Del_p.D2686fs NM_001164273 NP_001157745 Q8IWI9 MGAP_HUMAN MAX-interacting protein isoform 1 2856 MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 12 all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238) OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235) GGGGAGAGTGACTCTATCAGT 0.458 0.57 40 53 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.36 87 48 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.68 212 449 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 11 87 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.74 9 26 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.45 127 103 STK17B 9262 broad.mit.edu 37 2 197002245 197002247 + In_Frame_Del DEL TGC - - SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:197002245_197002247delTGC uc002utk.2 - 8 1367_1369 c.1043_1045delGCA c.(1042-1047)AGCATG>ATG p.S348del STK17B_uc010fsh.2_In_Frame_Del_p.S348del NM_004226 NP_004217 O94768 ST17B_HUMAN serine/threonine kinase 17B 348 apoptosis|induction of apoptosis|intracellular protein kinase cascade nucleus ATP binding|protein serine/threonine kinase activity lung(2) 2 OV - Ovarian serous cystadenocarcinoma(117;0.141) TTGGAAACCATGCTGCTATCCTC 0.404 0.46 87 74 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.36 9 5 CCNA2 890 broad.mit.edu 37 4 122743803 122743804 + Splice_Site INS - A A SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:122743803_122743804insA uc003iec.3 - 2 519 c.214_splice c.e2-1 p.V72_splice NM_001237 NP_001228 P20248 CCNA2_HUMAN cyclin A cell division|mitosis|mitotic cell cycle G2/M transition DNA damage checkpoint|Ras protein signal transduction|regulation of cyclin-dependent protein kinase activity cytoplasm|nucleoplasm protein kinase binding ovary(1) 1 GGGTGCAACCTAAAAAAAAATT 0.406 0.41 53 37 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.35 55 29 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 8 14 AIM1 202 broad.mit.edu 37 6 106968093 106968093 + Frame_Shift_Del DEL C - - SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:106968093delC uc003prh.2 + 2 2273 c.1786delC c.(1786-1788)CCCfs p.P596fs NM_001624 NP_001615 Q9Y4K1 AIM1_HUMAN absent in melanoma 1 596 sugar binding breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1) 9 Breast(9;0.0138)|all_epithelial(6;0.169) all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473) Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305) all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858) AAGTTGTGCTCCCCCACAAGA 0.512 0.57 20 27 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.70 3 7 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 11 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.53 534 601 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.36 7 4 FADD 8772 broad.mit.edu 37 11 70049816 70049817 + Frame_Shift_Ins INS - G G SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:70049816_70049817insG uc001opm.2 + 1 548_549 c.251_252insG c.(250-252)GCGfs p.A84fs NM_003824 NP_003815 Q13158 FADD_HUMAN Fas-associated via death domain 84 activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction cytosol death receptor binding|identical protein binding ovary(1)|lung(1)|pancreas(1) 3 Esophageal squamous(2;1.19e-45) LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) 0.000 0.10 504 54 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 76 15 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.30 35 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 389 1338 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 43 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 8 101 PIKFYVE 200576 broad.mit.edu 37 2 209204277 209204277 + Frame_Shift_Del DEL A - - SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr2:209204277delA uc002vcz.2 + 30 4966 c.4808delA c.(4807-4809)GAAfs p.E1603fs NM_015040 NP_055855 Q9Y2I7 FYV1_HUMAN phosphatidylinositol-3-phosphate 5-kinase type 1603 cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi early endosome membrane|membrane raft 1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1) 10 AGCAGTTCCGAAGGTAGAGGT 0.373 0.27 151 55 PASK 23178 broad.mit.edu 37 2 242051752 242051753 + Frame_Shift_Ins INS - T T SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr2:242051752_242051753insT uc002wao.1 - 15 3527_3528 c.3435_3436insA c.(3433-3438)ATAGACfs p.I1145fs PASK_uc010zol.1_Frame_Shift_Ins_p.I959fs|PASK_uc010zom.1_Frame_Shift_Ins_p.I1110fs|PASK_uc010fzl.1_Frame_Shift_Ins_p.I1152fs|PASK_uc010zon.1_Frame_Shift_Ins_p.I926fs NM_015148 NP_055963 Q96RG2 PASK_HUMAN PAS domain containing serine/threonine kinase 1145_1146 Protein kinase. regulation of transcription, DNA-dependent Golgi apparatus ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity ovary(4)|lung(1)|skin(1) 6 all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968) GAGCCAAAGTCTATCAGCTTGA 0.485 0.43 166 123 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.50 5 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 109 134 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 24 42 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.17 909 191 UBR5 51366 broad.mit.edu 37 8 103324592 103324592 + Frame_Shift_Del DEL A - - SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr8:103324592delA uc003ykr.1 - 17 2162 c.2129delT c.(2128-2130)TTAfs p.L710fs UBR5_uc003yks.1_Frame_Shift_Del_p.L710fs NM_015902 NP_056986 O95071 UBR5_HUMAN ubiquitin protein ligase E3 component n-recognin 710 cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus nucleus|soluble fraction protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1) 28 all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05) OV - Ovarian serous cystadenocarcinoma(57;0.000442) AATTCTAAGTAACCTACAATC 0.388 0.47 191 168 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 293 33 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 3 45 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 9 24 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 116 22 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 54 469 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SF126_CENTRAL_NERVOUS_SYSTEM NA SF126_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 98 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SF295_CENTRAL_NERVOUS_SYSTEM NA SF295_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 3 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SF295_CENTRAL_NERVOUS_SYSTEM NA SF295_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.46 44 37 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SF295_CENTRAL_NERVOUS_SYSTEM NA SF295_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 28 48 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SF295_CENTRAL_NERVOUS_SYSTEM NA SF295_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SF295_CENTRAL_NERVOUS_SYSTEM NA SF295_CENTRAL_NERVOUS_SYSTEM NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.43 17 13 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SF295_CENTRAL_NERVOUS_SYSTEM NA SF295_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.90 1 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SF295_CENTRAL_NERVOUS_SYSTEM NA SF295_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 175 69 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes SF295_CENTRAL_NERVOUS_SYSTEM NA SF295_CENTRAL_NERVOUS_SYSTEM NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.13 81 12 UBE2O 63893 broad.mit.edu 37 17 74395563 74395565 + In_Frame_Del DEL TTC - - SF295_CENTRAL_NERVOUS_SYSTEM NA SF295_CENTRAL_NERVOUS_SYSTEM NA g.chr17:74395563_74395565delTTC uc002jrm.3 - 9 1658_1660 c.1593_1595delGAA c.(1591-1596)AAGAAT>AAT p.K531del UBE2O_uc002jrn.3_In_Frame_Del_p.K531del|UBE2O_uc002jrl.3_In_Frame_Del_p.K134del NM_022066 NP_071349 Q9C0C9 UBE2O_HUMAN ubiquitin-conjugating enzyme E2O 531 ATP binding|ubiquitin-protein ligase activity breast(2)|skin(2)|lung(1) 5 AGTGATTTTATTCTTCTTCCTCT 0.557 0.57 101 133 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SF295_CENTRAL_NERVOUS_SYSTEM NA SF295_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 43 28 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SF295_CENTRAL_NERVOUS_SYSTEM NA SF295_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.35 64 34 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SF295_CENTRAL_NERVOUS_SYSTEM NA SF295_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 107 427 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SF295_CENTRAL_NERVOUS_SYSTEM NA SF295_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 4 41 TBX22 50945 broad.mit.edu 37 X 79282809 79282809 + Frame_Shift_Del DEL G - - SH10TC_STOMACH NA SH10TC_STOMACH NA g.chrX:79282809delG uc010nmg.1 + 7 987 c.853delG c.(853-855)GGAfs p.G285fs TBX22_uc004edi.1_Frame_Shift_Del_p.G165fs|TBX22_uc004edj.1_Frame_Shift_Del_p.G285fs NM_001109878 NP_001103348 Q9Y458 TBX22_HUMAN T-box 22 isoform 1 285 multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter nucleus DNA binding|sequence-specific DNA binding transcription factor activity lung(7)|large_intestine(3)|central_nervous_system(2)|breast(1)|skin(1)|ovary(1) 15 TAGAGATACTGGAAGAAACAG 0.264 0.23 344 105 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SH10TC_STOMACH NA SH10TC_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 6 82 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.51 732 770 SP140 11262 broad.mit.edu 37 2 231106184 231106184 + Frame_Shift_Del DEL C - - SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr2:231106184delC uc002vql.2 + 4 587 c.472delC c.(472-474)CTAfs p.L158fs SP140_uc010zma.1_RNA|SP140_uc002vqk.2_Frame_Shift_Del_p.L158fs|SP140_uc002vqn.2_Frame_Shift_Del_p.L158fs|SP140_uc002vqm.2_Frame_Shift_Del_p.L158fs|SP140_uc010fxl.2_Frame_Shift_Del_p.L158fs NM_007237 NP_009168 Q13342 LY10_HUMAN SP140 nuclear body protein isoform 1 158 defense response cytoplasm|nuclear envelope|nucleolus|nucleoplasm DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding 0 Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167) Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942) ACCCAGATTACTACCATATGG 0.358 0.39 612 391 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.28 31 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.39 128 81 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.56 43 54 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.80 5 20 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.50 6 6 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.24 250 79 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.83 4 19 PTEN 5728 broad.mit.edu 37 10 89624258 89624259 + Frame_Shift_Ins INS - A A SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr10:89624258_89624259insA uc001kfb.2 + 2 1063_1064 c.32_33insA c.(31-33)AGAfs p.R11fs KILLIN_uc009xti.2_5'Flank NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 11 activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.?(13)|p.0?(12)|p.I8_R14>LRLICIF(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) ATCGTTAGCAGAAACAAAAGGA 0.480 0.92 27 307 PIK3C2A 5286 broad.mit.edu 37 11 17139165 17139166 + Frame_Shift_Del DEL AC - - SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr11:17139165_17139166delAC uc001mmq.3 - 18 3154_3155 c.3088_3089delGT c.(3088-3090)GTTfs p.V1030fs PIK3C2A_uc009ygu.1_Intron|PIK3C2A_uc010rcw.1_Frame_Shift_Del_p.V650fs|PIK3C2A_uc001mmr.3_Intron NM_002645 NP_002636 O00443 P3C2A_HUMAN phosphoinositide-3-kinase, class 2 alpha 1030 cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity lung(4)|central_nervous_system(4)|stomach(1)|ovary(1) 10 Phosphatidylserine(DB00144) AGCACCCAAAACATGTTCGTAT 0.381 0.29 930 372 CHD4 1108 broad.mit.edu 37 12 6701651 6701651 + Frame_Shift_Del DEL C - - rs147796962 SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr12:6701651delC uc001qpo.2 - 19 3020 c.2856delG c.(2854-2856)CCGfs p.P952fs CHD4_uc001qpn.2_Frame_Shift_Del_p.P945fs|CHD4_uc001qpp.2_Frame_Shift_Del_p.P949fs NM_001273 NP_001264 Q14839 CHD4_HUMAN chromodomain helicase DNA binding protein 4 952 chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent microtubule organizing center|NuRD complex ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding central_nervous_system(2) 2 GCAACATGTGCGGCCCCAGCA 0.478 0.20 59 15 ATN1 1822 broad.mit.edu 37 12 7045885 7045886 + In_Frame_Ins INS - CAG CAG SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr12:7045885_7045886insCAG uc001qrw.1 + 5 1692_1693 c.1455_1456insCAG c.(1453-1458)insCAG p.502_503insQ ATN1_uc001qrx.1_In_Frame_Ins_p.502_503insQ|ATN1_uc001qry.1_In_Frame_Ins_p.486_487insQ NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 502_503 cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 ACCACcagcaacagcaacagca 0.441 0.69 28 61 NEK3 4752 broad.mit.edu 37 13 52725278 52725279 + Splice_Site INS - A A SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr13:52725278_52725279insA uc001vgi.2 - 7 783 c.548_splice c.e7+1 p.S183_splice NEK3_uc001vgg.2_Splice_Site_p.S177_splice|NEK3_uc001vgh.2_Splice_Site_p.S204_splice|NEK3_uc010tgx.1_Splice_Site|NEK3_uc010tgy.1_Splice_Site_p.S183_splice NM_152720 NP_689933 P51956 NEK3_HUMAN NIMA-related kinase 3 isoform a cell division|mitosis nucleus ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173) GBM - Glioblastoma multiforme(99;2.81e-08) ATGCAGCACTCACCTTTTATTG 0.421 0.92 43 489 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.30 16 7 ZNF573 126231 broad.mit.edu 37 19 38230440 38230442 + In_Frame_Del DEL AAG - - SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr19:38230440_38230442delAAG uc002ohe.2 - 4 971_973 c.949_951delCTT c.(949-951)CTTdel p.L317del ZNF573_uc010efs.2_In_Frame_Del_p.L230del|ZNF573_uc002ohd.2_In_Frame_Del_p.L315del|ZNF573_uc002ohf.2_In_Frame_Del_p.L259del|ZNF573_uc002ohg.2_In_Frame_Del_p.L229del NM_152360 NP_689573 Q86YE8 ZN573_HUMAN zinc finger protein 573 297 C2H2-type 7. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1) 1 UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146) GATGTACAGTAAGCTGGTGACCT 0.419 0.42 7 5 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.37 48 28 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 123 527 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SH10TC_STOMACH NA SH10TC_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 24 319 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SH4_SKIN NA SH4_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 32 MPL 4352 broad.mit.edu 37 1 43804946 43804947 + Frame_Shift_Ins INS - C C SH4_SKIN NA SH4_SKIN NA g.chr1:43804946_43804947insC uc001ciw.2 + 4 441_442 c.396_397insC c.(394-399)CTGCCGfs p.L132fs MPL_uc001civ.2_Frame_Shift_Ins_p.L132fs|MPL_uc009vwr.2_Frame_Shift_Ins_p.L125fs NM_005373 NP_005364 P40238 TPOR_HUMAN myeloproliferative leukemia virus oncogene 132_133 Extracellular (Potential).|Fibronectin type-III 1. cell proliferation|platelet activation integral to plasma membrane cytokine receptor activity haematopoietic_and_lymphoid_tissue(361)|upper_aerodigestive_tract(1)|pancreas(1) 363 all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0505) CCTCAGGCCTGCCGGCTCCCCC 0.599 0.10 132 14 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes SH4_SKIN NA SH4_SKIN NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.42 22 16 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 SH4_SKIN NA SH4_SKIN NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.52 12 13 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SH4_SKIN NA SH4_SKIN NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.13 93 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SH4_SKIN NA SH4_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 113 186 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SH4_SKIN NA SH4_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 38 80 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - SH4_SKIN NA SH4_SKIN NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 1.00 0 147 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SH4_SKIN NA SH4_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 3 26 ABL1 25 broad.mit.edu 37 9 133760527 133760528 + Frame_Shift_Ins INS - C C SH4_SKIN NA SH4_SKIN NA g.chr9:133760527_133760528insC uc004bzw.2 + 11 2853_2854 c.2850_2851insC c.(2848-2853)CAGCCGfs p.Q950fs ABL1_uc004bzv.2_Frame_Shift_Ins_p.Q969fs NM_005157 NP_005148 P00519 ABL1_HUMAN c-abl oncogene 1, receptor tyrosine kinase 950_951 DNA-binding (By similarity).|Pro-rich. actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1) 817 all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204) OV - Ovarian serous cystadenocarcinoma(145;5.4e-05) Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619) AGCCCAGCCAGCCGGGAGAGGG 0.678 0.24 26 8 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SH4_SKIN NA SH4_SKIN NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.65 6 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SH4_SKIN NA SH4_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 718 291 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SH4_SKIN NA SH4_SKIN NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.15 46 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SH4_SKIN NA SH4_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 28 220 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SH4_SKIN NA SH4_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 7 157 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 3 26 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.38 8 5 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.32 17 8 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.48 13 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.67 49 99 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 15 23 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.23 31 9 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.22 32 9 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.23 30 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 26 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.14 44 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 186 99 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 61 1144 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.32 48 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 107 273 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SIMA_AUTONOMIC_GANGLIA NA SIMA_AUTONOMIC_GANGLIA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 55 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 SJSA1_BONE NA SJSA1_BONE NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.53 31 35 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SJSA1_BONE NA SJSA1_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 46 CELF3 11189 broad.mit.edu 37 1 151678722 151678723 + In_Frame_Ins INS - TGCTGCTGC TGCTGCTGC SJSA1_BONE NA SJSA1_BONE NA g.chr1:151678722_151678723insTGCTGCTGC uc001eys.1 - 10 1897_1898 c.1103_1104insGCAGCAGCA c.(1102-1104)CAA>CAGCAGCAGCAA p.368_368Q>QQQQ CELF3_uc010pdh.1_In_Frame_Ins_p.154_154Q>QQQQ|CELF3_uc001eyr.2_In_Frame_Ins_p.367_367Q>QQQQ|CELF3_uc009wmy.2_In_Frame_Ins_p.318_318Q>QQQQ|CELF3_uc009wmx.1_In_Frame_Ins_p.367_367Q>QQQQ NM_007185 NP_009116 Q5SZQ8 CELF3_HUMAN trinucleotide repeat containing 4 368 Gln-rich. nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome cytoplasm|nucleus mRNA binding|nucleotide binding ovary(1)|central_nervous_system(1) 2 gctgctgctgttgctgctgctg 0.505 0.30 48 21 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SJSA1_BONE NA SJSA1_BONE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.14 56 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SJSA1_BONE NA SJSA1_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 92 109 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SJSA1_BONE NA SJSA1_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 17 39 ATXN1 6310 broad.mit.edu 37 6 16327915 16327916 + In_Frame_Ins INS - TGC TGC rs11969612 by1000genomes SJSA1_BONE NA SJSA1_BONE NA g.chr6:16327915_16327916insTGC uc003nbt.2 - 8 1597_1598 c.626_627insGCA c.(625-627)CAT>CAGCAT p.208_209insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.208_209insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 208_209 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) gctgatgctgatgctgctgctg 0.381 0.11 62 8 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SJSA1_BONE NA SJSA1_BONE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.25 21 7 ARID1B 57492 broad.mit.edu 37 6 157099426 157099427 + In_Frame_Ins INS - CAG CAG rs78253128 SJSA1_BONE NA SJSA1_BONE NA g.chr6:157099426_157099427insCAG uc003qqn.2 + 1 341_342 c.189_190insCAG c.(187-192)insCAG p.73_74insQ ARID1B_uc003qqo.2_In_Frame_Ins_p.73_74insQ|ARID1B_uc003qqp.2_In_Frame_Ins_p.73_74insQ NM_017519 NP_059989 Q8NFD5 ARI1B_HUMAN AT rich interactive domain 1B (SWI1-like) 131_132 chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent SWI/SNF complex DNA binding|protein binding|transcription coactivator activity ovary(1)|breast(1) 2 Breast(66;0.000162)|Ovarian(120;0.0265) OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05) agcagcagcaacagcagcagca 0.193 0.30 78 33 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SJSA1_BONE NA SJSA1_BONE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SJSA1_BONE NA SJSA1_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 31 MAMDC4 158056 broad.mit.edu 37 9 139750202 139750202 + Frame_Shift_Del DEL C - - SJSA1_BONE NA SJSA1_BONE NA g.chr9:139750202delC uc004cjs.2 + 13 1540 c.1490delC c.(1489-1491)TCCfs p.S497fs MAMDC4_uc011mej.1_5'UTR NM_206920 NP_996803 Q6UXC1 AEGP_HUMAN apical early endosomal glycoprotein precursor Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment protein transport integral to membrane breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1) 7 all_cancers(76;0.0763)|all_epithelial(76;0.198) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171) 0.000 0.55 420 515 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 SJSA1_BONE NA SJSA1_BONE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 1.00 0 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SJSA1_BONE NA SJSA1_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 290 132 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes SJSA1_BONE NA SJSA1_BONE NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.17 33 7 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SJSA1_BONE NA SJSA1_BONE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.30 45 19 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SJSA1_BONE NA SJSA1_BONE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.25 30 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SJSA1_BONE NA SJSA1_BONE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 11 80 TRIM37 4591 broad.mit.edu 37 17 57141768 57141769 + Splice_Site INS - A A rs147621691 SJSA1_BONE NA SJSA1_BONE NA g.chr17:57141768_57141769insA uc002iwy.3 - 10 1254 c.810_splice c.e10-1 p.S270_splice TRIM37_uc002iwz.3_Splice_Site_p.S270_splice|TRIM37_uc002ixa.3_Splice_Site_p.S148_splice|TRIM37_uc010woc.1_Splice_Site_p.S236_splice NM_001005207 NP_001005207 O94972 TRI37_HUMAN tripartite motif-containing 37 protein perinuclear region of cytoplasm|peroxisome ligase activity|protein binding|zinc ion binding lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1) 7 Medulloblastoma(34;0.0922)|all_neural(34;0.101) ACTAATTCACTAAAAAAAAAAA 0.272 0.47 8 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SJSA1_BONE NA SJSA1_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 37 117 NKX2-4 644524 broad.mit.edu 37 20 21376816 21376817 + Frame_Shift_Ins INS - G G SJSA1_BONE NA SJSA1_BONE NA g.chr20:21376816_21376817insG uc010gcz.2 - 2 807_808 c.797_798insC c.(796-798)CCGfs p.P266fs NM_033176 NP_149416 Q9H2Z4 NKX24_HUMAN NK2 homeobox 4 266 Poly-Pro. multicellular organismal development nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 gcggcggaggcggcggcgggcc 0.510 0.19 34 8 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SJSA1_BONE NA SJSA1_BONE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.23 61 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SJSA1_BONE NA SJSA1_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 55 326 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SJSA1_BONE NA SJSA1_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.86 10 63 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKBR3_BREAST NA SKBR3_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 14 GPR112 139378 broad.mit.edu 37 X 135428859 135428891 + In_Frame_Del DEL GCCTACAGCTGCTCATTCCTCAGCAACCCCTGT - - SKBR3_BREAST NA SKBR3_BREAST NA g.chrX:135428859_135428891delGCCTACAGCTGCTCATTCCTCAGCAACCCCTGT uc004ezu.1 + 6 3285_3317 c.2994_3026delGCCTACAGCTGCTCATTCCTCAGCAACCCCTGT c.(2992-3027)CAGCCTACAGCTGCTCATTCCTCAGCAACCCCTGTG>CAG p.PTAAHSSATPV999del GPR112_uc010nsb.1_In_Frame_Del_p.PTAAHSSATPV794del|GPR112_uc010nsc.1_In_Frame_Del_p.PTAAHSSATPV766del NM_153834 NP_722576 Q8IZF6 GP112_HUMAN G-protein coupled receptor 112 999_1009 Extracellular (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1) 12 Acute lymphoblastic leukemia(192;0.000127) TACCTCCACAGCCTACAGCTGCTCATTCCTCAGCAACCCCTGTGCCTGTTACT 0.515 0.30 42 18 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SKBR3_BREAST NA SKBR3_BREAST NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 46 12 YEATS2 55689 broad.mit.edu 37 3 183493744 183493746 + In_Frame_Del DEL GGA - - SKBR3_BREAST NA SKBR3_BREAST NA g.chr3:183493744_183493746delGGA uc003fly.2 + 18 2605_2607 c.2410_2412delGGA c.(2410-2412)GGAdel p.G814del YEATS2_uc003flz.2_5'UTR NM_018023 NP_060493 Q9ULM3 YETS2_HUMAN YEATS domain containing 2 814 Gly-rich. histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter Ada2/Gcn5/Ada3 transcription activator complex TBP-class protein binding ovary(3)|large_intestine(1) 4 all_cancers(143;6.55e-10)|Ovarian(172;0.0303) all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22) GAGTGGTGCCggaggaggaggag 0.236 0.55 5 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKBR3_BREAST NA SKBR3_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 58 32 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKBR3_BREAST NA SKBR3_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.18 32 7 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SKBR3_BREAST NA SKBR3_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.36 7 4 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SKBR3_BREAST NA SKBR3_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.26 365 126 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKBR3_BREAST NA SKBR3_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 170 47 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SKBR3_BREAST NA SKBR3_BREAST NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.46 13 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SKBR3_BREAST NA SKBR3_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.85 13 75 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKBR3_BREAST NA SKBR3_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 92 289 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKBR3_BREAST NA SKBR3_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 58 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKES1_BONE NA SKES1_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 43 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SKES1_BONE NA SKES1_BONE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.16 54 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKES1_BONE NA SKES1_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 128 159 CLPTM1L 81037 broad.mit.edu 37 5 1330413 1330414 + Frame_Shift_Ins INS - C C SKES1_BONE NA SKES1_BONE NA g.chr5:1330413_1330414insC uc003jch.2 - 9 1107_1108 c.1061_1062insG c.(1060-1062)GGTfs p.G354fs CLPTM1L_uc003jcg.2_Intron NM_030782 NP_110409 Q96KA5 CLP1L_HUMAN CLPTM1-like 354 Helical; (Potential). apoptosis integral to membrane breast(1)|central_nervous_system(1) 2 Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09) Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181) KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208) CGGCTCCAACACCCGCCGGGAC 0.624 0.12 110 15 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKES1_BONE NA SKES1_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.57 34 46 APC 324 broad.mit.edu 37 5 112177642 112177643 + In_Frame_Ins INS - GCT GCT SKES1_BONE NA SKES1_BONE NA g.chr5:112177642_112177643insGCT uc010jby.2 + 16 6731_6732 c.6351_6352insGCT c.(6349-6354)insGCT p.2122_2123insA APC_uc011cvt.1_In_Frame_Ins_p.2104_2105insA|APC_uc003kpz.3_In_Frame_Ins_p.2122_2123insA|APC_uc003kpy.3_In_Frame_Ins_p.2122_2123insA|APC_uc010jbz.2_In_Frame_Ins_p.1839_1840insA|APC_uc010jca.2_In_Frame_Ins_p.1422_1423insA NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 2122_2123 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.A2122_C2123insA(1)|p.?(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GTTTACATCAAGCTGCTGCTGC 0.406 0.65 42 79 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SKES1_BONE NA SKES1_BONE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.70 3 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SKES1_BONE NA SKES1_BONE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 2 24 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKES1_BONE NA SKES1_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.90 7 66 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SKES1_BONE NA SKES1_BONE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.59 9 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKES1_BONE NA SKES1_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 727 239 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SKES1_BONE NA SKES1_BONE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.50 26 26 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SKES1_BONE NA SKES1_BONE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 5 40 DNMT1 1786 broad.mit.edu 37 19 10257106 10257110 + Frame_Shift_Del DEL AGAGG - - SKES1_BONE NA SKES1_BONE NA g.chr19:10257106_10257110delAGAGG uc002mng.2 - 27 2943_2947 c.2763_2767delCCTCT c.(2761-2769)GTCCTCTACfs p.V921fs DNMT1_uc002mnf.2_5'Flank|DNMT1_uc010xlc.1_Frame_Shift_Del_p.V937fs|DNMT1_uc002mnh.2_Frame_Shift_Del_p.V816fs|DNMT1_uc010xld.1_Frame_Shift_Del_p.V921fs NM_001379 NP_001370 P26358 DNMT1_HUMAN DNA (cytosine-5-)-methyltransferase 1 isoform b 921_923 chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent nucleus DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1) 6 OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06) Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035) GCTGAGTAGTAGAGGACCCGGCTAT 0.571 0.33 64 31 PAK7 57144 broad.mit.edu 37 20 9560935 9560943 + In_Frame_Del DEL GCATGGTGG - - rs145132727 SKES1_BONE NA SKES1_BONE NA g.chr20:9560935_9560943delGCATGGTGG uc002wnl.2 - 5 1384_1392 c.839_847delCCACCATGC c.(838-849)CCCACCATGCGG>CGG p.PTM280del PAK7_uc002wnk.2_In_Frame_Del_p.PTM280del|PAK7_uc002wnj.2_In_Frame_Del_p.PTM280del|PAK7_uc010gby.1_In_Frame_Del_p.PTM280del NM_020341 NP_065074 Q9P286 PAK7_HUMAN p21-activated kinase 7 280_282 Linker. ATP binding|protein binding|protein serine/threonine kinase activity lung(11)|skin(5)|central_nervous_system(3)|ovary(2)|large_intestine(1)|stomach(1) 23 COAD - Colon adenocarcinoma(9;0.194) GACCTCTGCCGCATGGTGGGCTGAGGGCT 0.545 0.23 86 25 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKES1_BONE NA SKES1_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 84 440 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKES1_BONE NA SKES1_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 9 136 SHROOM4 57477 broad.mit.edu 37 X 50350728 50350729 + In_Frame_Ins INS - TCC TCC rs143151534 SKHEP1_LIVER NA SKHEP1_LIVER NA g.chrX:50350728_50350729insTCC uc004dpe.2 - 6 3439_3440 c.3413_3414insGGA c.(3412-3414)GAA>GAGGAA p.1138_1138E>EE SHROOM4_uc004dpd.3_RNA NM_020717 NP_065768 Q9ULL8 SHRM4_HUMAN shroom family member 4 1138 Glu-rich. actin filament organization|brain development|cell morphogenesis|cognition apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus actin filament binding upper_aerodigestive_tract(1) 1 Ovarian(276;0.236) cttcttcttcttcctcctcctc 0.223 0.69 4 9 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKHEP1_LIVER NA SKHEP1_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 3 151 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.22 181 52 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 55 40 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 156 176 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 55 105 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.25 232 79 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.31 9 4 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.67 4 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 357 49 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.50 14 14 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.10 753 82 ZNF30 90075 broad.mit.edu 37 19 35434880 35434881 + Frame_Shift_Del DEL TT - - SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr19:35434880_35434881delTT uc010edp.1 + 5 1388_1389 c.1010_1011delTT c.(1009-1011)ATTfs p.I337fs ZNF30_uc002nxf.2_Frame_Shift_Del_p.I256fs|ZNF30_uc010edq.1_Frame_Shift_Del_p.I338fs|ZNF30_uc010edr.1_Frame_Shift_Del_p.I338fs NM_194325 NP_919306 P17039 ZNF30_HUMAN zinc finger protein 30 isoform b 337 C2H2-type 8. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1)|central_nervous_system(1) 2 all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0849) GBM - Glioblastoma multiforme(1328;0.0265) CATCAGAGTATTCATACTGGTG 0.426 0.24 113 35 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.65 42 78 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.95 25 502 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKHEP1_LIVER NA SKHEP1_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 23 403 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 5 59 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.15 238 42 OBSCN 84033 broad.mit.edu 37 1 228473951 228473951 + Frame_Shift_Del DEL C - - SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr1:228473951delC uc009xez.1 + 34 9221 c.9177delC c.(9175-9177)GGCfs p.G3059fs OBSCN_uc001hsn.2_Frame_Shift_Del_p.G3059fs|OBSCN_uc001hsq.1_Frame_Shift_Del_p.G315fs NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 3059 Ig-like 30. apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) 0.000 0.97 22 702 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.54 16 19 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 19 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 135 187 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 24 46 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.80 2 8 MUC17 140453 broad.mit.edu 37 7 100674421 100674422 + Frame_Shift_Ins INS - C C SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr7:100674421_100674422insC uc003uxp.1 + 2 156_157 c.103_104insC c.(103-105)GTGfs p.V35fs MUC17_uc010lho.1_RNA NM_001040105 NP_001035194 Q685J3 MUC17_HUMAN mucin 17 precursor 35 Extracellular (Potential). extracellular region|integral to membrane|plasma membrane extracellular matrix constituent, lubricant activity ovary(14)|skin(8)|breast(3)|lung(2) 27 Lung NSC(181;0.136)|all_lung(186;0.182) 0.000 1.00 0 16 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 25 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.30 19 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 4 52 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.55 13 16 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.29 107 44 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 47 516 NF1 4763 broad.mit.edu 37 17 29562745 29562745 + Frame_Shift_Del DEL C - - SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr17:29562745delC uc002hgg.2 + 28 4158 c.3825delC c.(3823-3825)TTCfs p.F1275fs NF1_uc002hgh.2_Frame_Shift_Del_p.F1275fs|NF1_uc010csn.1_Frame_Shift_Del_p.F1135fs|NF1_uc002hgi.1_Frame_Shift_Del_p.F308fs NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 1275 Ras-GAP. actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) AGACTCTCTTCCGAGGCAACA 0.398 0.56 63 79 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.51 90 92 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.21 49 13 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKLMS1_SOFT_TISSUE NA SKLMS1_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 90 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKLU1_LUNG NA SKLU1_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 6 79 ARID1A 8289 broad.mit.edu 37 1 27099874 27099874 + Frame_Shift_Del DEL C - - SKLU1_LUNG NA SKLU1_LUNG NA g.chr1:27099874delC uc001bmv.1 + 15 4126 c.3753delC c.(3751-3753)GGCfs p.G1251fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.G1250fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.G1251fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.G868fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.G97fs|ARID1A_uc009vsm.1_5'UTR|ARID1A_uc009vsn.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1251 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CAGGGCAGGGCCCCAACGGCG 0.582 0.85 4 22 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SKLU1_LUNG NA SKLU1_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.60 4 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKLU1_LUNG NA SKLU1_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 105 94 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKLU1_LUNG NA SKLU1_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.29 48 20 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SKLU1_LUNG NA SKLU1_LUNG NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.70 36 85 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKLU1_LUNG NA SKLU1_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 2 32 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SKLU1_LUNG NA SKLU1_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 565 66 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKLU1_LUNG NA SKLU1_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 343 123 MLL2 8085 broad.mit.edu 37 12 49427265 49427266 + In_Frame_Ins INS - TGC TGC SKLU1_LUNG NA SKLU1_LUNG NA g.chr12:49427265_49427266insTGC uc001rta.3 - 39 11222_11223 c.11222_11223insGCA c.(11221-11223)CAA>CAGCAA p.3741_3741Q>QQ NM_003482 NP_003473 O14686 MLL2_HUMAN myeloid/lymphoid or mixed-lineage leukemia 2 3741 Potential.|Gln-rich. chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent histone methyltransferase complex histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2) 41 gctgctgctgttgctgctgctg 0.470 0.28 23 9 CIT 11113 broad.mit.edu 37 12 120295490 120295516 + Splice_Site DEL ATGGTGTCGGAATCTGCAAAAGATGCA - - rs139308004 byFrequency SKLU1_LUNG NA SKLU1_LUNG NA g.chr12:120295490_120295516delATGGTGTCGGAATCTGCAAAAGATGCA uc001txi.1 - 4 292 c.239_splice c.e4-1 p.Y80_splice CIT_uc001txj.1_Splice_Site_p.Y80_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAACTCAGCTATGGTGTCGGAATCTGCAAAAGATGCAAGAGTTAGCC 0.414 0.15 143 26 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SKLU1_LUNG NA SKLU1_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 18 262 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKLU1_LUNG NA SKLU1_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 222 678 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKLU1_LUNG NA SKLU1_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 60 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 1 20 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.14 344 58 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.28 106 42 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.27 35 13 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.31 49 22 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 20 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.31 527 240 TPH1 7166 broad.mit.edu 37 11 18048034 18048035 + Splice_Site INS - A A SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:18048034_18048035insA uc001mnp.2 - 6 829 c.803_splice c.e6+1 p.P268_splice TPH1_uc009yhe.2_Splice_Site NM_004179 NP_004170 P17752 TPH1_HUMAN tryptophan hydroxylase 1 aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process cytosol amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity 0 L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360) TAGAAGTACTTACGGCTCTGGG 0.337 0.81 5 21 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 142 21 AKAP6 9472 broad.mit.edu 37 14 33016139 33016139 + Frame_Shift_Del DEL A - - SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:33016139delA uc001wrq.2 + 4 2450 c.2280delA c.(2278-2280)TTAfs p.L760fs AKAP6_uc010aml.2_Frame_Shift_Del_p.L757fs NM_004274 NP_004265 Q13023 AKAP6_HUMAN A-kinase anchor protein 6 760 protein targeting calcium channel complex|nuclear membrane|sarcoplasmic reticulum protein kinase A binding|receptor binding breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1) 21 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) GBM - Glioblastoma multiforme(265;0.019) AATCAGCTTTAATTCAGAAAC 0.388 0.65 24 45 BCKDK 10295 broad.mit.edu 37 16 31122472 31122473 + Frame_Shift_Ins INS - G G SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:31122472_31122473insG uc002eaw.3 + 9 1093_1094 c.777_778insG c.(775-780)GCTGCCfs p.A259fs BCKDK_uc002eav.3_Frame_Shift_Ins_p.A259fs|BCKDK_uc010cah.2_RNA|BCKDK_uc010cai.2_Frame_Shift_Ins_p.A259fs NM_005881 NP_005872 O14874 BCKD_HUMAN branched chain ketoacid dehydrogenase kinase 259_260 Histidine kinase. branched chain family amino acid catabolic process|peptidyl-histidine phosphorylation mitochondrial alpha-ketoglutarate dehydrogenase complex [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity|ATP binding|protein binding|protein serine/threonine kinase activity|two-component sensor activity stomach(1)|breast(1) 2 GCCATGTGGCTGCCCGGTTCCC 0.624 0.20 49 12 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.60 22 33 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.24 90 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 117 454 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 93 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKMEL1_SKIN NA SKMEL1_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 3 44 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 255 100 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.42 7 5 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 119 27 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 82 93 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 24 34 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 2 37 ARHGEF10 9639 broad.mit.edu 37 8 1814725 1814726 + Frame_Shift_Ins INS - G G SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr8:1814725_1814726insG uc003wpr.2 + 6 757_758 c.579_580insG c.(577-582)CTTGCCfs p.L193fs ARHGEF10_uc003wpq.1_Frame_Shift_Ins_p.L218fs|ARHGEF10_uc003wps.2_Frame_Shift_Ins_p.L194fs|ARHGEF10_uc003wpt.2_Frame_Shift_Ins_p.L108fs|ARHGEF10_uc010lrd.1_Frame_Shift_Ins_p.L108fs|ARHGEF10_uc003wpu.2_Frame_Shift_Ins_p.L107fs NM_014629 NP_055444 O15013 ARHGA_HUMAN Rho guanine nucleotide exchange factor 10 218_219 centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis centrosome|cytosol|soluble fraction kinesin binding|Rho guanyl-nucleotide exchange factor activity large_intestine(1) 1 Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834) COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718) ACAGCGCACTTGCCCGCTGGGC 0.559 0.45 47 38 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.56 32 41 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 29 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.24 22 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 539 103 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.79 4 15 ING1 3621 broad.mit.edu 37 13 111372003 111372004 + Frame_Shift_Del DEL GC - - SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr13:111372003_111372004delGC uc001vri.2 + 2 1425_1426 c.993_994delGC c.(991-996)AAGCGCfs p.K331fs ING1_uc001vrf.2_Frame_Shift_Del_p.K144fs|ING1_uc001vrg.2_Frame_Shift_Del_p.K119fs|ING1_uc001vrh.2_Frame_Shift_Del_p.K188fs NM_005537 NP_005528 Q9UK53 ING1_HUMAN inhibitor of growth family, member 1 isoform D 331_332 cell cycle|negative regulation of cell growth|negative regulation of cell proliferation nucleus zinc ion binding ovary(1) 1 all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148) BRCA - Breast invasive adenocarcinoma(86;0.188) AGAAGAAGAAGCGCTCCAAGGC 0.624 0.41 16 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 21 171 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 61 38 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 194 653 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKMEL1_SKIN NA SKMEL1_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 93 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKMEL24_SKIN NA SKMEL24_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 6 57 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKMEL24_SKIN NA SKMEL24_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 133 107 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKMEL24_SKIN NA SKMEL24_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.52 37 40 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SKMEL24_SKIN NA SKMEL24_SKIN NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.36 21 12 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SKMEL24_SKIN NA SKMEL24_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 2 19 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKMEL24_SKIN NA SKMEL24_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 529 136 ATM 472 broad.mit.edu 37 11 108155075 108155091 + Frame_Shift_Del DEL ATTCTTGTAAATATTCT - - SKMEL24_SKIN NA SKMEL24_SKIN NA g.chr11:108155075_108155091delATTCTTGTAAATATTCT uc001pkb.1 + 26 4253_4269 c.3868_3884delATTCTTGTAAATATTCT c.(3868-3885)ATTCTTGTAAATATTCTTfs p.I1290fs ATM_uc009yxr.1_Frame_Shift_Del_p.I1290fs NM_000051 NP_000042 Q13315 ATM_HUMAN ataxia telangiectasia mutated isoform 1 1290_1295 cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence cytoplasmic membrane-bounded vesicle|nucleoplasm 1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding p.V1292_Q1331del(1) haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1) 240 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147) CTTTCCAAAGATTCTTGTAAATATTCTTCCTTATTTT 0.392 0.30 137 58 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SKMEL24_SKIN NA SKMEL24_SKIN NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.26 53 19 NFKBIA 4792 broad.mit.edu 37 14 35871662 35871663 + Frame_Shift_Ins INS - T T SKMEL24_SKIN NA SKMEL24_SKIN NA g.chr14:35871662_35871663insT uc001wtf.3 - 5 953_954 c.843_844insA c.(841-846)CCAGAGfs p.P281fs NFKBIA_uc001wte.3_Frame_Shift_Ins_p.P191fs|NFKBIA_uc001wtg.3_Frame_Shift_Ins_p.P238fs|NFKBIA_uc010amo.2_RNA NM_020529 NP_065390 P25963 IKBA_HUMAN nuclear factor of kappa light polypeptide gene 281_282 anti-apoptosis|apoptosis|cellular response to cold|cytoplasmic sequestering of NF-kappaB|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of DNA binding|negative regulation of lipid storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of NF-kappaB transcription factor activity|nerve growth factor receptor signaling pathway|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|I-kappaB/NF-kappaB complex|nucleus|plasma membrane identical protein binding|NF-kappaB binding|nuclear localization sequence binding|ubiquitin protein ligase binding breast(2) 2 Breast(36;0.0484)|Hepatocellular(127;0.158) Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891) GBM - Glioblastoma multiforme(112;0.0222) TCCTCACTCTCTGGCAGCATCT 0.559 0.44 211 169 ESR2 2100 broad.mit.edu 37 14 64735622 64735624 + In_Frame_Del DEL ATT - - SKMEL24_SKIN NA SKMEL24_SKIN NA g.chr14:64735622_64735624delATT uc001xha.1 - 4 1009_1011 c.541_543delAAT c.(541-543)AATdel p.N181del ESR2_uc001xgu.2_In_Frame_Del_p.N181del|ESR2_uc001xgv.2_In_Frame_Del_p.N181del|ESR2_uc001xgw.2_RNA|ESR2_uc001xgx.2_In_Frame_Del_p.N181del|ESR2_uc001xgy.1_In_Frame_Del_p.N181del|ESR2_uc001xgz.1_In_Frame_Del_p.N181del|ESR2_uc010aqb.1_RNA|ESR2_uc010aqc.1_In_Frame_Del_p.N181del NM_001437 NP_001428 Q92731 ESR2_HUMAN estrogen receptor beta isoform 1 181 Nuclear receptor. cell-cell signaling|negative regulation of cell growth|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor mitochondrion|nucleoplasm enzyme binding|estrogen receptor activity|receptor antagonist activity|sequence-specific DNA binding transcription factor activity|steroid binding|transcription coactivator activity|zinc ion binding central_nervous_system(2)|ovary(1) 3 all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437) Bicalutamide(DB01128)|Estradiol(DB00783)|Estramustine(DB01196)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108) AAATATAATCATTATGTCCTATA 0.429 0.45 120 99 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SKMEL24_SKIN NA SKMEL24_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 18 136 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKMEL24_SKIN NA SKMEL24_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 29 97 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKMEL24_SKIN NA SKMEL24_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 211 828 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKMEL24_SKIN NA SKMEL24_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 10 134 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKMEL28_SKIN NA SKMEL28_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.76 8 26 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.35 251 136 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.55 5 6 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.30 16 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.65 33 60 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 25 49 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 17 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.37 27 16 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 23 TSC1 7248 broad.mit.edu 37 9 135771987 135771988 + In_Frame_Ins INS - GCT GCT rs118203743 SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr9:135771987_135771988insGCT uc004cca.2 - 23 3363_3364 c.3129_3130insAGC c.(3127-3132)insAGC p.1043_1044insS TSC1_uc004ccb.3_In_Frame_Ins_p.1042_1043insS|TSC1_uc011mcq.1_In_Frame_Ins_p.992_993insS|TSC1_uc011mcr.1_In_Frame_Ins_p.236_236A>AA NM_000368 NP_000359 Q92574 TSC1_HUMAN tuberous sclerosis 1 protein isoform 1 1043_1044 activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus cell cortex|lamellipodium|membrane|TSC1-TSC2 complex chaperone binding|protein N-terminus binding p.S1043N(1)|p.?(1) lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1) 14 OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06) GTAGAAAGCTCgctgctgctgc 0.574 0.35 47 25 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 166 66 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.33 10 5 NAV3 89795 broad.mit.edu 37 12 78388627 78388630 + Frame_Shift_Del DEL CAAC - - SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr12:78388627_78388630delCAAC uc001syp.2 + 6 889_892 c.716_719delCAAC c.(715-720)GCAACCfs p.A239fs NAV3_uc001syo.2_Frame_Shift_Del_p.A239fs NM_014903 NP_055718 Q8IVL0 NAV3_HUMAN neuron navigator 3 239_240 nuclear outer membrane ATP binding|nucleoside-triphosphatase activity large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 17 AGTGGAATTGCAACCAGTCAAAAA 0.338 0.94 2 31 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.42 7 5 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.24 26 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 28 73 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKMEL28_SKIN NA SKMEL28_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 107 KIAA2022 340533 broad.mit.edu 37 X 73960934 73960934 + Frame_Shift_Del DEL T - - SKMEL2_SKIN NA SKMEL2_SKIN NA g.chrX:73960934delT uc004eby.2 - 3 4075 c.3458delA c.(3457-3459)AACfs p.N1153fs NM_001008537 NP_001008537 Q5QGS0 K2022_HUMAN hypothetical protein LOC340533 1153 base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle delta DNA polymerase complex 3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 CAGGCAAGGGTTTTTTTGGAG 0.403 0.39 120 78 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKMEL2_SKIN NA SKMEL2_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 8 73 MPL 4352 broad.mit.edu 37 1 43804953 43804953 + Frame_Shift_Del DEL C - - SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr1:43804953delC uc001ciw.2 + 4 448 c.403delC c.(403-405)CCCfs p.P135fs MPL_uc001civ.2_Frame_Shift_Del_p.P135fs|MPL_uc009vwr.2_Frame_Shift_Del_p.P128fs NM_005373 NP_005364 P40238 TPOR_HUMAN myeloproliferative leukemia virus oncogene 135 Extracellular (Potential).|Fibronectin type-III 1. cell proliferation|platelet activation integral to plasma membrane cytokine receptor activity haematopoietic_and_lymphoid_tissue(361)|upper_aerodigestive_tract(1)|pancreas(1) 363 all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0505) CCTGCCGGCTCCCCCCAGTAT 0.592 0.48 43 40 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 38 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.42 82 60 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 13 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 72 18 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.31 9 4 TBK1 29110 broad.mit.edu 37 12 64890787 64890787 + Frame_Shift_Del DEL A - - SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr12:64890787delA uc001ssc.1 + 17 1881 c.1819delA c.(1819-1821)AAAfs p.K607fs NM_013254 NP_037386 Q9UHD2 TBK1_HUMAN TANK-binding kinase 1 607 I-kappaB kinase/NF-kappaB cascade|innate immune response|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription from RNA polymerase II promoter|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|endosome membrane|plasma membrane ATP binding|phosphoprotein binding|protein serine/threonine kinase activity central_nervous_system(2)|ovary(1)|large_intestine(1)|breast(1) 5 GBM - Glioblastoma multiforme(28;0.0386) TGAATGTGTTAAAAAGTATGA 0.333 0.10 125 14 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.24 29 9 ZMYM2 7750 broad.mit.edu 37 13 20657094 20657094 + Frame_Shift_Del DEL A - - SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr13:20657094delA uc001umr.2 + 24 4040 c.3742delA c.(3742-3744)AAAfs p.K1248fs ZMYM2_uc001ums.2_Frame_Shift_Del_p.K1248fs|ZMYM2_uc001umt.2_Frame_Shift_Del_p.K1248fs|ZMYM2_uc001umv.2_Frame_Shift_Del_p.K628fs|ZMYM2_uc001umw.2_Frame_Shift_Del_p.K701fs NM_003453 NP_003444 Q9UBW7 ZMYM2_HUMAN zinc finger protein 198 1248 regulation of transcription, DNA-dependent|transcription, DNA-dependent PML body ubiquitin conjugating enzyme binding|zinc ion binding lung(3)|ovary(2)|prostate(1) 6 all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856) TAGGCATTGGAAAAAAAATCC 0.363 0.93 5 70 RCBTB2 1102 broad.mit.edu 37 13 49089459 49089460 + Frame_Shift_Ins INS - C C SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr13:49089459_49089460insC uc001vch.2 - 6 601_602 c.230_231insG c.(229-231)TGTfs p.C77fs RCBTB2_uc010tgg.1_Frame_Shift_Ins_p.C82fs|RCBTB2_uc001vci.2_Frame_Shift_Ins_p.C53fs|RCBTB2_uc010tgh.1_5'UTR|RCBTB2_uc001vcj.2_Frame_Shift_Ins_p.C81fs|RCBTB2_uc010acv.1_RNA|RCBTB2_uc010tgi.1_Frame_Shift_Ins_p.C53fs NM_001268 NP_001259 O95199 RCBT2_HUMAN regulator of chromosome condensation and BTB 77 RCC1 1. Ran guanyl-nucleotide exchange factor activity ovary(2)|lung(2)|skin(1) 5 all_cancers(8;4.86e-71)|all_epithelial(8;2.11e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;2.3e-10)|Lung NSC(96;1.07e-07)|Breast(56;1.53e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.00826)|Myeloproliferative disorder(33;0.0179)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(99;1.8e-09)|LUSC - Lung squamous cell carcinoma(3;0.116) CTAACCCCAAACAGCCACAGCA 0.421 0.13 81 12 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.16 59 11 NOTCH3 4854 broad.mit.edu 37 19 15296358 15296358 + Frame_Shift_Del DEL G - - SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr19:15296358delG uc002nan.2 - 13 2160 c.2084delC c.(2083-2085)CCGfs p.P695fs NOTCH3_uc002nao.1_Frame_Shift_Del_p.P695fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 695 Extracellular (Potential).|EGF-like 18. Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.44 690 536 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.37 31 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 103 620 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKMEL2_SKIN NA SKMEL2_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 17 179 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKMEL30_SKIN NA SKMEL30_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 3 32 TPR 7175 broad.mit.edu 37 1 186292981 186292983 + In_Frame_Del DEL GCA - - SKMEL30_SKIN NA SKMEL30_SKIN NA g.chr1:186292981_186292983delGCA uc001grv.2 - 43 6429_6431 c.6132_6134delTGC c.(6130-6135)GCTGCA>GCA p.2044_2045AA>A NM_003292 NP_003283 P12270 TPR_HUMAN nuclear pore complex-associated protein TPR 2044_2045 carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm ATP binding|protein binding|serine-tRNA ligase activity ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1) 7 Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157) Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553) AGAAGATTCTGCAGCACCTGTAT 0.424 0.34 86 44 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SKMEL30_SKIN NA SKMEL30_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.35 17 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKMEL30_SKIN NA SKMEL30_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 63 43 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKMEL30_SKIN NA SKMEL30_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 5 13 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SKMEL30_SKIN NA SKMEL30_SKIN NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.38 126 76 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKMEL30_SKIN NA SKMEL30_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 1 11 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SKMEL30_SKIN NA SKMEL30_SKIN NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.55 9 11 RPS6KB2 6199 broad.mit.edu 37 11 67200907 67200908 + Frame_Shift_Ins INS - T T SKMEL30_SKIN NA SKMEL30_SKIN NA g.chr11:67200907_67200908insT uc001old.2 + 10 977_978 c.895_896insT c.(895-897)CTTfs p.L299fs RPS6KB2_uc001olf.2_Frame_Shift_Ins_p.L99fs|RPS6KB2_uc001olg.2_Frame_Shift_Ins_p.L299fs|RPS6KB2_uc009yrq.2_Frame_Shift_Ins_p.L99fs|RPS6KB2_uc001ole.2_RNA|RPS6KB2_uc001olh.2_Intron|RPS6KB2_uc009yrr.2_Frame_Shift_Ins_p.L130fs NM_003952 NP_003943 Q9UBS0 KS6B2_HUMAN ribosomal protein S6 kinase, 70kDa, polypeptide 299 Protein kinase. nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of translational initiation|translation nucleoplasm ATP binding|protein serine/threonine kinase activity ovary(2)|central_nervous_system(2)|stomach(1)|lung(1)|salivary_gland(1) 7 BRCA - Breast invasive adenocarcinoma(15;3.26e-06) TGCCCGGGACCTTGTCAAAAAG 0.614 0.12 141 20 RABEP1 9135 broad.mit.edu 37 17 5257686 5257703 + In_Frame_Del DEL AAAGGATCACAAAAAAGC - - SKMEL30_SKIN NA SKMEL30_SKIN NA g.chr17:5257686_5257703delAAAGGATCACAAAAAAGC uc002gbm.3 + 8 1220_1237 c.996_1013delAAAGGATCACAAAAAAGC c.(994-1014)AGAAAGGATCACAAAAAAGCA>AGA p.KDHKKA333del RABEP1_uc010clc.1_In_Frame_Del_p.KDHKKA326del|RABEP1_uc010cld.1_In_Frame_Del_p.KDHKKA290del|RABEP1_uc010vsw.1_In_Frame_Del_p.KDHKKA290del|RABEP1_uc002gbl.3_In_Frame_Del_p.KDHKKA333del NM_004703 NP_004694 Q15276 RABE1_HUMAN rabaptin, RAB GTPase binding effector protein 1 333_338 Potential. apoptosis|cellular membrane fusion|endocytosis|protein transport centrosome|early endosome|endocytic vesicle|recycling endosome growth factor activity|GTPase activator activity|protein homodimerization activity large_intestine(1)|ovary(1) 2 TCAATAAGAGAAAGGATCACAAAAAAGCAGATGTTGAG 0.330 0.21 26 7 TP53 7157 broad.mit.edu 37 17 7577086 7577087 + Frame_Shift_Del DEL TG - - SKMEL30_SKIN NA SKMEL30_SKIN NA g.chr17:7577086_7577087delTG uc002gim.2 - 8 1045_1046 c.851_852delCA c.(850-852)ACAfs p.T284fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Frame_Shift_Del_p.T284fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.T152fs|TP53_uc010cng.1_Frame_Shift_Del_p.T152fs|TP53_uc002gii.1_Frame_Shift_Del_p.T152fs|TP53_uc010cnh.1_Frame_Shift_Del_p.T284fs|TP53_uc010cni.1_Frame_Shift_Del_p.T284fs|TP53_uc002gij.2_Frame_Shift_Del_p.T284fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 284 |Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). T -> A (in sporadic cancers; somatic mutation).|T -> K (in sporadic cancers; somatic mutation).|T -> P (in sporadic cancers; somatic mutation).|T -> I (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.T284P(7)|p.0?(7)|p.T284fs*61(3)|p.T284A(3)|p.T284T(3)|p.T284fs*21(2)|p.T284fs*62(2)|p.?(2)|p.R283fs*16(2)|p.R282_E287delRRTEEE(1)|p.T284_G293del10(1)|p.G279fs*59(1)|p.S269fs*21(1)|p.R283fs*59(1)|p.T284I(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.R283fs*56(1)|p.R283_T284>T(1)|p.V272_K292del21(1)|p.C275fs*20(1)|p.E285_L289delEEENL(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) TCTCTTCCTCTGTGCGCCGGTC 0.564 0.70 8 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKMEL30_SKIN NA SKMEL30_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 153 335 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKMEL30_SKIN NA SKMEL30_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 85 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 4 68 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.57 20 26 HTT 3064 broad.mit.edu 37 4 3076604 3076606 + In_Frame_Del DEL CAG - - rs10618869 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr4:3076604_3076606delCAG uc011bvq.1 + 2 203_205 c.58_60delCAG c.(58-60)CAGdel p.Q40del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagc 0.335 0.20 60 15 HTT 3064 broad.mit.edu 37 4 3076672 3076673 + In_Frame_Ins INS - CCGCCG CCGCCG rs76533208 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr4:3076672_3076673insCCGCCG uc011bvq.1 + 2 271_272 c.126_127insCCGCCG c.(124-129)insCCGCCG p.50_51insPP NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 48_49 Poly-Pro. establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) aacagccgccaccgccgccgcc 0.084 0.19 57 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.73 72 195 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 38 113 ATXN1 6310 broad.mit.edu 37 6 16327907 16327909 + In_Frame_Del DEL TGA - - rs59310777 by1000genomes SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr6:16327907_16327909delTGA uc003nbt.2 - 8 1604_1606 c.633_635delTCA c.(631-636)CATCAG>CAG p.H211del ATXN1_uc010jpi.2_In_Frame_Del_p.H211del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 211 Poly-Gln. H -> HQ (in Ref. 1; CAA55793). cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgctgctgctgatgctgatgct 0.384 0.11 185 22 POU3F2 5454 broad.mit.edu 37 6 99283172 99283173 + In_Frame_Ins INS - CAG CAG SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr6:99283172_99283173insCAG uc003ppe.2 + 1 593_594 c.423_424insCAG c.(421-426)insCAG p.149_150insQ NM_005604 NP_005595 P20265 PO3F2_HUMAN POU domain, class 3, transcription factor 2 149_150 positive regulation of cell proliferation identical protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197) BRCA - Breast invasive adenocarcinoma(108;0.0355) aacagcagcaacagcagcagca 0.465 0.15 121 22 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.10 292 34 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 4 35 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.70 3 7 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.25 65 22 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 43 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.49 515 495 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.68 19 40 MEF2A 4205 broad.mit.edu 37 15 100252745 100252746 + In_Frame_Ins INS - CCGCCA CCGCCA SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr15:100252745_100252746insCCGCCA uc010urw.1 + 11 1652_1653 c.1293_1294insCCGCCA c.(1291-1296)insCCGCCA p.435_436insPP MEF2A_uc010urv.1_In_Frame_Ins_p.365_366insPP|MEF2A_uc010bos.2_In_Frame_Ins_p.425_426insPP|MEF2A_uc002bvf.2_In_Frame_Ins_p.427_428insPP|MEF2A_uc002bve.2_In_Frame_Ins_p.433_434insPP|MEF2A_uc002bvg.2_In_Frame_Ins_p.425_426insPP|MEF2A_uc002bvi.2_In_Frame_Ins_p.425_426insPP|MEF2A_uc010bot.2_In_Frame_Ins_p.357_358insPP NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 435_436 Gln/Pro-rich. apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) agcagcagcCGCCGCCACCACC 0.520 0.41 17 12 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 26 288 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.77 29 95 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.13 208 32 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 126 453 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKMEL31_SKIN NA SKMEL31_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 6 113 SHROOM4 57477 broad.mit.edu 37 X 50350758 50350759 + In_Frame_Ins INS - TGCTGCTGCTGT TGCTGCTGCTGT SKMEL5_SKIN NA SKMEL5_SKIN NA g.chrX:50350758_50350759insTGCTGCTGCTGT uc004dpe.2 - 6 3409_3410 c.3383_3384insACAGCAGCAGCA c.(3382-3384)CAG>CAACAGCAGCAGCAG p.1128_1128Q>QQQQQ SHROOM4_uc004dpd.3_RNA NM_020717 NP_065768 Q9ULL8 SHRM4_HUMAN shroom family member 4 1128 Gln-rich. actin filament organization|brain development|cell morphogenesis|cognition apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus actin filament binding upper_aerodigestive_tract(1) 1 Ovarian(276;0.236) cctgttgcttctgctgctgctg 0.252 0.31 11 5 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKMEL5_SKIN NA SKMEL5_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 7 143 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.14 129 21 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 287 60 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 116 30 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 141 246 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.37 91 53 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.68 61 129 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.38 50 30 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 26 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 57 FNBP1 23048 broad.mit.edu 37 9 132686262 132686282 + In_Frame_Del DEL GGGGGAGGGGGAGGCTGATGG - - SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr9:132686262_132686282delGGGGGAGGGGGAGGCTGATGG uc004byw.1 - 10 1230_1250 c.1011_1031delCCATCAGCCTCCCCCTCCCCC c.(1009-1032)CCCCATCAGCCTCCCCCTCCCCCT>CCT p.337_344PHQPPPPP>P FNBP1_uc011mbv.1_Splice_Site_p.P330_splice|FNBP1_uc011mbw.1_In_Frame_Del_p.337_344PHQPPPPP>P|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc004byx.1_In_Frame_Del_p.258_265PHQPPPPP>P|FNBP1_uc004byy.1_Splice_Site_p.P251_splice NM_015033 NP_055848 Q96RU3 FNBP1_HUMAN formin binding protein 1 337_344 Required for self-association and induction of membrane tubulation.|Poly-Pro. endocytosis cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane identical protein binding|lipid binding 0 Ovarian(14;0.000536) GBM - Glioblastoma multiforme(294;0.0378) agaggcaggagggggagggggaggctgatggggggATGTTA 0.353 0.38 70 42 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 265 132 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 9 55 TRIM37 4591 broad.mit.edu 37 17 57141768 57141769 + Splice_Site INS - A A rs147621691 SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr17:57141768_57141769insA uc002iwy.3 - 10 1254 c.810_splice c.e10-1 p.S270_splice TRIM37_uc002iwz.3_Splice_Site_p.S270_splice|TRIM37_uc002ixa.3_Splice_Site_p.S148_splice|TRIM37_uc010woc.1_Splice_Site_p.S236_splice NM_001005207 NP_001005207 O94972 TRI37_HUMAN tripartite motif-containing 37 protein perinuclear region of cytoplasm|peroxisome ligase activity|protein binding|zinc ion binding lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1) 7 Medulloblastoma(34;0.0922)|all_neural(34;0.101) ACTAATTCACTAAAAAAAAAAA 0.272 0.19 126 30 SMARCA4 6597 broad.mit.edu 37 19 11136172 11136172 + Frame_Shift_Del DEL C - - SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr19:11136172delC uc002mqf.3 + 22 3440 c.3156delC c.(3154-3156)TTCfs p.F1052fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.F1052fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.F1052fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.F1052fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.F1052fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.F1052fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.F1052fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.F1052fs|SMARCA4_uc010dxt.1_Frame_Shift_Del_p.F272fs|SMARCA4_uc002mqh.3_Frame_Shift_Del_p.F175fs|SMARCA4_uc002mqi.1_Frame_Shift_Del_p.F255fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 1052 chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) 0.000 0.42 387 284 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 33 128 LMTK3 114783 broad.mit.edu 37 19 49012148 49012148 + Frame_Shift_Del DEL G - - SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr19:49012148delG uc002pjk.2 - 6 604 c.604delC c.(604-606)CTGfs p.L202fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) CGTTGCTCCAGGGGCCCCGCG 0.577 0.61 103 159 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.41 23 16 PTPRT 11122 broad.mit.edu 37 20 40739124 40739125 + Frame_Shift_Ins INS - T T SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr20:40739124_40739125insT uc002xkg.2 - 23 3286_3287 c.3102_3103insA c.(3100-3105)AAAGGCfs p.K1034fs PTPRT_uc010ggj.2_Frame_Shift_Ins_p.K1053fs|PTPRT_uc010ggi.2_Frame_Shift_Ins_p.K237fs NM_007050 NP_008981 O14522 PTPRT_HUMAN protein tyrosine phosphatase, receptor type, T 1034_1035 Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential). homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway cell surface|integral to membrane|plasma membrane alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity skin(8)|ovary(7)|lung(5) 20 Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783) TCATGGTAGCCTTTCTGAGGAA 0.619 0.38 23 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 37 319 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKMEL5_SKIN NA SKMEL5_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 22 461 HTT 3064 broad.mit.edu 37 4 3076604 3076606 + In_Frame_Del DEL CAG - - rs10618869 SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr4:3076604_3076606delCAG uc011bvq.1 + 2 203_205 c.58_60delCAG c.(58-60)CAGdel p.Q40del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagc 0.335 0.10 137 16 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 57 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.75 97 288 NKD2 85409 broad.mit.edu 37 5 1038446 1038447 + In_Frame_Ins INS - CACCAC CACCAC rs3840989 SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr5:1038446_1038447insCACCAC uc003jbt.1 + 10 1319_1320 c.1314_1315insCACCAC c.(1312-1317)insCACCAC p.446_447insHH NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 446_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.31 194 88 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.48 67 63 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.33 12 6 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.28 97 37 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.11 253 31 PMS2CL 441194 broad.mit.edu 37 7 6776798 6776800 + In_Frame_Del DEL AAG - - SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr7:6776798_6776800delAAG uc011jxb.1 + 5 852_854 c.78_80delAAG c.(76-81)AAAAGG>AAG p.R27del PMS2CL_uc003squ.2_RNA|PMS2CL_uc003sqv.1_RNA SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2; 0 GAGAAGAAAAAAGGGACGTGTCC 0.458 0.43 213 161 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 21 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.49 601 587 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.41 10 7 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.15 191 35 SALL1 6299 broad.mit.edu 37 16 51175655 51175656 + In_Frame_Ins INS - GCT GCT rs113614842 SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr16:51175655_51175656insGCT uc010vgs.1 - 2 508_509 c.477_478insAGC c.(475-480)insAGC p.159_160insS SALL1_uc010vgr.1_In_Frame_Ins_p.62_63insS|SALL1_uc010cbv.2_Intron NM_002968 NP_002959 Q9NSC2 SALL1_HUMAN sal-like 1 isoform a 159_160 Poly-Gly. adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development chromocenter|cytoplasm|heterochromatin|nucleus beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding skin(5)|ovary(3) 8 all_cancers(37;0.0322) COAD - Colon adenocarcinoma(2;0.24) ccgccgccgccgctgctgctgc 0.460 0.31 18 8 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 23 266 NF1 4763 broad.mit.edu 37 17 29552254 29552267 + Frame_Shift_Del DEL GGGAACTCCTCTAT - - rs140653372;rs145891889 byFrequency;byFrequency SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr17:29552254_29552267delGGGAACTCCTCTAT uc002hgg.2 + 17 2320_2333 c.1987_2000delGGGAACTCCTCTAT c.(1987-2001)GGGAACTCCTCTATGfs p.G663fs NF1_uc002hgh.2_Frame_Shift_Del_p.G663fs|NF1_uc010csn.1_Frame_Shift_Del_p.G523fs|NF1_uc002hgi.1_5'UTR NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 663_667 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) GAAGGGAAAAGGGAACTCCTCTATGGTCAGCTTC 0.379 0.70 31 72 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.46 100 84 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 68 391 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKNBE2_AUTONOMIC_GANGLIA NA SKNBE2_AUTONOMIC_GANGLIA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 123 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 1 13 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.15 129 23 LRP1B 53353 broad.mit.edu 37 2 141625834 141625835 + Splice_Site INS - A A SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr2:141625834_141625835insA uc002tvj.1 - 26 5142 c.4170_splice c.e26-1 p.G1390_splice LRP1B_uc010fnl.1_Splice_Site_p.G572_splice NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) AAAAGAATTCTaaaaaaaaaaa 0.223 0.28 18 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 35 43 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.50 14 14 ATXN1 6310 broad.mit.edu 37 6 16327916 16327918 + In_Frame_Del DEL TGC - - rs28555263 SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr6:16327916_16327918delTGC uc003nbt.2 - 8 1595_1597 c.624_626delGCA c.(622-627)CAGCAT>CAT p.Q208del ATXN1_uc010jpi.2_In_Frame_Del_p.Q208del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 208 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgatgctgatgctgctgctgct 0.379 0.42 7 5 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 NUMA1 4926 broad.mit.edu 37 11 71723446 71723448 + Splice_Site DEL CCT - - SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr11:71723446_71723448delCCT uc001orl.1 - 16 4822 c.4650_splice c.e16+1 p.Q1550_splice NUMA1_uc009ysw.1_Intron|NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Intron|NUMA1_uc001orn.2_Splice_Site_p.Q1113_splice NM_006185 NP_006176 Q14980 NUMA1_HUMAN nuclear mitotic apparatus protein 1 G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole protein binding|structural molecule activity ovary(3)|lung(2)|skin(2)|central_nervous_system(1) 8 TCAGGCATTACCTGCTTAGTTTG 0.552 0.38 63 39 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 242 43 SIK2 23235 broad.mit.edu 37 11 111590625 111590651 + In_Frame_Del DEL GACCCCGCTCATGCCTTTGAGGCATTT - - SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr11:111590625_111590651delGACCCCGCTCATGCCTTTGAGGCATTT uc001plt.2 + 10 1511_1537 c.1393_1419delGACCCCGCTCATGCCTTTGAGGCATTT c.(1393-1419)GACCCCGCTCATGCCTTTGAGGCATTTdel p.DPAHAFEAF465del NM_015191 NP_056006 Q9H0K1 SIK2_HUMAN SNF1-like kinase 2 465_473 intracellular protein kinase cascade|regulation of insulin receptor signaling pathway Golgi apparatus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|skin(1) 3 GGCCGAGGAAGACCCCGCTCATGCCTTTGAGGCATTTCAGTCCACAC 0.595 0.38 8 5 PIK3C2G 5288 broad.mit.edu 37 12 18747475 18747478 + Frame_Shift_Del DEL AGTT - - SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr12:18747475_18747478delAGTT uc001rdt.2 + 29 4052_4055 c.3936_3939delAGTT c.(3934-3939)ACAGTTfs p.T1312fs PIK3C2G_uc010sia.1_RNA|PIK3C2G_uc010sib.1_Frame_Shift_Del_p.T1353fs|PIK3C2G_uc010sic.1_Frame_Shift_Del_p.T1131fs NM_004570 NP_004561 O75747 P3C2G_HUMAN phosphoinositide-3-kinase, class 2 gamma 1312_1313 cell communication|phosphatidylinositol-mediated signaling membrane|phosphatidylinositol 3-kinase complex 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2) 21 Hepatocellular(102;0.194) TGCAACAAACAGTTGAAGAATCAT 0.294 0.29 71 29 RB1 5925 broad.mit.edu 37 13 48878076 48878084 + In_Frame_Del DEL GCCGCCACC - - SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr13:48878076_48878084delGCCGCCACC uc001vcb.2 + 1 194_202 c.28_36delGCCGCCACC c.(28-36)GCCGCCACCdel p.AAT10del RB1_uc010acs.1_RNA|uc001vca.2_5'Flank NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 10_12 Poly-Ala. androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.0?(13)|p.?(1) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) 0.000 0.17 436 89 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 52 546 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.78 5 18 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.26 23 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.53 265 304 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKNDZ_AUTONOMIC_GANGLIA NA SKNDZ_AUTONOMIC_GANGLIA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 35 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.46 32 27 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 28 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.30 130 56 SATB1 6304 broad.mit.edu 37 3 18391132 18391133 + In_Frame_Ins INS - CTG CTG SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr3:18391132_18391133insCTG uc003cbh.2 - 11 3556_3557 c.1821_1822insCAG c.(1819-1824)insCAG p.607_608insQ SATB1_uc003cbi.2_In_Frame_Ins_p.639_640insQ|SATB1_uc003cbj.2_In_Frame_Ins_p.607_608insQ NM_002971 NP_002962 Q01826 SATB1_HUMAN special AT-rich sequence binding protein 1 607_608 cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter nuclear matrix|PML body double-stranded DNA binding|sequence-specific DNA binding skin(2)|ovary(1)|lung(1) 4 GGCGGCGGTGCctgctgctgct 0.465 0.40 6 4 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.33 8 4 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 46 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 95 154 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.56 14 18 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 27 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 56 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.29 22 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 615 125 ZNF384 171017 broad.mit.edu 37 12 6777070 6777081 + In_Frame_Del DEL TGCTGCTGCTGC - - rs151322806;rs111332695;rs78573212;rs1052680;rs149757410;rs72393318 SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr12:6777070_6777081delTGCTGCTGCTGC uc010sfh.1 - 11 1741_1752 c.1533_1544delGCAGCAGCAGCA c.(1531-1545)CAGCAGCAGCAGCAA>CAA p.511_515QQQQQ>Q ZNF384_uc001qpz.2_In_Frame_Del_p.450_454QQQQQ>Q|ZNF384_uc001qqa.2_In_Frame_Del_p.450_454QQQQQ>Q|ZNF384_uc001qqb.2_In_Frame_Del_p.434_438QQQQQ>Q|ZNF384_uc001qqc.2_In_Frame_Del_p.450_454QQQQQ>Q|ZNF384_uc001qqd.2_In_Frame_Del_p.395_399QQQQQ>Q|ZNF384_uc001qqe.2_In_Frame_Del_p.434_438QQQQQ>Q NM_001135734 NP_001129206 Q8TF68 ZN384_HUMAN nuclear matrix transcription factor 4 isoform d 511_515 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding EWSR1/ZNF384(4) haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1) 8 TGGTGgctgttgctgctgctgctgctgctgct 0.325 0.22 301 85 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.17 110 23 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 38 284 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.49 62 59 NCOA3 8202 broad.mit.edu 37 20 46279860 46279861 + In_Frame_Ins INS - CAA CAA rs151060280 byFrequency SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr20:46279860_46279861insCAA uc002xtk.2 + 20 3991_3992 c.3786_3787insCAA c.(3784-3789)insCAA p.1276_1277insQ NCOA3_uc010ght.1_In_Frame_Ins_p.1267_1268insQ|NCOA3_uc002xtl.2_In_Frame_Ins_p.1272_1273insQ|NCOA3_uc002xtm.2_In_Frame_Ins_p.1271_1272insQ|NCOA3_uc002xtn.2_In_Frame_Ins_p.1275_1276insQ|NCOA3_uc010zyc.1_In_Frame_Ins_p.1071_1072insQ NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 1276_1277 Poly-Gln.|Acetyltransferase. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 agcagcagcagcagcaacagca 0.307 0.43 155 116 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 129 577 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKNFI_AUTONOMIC_GANGLIA NA SKNFI_AUTONOMIC_GANGLIA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 3 94 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 SKNMC_BONE NA SKNMC_BONE NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.15 102 18 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKNMC_BONE NA SKNMC_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 62 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SKNMC_BONE NA SKNMC_BONE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 304 91 LRP1B 53353 broad.mit.edu 37 2 141986749 141986750 + Splice_Site INS - A A SKNMC_BONE NA SKNMC_BONE NA g.chr2:141986749_141986750insA uc002tvj.1 - 6 1822 c.850_splice c.e6+1 p.N284_splice LRP1B_uc010fnl.1_Intron NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) TTGAAACACTTACTGTGGAAGG 0.351 0.34 23 12 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 SKNMC_BONE NA SKNMC_BONE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.22 29 8 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SKNMC_BONE NA SKNMC_BONE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.18 45 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKNMC_BONE NA SKNMC_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 150 207 POU3F2 5454 broad.mit.edu 37 6 99283172 99283173 + In_Frame_Ins INS - CAG CAG SKNMC_BONE NA SKNMC_BONE NA g.chr6:99283172_99283173insCAG uc003ppe.2 + 1 593_594 c.423_424insCAG c.(421-426)insCAG p.149_150insQ NM_005604 NP_005595 P20265 PO3F2_HUMAN POU domain, class 3, transcription factor 2 149_150 positive regulation of cell proliferation identical protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197) BRCA - Breast invasive adenocarcinoma(108;0.0355) aacagcagcaacagcagcagca 0.465 0.22 141 39 UBR5 51366 broad.mit.edu 37 8 103297367 103297375 + In_Frame_Del DEL AGTGTTCGT - - SKNMC_BONE NA SKNMC_BONE NA g.chr8:103297367_103297375delAGTGTTCGT uc003ykr.1 - 40 5709_5717 c.5676_5684delACGAACACT c.(5674-5685)TTACGAACACTT>TTT p.1892_1895LRTL>F UBR5_uc003yks.1_In_Frame_Del_p.1892_1895LRTL>F NM_015902 NP_056986 O95071 UBR5_HUMAN ubiquitin protein ligase E3 component n-recognin 1892_1895 cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus nucleus|soluble fraction protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1) 28 all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05) OV - Ovarian serous cystadenocarcinoma(57;0.000442) TCTGCCTTCAAGTGTTCGTAAGCTAGCTT 0.354 0.39 124 78 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKNMC_BONE NA SKNMC_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 69 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SKNMC_BONE NA SKNMC_BONE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.36 463 262 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKNMC_BONE NA SKNMC_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 971 172 DAPK2 23604 broad.mit.edu 37 15 64275868 64275868 + Frame_Shift_Del DEL G - - rs56047843 SKNMC_BONE NA SKNMC_BONE NA g.chr15:64275868delG uc002amr.2 - 3 209 c.178delC c.(178-180)CGGfs p.R60fs DAPK2_uc010uim.1_RNA|DAPK2_uc010bgu.1_Frame_Shift_Del_p.R50fs NM_014326 NP_055141 Q9UIK4 DAPK2_HUMAN death-associated kinase 2 60 Protein kinase. apoptosis|induction of apoptosis|intracellular protein kinase cascade cytoplasm ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|identical protein binding stomach(1)|central_nervous_system(1) 2 LUAD - Lung adenocarcinoma(2;0.215) CGGCTCGCCCGGCTCTGCCGC 0.622 0.39 204 131 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes SKNMC_BONE NA SKNMC_BONE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.29 34 14 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKNMC_BONE NA SKNMC_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.41 119 82 LMTK3 114783 broad.mit.edu 37 19 49001791 49001792 + Frame_Shift_Ins INS - G G SKNMC_BONE NA SKNMC_BONE NA g.chr19:49001791_49001792insG uc002pjk.2 - 12 2621_2622 c.2621_2622insC c.(2620-2622)CCGfs p.P874fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) CCCGGGGCCCCGGGAGTGGGAG 0.718 0.13 92 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKNMC_BONE NA SKNMC_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.53 224 252 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKNMC_BONE NA SKNMC_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 7 128 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKNSH_AUTONOMIC_GANGLIA NA SKNSH_AUTONOMIC_GANGLIA NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 26 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SKNSH_AUTONOMIC_GANGLIA NA SKNSH_AUTONOMIC_GANGLIA NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 188 50 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SKNSH_AUTONOMIC_GANGLIA NA SKNSH_AUTONOMIC_GANGLIA NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 55 11 PHOX2B 8929 broad.mit.edu 37 4 41748048 41748049 + Frame_Shift_Ins INS - G G SKNSH_AUTONOMIC_GANGLIA NA SKNSH_AUTONOMIC_GANGLIA NA g.chr4:41748048_41748049insG uc003gwf.3 - 3 1080_1081 c.720_721insC c.(718-723)GGCGCAfs p.G240fs NM_003924 NP_003915 Q99453 PHX2B_HUMAN paired-like homeobox 2b 240_241 Poly-Ala. A -> AAAAAAAAAAA (in CCHS). positive regulation of transcription from RNA polymerase II promoter nuclear chromatin RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity p.A241fs*69(3)|p.A241fs*64(1) autonomic_ganglia(7)|lung(2)|ovary(2)|central_nervous_system(1) 12 0.000 0.34 335 171 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKNSH_AUTONOMIC_GANGLIA NA SKNSH_AUTONOMIC_GANGLIA NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 49 64 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SKNSH_AUTONOMIC_GANGLIA NA SKNSH_AUTONOMIC_GANGLIA NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKNSH_AUTONOMIC_GANGLIA NA SKNSH_AUTONOMIC_GANGLIA NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 186 75 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SKNSH_AUTONOMIC_GANGLIA NA SKNSH_AUTONOMIC_GANGLIA NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.56 7 9 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SKNSH_AUTONOMIC_GANGLIA NA SKNSH_AUTONOMIC_GANGLIA NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 21 307 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKNSH_AUTONOMIC_GANGLIA NA SKNSH_AUTONOMIC_GANGLIA NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.66 16 31 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKNSH_AUTONOMIC_GANGLIA NA SKNSH_AUTONOMIC_GANGLIA NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 466 1084 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKNSH_AUTONOMIC_GANGLIA NA SKNSH_AUTONOMIC_GANGLIA NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 32 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKOV3_OVARY NA SKOV3_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.79 43 160 NOTCH2 4853 broad.mit.edu 37 1 120466308 120466309 + Frame_Shift_Del DEL CT - - SKOV3_OVARY NA SKOV3_OVARY NA g.chr1:120466308_120466309delCT uc001eik.2 - 26 5066_5067 c.4810_4811delAG c.(4810-4812)AGGfs p.R1604fs NM_024408 NP_077719 Q04721 NOTC2_HUMAN notch 2 preproprotein 1604 Negative regulatory region (NRR).|Extracellular (Potential). anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1) 27 all_neural(166;0.153) all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809) Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133) GCGTGTCATCCTCTGTTTCTTC 0.500 0.47 135 118 RNASEL 6041 broad.mit.edu 37 1 182554909 182554909 + Frame_Shift_Del DEL C - - SKOV3_OVARY NA SKOV3_OVARY NA g.chr1:182554909delC uc001gpj.1 - 1 1200 c.1033delG c.(1033-1035)GCAfs p.A345fs RNASEL_uc009wxz.1_Frame_Shift_Del_p.A345fs|RNASEL_uc001gpk.2_Frame_Shift_Del_p.A345fs|RNASEL_uc009wya.1_Frame_Shift_Del_p.A345fs NM_021133 NP_066956 Q05823 RN5A_HUMAN ribonuclease L 345 mRNA processing|response to virus|type I interferon-mediated signaling pathway mitochondrion ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding ovary(4)|stomach(1) 5 TTCAGGGCTGCCCCCCAGTGT 0.453 0.22 117 33 TRIB2 28951 broad.mit.edu 37 2 12863620 12863620 + Frame_Shift_Del DEL G - - SKOV3_OVARY NA SKOV3_OVARY NA g.chr2:12863620delG uc002rbv.3 + 2 1941 c.505delG c.(505-507)GGGfs p.G169fs TRIB2_uc010yjp.1_Frame_Shift_Del_p.G33fs NM_021643 NP_067675 Q92519 TRIB2_HUMAN tribbles homolog 2 169 Protein kinase. negative regulation of fat cell differentiation|negative regulation of interleukin-10 biosynthetic process|negative regulation of protein kinase activity|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|regulation of MAP kinase activity cytoplasm|cytoskeleton|nucleus ATP binding|protein kinase activity|protein kinase inhibitor activity|transcription factor binding|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity stomach(1) 1 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) CTGCCATGACGGGGGGCTGGT 0.577 0.57 80 107 SMARCC1 6599 broad.mit.edu 37 3 47676782 47676785 + Frame_Shift_Del DEL TCTT - - SKOV3_OVARY NA SKOV3_OVARY NA g.chr3:47676782_47676785delTCTT uc003crq.2 - 24 2659_2662 c.2541_2544delAAGA c.(2539-2544)GAAAGAfs p.E847fs SMARCC1_uc011bbc.1_RNA|SMARCC1_uc011bbd.1_Frame_Shift_Del_p.E738fs NM_003074 NP_003065 Q92922 SMRC1_HUMAN SWI/SNF-related matrix-associated 847_848 Glu-rich. chromatin remodeling|nervous system development|transcription, DNA-dependent nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex DNA binding|protein N-terminus binding|transcription coactivator activity skin(2)|lung(1) 3 BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01) 0.000 0.59 226 331 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SKOV3_OVARY NA SKOV3_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.15 45 8 CCKAR 886 broad.mit.edu 37 4 26483342 26483343 + Frame_Shift_Ins INS - C C SKOV3_OVARY NA SKOV3_OVARY NA g.chr4:26483342_26483343insC uc003gse.1 - 5 1357_1358 c.1204_1205insG c.(1204-1206)GAGfs p.E402fs NM_000730 NP_000721 P32238 CCKAR_HUMAN cholecystokinin A receptor 402 Cytoplasmic (Potential). activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|elevation of cytosolic calcium ion concentration|response to nutrient integral to plasma membrane cholecystokinin receptor activity lung(3)|pancreas(1) 4 Breast(46;0.0503) Ceruletide(DB00403) 0.000 0.14 481 76 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SKOV3_OVARY NA SKOV3_OVARY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.54 62 74 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKOV3_OVARY NA SKOV3_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.37 174 103 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKOV3_OVARY NA SKOV3_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 70 187 APC 324 broad.mit.edu 37 5 112175952 112175952 + Frame_Shift_Del DEL A - - SKOV3_OVARY NA SKOV3_OVARY NA g.chr5:112175952delA uc010jby.2 + 16 5041 c.4661delA c.(4660-4662)GAAfs p.E1554fs APC_uc011cvt.1_Frame_Shift_Del_p.E1536fs|APC_uc003kpz.3_Frame_Shift_Del_p.E1554fs|APC_uc003kpy.3_Frame_Shift_Del_p.E1554fs|APC_uc010jbz.2_Frame_Shift_Del_p.E1271fs|APC_uc010jca.2_Frame_Shift_Del_p.E854fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1554 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.T1556fs*3(35)|p.E1554fs*5(2)|p.E1554*(2)|p.?(1)|p.T1556fs*9(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1554fs*11(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) AAAGAGGCAGAAAAAACTATT 0.338 0.20 174 43 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SKOV3_OVARY NA SKOV3_OVARY NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.90 1 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKOV3_OVARY NA SKOV3_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 15 MASTL 84930 broad.mit.edu 37 10 27447484 27447484 + Frame_Shift_Del DEL A - - SKOV3_OVARY NA SKOV3_OVARY NA g.chr10:27447484delA uc001itm.2 + 2 832 c.193delA c.(193-195)AAAfs p.K65fs MASTL_uc001itl.2_Frame_Shift_Del_p.K65fs|MASTL_uc009xkw.1_Frame_Shift_Del_p.K65fs|MASTL_uc009xkx.1_RNA NM_032844 NP_116233 Q96GX5 GWL_HUMAN microtubule associated serine/threonine 65 Protein kinase. cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus centrosome|cleavage furrow|nucleus ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity stomach(1)|ovary(1)|lung(1) 3 ACAGGTTGTTAAAAAAGCAGA 0.239 0.46 417 362 CHUK 1147 broad.mit.edu 37 10 101980369 101980370 + Frame_Shift_Del DEL TA - - SKOV3_OVARY NA SKOV3_OVARY NA g.chr10:101980369_101980370delTA uc001kqp.2 - 5 504_505 c.449_450delTA c.(448-450)ATAfs p.I150fs NM_001278 NP_001269 O15111 IKKA_HUMAN conserved helix-loop-helix ubiquitous kinase 150 Protein kinase. I-kappaB phosphorylation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway CD40 receptor complex|cytosol|internal side of plasma membrane|nucleus ATP binding|identical protein binding|IkappaB kinase activity ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|breast(1) 7 Colorectal(252;0.117) Epithelial(162;2.05e-10)|all cancers(201;1.91e-08) CCTGAAGAACTATGTTTTCAGG 0.307 0.97 17 562 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKOV3_OVARY NA SKOV3_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 213 36 NPAT 4863 broad.mit.edu 37 11 108031706 108031707 + Frame_Shift_Ins INS - T T SKOV3_OVARY NA SKOV3_OVARY NA g.chr11:108031706_108031707insT uc001pjz.3 - 17 4208_4209 c.4106_4107insA c.(4105-4107)AAGfs p.K1369fs NPAT_uc010rvv.1_Frame_Shift_Ins_p.K425fs NM_002519 NP_002510 Q14207 NPAT_HUMAN nuclear protein, ataxia-telangiectasia locus 1369 positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle Cajal body protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity ovary(2) 2 all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116) CAATTTTCCGCTTTTTTGTGGT 0.381 0.12 1023 134 RASGRF1 5923 broad.mit.edu 37 15 79310201 79310201 + Frame_Shift_Del DEL C - - SKOV3_OVARY NA SKOV3_OVARY NA g.chr15:79310201delC uc002beq.2 - 12 2029 c.1654delG c.(1654-1656)GTGfs p.V552fs RASGRF1_uc002bep.2_Frame_Shift_Del_p.V552fs|RASGRF1_uc010blm.1_Frame_Shift_Del_p.V474fs|RASGRF1_uc002ber.3_Frame_Shift_Del_p.V552fs|RASGRF1_uc010unh.1_5'UTR NM_002891 NP_002882 Q13972 RGRF1_HUMAN Ras protein-specific guanine 552 PH 2. activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission cytosol|growth cone|plasma membrane|synaptosome Rho guanyl-nucleotide exchange factor activity skin(4)|ovary(1)|central_nervous_system(1) 6 TTTGGCTCCACCCCGATTTTA 0.507 0.38 72 44 TP53 7157 broad.mit.edu 37 17 7579420 7579420 + Frame_Shift_Del DEL G - - SKOV3_OVARY NA SKOV3_OVARY NA g.chr17:7579420delG uc002gim.2 - 4 461 c.267delC c.(265-267)CCCfs p.P89fs TP53_uc002gig.1_Frame_Shift_Del_p.P89fs|TP53_uc002gih.2_Frame_Shift_Del_p.P89fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.P89fs|TP53_uc010cni.1_Frame_Shift_Del_p.P89fs|TP53_uc002gij.2_Frame_Shift_Del_p.P89fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.P50fs|TP53_uc010cnk.1_Frame_Shift_Del_p.P104fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 89 Interaction with WWOX. P -> L (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.A76_S90del15(3)|p.P89S(3)|p.G59fs*23(3)|p.P89fs*60(1)|p.V73fs*9(1)|p.D48fs*55(1)|p.P85fs*58(1)|p.S33fs*23(1)|p.A86fs*33(1)|p.A86fs*32(1)|p.P87fs*54(1)|p.P13fs*18(1)|p.A88fs*52(1)|p.P89L(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.77 113 370 MALT1 10892 broad.mit.edu 37 18 56376774 56376774 + Frame_Shift_Del DEL A - - SKOV3_OVARY NA SKOV3_OVARY NA g.chr18:56376774delA uc002lhm.1 + 5 1072 c.814delA c.(814-816)AAAfs p.K272fs MALT1_uc002lhn.1_Frame_Shift_Del_p.K272fs NM_006785 NP_006776 Q9UDY8 MALT1_HUMAN mucosa associated lymphoid tissue lymphoma 272 Ig-like C2-type 2. activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway CBM complex|cytosol|nucleus|perinuclear region of cytoplasm cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity ovary(2)|lung(1)|central_nervous_system(1) 4 ACATGAGACCAAAAAGCTATA 0.383 0.42 434 319 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKOV3_OVARY NA SKOV3_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.45 41 33 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes SKOV3_OVARY NA SKOV3_OVARY NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.32 15 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKOV3_OVARY NA SKOV3_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.66 249 494 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKOV3_OVARY NA SKOV3_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 22 241 FOXO4 4303 broad.mit.edu 37 X 70321276 70321277 + Frame_Shift_Ins INS - G G SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chrX:70321276_70321277insG uc004dys.1 + 2 1549_1550 c.1196_1197insG c.(1195-1197)CTGfs p.L399fs FOXO4_uc010nkz.2_Intron|FOXO4_uc004dyt.1_Frame_Shift_Ins_p.L344fs NM_005938 NP_005929 P98177 FOXO4_HUMAN forkhead box O4 399 cell cycle arrest|cell differentiation|embryo development|G1 phase of mitotic cell cycle|insulin receptor signaling pathway|mitotic cell cycle G2/M transition DNA damage checkpoint|muscle organ development|negative regulation of angiogenesis|negative regulation of cell proliferation|negative regulation of smooth muscle cell differentiation|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding central_nervous_system(2)|prostate(1) 3 Renal(35;0.156) CTTCTGTTGCTGGGGGGGCTTC 0.634 0.43 111 85 Unknown 0 broad.mit.edu 37 X 80185321 80185321 + Frame_Shift_Del DEL A - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chrX:80185321delA uc004eec.1 + 1 394 c.220delA c.(220-222)AAAfs p.K74fs SubName: Full=cDNA FLJ16670 fis, clone THYMU3001133, highly similar to Voltage-dependent anion-selective channel protein 1; SubName: Full=Voltage-dependent anion channel 1, isoform CRA_a; TAACACTGGGAAAAAAAATGC 0.483 0.47 90 81 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 4 55 DVL1 1855 broad.mit.edu 37 1 1271642 1271642 + Frame_Shift_Del DEL C - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr1:1271642delC uc001aer.3 - 15 1940 c.1893delG c.(1891-1893)GGGfs p.G631fs DVL1_uc002quu.2_Frame_Shift_Del_p.G373fs|DVL1_uc009vka.2_Frame_Shift_Del_p.G314fs|DVL1_uc001aeu.1_3'UTR NM_004421 NP_004412 O14640 DVL1_HUMAN dishevelled 1 656 canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome frizzled binding|identical protein binding|protein kinase binding|signal transducer activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145) 0.000 0.44 396 309 ARID1A 8289 broad.mit.edu 37 1 27100176 27100176 + Frame_Shift_Del DEL C - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr1:27100176delC uc001bmv.1 + 16 4345 c.3972delC c.(3970-3972)TACfs p.Y1324fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.Y1323fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.Y1324fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.Y941fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.Y170fs|ARID1A_uc009vsm.1_5'UTR|ARID1A_uc009vsn.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1324 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.Y1324fs*1(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CTAGCCGCTACCCCCCgcagc 0.517 0.27 45 17 TIE1 7075 broad.mit.edu 37 1 43778141 43778141 + Frame_Shift_Del DEL C - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr1:43778141delC uc001ciu.2 + 12 1875 c.1796delC c.(1795-1797)TCCfs p.S599fs TIE1_uc010okd.1_Frame_Shift_Del_p.S599fs|TIE1_uc010oke.1_Frame_Shift_Del_p.S554fs|TIE1_uc009vwq.2_Frame_Shift_Del_p.S555fs|TIE1_uc010okf.1_Frame_Shift_Del_p.S244fs|TIE1_uc010okg.1_Frame_Shift_Del_p.S244fs NM_005424 NP_005415 P35590 TIE1_HUMAN tyrosine kinase with immunoglobulin-like and 599 Fibronectin type-III 2.|Extracellular (Potential). mesoderm development integral to plasma membrane ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity lung(3)|stomach(1)|salivary_gland(1)|ovary(1)|skin(1) 7 Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0505) AACGTCTCATCCCCCCAGGCC 0.706 0.35 13 7 TIE1 7075 broad.mit.edu 37 1 43778263 43778263 + Frame_Shift_Del DEL C - - rs143037217 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr1:43778263delC uc001ciu.2 + 12 1997 c.1918delC c.(1918-1920)CCCfs p.P640fs TIE1_uc010okd.1_Frame_Shift_Del_p.P640fs|TIE1_uc010oke.1_Frame_Shift_Del_p.P595fs|TIE1_uc009vwq.2_Frame_Shift_Del_p.P596fs|TIE1_uc010okf.1_Frame_Shift_Del_p.P285fs|TIE1_uc010okg.1_Frame_Shift_Del_p.P285fs NM_005424 NP_005415 P35590 TIE1_HUMAN tyrosine kinase with immunoglobulin-like and 640 Extracellular (Potential). mesoderm development integral to plasma membrane ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity lung(3)|stomach(1)|salivary_gland(1)|ovary(1)|skin(1) 7 Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0505) CGTGCTTCTGCCCCCCAGTGG 0.652 0.50 17 17 PIP5K1A 8394 broad.mit.edu 37 1 151206914 151206914 + Frame_Shift_Del DEL T - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr1:151206914delT uc001exj.2 + 8 1333 c.881delT c.(880-882)CTTfs p.L294fs PIP5K1A_uc001exi.2_Frame_Shift_Del_p.L281fs|PIP5K1A_uc010pcu.1_Frame_Shift_Del_p.L282fs|PIP5K1A_uc001exk.2_Frame_Shift_Del_p.L281fs|PIP5K1A_uc010pcv.1_Frame_Shift_Del_p.L51fs NM_001135638 NP_001129110 Q99755 PI51A_HUMAN phosphatidylinositol-4-phosphate 5-kinase, type 294 PIPK. phospholipid biosynthetic process|signal transduction endomembrane system|Golgi stack|lamellipodium|nuclear speck 1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|kinase binding ovary(1)|central_nervous_system(1)|skin(1) 3 Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.181) CCTGATGGTCTTTTTTTGGAT 0.438 0.48 55 51 FMO4 2329 broad.mit.edu 37 1 171303551 171303551 + Frame_Shift_Del DEL A - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr1:171303551delA uc001gho.2 + 8 1046 c.829delA c.(829-831)AAAfs p.K277fs NM_002022 NP_002013 P31512 FMO4_HUMAN flavin containing monooxygenase 4 277 xenobiotic metabolic process integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding kidney(2)|skin(1) 3 all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181) GTGTCAAAGGAAAAAAGCAAA 0.373 0.44 41 32 OBSCN 84033 broad.mit.edu 37 1 228504466 228504466 + Frame_Shift_Del DEL C - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr1:228504466delC uc009xez.1 + 51 13386 c.13342delC c.(13342-13344)CAGfs p.Q4448fs OBSCN_uc001hsn.2_Frame_Shift_Del_p.Q4448fs NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 4448 Ig-like 46. apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) 0.000 0.42 164 117 PXDN 7837 broad.mit.edu 37 2 1638058 1638058 + Frame_Shift_Del DEL G - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr2:1638058delG uc002qxa.2 - 23 4422 c.4358delC c.(4357-4359)CCTfs p.P1453fs NM_012293 NP_036425 Q92626 PXDN_HUMAN peroxidasin precursor 1453 VWFC. extracellular matrix organization|hydrogen peroxide catabolic process|immune response endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity pancreas(6)|ovary(2) 8 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716) all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228) 0.000 0.45 282 230 PXDN 7837 broad.mit.edu 37 2 1652983 1652984 + Frame_Shift_Ins INS - G G SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr2:1652983_1652984insG uc002qxa.2 - 17 2632_2633 c.2568_2569insC c.(2566-2571)CCCTGCfs p.P856fs NM_012293 NP_036425 Q92626 PXDN_HUMAN peroxidasin precursor 856_857 extracellular matrix organization|hydrogen peroxide catabolic process|immune response endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity pancreas(6)|ovary(2) 8 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716) all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228) 0.000 0.37 272 163 MSH2 4436 broad.mit.edu 37 2 47705563 47705564 + Frame_Shift_Del DEL CT - - rs63750937 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr2:47705563_47705564delCT uc002rvy.1 + 14 2431_2432 c.2363_2364delCT c.(2362-2364)ACTfs p.T788fs MSH2_uc010yoh.1_Frame_Shift_Del_p.T722fs|MSH2_uc002rvz.2_Frame_Shift_Del_p.T788fs|MSH2_uc010fbg.2_Frame_Shift_Del_p.T598fs NM_000251 NP_000242 P43246 MSH2_HUMAN mutS homolog 2 788 B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes MutSalpha complex|MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding p.?(2) large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1) 55 all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) CATGAACTTACTGCCTTGGCCA 0.396 1.00 0 45 TTN 7273 broad.mit.edu 37 2 179542390 179542392 + In_Frame_Del DEL CTT - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr2:179542390_179542392delCTT uc010zfg.1 - 143 30739_30741 c.30515_30517delAAG c.(30514-30519)GAAGTC>GTC p.E10172del TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Del_p.E6833del|TTN_uc010fre.1_Intron|TTN_uc002una.1_RNA|TTN_uc010frf.1_RNA NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 11099 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCTGGAAGGACTTCTTCTTCAGG 0.443 0.53 27 31 TTN 7273 broad.mit.edu 37 2 179600384 179600384 + Frame_Shift_Del DEL G - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr2:179600384delG uc010zfg.1 - 47 11281 c.11057delC c.(11056-11058)CCAfs p.P3686fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.P347fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 4613 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) ATCTTTCCCTGGGGGGAGTTT 0.423 0.48 164 152 TTN 7273 broad.mit.edu 37 2 179611963 179611963 + Frame_Shift_Del DEL G - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr2:179611963delG uc002unb.2 - 46 15388 c.15164delC c.(15163-15165)CCAfs p.P5055fs TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron NM_133379 NP_596870 Q8WZ42 TITIN_HUMAN titin isoform novex-3 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TGTCTCCCCTGGGGGTGTGGA 0.498 0.39 60 39 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.26 20 7 MECOM 2122 broad.mit.edu 37 3 168834348 168834349 + Frame_Shift_Ins INS - C C SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr3:168834348_168834349insC uc003ffi.3 - 7 1016_1017 c.747_748insG c.(745-750)GGATTTfs p.G249fs MECOM_uc010hwk.1_Frame_Shift_Ins_p.G272fs|MECOM_uc003ffj.3_Frame_Shift_Ins_p.G314fs|MECOM_uc011bpi.1_Frame_Shift_Ins_p.G250fs|MECOM_uc003ffn.3_Frame_Shift_Ins_p.G249fs|MECOM_uc003ffk.2_Frame_Shift_Ins_p.G249fs|MECOM_uc003ffl.2_Frame_Shift_Ins_p.G409fs|MECOM_uc011bpj.1_Frame_Shift_Ins_p.G437fs|MECOM_uc011bpk.1_Frame_Shift_Ins_p.G239fs|MECOM_uc010hwn.2_Frame_Shift_Ins_p.G437fs NM_005241 NP_005232 Q03112 EVI1_HUMAN MDS1 and EVI1 complex locus isoform b 249_250 Interaction with MAPK9, SMAD3 and probably SUV39H1. apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle nuclear speck DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1) 14 TGGCCAAAAAATCCACCTGCCG 0.450 0.10 156 17 TACC3 10460 broad.mit.edu 37 4 1730308 1730308 + Frame_Shift_Del DEL C - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr4:1730308delC uc003gdo.2 + 4 1287 c.1179delC c.(1177-1179)GACfs p.D393fs TACC3_uc010ibz.2_Frame_Shift_Del_p.D393fs|TACC3_uc003gdp.2_Intron|TACC3_uc010ica.2_5'Flank NM_006342 NP_006333 Q9Y6A5 TACC3_HUMAN transforming, acidic coiled-coil containing 393 centrosome ovary(1)|central_nervous_system(1) 2 Breast(71;0.212)|all_epithelial(65;0.241) OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126) 0.000 0.47 300 266 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.37 95 55 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 10 25 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.15 148 26 APC 324 broad.mit.edu 37 5 112175952 112175952 + Frame_Shift_Del DEL A - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr5:112175952delA uc010jby.2 + 16 5041 c.4661delA c.(4660-4662)GAAfs p.E1554fs APC_uc011cvt.1_Frame_Shift_Del_p.E1536fs|APC_uc003kpz.3_Frame_Shift_Del_p.E1554fs|APC_uc003kpy.3_Frame_Shift_Del_p.E1554fs|APC_uc010jbz.2_Frame_Shift_Del_p.E1271fs|APC_uc010jca.2_Frame_Shift_Del_p.E854fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1554 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.T1556fs*3(35)|p.E1554fs*5(2)|p.E1554*(2)|p.?(1)|p.T1556fs*9(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1554fs*11(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) AAAGAGGCAGAAAAAACTATT 0.338 0.50 10 10 HNRNPH1 3187 broad.mit.edu 37 5 179043935 179043937 + In_Frame_Del DEL AAG - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr5:179043935_179043937delAAG uc003mkf.3 - 11 1246_1248 c.1140_1142delCTT c.(1138-1143)TTCTTG>TTG p.F380del HNRNPH1_uc011dgn.1_Intron|HNRNPH1_uc003mkg.3_In_Frame_Del_p.F288del|HNRNPH1_uc003mke.3_In_Frame_Del_p.F380del|HNRNPH1_uc003mkh.3_In_Frame_Del_p.F380del NM_005520 NP_005511 P31943 HNRH1_HUMAN heterogeneous nuclear ribonucleoprotein H1 380 2 X 16 AA Gly-rich approximate repeats.|2 X 19 AA perfect repeats.|2-2. regulation of RNA splicing actin cytoskeleton|catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm nucleotide binding|poly(U) RNA binding|protein binding 0 TGTAGAATTCAAGAAGAGTTCTA 0.384 0.43 88 67 AKAP12 9590 broad.mit.edu 37 6 151671303 151671305 + In_Frame_Del DEL GAA - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr6:151671303_151671305delGAA uc011eep.1 + 4 2017_2019 c.1777_1779delGAA c.(1777-1779)GAAdel p.E594del AKAP12_uc003qoe.2_In_Frame_Del_p.E594del|AKAP12_uc003qof.2_In_Frame_Del_p.E496del|AKAP12_uc010kim.2_Intron|AKAP12_uc003qog.2_In_Frame_Del_p.E489del NM_005100 NP_005091 Q02952 AKA12_HUMAN A kinase (PRKA) anchor protein 12 isoform 1 594 G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting cell cortex|cytoskeleton|plasma membrane adenylate cyclase binding|protein kinase A binding large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1) 8 Ovarian(120;0.125) BRCA - Breast invasive adenocarcinoma(37;0.175) OV - Ovarian serous cystadenocarcinoma(155;2.98e-11) 0.000 0.31 494 219 HOXA13 3209 broad.mit.edu 37 7 27239299 27239301 + In_Frame_Del DEL GCG - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr7:27239299_27239301delGCG uc003szb.1 - 1 425_427 c.396_398delCGC c.(394-399)GCCGCG>GCG p.132_133AA>A uc003szc.1_5'Flank NM_000522 NP_000513 P31271 HXA13_HUMAN homeobox A13 132_133 Poly-Ala. skeletal system development nucleus sequence-specific DNA binding breast(1) 1 0.000 0.25 156 51 EGFR 1956 broad.mit.edu 37 7 55240709 55240709 + Frame_Shift_Del DEL G - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr7:55240709delG uc003tqk.2 + 17 2199 c.1953delG c.(1951-1953)GTGfs p.V651fs EGFR_uc010kzg.1_Frame_Shift_Del_p.V606fs|EGFR_uc011kco.1_Frame_Shift_Del_p.V598fs NM_005228 NP_005219 P00533 EGFR_HUMAN epidermal growth factor receptor isoform a 651 Helical; (Potential). activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity p.V651M(2) lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1) 9571 all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318) GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607) Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072) 0.000 0.47 354 317 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 2 12 BLK 640 broad.mit.edu 37 8 11412348 11412348 + Frame_Shift_Del DEL C - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr8:11412348delC uc003wty.2 + 7 1150 c.569delC c.(568-570)TCCfs p.S190fs BLK_uc003wtz.2_Frame_Shift_Del_p.S119fs NM_001715 NP_001706 P51451 BLK_HUMAN B lymphoid tyrosine kinase 190 SH2. intracellular protein kinase cascade|positive regulation of insulin secretion ATP binding|non-membrane spanning protein tyrosine kinase activity large_intestine(1)|stomach(1)|ovary(1) 3 STAD - Stomach adenocarcinoma(15;0.00391) COAD - Colon adenocarcinoma(149;0.207) TACTACATCTCCCCCCGGATC 0.607 0.46 68 57 PRKDC 5591 broad.mit.edu 37 8 48805866 48805866 + Frame_Shift_Del DEL C - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr8:48805866delC uc003xqi.2 - 31 3737 c.3680delG c.(3679-3681)GGTfs p.G1227fs PRKDC_uc003xqj.2_Frame_Shift_Del_p.G1227fs|PRKDC_uc011ldh.1_Intron NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic 1227 cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) GCCACAGCCACCCCCCTCAAA 0.542 0.41 101 70 SULF1 23213 broad.mit.edu 37 8 70488249 70488249 + Frame_Shift_Del DEL G - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr8:70488249delG uc010lza.1 + 6 934 c.217delG c.(217-219)GGGfs p.G73fs SULF1_uc003xyd.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xye.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xyf.2_Frame_Shift_Del_p.G73fs|SULF1_uc003xyg.2_Frame_Shift_Del_p.G73fs NM_015170 NP_055985 Q8IWU6 SULF1_HUMAN sulfatase 1 precursor 73 apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway cell surface|endoplasmic reticulum|extracellular space|Golgi stack arylsulfatase activity|calcium ion binding central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1) 7 Breast(64;0.0654) Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534) TATGGAACATGGGGGGGCCAC 0.493 0.40 41 27 VPS13B 157680 broad.mit.edu 37 8 100050671 100050671 + Frame_Shift_Del DEL T - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr8:100050671delT uc003yiv.2 + 3 279 c.168delT c.(166-168)ACTfs p.T56fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.T56fs|VPS13B_uc003yit.2_Frame_Shift_Del_p.T56fs|VPS13B_uc003yiu.1_Frame_Shift_Del_p.T56fs|VPS13B_uc003yis.2_Frame_Shift_Del_p.T56fs|VPS13B_uc011lgy.1_5'UTR NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 56 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TACCATTCACTTTTTTAAGTG 0.254 0.53 31 35 RIMS2 9699 broad.mit.edu 37 8 104513270 104513271 + Frame_Shift_Ins INS - A A SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr8:104513270_104513271insA uc003ylp.2 + 1 295_296 c.156_157insA c.(154-159)GAGAAGfs p.E52fs NM_001100117 NP_001093587 Q9UQ26 RIMS2_HUMAN regulating synaptic membrane exocytosis 2 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment_56 intracellular protein transport cell junction|presynaptic membrane metal ion binding|Rab GTPase binding ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1) 15 OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229) AAGAAGAGGAGAAGGAGCAGTC 0.644 0.49 20 19 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 24 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.37 322 192 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.27 99 37 PTEN 5728 broad.mit.edu 37 10 89720799 89720802 + Frame_Shift_Del DEL TACT - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr10:89720799_89720802delTACT uc001kfb.2 + 9 1981_1984 c.950_953delTACT c.(949-954)GTACTTfs p.V317fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 317_318 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.L318fs*2(17)|p.V317fs*3(16)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.V317fs*6(2)|p.G165_*404del(1)|p.G165_K342del(1)|p.L316fs*1(1)|p.W274_F341del(1)|p.V317_K322del(1)|p.L318F(1)|p.T318fs*2(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GAATATCTAGTACTTACTTTAACA 0.333 0.36 70 39 PTEN 5728 broad.mit.edu 37 10 89720811 89720812 + Frame_Shift_Ins INS - A A SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr10:89720811_89720812insA uc001kfb.2 + 9 1993_1994 c.962_963insA c.(961-963)ACAfs p.T321fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 321 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.T321fs*23(9)|p.T321fs*3(7)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.N323fs*2(2)|p.T319_K332del(1)|p.T321fs*22(1)|p.G165_*404del(1)|p.G165_K342del(1)|p.L316fs*1(1)|p.W274_F341del(1)|p.V317_K322del(1)|p.T321fs*4(1)|p.T321fs*6(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) CTTACTTTAACAAAAAATGATC 0.327 0.46 59 51 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 267 73 DYRK4 8798 broad.mit.edu 37 12 4719362 4719362 + Frame_Shift_Del DEL A - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr12:4719362delA uc001qmx.2 + 11 1217 c.1057delA c.(1057-1059)AAAfs p.K353fs DYRK4_uc009zeh.1_Frame_Shift_Del_p.K468fs|DYRK4_uc001qmy.1_Frame_Shift_Del_p.K353fs|DYRK4_uc001qmz.1_Frame_Shift_Del_p.K67fs|DYRK4_uc001qna.1_5'UTR|DYRK4_uc010ser.1_5'UTR NM_003845 NP_003836 Q9NR20 DYRK4_HUMAN dual-specificity tyrosine-(Y)-phosphorylation 353 Protein kinase. Golgi apparatus ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(2)|skin(1) 3 Colorectal(7;0.103) CAACAGGGGGAAAAAAAGATA 0.398 0.49 33 32 ITPR2 3709 broad.mit.edu 37 12 26568292 26568292 + Frame_Shift_Del DEL A - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr12:26568292delA uc001rhg.2 - 51 7667 c.7250delT c.(7249-7251)TTGfs p.L2417fs ITPR2_uc009zjg.1_Frame_Shift_Del_p.L568fs NM_002223 NP_002214 Q14571 ITPR2_HUMAN inositol 1,4,5-triphosphate receptor, type 2 2417 Extracellular (Potential). activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 14 Colorectal(261;0.0847) GTCATCCTTCAAAAAAAGGAA 0.408 0.58 45 61 WNT1 7471 broad.mit.edu 37 12 49374348 49374348 + Frame_Shift_Del DEL G - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr12:49374348delG uc001rsu.2 + 3 698 c.500delG c.(499-501)TGGfs p.W167fs NM_005430 NP_005421 P04628 WNT1_HUMAN wingless-type MMTV integration site family, 167 brain segmentation|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|central nervous system morphogenesis|cerebellum formation|dermatome development|diencephalon development|embryonic axis specification|forebrain anterior/posterior pattern formation|fourth ventricle development|hemopoietic stem cell proliferation|hepatocyte differentiation|inner ear morphogenesis|mesoderm morphogenesis|midbrain development|midbrain-hindbrain boundary maturation during brain development|negative regulation of cell-cell adhesion|negative regulation of cell-substrate adhesion|negative regulation of DNA damage checkpoint|negative regulation of fat cell differentiation|neuron fate determination|positive regulation of fibroblast proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of lamellipodium assembly|positive regulation of Notch signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to wounding|signal transduction in response to DNA damage|Spemann organizer formation|T cell differentiation in thymus|Wnt receptor signaling pathway, calcium modulating pathway early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix cytokine activity|frizzled-2 binding|transcription regulatory region DNA binding kidney(1) 1 BRCA - Breast invasive adenocarcinoma(357;0.244) 0.000 0.42 224 160 LRP1 4035 broad.mit.edu 37 12 57603940 57603940 + Frame_Shift_Del DEL C - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr12:57603940delC uc001snd.2 + 81 13034 c.12568delC c.(12568-12570)CCCfs p.P4190fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 4190 Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CTCTCCAACGCCCCCCCCAGA 0.637 0.37 24 14 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.21 68 18 ZMYM2 7750 broad.mit.edu 37 13 20657094 20657094 + Frame_Shift_Del DEL A - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr13:20657094delA uc001umr.2 + 24 4040 c.3742delA c.(3742-3744)AAAfs p.K1248fs ZMYM2_uc001ums.2_Frame_Shift_Del_p.K1248fs|ZMYM2_uc001umt.2_Frame_Shift_Del_p.K1248fs|ZMYM2_uc001umv.2_Frame_Shift_Del_p.K628fs|ZMYM2_uc001umw.2_Frame_Shift_Del_p.K701fs NM_003453 NP_003444 Q9UBW7 ZMYM2_HUMAN zinc finger protein 198 1248 regulation of transcription, DNA-dependent|transcription, DNA-dependent PML body ubiquitin conjugating enzyme binding|zinc ion binding lung(3)|ovary(2)|prostate(1) 6 all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856) TAGGCATTGGAAAAAAAATCC 0.363 0.84 11 59 CDX2 1045 broad.mit.edu 37 13 28537278 28537278 + Frame_Shift_Del DEL C - - rs142861632 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr13:28537278delC uc001urv.2 - 3 1090 c.916delG c.(916-918)GTGfs p.V306fs NM_001265 NP_001256 Q99626 CDX2_HUMAN caudal type homeobox 2 306 organ morphogenesis|transcription from RNA polymerase II promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity lung(1) 1 all_cancers(110;0.191)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155) Lung SC(185;0.0156) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199) GGGTTTAGCACCCCCCCAGTT 0.627 0.93 1 14 RB1 5925 broad.mit.edu 37 13 49030479 49030479 + Frame_Shift_Del DEL A - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr13:49030479delA uc001vcb.2 + 19 2120 c.1954delA c.(1954-1956)AAAfs p.K652fs NM_000321 NP_000312 P06400 RB_HUMAN retinoblastoma 1 652 Pocket; binds T and E1A.|Domain B. androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation chromatin|PML body|Rb-E2F complex|SWI/SNF complex androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding p.?(6)|p.V654fs*4(1) lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1) 358 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) ACTGTTTTATAAAAAAGGTTA 0.239 0.86 5 32 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.30 21 9 SPRED1 161742 broad.mit.edu 37 15 38614463 38614463 + Frame_Shift_Del DEL A - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr15:38614463delA uc001zka.3 + 3 564 c.229delA c.(229-231)AAAfs p.K77fs NM_152594 NP_689807 Q7Z699 SPRE1_HUMAN sprouty-related protein 1 with EVH-1 domain 77 WH1. inactivation of MAPK activity|multicellular organismal development caveola|nucleus stem cell factor receptor binding ovary(2)|lung(2)|skin(1) 5 all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091) GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244) 0.000 0.62 35 56 TP53BP1 7158 broad.mit.edu 37 15 43730536 43730536 + Frame_Shift_Del DEL G - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr15:43730536delG uc001zrs.2 - 16 3310 c.3162delC c.(3160-3162)CCCfs p.P1054fs TP53BP1_uc010udp.1_Frame_Shift_Del_p.P1054fs|TP53BP1_uc001zrq.3_Frame_Shift_Del_p.P1059fs|TP53BP1_uc001zrr.3_Frame_Shift_Del_p.P1059fs|TP53BP1_uc010udq.1_Frame_Shift_Del_p.P1059fs NM_005657 NP_005648 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 isoform 3 1054 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1) 7 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) TGGGTGTGGTGGGGGGATCCT 0.413 0.39 75 47 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.82 17 79 MLLT6 4302 broad.mit.edu 37 17 36872047 36872048 + In_Frame_Ins INS - TCC TCC SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr17:36872047_36872048insTCC uc002hqi.3 + 9 1015_1016 c.1002_1003insTCC c.(1000-1005)insTCC p.338_339insS MLLT6_uc010cvm.1_In_Frame_Ins_p.338_339insS|MLLT6_uc002hqj.2_5'UTR|MLLT6_uc002hqk.3_5'Flank NM_005937 NP_005928 P55198 AF17_HUMAN myeloid/lymphoid or mixed-lineage leukemia 338_339 regulation of transcription, DNA-dependent nucleus protein binding|zinc ion binding breast(3)|prostate(1)|lung(1)|skin(1) 6 Breast(7;4.43e-21) cctcctcctcttcctcctcctc 0.431 0.38 44 27 WNK4 65266 broad.mit.edu 37 17 40939870 40939870 + Frame_Shift_Del DEL G - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr17:40939870delG uc002ibj.2 + 8 1837 c.1816delG c.(1816-1818)GGGfs p.G606fs WNK4_uc010wgx.1_Frame_Shift_Del_p.G270fs|WNK4_uc002ibk.1_Frame_Shift_Del_p.G378fs|WNK4_uc010wgy.1_Intron NM_032387 NP_115763 Q96J92 WNK4_HUMAN WNK lysine deficient protein kinase 4 606 intracellular protein kinase cascade tight junction ATP binding|protein serine/threonine kinase activity ovary(3)|skin(3)|stomach(1) 7 Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.0749) TCAGCCCCCTGGGGGGGTGCC 0.637 0.39 56 36 TRIM37 4591 broad.mit.edu 37 17 57141768 57141769 + Splice_Site INS - A A rs147621691 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr17:57141768_57141769insA uc002iwy.3 - 10 1254 c.810_splice c.e10-1 p.S270_splice TRIM37_uc002iwz.3_Splice_Site_p.S270_splice|TRIM37_uc002ixa.3_Splice_Site_p.S148_splice|TRIM37_uc010woc.1_Splice_Site_p.S236_splice NM_001005207 NP_001005207 O94972 TRI37_HUMAN tripartite motif-containing 37 protein perinuclear region of cytoplasm|peroxisome ligase activity|protein binding|zinc ion binding lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1) 7 Medulloblastoma(34;0.0922)|all_neural(34;0.101) ACTAATTCACTAAAAAAAAAAA 0.272 0.50 5 5 CLTC 1213 broad.mit.edu 37 17 57746241 57746244 + Frame_Shift_Del DEL AGAA - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr17:57746241_57746244delAGAA uc002ixq.1 + 14 2675_2678 c.2232_2235delAGAA c.(2230-2235)GTAGAAfs p.V744fs CLTC_uc002ixp.2_Frame_Shift_Del_p.V744fs|CLTC_uc002ixr.1_Frame_Shift_Del_p.V748fs NM_004859 NP_004850 Q00610 CLH1_HUMAN clathrin heavy chain 1 744_745 Heavy chain arm.|Proximal segment. axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle protein binding|structural molecule activity CLTC/ALK(44)|CLTC/TFE3(2) haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1) 48 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) TCAAAGAAGTAGAAAGAATCTGTA 0.392 0.47 40 35 AATK 9625 broad.mit.edu 37 17 79094046 79094048 + In_Frame_Del DEL CTT - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr17:79094046_79094048delCTT uc010dia.2 - 11 3768_3770 c.3688_3690delAAG c.(3688-3690)AAGdel p.K1230del AATK_uc010dhz.2_RNA NM_001080395 NP_001073864 Q6ZMQ8 LMTK1_HUMAN apoptosis-associated tyrosine kinase 1230 integral to membrane|mitochondrion|perinuclear region of cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1) 9 all_neural(118;0.101) BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524) AGGACACGGCCTTCTTCTTGCGT 0.680 0.55 25 31 RBBP8 5932 broad.mit.edu 37 18 20572852 20572853 + Frame_Shift_Ins INS - A A SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr18:20572852_20572853insA uc002ktw.2 + 11 1393_1394 c.1062_1063insA c.(1060-1065)GGGAAAfs p.G354fs RBBP8_uc002kty.2_Frame_Shift_Ins_p.G354fs|RBBP8_uc002ktz.2_Frame_Shift_Ins_p.G354fs|RBBP8_uc002kua.2_Frame_Shift_Ins_p.G354fs|RBBP8_uc002ktx.1_Frame_Shift_Ins_p.G354fs NM_002894 NP_002885 Q99708 COM1_HUMAN retinoblastoma binding protein 8 isoform a 354_355 cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter nucleus damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity ovary(1)|lung(1)|skin(1) 3 all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19) OV - Ovarian serous cystadenocarcinoma(1;0.00196) TACAGCCTGGGAAAAAAAAACA 0.361 0.47 48 43 ALPK2 115701 broad.mit.edu 37 18 56246440 56246440 + Frame_Shift_Del DEL T - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr18:56246440delT uc002lhj.3 - 4 1782 c.1568delA c.(1567-1569)AAGfs p.K523fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 523 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 CCATAAGTCCTTTCCCCCCAC 0.522 0.41 185 131 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.31 72 33 GLTSCR1 29998 broad.mit.edu 37 19 48183094 48183094 + Frame_Shift_Del DEL G - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr19:48183094delG uc002phh.3 + 6 861 c.667delG c.(667-669)GGGfs p.G223fs GLTSCR1_uc002phi.3_5'UTR NM_015711 NP_056526 Q9NZM4 GSCR1_HUMAN glioma tumor suppressor candidate region gene 1 223 protein binding pancreas(3) 3 all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086) all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355) TGGCAGCCCTGGGGGTGCCAC 0.701 0.42 15 11 RBL1 5933 broad.mit.edu 37 20 35695259 35695259 + Frame_Shift_Del DEL G - - SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr20:35695259delG uc002xgi.2 - 6 793 c.714delC c.(712-714)GACfs p.D238fs RBL1_uc010zvt.1_RNA|RBL1_uc002xgj.1_Frame_Shift_Del_p.D238fs|RBL1_uc010gfv.1_RNA NM_002895 NP_002886 P28749 RBL1_HUMAN retinoblastoma-like protein 1 isoform a 238 cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent transcription factor binding lung(5)|skin(3)|ovary(2) 10 Myeloproliferative disorder(115;0.00878) AAGCCGTAAAGTCAGCAGTAT 0.388 0.50 104 102 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 55 267 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SKUT1_SOFT_TISSUE NA SKUT1_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 77 ITIH5L 347365 broad.mit.edu 37 X 54780182 54780183 + Frame_Shift_Ins INS - G G SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chrX:54780182_54780183insG uc004dtj.2 - 11 3283_3284 c.3253_3254insC c.(3253-3255)CACfs p.H1085fs NM_198510 NP_940912 Q6UXX5 ITH5L_HUMAN inter-alpha (globulin) inhibitor H5-like 1085 hyaluronan metabolic process extracellular region serine-type endopeptidase inhibitor activity lung(2)|skin(2)|ovary(1)|breast(1) 6 GATCACAAAGTGGGGGTCCCCG 0.500 0.33 8 4 ATRX 546 broad.mit.edu 37 X 76890149 76890150 + Frame_Shift_Ins INS - T T SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chrX:76890149_76890150insT uc004ecp.3 - 17 4976_4977 c.4744_4745insA c.(4744-4746)ACAfs p.T1582fs ATRX_uc004ecq.3_Frame_Shift_Ins_p.T1544fs|ATRX_uc004eco.3_Frame_Shift_Ins_p.T1367fs NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 1582 Helicase ATP-binding. DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) AGATTTCTTTGTTTTTTTCACA 0.371 0.34 23 12 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 7 69 SPEN 23013 broad.mit.edu 37 1 16256610 16256610 + Frame_Shift_Del DEL A - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr1:16256610delA uc001axk.1 + 11 4079 c.3875delA c.(3874-3876)GAAfs p.E1292fs SPEN_uc010obp.1_Frame_Shift_Del_p.E1251fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 1292 interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) AAAGTAGATGAAAAAGTCCTC 0.443 0.45 59 48 ARID1A 8289 broad.mit.edu 37 1 27105931 27105931 + Frame_Shift_Del DEL G - - rs140055856 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr1:27105931delG uc001bmv.1 + 20 5915 c.5542delG c.(5542-5544)GGGfs p.G1848fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.G1631fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.G694fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.G176fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.G90fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1848 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.G1848fs*6(3) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GCGGATTGGTGGGGGGGACAC 0.582 0.43 192 142 ARID1A 8289 broad.mit.edu 37 1 27106804 27106804 + Frame_Shift_Del DEL C - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr1:27106804delC uc001bmv.1 + 20 6788 c.6415delC c.(6415-6417)CCCfs p.P2139fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.P1922fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.P985fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.P467fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.P381fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 2139 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.F2141fs*59(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) TCTGGCCACACCCCCCTTCAG 0.587 0.43 163 121 MAP3K6 9064 broad.mit.edu 37 1 27685012 27685012 + Frame_Shift_Del DEL G - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr1:27685012delG uc001bny.1 - 20 2923 c.2674delC c.(2674-2676)CGCfs p.R892fs MAP3K6_uc009vsw.1_Frame_Shift_Del_p.R884fs|MAP3K6_uc001bnz.1_Frame_Shift_Del_p.R415fs NM_004672 NP_004663 O95382 M3K6_HUMAN mitogen-activated protein kinase kinase kinase 892 Protein kinase. activation of JUN kinase activity ATP binding|magnesium ion binding|MAP kinase kinase kinase activity breast(4)|lung(3)|ovary(1)|central_nervous_system(1) 9 all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419) 0.000 0.50 290 294 MAP3K6 9064 broad.mit.edu 37 1 27685239 27685239 + Frame_Shift_Del DEL G - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr1:27685239delG uc001bny.1 - 19 2793 c.2544delC c.(2542-2544)CCCfs p.P848fs MAP3K6_uc009vsw.1_Frame_Shift_Del_p.P840fs|MAP3K6_uc001bnz.1_Frame_Shift_Del_p.P371fs NM_004672 NP_004663 O95382 M3K6_HUMAN mitogen-activated protein kinase kinase kinase 848 Protein kinase. activation of JUN kinase activity ATP binding|magnesium ion binding|MAP kinase kinase kinase activity p.F709fs*40(1) breast(4)|lung(3)|ovary(1)|central_nervous_system(1) 9 all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419) GCTCGTGGAAGGGGGGGCGAC 0.622 0.40 67 44 THBS3 7059 broad.mit.edu 37 1 155165845 155165845 + Frame_Shift_Del DEL C - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr1:155165845delC uc001fix.2 - 22 2768 c.2745delG c.(2743-2745)GGGfs p.G915fs RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Frame_Shift_Del_p.G906fs|THBS3_uc001fiz.2_Frame_Shift_Del_p.G878fs|THBS3_uc001fiy.2_Frame_Shift_Del_p.G444fs|THBS3_uc010pfu.1_Frame_Shift_Del_p.G795fs NM_007112 NP_009043 P49746 TSP3_HUMAN thrombospondin 3 precursor 915 TSP C-terminal. cell-matrix adhesion extracellular region|perinuclear region of cytoplasm calcium ion binding|heparin binding|structural molecule activity breast(3)|ovary(2) 5 all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) CACCAAGACGCCCCCCTCGCA 0.498 0.40 155 102 CDK18 5129 broad.mit.edu 37 1 205492734 205492735 + Frame_Shift_Ins INS - GC GC SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr1:205492734_205492735insGC uc001hcr.2 + 3 473_474 c.254_255insGC c.(253-255)CAGfs p.Q85fs CDK18_uc009xbk.1_RNA|CDK18_uc009xbl.1_RNA|CDK18_uc010pri.1_Frame_Shift_Ins_p.P105fs|CDK18_uc001hcp.2_Frame_Shift_Ins_p.Q85fs|CDK18_uc001hcq.2_Frame_Shift_Ins_p.Q85fs|CDK18_uc010prj.1_5'UTR|CDK18_uc001hcs.2_5'UTR|CDK18_uc009xbm.1_5'UTR NM_212503 NP_997668 Q07002 CDK18_HUMAN PCTAIRE protein kinase 3 isoform a 83 ATP binding|cyclin-dependent protein kinase activity|protein binding|signal transducer activity stomach(2) 2 CGGCAGAACCAGCGCCGCTTCT 0.574 0.45 31 25 FMN2 56776 broad.mit.edu 37 1 240371002 240371034 + In_Frame_Del DEL ATACCCCTTCCTCCCCCTCTTCCCGGAGCAGGA - - rs142052746;rs150923193;rs138468405;rs140720010;rs150102515 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr1:240371002_240371034delATACCCCTTCCTCCCCCTCTTCCCGGAGCAGGA uc010pyd.1 + 5 3115_3147 c.2890_2922delATACCCCTTCCTCCCCCTCTTCCCGGAGCAGGA c.(2890-2922)ATACCCCTTCCTCCCCCTCTTCCCGGAGCAGGAdel p.IPLPPPLPGAG964del FMN2_uc010pye.1_In_Frame_Del_p.IPLPPPLPGAG968del NM_020066 NP_064450 Q9NZ56 FMN2_HUMAN formin 2 964_974 Pro-rich.|FH1. actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions actin binding ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) CGGGGCAGGCATACCCCTTCCTCCCCCTCTTCCCGGAGCAGGAATACCTCCTC 0.704 0.60 6 9 CDKL4 344387 broad.mit.edu 37 2 39406312 39406312 + Frame_Shift_Del DEL T - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr2:39406312delT uc002rrm.2 - 8 943 c.943delA c.(943-945)AGTfs p.S315fs CDKL4_uc010fal.1_Intron NM_001009565 NP_001009565 Q5MAI5 CDKL4_HUMAN cyclin-dependent kinase-like 4 315 cytoplasm ATP binding|cyclin-dependent protein kinase activity ovary(1) 1 all_hematologic(82;0.248) GCACTTTAACTTTTGAGCGGA 0.383 0.23 49 15 TTN 7273 broad.mit.edu 37 2 179401107 179401107 + Frame_Shift_Del DEL T - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr2:179401107delT uc010zfg.1 - 306 92887 c.92663delA c.(92662-92664)AACfs p.N30888fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.N24583fs|TTN_uc010zfi.1_Frame_Shift_Del_p.N24516fs|TTN_uc010zfj.1_Frame_Shift_Del_p.N24391fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 31815 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTCAATAAGGTTTTTCACTGA 0.368 0.16 158 31 TTN 7273 broad.mit.edu 37 2 179435296 179435296 + Frame_Shift_Del DEL T - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr2:179435296delT uc010zfg.1 - 275 68083 c.67859delA c.(67858-67860)AATfs p.N22620fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.N16315fs|TTN_uc010zfi.1_Frame_Shift_Del_p.N16248fs|TTN_uc010zfj.1_Frame_Shift_Del_p.N16123fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 23547 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCCTGCAACATTTTTGGCCTT 0.438 0.28 126 48 TTN 7273 broad.mit.edu 37 2 179604379 179604379 + Frame_Shift_Del DEL T - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr2:179604379delT uc010zfh.1 - 46 13292 c.13068delA c.(13066-13068)AAAfs p.K4356fs TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Frame_Shift_Del_p.K4289fs|TTN_uc010zfj.1_Frame_Shift_Del_p.K4164fs|TTN_uc002umz.1_Intron NM_133437 NP_597681 Q8WZ42 TITIN_HUMAN titin isoform novex-2 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AGATCAGATATTTAGATTCAA 0.393 0.53 61 68 BMPR2 659 broad.mit.edu 37 2 203420325 203420326 + Frame_Shift_Del DEL CA - - rs147792289 by1000genomes SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr2:203420325_203420326delCA uc002uzf.3 + 12 3085_3086 c.1937_1938delCA c.(1936-1938)GCAfs p.A646fs BMPR2_uc010ftr.2_Intron NM_001204 NP_001195 Q13873 BMPR2_HUMAN bone morphogenetic protein receptor type II 646 Cytoplasmic (Potential). anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway integral to plasma membrane ATP binding|metal ion binding|transforming growth factor beta receptor activity ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1) 9 ACAAATGTTGCACAGTCAATTG 0.446 0.15 46 8 ROBO1 6091 broad.mit.edu 37 3 78987928 78987929 + Frame_Shift_Del DEL CT - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr3:78987928_78987929delCT uc003dqe.2 - 4 529_530 c.321_322delAG c.(319-324)AGAGTGfs p.R107fs ROBO1_uc003dqb.2_Frame_Shift_Del_p.R68fs|ROBO1_uc003dqc.2_Frame_Shift_Del_p.R68fs|ROBO1_uc003dqd.2_Frame_Shift_Del_p.R68fs NM_002941 NP_002932 Q9Y6N7 ROBO1_HUMAN roundabout 1 isoform a 107_108 Extracellular (Potential).|Ig-like C2-type 1. activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway cell surface|cytoplasm|integral to plasma membrane axon guidance receptor activity|identical protein binding|LRR domain binding large_intestine(2) 2 Lung SC(41;0.0257)|Lung NSC(201;0.0439) LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274) TCTGTCTCCACTCTCTCTCCCC 0.475 0.16 147 27 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.21 26 7 AFF1 4299 broad.mit.edu 37 4 88048824 88048825 + Frame_Shift_Ins INS - A A SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr4:88048824_88048825insA uc003hqj.3 + 15 3319_3320 c.2912_2913insA c.(2911-2913)GCAfs p.A971fs AFF1_uc011ccz.1_Frame_Shift_Ins_p.A978fs|AFF1_uc003hqk.3_Frame_Shift_Ins_p.A971fs|AFF1_uc011cda.1_Frame_Shift_Ins_p.A609fs NM_005935 NP_005926 P51825 AFF1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 971 nucleus sequence-specific DNA binding transcription factor activity breast(1) 1 Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114) OV - Ovarian serous cystadenocarcinoma(123;0.000233) ATGAGGGAGGCAAAAAAGATGA 0.381 0.45 62 50 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 98 157 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.57 134 181 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.34 128 65 STK32A 202374 broad.mit.edu 37 5 146754725 146754725 + Frame_Shift_Del DEL A - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr5:146754725delA uc010jgn.1 + 11 1256 c.976delA c.(976-978)AAAfs p.K326fs STK32A_uc003lom.2_Frame_Shift_Del_p.K326fs|STK32A_uc011dbw.1_Frame_Shift_Del_p.K326fs NM_001112724 NP_001106195 Q8WU08 ST32A_HUMAN serine/threonine kinase 32A isoform 1 326 ATP binding|metal ion binding|protein serine/threonine kinase activity lung(2)|skin(1) 3 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) 0.000 0.16 695 129 HMMR 3161 broad.mit.edu 37 5 162917425 162917426 + Frame_Shift_Ins INS - A A SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr5:162917425_162917426insA uc003lzf.2 + 17 2171_2172 c.1989_1990insA c.(1987-1992)GCTAAAfs p.A663fs HMMR_uc003lzh.2_Frame_Shift_Ins_p.A664fs|HMMR_uc003lzg.2_Frame_Shift_Ins_p.A648fs|HMMR_uc011dem.1_Frame_Shift_Ins_p.A577fs|uc003lzi.2_Intron NM_012484 NP_036616 O75330 HMMR_HUMAN hyaluronan-mediated motility receptor isoform b 663_664 Hyaluronic acid-binding (Potential). cell surface|cytoplasm hyaluronic acid binding 0 Renal(175;0.000281) Medulloblastoma(196;0.00853)|all_neural(177;0.0408) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848) GTCAGCTTGCTAAAAAAAAACA 0.307 0.50 5 5 GRM6 2916 broad.mit.edu 37 5 178418555 178418555 + Frame_Shift_Del DEL C - - rs63062360 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr5:178418555delC uc003mjr.2 - 3 906 c.727delG c.(727-729)GTCfs p.V243fs GRM6_uc010jla.1_5'Flank|GRM6_uc003mjs.1_5'Flank NM_000843 NP_000834 O15303 GRM6_HUMAN glutamate receptor, metabotropic 6 precursor 243 Extracellular (Potential). detection of visible light|visual perception integral to plasma membrane lung(4)|ovary(2)|breast(1)|pancreas(1) 8 all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351) all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) all cancers(165;0.245) 0.000 0.15 858 147 PRPF4B 8899 broad.mit.edu 37 6 4031880 4031881 + Frame_Shift_Ins INS - A A SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr6:4031880_4031881insA uc003mvv.2 + 2 220_221 c.129_130insA c.(127-132)CACAAAfs p.H43fs PRPF4B_uc011dhv.1_RNA NM_003913 NP_003904 Q13523 PRP4B_HUMAN serine/threonine-protein kinase PRP4K 43_44 His-rich.|Arg/Lys-rich (basic). catalytic step 2 spliceosome ATP binding|protein binding|protein serine/threonine kinase activity breast(5) 5 Ovarian(93;0.0925) all_hematologic(90;0.0895) ACAGTCGTCACaaaaaaaagaa 0.168 0.62 5 8 RANBP9 10048 broad.mit.edu 37 6 13632610 13632610 + Frame_Shift_Del DEL T - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr6:13632610delT uc003nbb.2 - 12 1998 c.1939delA c.(1939-1941)ATGfs p.M647fs RANBP9_uc003nba.2_Frame_Shift_Del_p.M306fs NM_005493 NP_005484 Q96S59 RANB9_HUMAN RAN binding protein 9 647 Interaction with FMR1. axon guidance|microtubule nucleation|protein complex assembly cytosol|microtubule associated complex|nucleus Ran GTPase binding lung(1)|skin(1) 2 Breast(50;0.00669)|Ovarian(93;0.0634) all_hematologic(90;0.117) Epithelial(50;0.223) ACCTTCAACATTTTTTTGTTT 0.378 0.51 59 61 HOXA9 3205 broad.mit.edu 37 7 27204794 27204794 + Frame_Shift_Del DEL G - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr7:27204794delG uc003syt.2 - 1 356 c.283delC c.(283-285)CAGfs p.Q95fs NM_152739 NP_689952 P31269 HXA9_HUMAN homeobox A9 95 protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity lung(1)|central_nervous_system(1) 2 0.000 0.48 357 331 TRRAP 8295 broad.mit.edu 37 7 98528336 98528336 + Frame_Shift_Del DEL G - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr7:98528336delG uc003upp.2 + 25 3683 c.3474delG c.(3472-3474)CTGfs p.L1158fs TRRAP_uc011kis.1_Frame_Shift_Del_p.L1158fs|TRRAP_uc003upr.2_Frame_Shift_Del_p.L850fs NM_003496 NP_003487 Q9Y4A5 TRRAP_HUMAN transformation/transcription domain-associated 1158 histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1) 37 all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274) STAD - Stomach adenocarcinoma(171;0.215) ATGCAAAGCTGGGGGGTGTGG 0.507 0.32 171 80 EXT1 2131 broad.mit.edu 37 8 119123094 119123094 + Frame_Shift_Del DEL G - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr8:119123094delG uc003yok.1 - 1 965 c.192delC c.(190-192)CCCfs p.P64fs NM_000127 NP_000118 Q16394 EXT1_HUMAN exostosin 1 64 Lumenal (Potential). glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development Golgi membrane|integral to endoplasmic reticulum membrane glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity ovary(2)|lung(2) 4 all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173) STAD - Stomach adenocarcinoma(47;0.012) AAGGAACGAAGGGGCGCAGAG 0.582 0.23 88 26 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 3 55 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.24 81 26 TSC1 7248 broad.mit.edu 37 9 135771987 135771988 + In_Frame_Ins INS - GCT GCT rs118203743 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr9:135771987_135771988insGCT uc004cca.2 - 23 3363_3364 c.3129_3130insAGC c.(3127-3132)insAGC p.1043_1044insS TSC1_uc004ccb.3_In_Frame_Ins_p.1042_1043insS|TSC1_uc011mcq.1_In_Frame_Ins_p.992_993insS|TSC1_uc011mcr.1_In_Frame_Ins_p.236_236A>AA NM_000368 NP_000359 Q92574 TSC1_HUMAN tuberous sclerosis 1 protein isoform 1 1043_1044 activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus cell cortex|lamellipodium|membrane|TSC1-TSC2 complex chaperone binding|protein N-terminus binding p.S1043N(1)|p.?(1) lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1) 14 OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06) GTAGAAAGCTCgctgctgctgc 0.574 0.32 73 34 PTEN 5728 broad.mit.edu 37 10 89693003 89693003 + Frame_Shift_Del DEL A - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr10:89693003delA uc001kfb.2 + 6 1518 c.487delA c.(487-489)AAAfs p.K163fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 163 Phosphatase tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R55fs*1(4)|p.?(2)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.K163_V166>NKGE(1)|p.F56fs*2(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GACCAGAGACAAAAAGGTAAG 0.328 0.50 29 29 PTEN 5728 broad.mit.edu 37 10 89720712 89720712 + Frame_Shift_Del DEL A - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr10:89720712delA uc001kfb.2 + 9 1894 c.863delA c.(862-864)GAAfs p.E288fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 288 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.E288fs*3(6)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.E288*(2)|p.G165_*404del(1)|p.S287fs*1(1)|p.G165_K342del(1)|p.E288fs*8(1)|p.S287fs*8(1)|p.W274_F341del(1)|p.E288K(1)|p.E288fs*9(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GAAACCTCAGAAAAAGTAGAA 0.299 0.52 29 31 LDHA 3939 broad.mit.edu 37 11 18424538 18424539 + Frame_Shift_Ins INS - G G SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr11:18424538_18424539insG uc001mok.3 + 5 842_843 c.570_571insG c.(568-573)CTTGGGfs p.L190fs LDHA_uc010rdc.1_Frame_Shift_Ins_p.L132fs|LDHA_uc009yhn.2_Frame_Shift_Ins_p.L190fs|LDHA_uc009yho.2_Frame_Shift_Ins_p.L17fs|LDHA_uc001mol.3_Frame_Shift_Ins_p.L190fs|LDHA_uc010rdd.1_Frame_Shift_Ins_p.L219fs NM_005566 NP_005557 P00338 LDHA_HUMAN lactate dehydrogenase A isoform 1 190_191 glycolysis|pyruvate metabolic process cytosol L-lactate dehydrogenase activity|protein binding central_nervous_system(3) 3 NADH(DB00157) GGTGGGTCCTTGGGGAACATGG 0.411 0.19 132 30 NUMA1 4926 broad.mit.edu 37 11 71718403 71718403 + Frame_Shift_Del DEL G - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr11:71718403delG uc001orl.1 - 21 5467 c.5295delC c.(5293-5295)CCCfs p.P1765fs NUMA1_uc001orj.2_5'UTR|NUMA1_uc009ysw.1_Frame_Shift_Del_p.P1332fs|NUMA1_uc001ork.1_Frame_Shift_Del_p.P629fs|NUMA1_uc001orm.1_Frame_Shift_Del_p.P1751fs|NUMA1_uc001orn.2_3'UTR NM_006185 NP_006176 Q14980 NUMA1_HUMAN nuclear mitotic apparatus protein 1 1765 G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole protein binding|structural molecule activity ovary(3)|lung(2)|skin(2)|central_nervous_system(1) 8 ATTCTACCTTGGGGGGCAGGC 0.622 0.46 58 50 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 813 372 MLL 4297 broad.mit.edu 37 11 118307387 118307387 + Frame_Shift_Del DEL C - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr11:118307387delC uc001pta.2 + 1 183 c.160delC c.(160-162)CCCfs p.P54fs MLL_uc001ptb.2_Frame_Shift_Del_p.P54fs|uc001psy.2_5'Flank|MLL_uc001psz.1_Frame_Shift_Del_p.P54fs NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 54 Ala/Gly/Ser-rich. apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) 0.000 0.17 396 84 LRP1 4035 broad.mit.edu 37 12 57603940 57603940 + Frame_Shift_Del DEL C - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr12:57603940delC uc001snd.2 + 81 13034 c.12568delC c.(12568-12570)CCCfs p.P4190fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 4190 Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CTCTCCAACGCCCCCCCCAGA 0.637 0.40 88 59 XPO4 64328 broad.mit.edu 37 13 21357948 21357950 + In_Frame_Del DEL AGG - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr13:21357948_21357950delAGG uc001unq.3 - 23 3403_3405 c.3367_3369delCCT c.(3367-3369)CCTdel p.P1123del NM_022459 NP_071904 Q9C0E2 XPO4_HUMAN exportin 4 1123 protein transport cytoplasm|nucleus protein binding large_intestine(1)|ovary(1)|kidney(1) 3 all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244) all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548) GATCCAGCGTAGGAGGAGTGCTG 0.414 0.13 144 22 NIN 51199 broad.mit.edu 37 14 51237236 51237236 + Frame_Shift_Del DEL T - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr14:51237236delT uc001wym.2 - 12 1495 c.1304delA c.(1303-1305)AATfs p.N435fs NIN_uc001wyi.2_Frame_Shift_Del_p.N435fs|NIN_uc001wyj.2_RNA|NIN_uc001wyk.2_Frame_Shift_Del_p.N435fs|NIN_uc010tqp.1_Frame_Shift_Del_p.N441fs|NIN_uc001wyo.2_Frame_Shift_Del_p.N435fs|NIN_uc001wyp.1_Frame_Shift_Del_p.N397fs NM_182946 NP_891991 Q8N4C6 NIN_HUMAN ninein isoform 5 435 Potential. centrosome localization centrosome|microtubule calcium ion binding|GTP binding|protein binding skin(3)|ovary(1)|kidney(1)|central_nervous_system(1) 6 all_epithelial(31;0.00244)|Breast(41;0.127) TCGGAGTTCATTTTTTAAGGC 0.438 0.52 163 180 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.29 61 25 TRIP11 9321 broad.mit.edu 37 14 92465620 92465620 + Frame_Shift_Del DEL T - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr14:92465620delT uc001xzy.2 - 13 5644 c.4856delA c.(4855-4857)AAGfs p.K1619fs TRIP11_uc010auf.1_Frame_Shift_Del_p.K1355fs NM_004239 NP_004230 Q15643 TRIPB_HUMAN thyroid hormone receptor interactor 11 1619 Potential. transcription from RNA polymerase II promoter cytoskeleton|Golgi apparatus|membrane|nucleus protein binding|transcription coactivator activity ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1) 13 COAD - Colon adenocarcinoma(157;0.223) TGAAACTAGCTTTTCCTCCAA 0.279 0.26 107 38 BCAR1 9564 broad.mit.edu 37 16 75269097 75269097 + Frame_Shift_Del DEL C - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr16:75269097delC uc002fdv.2 - 5 1823 c.1700delG c.(1699-1701)GGAfs p.G567fs BCAR1_uc002fdt.2_Frame_Shift_Del_p.G20fs|BCAR1_uc002fdu.2_Frame_Shift_Del_p.G357fs|BCAR1_uc010cgu.2_Frame_Shift_Del_p.G556fs|BCAR1_uc010vna.1_Frame_Shift_Del_p.G565fs|BCAR1_uc010vnb.1_Frame_Shift_Del_p.G613fs|BCAR1_uc002fdw.2_Frame_Shift_Del_p.G567fs|BCAR1_uc010vnc.1_Frame_Shift_Del_p.G419fs|BCAR1_uc010vnd.1_Frame_Shift_Del_p.G585fs|BCAR1_uc002fdx.2_Frame_Shift_Del_p.G585fs NM_014567 NP_055382 P56945 BCAR1_HUMAN breast cancer anti-estrogen resistance 1 567 Ser-rich. actin filament organization|B cell receptor signaling pathway|blood coagulation|cell adhesion|cell division|cell migration|cell proliferation|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|integrin-mediated signaling pathway|nerve growth factor receptor signaling pathway|platelet-derived growth factor receptor signaling pathway|positive regulation of cell migration|regulation of apoptosis|regulation of cell growth|T cell receptor signaling pathway cytosol|focal adhesion|membrane fraction|ruffle protein kinase binding|protein phosphatase binding|SH3 domain binding|signal transducer activity central_nervous_system(5)|breast(2)|prostate(1) 8 BRCA - Breast invasive adenocarcinoma(221;0.169) 0.000 0.48 187 173 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 37 502 MAP2K3 5606 broad.mit.edu 37 17 21215536 21215536 + Frame_Shift_Del DEL C - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr17:21215536delC uc002gys.2 + 10 1122 c.857delC c.(856-858)TCCfs p.S286fs MAP2K3_uc002gyt.2_Frame_Shift_Del_p.S257fs|MAP2K3_uc002gyu.2_Frame_Shift_Del_p.S257fs NM_145109 NP_659731 P46734 MP2K3_HUMAN mitogen-activated protein kinase kinase 3 286 Protein kinase. activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity 0 COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553) GAGGAGCCGTCCCCCCAGCTC 0.652 0.12 348 46 USP32 84669 broad.mit.edu 37 17 58285492 58285492 + Frame_Shift_Del DEL T - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr17:58285492delT uc002iyo.1 - 24 3139 c.2853delA c.(2851-2853)AAAfs p.K951fs USP32_uc002iyn.1_Frame_Shift_Del_p.K621fs NM_032582 NP_115971 Q8NFA0 UBP32_HUMAN ubiquitin specific protease 32 951 protein deubiquitination|ubiquitin-dependent protein catabolic process Golgi apparatus|membrane calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity lung(2)|breast(2)|large_intestine(1) 5 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198) CACTCAGCTGTTTTTTTAAAC 0.343 0.31 9 4 GRB2 2885 broad.mit.edu 37 17 73322091 73322092 + Frame_Shift_Ins INS - A A SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr17:73322091_73322092insA uc002jnx.3 - 4 543_544 c.186_187insT c.(184-189)TTTGGCfs p.F62fs GRB2_uc002jny.3_Intron NM_002086 NP_002077 P62993 GRB2_HUMAN growth factor receptor-bound protein 2 isoform 62_63 SH2. axon guidance|blood coagulation|cell junction assembly|cell-cell signaling|cellular response to ionizing radiation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|receptor internalization|signal transduction in response to DNA damage|T cell costimulation cytosol|Golgi apparatus epidermal growth factor receptor binding|insulin receptor substrate binding|SH3/SH2 adaptor activity ovary(3) 3 all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222) all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185) Pegademase bovine(DB00061) GGGATTTTGCCAAAAAACCACC 0.500 0.43 66 50 ITGB4 3691 broad.mit.edu 37 17 73725372 73725373 + Frame_Shift_Ins INS - C C SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr17:73725372_73725373insC uc002jpg.2 + 7 780_781 c.593_594insC c.(592-594)GACfs p.D198fs ITGB4_uc002jph.2_Frame_Shift_Ins_p.D198fs|ITGB4_uc010dgo.2_Frame_Shift_Ins_p.D198fs|ITGB4_uc002jpi.3_Frame_Shift_Ins_p.D198fs|ITGB4_uc010dgp.1_Frame_Shift_Ins_p.D198fs|ITGB4_uc002jpj.2_Frame_Shift_Ins_p.D198fs|ITGB4_uc010wsh.1_5'Flank NM_000213 NP_000204 P16144 ITB4_HUMAN integrin beta 4 isoform 1 precursor 198 VWFA.|Extracellular (Potential). cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding cell leading edge|cell surface|hemidesmosome|integrin complex protein binding|receptor activity lung(4) 4 all_cancers(13;1.5e-07) all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154) CCCAACAGTGACCCCCCCTTCT 0.599 0.47 70 63 AATK 9625 broad.mit.edu 37 17 79095285 79095285 + Frame_Shift_Del DEL G - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr17:79095285delG uc010dia.2 - 11 2531 c.2451delC c.(2449-2451)CCCfs p.P817fs AATK_uc010dhz.2_RNA NM_001080395 NP_001073864 Q6ZMQ8 LMTK1_HUMAN apoptosis-associated tyrosine kinase 817 Pro-rich. integral to membrane|mitochondrion|perinuclear region of cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1) 9 all_neural(118;0.101) BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524) 0.000 0.11 834 100 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.82 34 153 CYP2B6 1555 broad.mit.edu 37 19 41510031 41510031 + Frame_Shift_Del DEL A - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr19:41510031delA uc002opr.1 + 2 304 c.297delA c.(295-297)GGAfs p.G99fs CYP2A7_uc002opo.2_Intron|CYP2B6_uc010xvu.1_Frame_Shift_Del_p.G59fs NM_000767 NP_000758 P20813 CP2B6_HUMAN cytochrome P450, family 2, subfamily B, 99 cellular ketone metabolic process|exogenous drug catabolic process|steroid metabolic process|xenobiotic metabolic process endoplasmic reticulum membrane|microsome aromatase activity|electron carrier activity|heme binding|oxygen binding ovary(1)|skin(1) 2 LUSC - Lung squamous cell carcinoma(20;0.00322) Bupropion(DB01156)|Butalbital(DB00241)|Carbamazepine(DB00564)|Clopidogrel(DB00758)|Cyclophosphamide(DB00531)|Efavirenz(DB00625)|Ifosfamide(DB01181)|Memantine(DB01043)|Meperidine(DB00454)|Mephenytoin(DB00532)|Methadone(DB00333)|Methylphenobarbital(DB00849)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicotine(DB00184)|Orphenadrine(DB01173)|Phenytoin(DB00252)|Propofol(DB00818)|Ritonavir(DB00503)|Selegiline(DB01037)|Sertraline(DB01104)|Ticlopidine(DB00208)|Troleandomycin(DB01361) 0.000 0.49 299 285 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 38 7 COL18A1 80781 broad.mit.edu 37 21 46917559 46917559 + Frame_Shift_Del DEL C - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr21:46917559delC uc011afs.1 + 31 3933 c.3912delC c.(3910-3912)GGCfs p.G1304fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.G889fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.G1069fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1304 Triple-helical region 7 (COL7). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.43 585 449 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 107 411 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 104 XBP1 7494 broad.mit.edu 37 22 29196351 29196351 + Frame_Shift_Del DEL C - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr22:29196351delC uc011akl.1 - 1 210 c.162delG c.(160-162)GGGfs p.G54fs XBP1_uc003aed.2_5'Flank|XBP1_uc003aef.2_5'UTR NM_001079539 NP_001073007 P17861 XBP1_HUMAN X-box binding protein 1 isoform XBP1(S) 54 immune response nucleus protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity breast(1) 1 0.000 0.29 218 88 PATZ1 23598 broad.mit.edu 37 22 31741482 31741482 + Frame_Shift_Del DEL T - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr22:31741482delT uc003akq.2 - 1 768 c.107delA c.(106-108)AACfs p.N36fs PATZ1_uc003akp.2_Frame_Shift_Del_p.N36fs|PATZ1_uc003akr.2_Frame_Shift_Del_p.N36fs|PATZ1_uc003aks.2_Frame_Shift_Del_p.N36fs|uc003akt.2_5'Flank NM_014323 NP_055138 Q9HBE1 PATZ1_HUMAN POZ (BTB) and AT hook containing zinc finger 1 36 negative regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding EWSR1/PATZ1(2) soft_tissue(2) 2 GCGCCCGCCGTTTTTGCGCTG 0.647 0.14 94 15 TNRC6B 23112 broad.mit.edu 37 22 40662764 40662764 + Frame_Shift_Del DEL C - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr22:40662764delC uc011aor.1 + 5 2741 c.2530delC c.(2530-2532)CCCfs p.P844fs TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Frame_Shift_Del_p.P844fs|TNRC6B_uc003ayo.2_Frame_Shift_Del_p.P648fs NM_001162501 NP_001155973 Q9UPQ9 TNR6B_HUMAN trinucleotide repeat containing 6B isoform 1 844 Pro-rich. gene silencing by RNA|regulation of translation cytoplasmic mRNA processing body nucleotide binding|RNA binding 0 GGGAGGCCCACCCCCACCACC 0.612 0.36 18 10 MAPK8IP2 23542 broad.mit.edu 37 22 51045156 51045156 + Frame_Shift_Del DEL G - - SNGM_ENDOMETRIUM NA SNGM_ENDOMETRIUM NA g.chr22:51045156delG uc003bmx.2 + 10 2312 c.2195delG c.(2194-2196)CGGfs p.R732fs MAPK8IP2_uc003bmy.2_Frame_Shift_Del_p.R705fs|MAPK8IP2_uc011asc.1_Frame_Shift_Del_p.R86fs NM_012324 NP_036456 Q13387 JIP2_HUMAN mitogen-activated protein kinase 8 interacting 732 PID. behavioral fear response|dendrite morphogenesis|MAPKKK cascade|nonassociative learning|positive regulation of anti-apoptosis|regulation of excitatory postsynaptic membrane potential|regulation of JNK cascade|regulation of receptor activity|regulation of synaptic transmission, glutamatergic|signal complex assembly|social behavior cytoplasm|postsynaptic density beta-amyloid binding|kinesin binding|MAP-kinase scaffold activity|protein kinase activator activity|protein kinase binding large_intestine(2)|central_nervous_system(1) 3 all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) OV - Ovarian serous cystadenocarcinoma(4;1.28e-70)|Epithelial(4;3.46e-65)|GBM - Glioblastoma multiforme(4;4.83e-06)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247) ATCTCTCTTCGGGGGGTCAAG 0.647 0.44 101 79 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.62 20 33 NFIA 4774 broad.mit.edu 37 1 61872302 61872303 + In_Frame_Ins INS - CCACCA CCACCA SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr1:61872302_61872303insCCACCA uc001czw.2 + 9 1807_1808 c.1323_1324insCCACCA c.(1321-1326)insCCACCA p.443_444insPP NFIA_uc001czy.2_In_Frame_Ins_p.435_436insPP|NFIA_uc010oos.1_In_Frame_Ins_p.488_489insPP|NFIA_uc001czv.2_In_Frame_Ins_p.443_444insPP|NFIA_uc001czx.2_In_Frame_Ins_p.91_92insPP|NFIA_uc009wae.2_RNA NM_001134673 NP_001128145 Q12857 NFIA_HUMAN nuclear factor I/A isoform 1 443_444 DNA replication|viral genome replication cell junction|nucleus DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding pancreas(1)|skin(1) 2 CACCGCCACCGCCACCACCGAT 0.634 0.26 98 34 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 302 64 KIAA1804 84451 broad.mit.edu 37 1 233464274 233464280 + Frame_Shift_Del DEL GCGTGCG - - SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr1:233464274_233464280delGCGTGCG uc001hvt.3 + 1 761_767 c.500_506delGCGTGCG c.(499-507)AGCGTGCGGfs p.S167fs KIAA1804_uc001hvs.1_Frame_Shift_Del_p.S167fs NM_032435 NP_115811 Q5TCX8 M3KL4_HUMAN mixed lineage kinase 4 167_169 Protein kinase. activation of JUN kinase activity|protein autophosphorylation ATP binding|MAP kinase kinase kinase activity|protein homodimerization activity lung(5)|central_nervous_system(2)|skin(1) 8 all_cancers(173;0.000405)|all_epithelial(177;0.0345)|Prostate(94;0.122) 0.000 0.30 1033 451 RIF1 55183 broad.mit.edu 37 2 152320713 152320715 + In_Frame_Del DEL AAG - - SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr2:152320713_152320715delAAG uc002txm.2 + 30 4809_4811 c.4679_4681delAAG c.(4678-4683)AAAGAA>AAA p.E1562del RIF1_uc002txl.2_In_Frame_Del_p.E1562del|RIF1_uc002txn.2_In_Frame_Del_p.E1562del|RIF1_uc002txo.2_In_Frame_Del_p.E1562del|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1562 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) TCGGAGGCAAAAGAAGAAGGTTC 0.404 0.27 43 16 STK17B 9262 broad.mit.edu 37 2 197021291 197021293 + In_Frame_Del DEL TCT - - rs144100898 by1000genomes SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr2:197021291_197021293delTCT uc002utk.2 - 3 529_531 c.205_207delAGA c.(205-207)AGAdel p.R69del STK17B_uc010fsh.2_In_Frame_Del_p.R69del NM_004226 NP_004217 O94768 ST17B_HUMAN serine/threonine kinase 17B 69 Protein kinase. apoptosis|induction of apoptosis|intracellular protein kinase cascade nucleus ATP binding|protein serine/threonine kinase activity lung(2) 2 OV - Ovarian serous cystadenocarcinoma(117;0.141) AATCCTGTCCTCTTCTTCTCTTT 0.379 0.33 116 58 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.27 54 20 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.46 19 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.32 51 24 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.90 1 9 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.70 3 7 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 21 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 2 29 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 181 26 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.34 31 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 62 527 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.33 58 28 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 99 391 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU1033_LARGE_INTESTINE NA SNU1033_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 58 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 18 TAL1 6886 broad.mit.edu 37 1 47691411 47691412 + Frame_Shift_Ins INS - G G SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr1:47691411_47691412insG uc001cqx.2 - 2 726_727 c.149_150insC c.(148-150)CCAfs p.P50fs TAL1_uc009vyq.2_5'Flank|TAL1_uc001cqy.2_Frame_Shift_Ins_p.P50fs|TAL1_uc001cra.1_Intron|TAL1_uc001cqz.1_Intron NM_003189 NP_003180 P17542 TAL1_HUMAN T-cell acute lymphocytic leukemia 1 50 basophil differentiation|cell fate commitment|cell proliferation|embryonic hemopoiesis|erythrocyte differentiation|megakaryocyte differentiation|positive regulation of cell division|positive regulation of chromatin assembly or disassembly|positive regulation of erythrocyte differentiation|positive regulation of mitotic cell cycle|positive regulation of protein complex assembly|positive regulation of transcription from RNA polymerase II promoter nuclear chromatin E-box binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity lung(1) 1 0.000 0.28 296 116 TAL1 6886 broad.mit.edu 37 1 47691475 47691475 + Frame_Shift_Del DEL G - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr1:47691475delG uc001cqx.2 - 2 663 c.86delC c.(85-87)CCGfs p.P29fs TAL1_uc009vyq.2_5'Flank|TAL1_uc001cqy.2_Frame_Shift_Del_p.P29fs|TAL1_uc001cra.1_Intron|TAL1_uc001cqz.1_Intron NM_003189 NP_003180 P17542 TAL1_HUMAN T-cell acute lymphocytic leukemia 1 29 basophil differentiation|cell fate commitment|cell proliferation|embryonic hemopoiesis|erythrocyte differentiation|megakaryocyte differentiation|positive regulation of cell division|positive regulation of chromatin assembly or disassembly|positive regulation of erythrocyte differentiation|positive regulation of mitotic cell cycle|positive regulation of protein complex assembly|positive regulation of transcription from RNA polymerase II promoter nuclear chromatin E-box binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity lung(1) 1 0.000 0.51 500 523 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.26 214 74 NUAK2 81788 broad.mit.edu 37 1 205273141 205273141 + Frame_Shift_Del DEL G - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr1:205273141delG uc001hce.2 - 7 1451 c.1324delC c.(1324-1326)CTGfs p.L442fs NM_030952 NP_112214 Q9H093 NUAK2_HUMAN NUAK family, SNF1-like kinase, 2 442 actin cytoskeleton organization|apoptosis|cellular response to glucose starvation|negative regulation of apoptosis ATP binding|magnesium ion binding|protein serine/threonine kinase activity ovary(3)|stomach(1)|breast(1) 5 Breast(84;0.186) BRCA - Breast invasive adenocarcinoma(75;0.117) TTGGGGAGCAGGGGGGCAGCC 0.632 0.54 37 43 PARP1 142 broad.mit.edu 37 1 226570820 226570820 + Frame_Shift_Del DEL G - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr1:226570820delG uc001hqd.3 - 8 1247 c.1076delC c.(1075-1077)CCAfs p.P359fs NM_001618 NP_001609 P09874 PARP1_HUMAN poly (ADP-ribose) polymerase family, member 1 359 cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter nuclear envelope|nucleolus|transcription factor complex DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding lung(3)|ovary(2)|breast(2)|skin(2)|upper_aerodigestive_tract(1) 10 Breast(184;0.133) GBM - Glioblastoma multiforme(131;0.0531) GCTGGTTTCTGGGGGGAATAT 0.502 0.58 22 30 ROCK2 9475 broad.mit.edu 37 2 11427810 11427810 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr2:11427810delT uc002rbd.1 - 2 643 c.194delA c.(193-195)AACfs p.N65fs NM_004850 NP_004841 O75116 ROCK2_HUMAN Rho-associated, coiled-coil containing protein 65 axon guidance|cytokinesis|intracellular signal transduction cytosol|plasma membrane ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity stomach(2)|skin(2) 4 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162) TATGTTCTTGTTTTTCCTCAA 0.274 0.57 17 23 CYP1B1 1545 broad.mit.edu 37 2 38301664 38301664 + Frame_Shift_Del DEL G - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr2:38301664delG uc002rqo.2 - 3 1271 c.868delC c.(868-870)CGCfs p.R290fs NM_000104 NP_000095 Q16678 CP1B1_HUMAN cytochrome P450, family 1, subfamily B, 290 visual perception|xenobiotic metabolic process endoplasmic reticulum membrane|microsome aromatase activity|electron carrier activity|heme binding|oxygen binding|protein binding ovary(1)|central_nervous_system(1) 2 all_hematologic(82;0.21) Estrone(DB00655) 0.000 0.40 945 624 LRP2 4036 broad.mit.edu 37 2 169997025 169997025 + Frame_Shift_Del DEL G - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr2:169997025delG uc002ues.2 - 72 13352 c.13139delC c.(13138-13140)CCAfs p.P4380fs NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 4380 EGF-like 17.|Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) 0.000 0.51 204 211 TTN 7273 broad.mit.edu 37 2 179549440 179549440 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr2:179549440delT uc010zfg.1 - 128 29083 c.28859delA c.(28858-28860)AAGfs p.K9620fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.K6281fs|TTN_uc010fre.1_Intron NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10547 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TGGAGGAACCTTTTTTTCTGG 0.408 0.48 27 25 SMARCC1 6599 broad.mit.edu 37 3 47677559 47677559 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr3:47677559delT uc003crq.2 - 23 2562 c.2444delA c.(2443-2445)AATfs p.N815fs SMARCC1_uc011bbc.1_RNA|SMARCC1_uc011bbd.1_Frame_Shift_Del_p.N706fs NM_003074 NP_003065 Q92922 SMRC1_HUMAN SWI/SNF-related matrix-associated 815 Glu-rich. chromatin remodeling|nervous system development|transcription, DNA-dependent nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex DNA binding|protein N-terminus binding|transcription coactivator activity skin(2)|lung(1) 3 BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01) 0.000 0.37 129 77 NEK11 79858 broad.mit.edu 37 3 130828691 130828691 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr3:130828691delA uc003eny.2 + 5 707 c.381delA c.(379-381)GGAfs p.G127fs NEK11_uc003enx.2_Frame_Shift_Del_p.G127fs|NEK11_uc003eoa.2_Frame_Shift_Del_p.G127fs|NEK11_uc003enz.2_5'UTR|NEK11_uc010htn.2_RNA|NEK11_uc011blk.1_5'UTR|NEK11_uc011bll.1_Frame_Shift_Del_p.G127fs|NEK11_uc003enw.1_Frame_Shift_Del_p.G127fs|NEK11_uc011blm.1_Frame_Shift_Del_p.G127fs|NEK11_uc010hto.1_5'UTR NM_024800 NP_079076 Q8NG66 NEK11_HUMAN NIMA-related kinase 11 isoform 1 127 Protein kinase. cell cycle|intra-S DNA damage checkpoint|intracellular protein kinase cascade nucleolus ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity large_intestine(4)|stomach(1)|central_nervous_system(1) 6 AACAAGCTGGAAAAATCTTTC 0.368 0.40 58 39 GPR87 53836 broad.mit.edu 37 3 151012006 151012007 + Frame_Shift_Ins INS - T T SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr3:151012006_151012007insT uc003eyt.2 - 3 1388_1389 c.1027_1028insA c.(1027-1029)AGTfs p.S343fs MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron NM_023915 NP_076404 Q9BY21 GPR87_HUMAN G protein-coupled receptor 87 343 Cytoplasmic (Potential). integral to membrane|plasma membrane purinergic nucleotide receptor activity, G-protein coupled large_intestine(1) 1 LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517) TCTTCTCACACTTTGCAGTGAT 0.337 0.39 48 31 TACC3 10460 broad.mit.edu 37 4 1737038 1737038 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr4:1737038delT uc003gdo.2 + 7 1738 c.1630delT c.(1630-1632)TTTfs p.F544fs TACC3_uc010ibz.2_Frame_Shift_Del_p.F544fs|TACC3_uc003gdp.2_Frame_Shift_Del_p.F184fs|TACC3_uc010ica.2_5'UTR NM_006342 NP_006333 Q9Y6A5 TACC3_HUMAN transforming, acidic coiled-coil containing 544 centrosome ovary(1)|central_nervous_system(1) 2 Breast(71;0.212)|all_epithelial(65;0.241) OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126) 0.000 0.52 815 883 FGFR3 2261 broad.mit.edu 37 4 1806180 1806181 + Frame_Shift_Ins INS - C C SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr4:1806180_1806181insC uc003gdr.3 + 9 1455_1456 c.1199_1200insC c.(1198-1200)AGCfs p.S400fs FGFR3_uc003gdu.2_Frame_Shift_Ins_p.S402fs|FGFR3_uc003gds.3_Intron|FGFR3_uc003gdq.3_Frame_Shift_Ins_p.S400fs NM_000142 NP_000133 P22607 FGFR3_HUMAN fibroblast growth factor receptor 3 isoform 1 400 Cytoplasmic (Potential). bone maturation|cell growth|insulin receptor signaling pathway|JAK-STAT cascade|MAPKKK cascade|negative regulation of developmental growth|positive regulation of cell proliferation integral to plasma membrane ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|identical protein binding urinary_tract(2177)|skin(314)|upper_aerodigestive_tract(57)|haematopoietic_and_lymphoid_tissue(24)|prostate(9)|cervix(6)|central_nervous_system(4)|large_intestine(3)|lung(3)|testis(2)|pancreas(1) 2600 Breast(71;0.212)|all_epithelial(65;0.241) all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234) Palifermin(DB00039) CGCCTGCGCAGCCCCCCCAAGA 0.629 0.40 24 16 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.45 18 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.34 77 40 INPP4B 8821 broad.mit.edu 37 4 143007332 143007332 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr4:143007332delT uc003iix.3 - 25 3047 c.2452delA c.(2452-2454)AGAfs p.R818fs INPP4B_uc003iiw.3_Frame_Shift_Del_p.R818fs|INPP4B_uc011chm.1_RNA|INPP4B_uc011chn.1_Frame_Shift_Del_p.R633fs|INPP4B_uc011cho.1_RNA NM_003866 NP_003857 O15327 INP4B_HUMAN inositol polyphosphate-4-phosphatase, type II, 818 signal transduction phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity ovary(1)|lung(1) 2 all_hematologic(180;0.158) ACATTCTTTCTTTTTTTGGAT 0.343 0.51 38 39 FBXW7 55294 broad.mit.edu 37 4 153332463 153332463 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr4:153332463delT uc003ims.2 - 2 642 c.493delA c.(493-495)ACAfs p.T165fs FBXW7_uc011cii.1_Frame_Shift_Del_p.T165fs|FBXW7_uc003imt.2_Frame_Shift_Del_p.T165fs|FBXW7_uc003imu.2_Frame_Shift_Del_p.T165fs NM_033632 NP_361014 Q969H0 FBXW7_HUMAN F-box and WD repeat domain containing 7 isoform 165 interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex protein binding|protein binding haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1) 308 all_hematologic(180;0.093) Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067) ACTTTTGTTGTTTTTGTATAG 0.343 0.50 60 61 NKD2 85409 broad.mit.edu 37 5 1009175 1009175 + Frame_Shift_Del DEL G - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr5:1009175delG uc003jbt.1 + 1 8 c.3delG c.(1-3)ATGfs p.M1fs NKD2_uc010itf.1_Frame_Shift_Del_p.M1fs NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 1 exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.27 624 232 TRIO 7204 broad.mit.edu 37 5 14477003 14477004 + Frame_Shift_Ins INS - T T SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr5:14477003_14477004insT uc003jff.2 + 41 6090_6091 c.6084_6085insT c.(6082-6087)GACTTTfs p.D2028fs TRIO_uc003jfg.2_RNA|TRIO_uc003jfh.1_Frame_Shift_Ins_p.D1677fs NM_007118 NP_009049 O75962 TRIO_HUMAN triple functional domain (PTPRF interacting) 2028_2029 DH 2. apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway cytosol ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1) 18 Lung NSC(4;0.000742) TTCTTTCCAGCTTTTTTTTAGG 0.292 0.31 53 24 NIPBL 25836 broad.mit.edu 37 5 37064899 37064899 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr5:37064899delA uc003jkl.3 + 47 8819 c.8320delA c.(8320-8322)AAAfs p.K2774fs NIPBL_uc003jkk.3_3'UTR|NIPBL_uc003jkn.2_3'UTR NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 2774 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) CATTATTTACAAAAAAATTGC 0.463 0.33 81 39 APC 324 broad.mit.edu 37 5 112178033 112178033 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr5:112178033delA uc010jby.2 + 16 7122 c.6742delA c.(6742-6744)AAAfs p.K2248fs APC_uc011cvt.1_Frame_Shift_Del_p.K2230fs|APC_uc003kpz.3_Frame_Shift_Del_p.K2248fs|APC_uc003kpy.3_Frame_Shift_Del_p.K2248fs|APC_uc010jbz.2_Frame_Shift_Del_p.K1965fs|APC_uc010jca.2_Frame_Shift_Del_p.K1548fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 2248 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.?(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) TCCTGTTTCTAAAAAAGGCCC 0.478 0.41 44 30 ZNF608 57507 broad.mit.edu 37 5 123983146 123983146 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr5:123983146delT uc003ktq.1 - 4 3054 c.2931delA c.(2929-2931)AAAfs p.K977fs ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Frame_Shift_Del_p.K977fs|ZNF608_uc003ktt.1_Frame_Shift_Del_p.K977fs|ZNF608_uc003ktp.1_5'Flank NM_020747 NP_065798 Q9ULD9 ZN608_HUMAN zinc finger protein 608 977 Ser-rich. intracellular zinc ion binding skin(3)|ovary(2)|lung(1) 6 all_cancers(142;0.186)|Prostate(80;0.081) KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221) OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783) AAGAATGCCCTTTTACAACAC 0.438 0.46 67 58 FBN2 2201 broad.mit.edu 37 5 127610311 127610311 + Frame_Shift_Del DEL C - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr5:127610311delC uc003kuu.2 - 60 8098 c.7659delG c.(7657-7659)GGGfs p.G2553fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 2553 EGF-like 43; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) TACAGGTAAACCCCCCCAGGG 0.423 0.40 96 63 CDC25C 995 broad.mit.edu 37 5 137627690 137627690 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr5:137627690delT uc003lcp.1 - 8 1002 c.731delA c.(730-732)AAGfs p.K244fs CDC25C_uc003lcq.1_Frame_Shift_Del_p.K171fs|CDC25C_uc003lcr.1_Frame_Shift_Del_p.K244fs|CDC25C_uc011cyp.1_Frame_Shift_Del_p.K261fs|CDC25C_uc003lcs.1_Frame_Shift_Del_p.K322fs NM_001790 NP_001781 P30307 MPIP3_HUMAN cell division cycle 25C isoform a 244 cell cycle checkpoint|cell division|cell proliferation|DNA replication|G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis|traversing start control point of mitotic cell cycle cytosol|nucleoplasm protein tyrosine phosphatase activity|WW domain binding lung(3) 3 KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592) AGAAAAATACTTTTTTTTAAC 0.388 0.40 75 51 DCTN4 51164 broad.mit.edu 37 5 150135984 150135985 + Frame_Shift_Ins INS - T T SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr5:150135984_150135985insT uc003lsv.2 - 2 302_303 c.200_201insA c.(199-201)AAGfs p.K67fs DCTN4_uc003lsu.2_Frame_Shift_Ins_p.K10fs|DCTN4_uc010jhi.2_Frame_Shift_Ins_p.K67fs|DCTN4_uc010jhj.2_RNA|DCTN4_uc011dck.1_Frame_Shift_Ins_p.K10fs NM_016221 NP_057305 Q9UJW0 DCTN4_HUMAN dynactin 4 (p62) isoform b 67 centrosome|nucleus protein N-terminus binding central_nervous_system(1) 1 Medulloblastoma(196;0.167) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) 0.000 0.11 73 9 HNRNPH1 3187 broad.mit.edu 37 5 179044644 179044644 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr5:179044644delA uc003mkf.3 - 9 1034 c.928delT c.(928-930)TCAfs p.S310fs HNRNPH1_uc011dgn.1_Frame_Shift_Del_p.S40fs|HNRNPH1_uc003mkg.3_Frame_Shift_Del_p.S218fs|HNRNPH1_uc003mke.3_Frame_Shift_Del_p.S310fs|HNRNPH1_uc003mkh.3_Frame_Shift_Del_p.S310fs NM_005520 NP_005511 P31943 HNRH1_HUMAN heterogeneous nuclear ribonucleoprotein H1 310 RRM 3.|2 X 16 AA Gly-rich approximate repeats. regulation of RNA splicing actin cytoskeleton|catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm nucleotide binding|poly(U) RNA binding|protein binding 0 TTGAGCGGTGAAAAAAACTAC 0.383 0.40 81 54 NUP153 9972 broad.mit.edu 37 6 17629508 17629508 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr6:17629508delT uc003ncd.1 - 18 3122 c.2922delA c.(2920-2922)AAAfs p.K974fs NUP153_uc011dje.1_Frame_Shift_Del_p.K1005fs|NUP153_uc010jpl.1_Frame_Shift_Del_p.K932fs NM_005124 NP_005115 P49790 NU153_HUMAN nucleoporin 153kDa 974 carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm DNA binding|protein binding|transporter activity|zinc ion binding lung(4)|ovary(2)|breast(2)|skin(1) 9 Breast(50;0.0259)|Ovarian(93;0.0584) all_hematologic(90;0.125) all cancers(50;0.0981)|Epithelial(50;0.112) TCTTACTATCTTTTTTAACTT 0.333 0.46 79 68 DNAH8 1769 broad.mit.edu 37 6 38773275 38773275 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr6:38773275delT uc003ooe.1 + 21 3002 c.2402delT c.(2401-2403)GTTfs p.V801fs NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 AAACACGTTGTTTTTGGAAGT 0.323 0.52 28 30 CDC5L 988 broad.mit.edu 37 6 44371563 44371563 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr6:44371563delA uc003oxl.2 + 6 816 c.557delA c.(556-558)CAAfs p.Q186fs NM_001253 NP_001244 Q99459 CDC5L_HUMAN CDC5-like 186 Potential. cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus DNA binding|RNA binding lung(3)|ovary(1)|kidney(1)|skin(1) 6 all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208) Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536) GCTGCCCTCCAAAAAAGAAGA 0.353 0.53 40 46 CDC5L 988 broad.mit.edu 37 6 44374080 44374081 + Frame_Shift_Ins INS - A A SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr6:44374080_44374081insA uc003oxl.2 + 7 1038_1039 c.779_780insA c.(778-780)AGAfs p.R260fs NM_001253 NP_001244 Q99459 CDC5L_HUMAN CDC5-like 260 Interaction with PPP1R8. cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus DNA binding|RNA binding lung(3)|ovary(1)|kidney(1)|skin(1) 6 all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208) Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536) GGAAGAGATAGAAAAAAAGACA 0.297 0.43 47 35 PKHD1 5314 broad.mit.edu 37 6 51890015 51890015 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr6:51890015delA uc003pah.1 - 32 4869 c.4593delT c.(4591-4593)TTTfs p.F1531fs PKHD1_uc003pai.2_Frame_Shift_Del_p.F1531fs NM_138694 NP_619639 P08F94 PKHD1_HUMAN fibrocystin isoform 1 1531 Extracellular (Potential).|IPT/TIG 10. cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body protein binding|receptor activity lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1) 44 Lung NSC(77;0.0605) GGCTTGCATTAAAAAAAGTTA 0.463 0.16 138 27 MLLT4 4301 broad.mit.edu 37 6 168352151 168352159 + In_Frame_Del DEL CCGCCACCC - - rs78309125 byFrequency;by1000genomes SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr6:168352151_168352159delCCGCCACCC uc003qwd.2 + 29 4235_4243 c.4093_4101delCCGCCACCC c.(4093-4101)CCGCCACCCdel p.PPP1368del MLLT4_uc003qwb.1_In_Frame_Del_p.PPP1353del|MLLT4_uc003qwc.1_In_Frame_Del_p.PPP1369del|MLLT4_uc003qwg.1_In_Frame_Del_p.PPP678del NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 1369_1371 Pro-rich. adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) AGACCTGCCTCCGCCACCCCCGCCACCTC 0.617 0.48 68 63 HOXA13 3209 broad.mit.edu 37 7 27237846 27237847 + Frame_Shift_Ins INS - T T SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr7:27237846_27237847insT uc003szb.1 - 2 1166_1167 c.1137_1138insA c.(1135-1140)AAAGTCfs p.K379fs uc003szc.1_5'Flank NM_000522 NP_000513 P31271 HXA13_HUMAN homeobox A13 379_380 Homeobox. skeletal system development nucleus sequence-specific DNA binding breast(1) 1 TTGTTGATGACTTTTTTCTCTT 0.426 0.40 103 68 HECW1 23072 broad.mit.edu 37 7 43351380 43351380 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr7:43351380delT uc003tid.1 + 4 651 c.46delT c.(46-48)TTTfs p.F16fs HECW1_uc011kbi.1_Frame_Shift_Del_p.F16fs|HECW1_uc003tie.1_Frame_Shift_Del_p.F48fs NM_015052 NP_055867 Q76N89 HECW1_HUMAN NEDD4-like ubiquitin-protein ligase 1 16 protein ubiquitination involved in ubiquitin-dependent protein catabolic process cytoplasm|nucleus ubiquitin-protein ligase activity ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1) 23 CCAGAACAGGTTTTTAGGCCT 0.572 0.59 9 13 AKAP9 10142 broad.mit.edu 37 7 91732039 91732039 + Frame_Shift_Del DEL G - - rs143306820 SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr7:91732039delG uc003ulg.2 + 46 11454 c.11229delG c.(11227-11229)ATGfs p.M3743fs AKAP9_uc003ulf.2_Frame_Shift_Del_p.M3735fs|AKAP9_uc003uli.2_Frame_Shift_Del_p.M3366fs|AKAP9_uc003ulj.2_Frame_Shift_Del_p.M1513fs|AKAP9_uc003ull.2_Frame_Shift_Del_p.M639fs NM_005751 NP_005742 Q99996 AKAP9_HUMAN A-kinase anchor protein 9 isoform 2 3747 G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport centrosome|cytosol|Golgi apparatus receptor binding breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1) 26 all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) TTGCCCGGATGGGGGGGCAGC 0.537 0.50 56 57 TRIM24 8805 broad.mit.edu 37 7 138213951 138213951 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr7:138213951delA uc003vuc.2 + 6 1187 c.972delA c.(970-972)GGAfs p.G324fs TRIM24_uc003vub.2_Frame_Shift_Del_p.G324fs NM_015905 NP_056989 O15164 TIF1A_HUMAN transcriptional intermediary factor 1 alpha 324 Potential. cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter cytoplasm chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1) 8 ATAAAAAAGGAAAAGCTCTAC 0.308 0.36 30 17 KIAA1549 57670 broad.mit.edu 37 7 138602537 138602538 + Frame_Shift_Ins INS - A A SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr7:138602537_138602538insA uc011kql.1 - 2 1883_1884 c.1834_1835insT c.(1834-1836)TCTfs p.S612fs KIAA1549_uc003vuk.3_Frame_Shift_Ins_p.S562fs|KIAA1549_uc011kqj.1_Frame_Shift_Ins_p.S612fs NM_020910 NP_065961 Q9HCM3 K1549_HUMAN hypothetical protein LOC57670 isoform 1 612 Ser-rich. integral to membrane KIAA1549/BRAF(229) central_nervous_system(229)|pancreas(1) 230 TTTATGCTCAGAAAAACTGGAA 0.505 0.50 28 28 KIAA1549 57670 broad.mit.edu 37 7 138603524 138603524 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr7:138603524delA uc011kql.1 - 2 897 c.848delT c.(847-849)TTAfs p.L283fs KIAA1549_uc003vuk.3_Frame_Shift_Del_p.L233fs|KIAA1549_uc011kqj.1_Frame_Shift_Del_p.L283fs NM_020910 NP_065961 Q9HCM3 K1549_HUMAN hypothetical protein LOC57670 isoform 1 283 integral to membrane KIAA1549/BRAF(229) central_nervous_system(229)|pancreas(1) 230 CCGGGAGCTTAAAAAAAGGGT 0.517 0.41 36 25 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.58 19 26 PPP3CC 5533 broad.mit.edu 37 8 22332542 22332543 + Frame_Shift_Ins INS - A A SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr8:22332542_22332543insA uc003xbs.2 + 2 452_453 c.125_126insA c.(124-126)TTAfs p.L42fs PPP3CC_uc003xbr.1_Frame_Shift_Ins_p.L42fs|PPP3CC_uc011kzi.1_Frame_Shift_Ins_p.L42fs|PPP3CC_uc003xbt.2_Frame_Shift_Ins_p.L42fs NM_005605 NP_005596 P48454 PP2BC_HUMAN protein phosphatase 3, catalytic subunit, gamma 42 activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals cytosol calmodulin binding|metal ion binding|phosphoprotein phosphatase activity ovary(1) 1 Prostate(55;0.104) BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835) GTTGATGTTTTAAAAAACCATT 0.381 0.50 52 53 ADAM18 8749 broad.mit.edu 37 8 39564382 39564382 + Frame_Shift_Del DEL C - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr8:39564382delC uc003xni.2 + 18 1976 c.1976delC c.(1975-1977)TCCfs p.S659fs ADAM18_uc010lww.2_RNA|ADAM18_uc010lwx.2_Frame_Shift_Del_p.S635fs NM_014237 NP_055052 Q9Y3Q7 ADA18_HUMAN a disintegrin and metalloprotease domain 18 659 Extracellular (Potential). cell differentiation|multicellular organismal development|proteolysis|spermatogenesis integral to membrane|membrane fraction metalloendopeptidase activity|zinc ion binding central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1) 6 all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112) LUSC - Lung squamous cell carcinoma(45;0.000199) CAGTTTGGTTCCCCAGGGGGT 0.318 0.52 46 49 MYST3 7994 broad.mit.edu 37 8 41836184 41836184 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr8:41836184delT uc010lxb.2 - 7 1563 c.1019delA c.(1018-1020)AACfs p.N340fs MYST3_uc010lxc.2_Frame_Shift_Del_p.N340fs|MYST3_uc003xon.3_Frame_Shift_Del_p.N340fs|MYST3_uc010lxd.2_Frame_Shift_Del_p.N340fs NM_001099412 NP_001092882 Q92794 MYST3_HUMAN MYST histone acetyltransferase (monocytic 340 Interaction with RUNX1-1. histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1) 7 all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211) all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983) Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171) CTTTAACCTGTTTTTTGGACG 0.398 0.49 67 65 TOX 9760 broad.mit.edu 37 8 59750826 59750826 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr8:59750826delT uc003xtw.1 - 5 959 c.738delA c.(736-738)AAAfs p.K246fs NM_014729 NP_055544 O94900 TOX_HUMAN thymus high mobility group box protein TOX 246 Nuclear localization signal (Potential). nucleus DNA binding kidney(2)|lung(1)|skin(1) 4 all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607) GAGTTTTTGGTTTTTTCCCCA 0.453 0.38 93 57 SGK3 23678 broad.mit.edu 37 8 67763086 67763086 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr8:67763086delT uc003xwr.2 + 16 1550 c.1251delT c.(1249-1251)CCTfs p.P417fs SGK3_uc003xwp.2_Frame_Shift_Del_p.P411fs|SGK3_uc003xwt.2_Frame_Shift_Del_p.P417fs|SGK3_uc003xwu.2_Frame_Shift_Del_p.P385fs NM_001033578 NP_001028750 Q96BR1 SGK3_HUMAN serum/glucocorticoid regulated kinase 3 isoform 417 Protein kinase. cell communication|response to stress cytoplasmic membrane-bounded vesicle|early endosome ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity ovary(1)|large_intestine(1)|lung(1)|breast(1) 4 Breast(64;0.186) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206) AGAATCATCCTTTTTTTGAAT 0.308 0.39 57 36 NBN 4683 broad.mit.edu 37 8 90967753 90967754 + Frame_Shift_Del DEL TT - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr8:90967753_90967754delTT uc003yej.1 - 10 1264_1265 c.1154_1155delAA c.(1153-1155)AAAfs p.K385fs NBN_uc003yei.1_Frame_Shift_Del_p.K303fs|NBN_uc011lgb.1_Frame_Shift_Del_p.K385fs NM_002485 NP_002476 O60934 NBN_HUMAN nibrin 385 cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm protein N-terminus binding|transcription factor binding central_nervous_system(3)|kidney(3)|lung(1) 7 BRCA - Breast invasive adenocarcinoma(11;0.0344) TTTTGGAGACTTTGATTTCTTT 0.337 0.10 62 7 RIMS2 9699 broad.mit.edu 37 8 104927779 104927779 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr8:104927779delA uc003yls.2 + 5 1444 c.1203delA c.(1201-1203)GTAfs p.V401fs RIMS2_uc003ylp.2_Frame_Shift_Del_p.V623fs|RIMS2_uc003ylw.2_Frame_Shift_Del_p.V431fs|RIMS2_uc003ylq.2_Frame_Shift_Del_p.V431fs|RIMS2_uc003ylr.2_Frame_Shift_Del_p.V478fs|RIMS2_uc003ylt.2_Frame_Shift_Del_p.V24fs|RIMS2_uc003ylu.1_Frame_Shift_Del_p.V14fs|RIMS2_uc003ylv.1_Frame_Shift_Del_p.V14fs NM_014677 NP_055492 Q9UQ26 RIMS2_HUMAN regulating synaptic membrane exocytosis 2 701 PDZ. intracellular protein transport cell junction|presynaptic membrane metal ion binding|Rab GTPase binding ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1) 15 OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229) TTACTAAAGTAAAAAAAGGAA 0.323 0.16 105 20 COL14A1 7373 broad.mit.edu 37 8 121293192 121293193 + Frame_Shift_Ins INS - A A SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr8:121293192_121293193insA uc003yox.2 + 31 3983_3984 c.3718_3719insA c.(3718-3720)GAAfs p.E1240fs COL14A1_uc003yoz.2_Frame_Shift_Ins_p.E205fs NM_021110 NP_066933 Q05707 COEA1_HUMAN collagen, type XIV, alpha 1 precursor 1240 Nonhelical region (NC4).|TSP N-terminal. cell-cell adhesion|collagen fibril organization collagen type XIV|extracellular space collagen binding|extracellular matrix structural constituent|protein binding, bridging ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1) 12 Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503) TGGTTTGGTTGAAAAAGATTTT 0.332 0.33 53 26 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 11 WNK2 65268 broad.mit.edu 37 9 96019304 96019305 + Frame_Shift_Ins INS - C C SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr9:96019304_96019305insC uc004ati.1 + 10 2265_2266 c.2265_2266insC c.(2263-2268)GTTCCCfs p.V755fs WNK2_uc011lud.1_Frame_Shift_Ins_p.V755fs|WNK2_uc004atj.2_Frame_Shift_Ins_p.V755fs|WNK2_uc004atk.2_Frame_Shift_Ins_p.V392fs|WNK2_uc010mrc.1_Frame_Shift_Ins_p.V703fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 755_756 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 0.000 0.45 1619 1316 SMC2 10592 broad.mit.edu 37 9 106864418 106864418 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr9:106864418delA uc004bbv.2 + 8 1102 c.814delA c.(814-816)AAAfs p.K272fs SMC2_uc004bbu.1_Frame_Shift_Del_p.K272fs|SMC2_uc004bbw.2_Frame_Shift_Del_p.K272fs|SMC2_uc011lvl.1_Frame_Shift_Del_p.K272fs|SMC2_uc010mtg.1_Frame_Shift_Del_p.K127fs|SMC2_uc010mth.1_Frame_Shift_Del_p.K222fs|SMC2_uc004bbx.2_Frame_Shift_Del_p.K272fs NM_001042551 NP_001036016 O95347 SMC2_HUMAN structural maintenance of chromosomes 2 272 Potential. cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism condensin complex|cytoplasm|nuclear chromosome ATP binding|protein heterodimerization activity ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1) 9 TGAGAATGATAAAAAAATAAA 0.299 0.45 21 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 138 15 BIRC2 329 broad.mit.edu 37 11 102239231 102239232 + Frame_Shift_Ins INS - A A SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr11:102239231_102239232insA uc001pgy.2 + 6 2717_2718 c.1318_1319insA c.(1318-1320)GAAfs p.E440fs BIRC2_uc010ruq.1_Frame_Shift_Ins_p.E391fs|BIRC2_uc010rur.1_Frame_Shift_Ins_p.E440fs NM_001166 NP_001157 Q13490 BIRC2_HUMAN baculoviral IAP repeat-containing protein 2 440 cell surface receptor linked signaling pathway|cellular component disassembly involved in apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteasomal ubiquitin-dependent protein catabolic process|protein polyubiquitination CD40 receptor complex|cytosol|internal side of plasma membrane protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding ovary(1)|lung(1)|breast(1) 3 all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227) Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093) Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151) BRCA - Breast invasive adenocarcinoma(274;0.0144) TGCTGAAGATGAAAAAAGAGAA 0.386 0.36 114 63 LTBR 4055 broad.mit.edu 37 12 6499901 6499902 + Frame_Shift_Ins INS - G G SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr12:6499901_6499902insG uc001qny.1 + 10 1274_1275 c.1106_1107insG c.(1105-1107)CTGfs p.L369fs LTBR_uc010sfc.1_Frame_Shift_Ins_p.L350fs|LTBR_uc001qnz.1_Frame_Shift_Ins_p.L364fs NM_002342 NP_002333 P36941 TNR3_HUMAN lymphotoxin beta receptor precursor 369 Cytoplasmic (Potential). apoptosis|cellular response to mechanical stimulus|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade integral to membrane protein binding|receptor activity lung(2) 2 GGACCAGTACTGGGGGGACCAC 0.599 0.36 68 38 MBD6 114785 broad.mit.edu 37 12 57919306 57919306 + Frame_Shift_Del DEL C - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr12:57919306delC uc001soj.1 + 6 779 c.555delC c.(553-555)TTCfs p.F185fs MBD6_uc001sok.1_Frame_Shift_Del_p.F52fs|MBD6_uc001sol.1_5'Flank NM_052897 NP_443129 Q96DN6 MBD6_HUMAN methyl-CpG binding domain protein 6 185 Pro-rich. chromosome|nucleus chromatin binding|DNA binding central_nervous_system(3)|ovary(1) 4 GGGGGCTTTTCCCCCCAAGGC 0.642 0.50 8 8 MDM2 4193 broad.mit.edu 37 12 69233240 69233240 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr12:69233240delA uc001sui.2 + 11 1392 c.1105delA c.(1105-1107)AAAfs p.K369fs MDM2_uc009zri.2_Frame_Shift_Del_p.K324fs|MDM2_uc009zqx.2_Frame_Shift_Del_p.K314fs|MDM2_uc009zqw.2_Intron|MDM2_uc001suk.2_Intron|MDM2_uc001sun.3_Frame_Shift_Del_p.K188fs|MDM2_uc009zqz.2_Frame_Shift_Del_p.K316fs|MDM2_uc009zra.2_Frame_Shift_Del_p.K167fs|MDM2_uc001sum.1_Intron|MDM2_uc009zrd.2_Frame_Shift_Del_p.K53fs|MDM2_uc009zrc.2_Frame_Shift_Del_p.K53fs|MDM2_uc009zre.2_Frame_Shift_Del_p.K110fs|MDM2_uc009zrf.2_Frame_Shift_Del_p.K53fs|MDM2_uc001suo.2_Frame_Shift_Del_p.K163fs|MDM2_uc009zrg.2_Frame_Shift_Del_p.K85fs|MDM2_uc009zrh.2_Frame_Shift_Del_p.K137fs NM_002392 NP_002383 Q00987 MDM2_HUMAN mouse double minute 2 homolog isoform MDM2 363 Necessary for interaction with USP2. cellular response to hypoxia|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|establishment of protein localization|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein complex assembly|protein destabilization|protein localization to nucleus|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to antibiotic|synaptic transmission cytosol|endocytic vesicle membrane|insoluble fraction|nucleolus|nucleoplasm|plasma membrane|protein complex enzyme binding|identical protein binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding lung(2)|central_nervous_system(1) 3 all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684) all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143) TCCTGATTGTAAAAAAACTAT 0.368 0.41 119 84 UBE3B 89910 broad.mit.edu 37 12 109967742 109967743 + Frame_Shift_Ins INS - A A SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr12:109967742_109967743insA uc001top.2 + 25 3278_3279 c.2675_2676insA c.(2674-2676)ATAfs p.I892fs UBE3B_uc001toq.2_Frame_Shift_Ins_p.I892fs|UBE3B_uc001tos.2_Frame_Shift_Ins_p.I319fs|UBE3B_uc001tot.2_Frame_Shift_Ins_p.I10fs|UBE3B_uc010sxp.1_Frame_Shift_Ins_p.I10fs NM_130466 NP_569733 Q7Z3V4 UBE3B_HUMAN ubiquitin protein ligase E3B 892 HECT. protein ubiquitination involved in ubiquitin-dependent protein catabolic process intracellular ubiquitin-protein ligase activity ovary(2)|lung(2) 4 CACACTCAAATAAAAAACCAAA 0.450 0.36 113 64 ZMYM2 7750 broad.mit.edu 37 13 20638677 20638678 + Frame_Shift_Del DEL AA - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr13:20638677_20638678delAA uc001umr.2 + 20 3422_3423 c.3124_3125delAA c.(3124-3126)AAAfs p.K1042fs ZMYM2_uc001ums.2_Frame_Shift_Del_p.K1042fs|ZMYM2_uc001umt.2_Frame_Shift_Del_p.K1042fs|ZMYM2_uc001umv.2_Frame_Shift_Del_p.K422fs|ZMYM2_uc001umw.2_Frame_Shift_Del_p.K495fs NM_003453 NP_003444 Q9UBW7 ZMYM2_HUMAN zinc finger protein 198 1042 regulation of transcription, DNA-dependent|transcription, DNA-dependent PML body ubiquitin conjugating enzyme binding|zinc ion binding lung(3)|ovary(2)|prostate(1) 6 all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856) ACCTCGATCTAAAAAAAAGGTA 0.366 0.49 36 34 XPO4 64328 broad.mit.edu 37 13 21371027 21371027 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr13:21371027delA uc001unq.3 - 17 2528 c.2492delT c.(2491-2493)TTAfs p.L831fs NM_022459 NP_071904 Q9C0E2 XPO4_HUMAN exportin 4 831 protein transport cytoplasm|nucleus protein binding large_intestine(1)|ovary(1)|kidney(1) 3 all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244) all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548) GAAGTCCATTAAAAAATTAAA 0.413 0.41 92 64 SACS 26278 broad.mit.edu 37 13 23905486 23905486 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr13:23905486delA uc001uon.2 - 10 13118 c.12529delT c.(12529-12531)TACfs p.Y4177fs SACS_uc001uoo.2_Frame_Shift_Del_p.Y4030fs|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 4177 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) TCTCCCGGGTAAAAAACATTC 0.418 0.46 135 113 FLT1 2321 broad.mit.edu 37 13 28964206 28964206 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr13:28964206delT uc001usb.3 - 13 1981 c.1696delA c.(1696-1698)ATGfs p.M566fs FLT1_uc010aar.1_Frame_Shift_Del_p.M566fs|FLT1_uc001usc.3_Frame_Shift_Del_p.M566fs|FLT1_uc010aas.1_RNA|FLT1_uc010aat.1_Frame_Shift_Del_p.M49fs NM_002019 NP_002010 P17948 VGFR1_HUMAN fms-related tyrosine kinase 1 isoform 1 566 Ig-like C2-type 6.|Extracellular (Potential). cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway extracellular space|Golgi apparatus|integral to plasma membrane|nucleus ATP binding|growth factor binding|vascular endothelial growth factor receptor activity lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1) 24 Acute lymphoblastic leukemia(6;0.04) Lung SC(185;0.0262)|Breast(139;0.188) Colorectal(13;0.000674) all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207) Sunitinib(DB01268) TCCGTCGGCATTTTTTCCAAG 0.353 0.52 83 91 WBP4 11193 broad.mit.edu 37 13 41642790 41642791 + Frame_Shift_Ins INS - A A SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr13:41642790_41642791insA uc001uxt.2 + 5 469_470 c.356_357insA c.(355-357)AGAfs p.R119fs WBP4_uc010tfd.1_Frame_Shift_Ins_p.R98fs NM_007187 NP_009118 O75554 WBP4_HUMAN WW domain-containing binding protein 4 119 Lys-rich. nuclear mRNA cis splicing, via spliceosome nuclear speck|spliceosomal complex nucleic acid binding|proline-rich region binding|zinc ion binding breast(2)|kidney(1) 3 Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114) all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07) aagaagaaaagaaaaaaagaTC 0.342 0.36 84 48 MAP4K5 11183 broad.mit.edu 37 14 50910676 50910676 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr14:50910676delT uc001wya.2 - 19 1738 c.1418delA c.(1417-1419)AAGfs p.K473fs MAP4K5_uc001wyb.2_Frame_Shift_Del_p.K473fs|MAP4K5_uc010anv.1_Frame_Shift_Del_p.K473fs|MAP4K5_uc001wyc.1_Frame_Shift_Del_p.K147fs NM_006575 NP_006566 Q9Y4K4 M4K5_HUMAN mitogen-activated protein kinase kinase kinase 473 activation of JUN kinase activity cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity large_intestine(1) 1 all_epithelial(31;0.000415)|Breast(41;0.0102) TCGTTTGTCCTTTTTTCGTGG 0.353 0.48 83 76 PRKCH 5583 broad.mit.edu 37 14 62014535 62014535 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr14:62014535delT uc001xfn.2 + 13 2141 c.1836delT c.(1834-1836)CCTfs p.P612fs PRKCH_uc010tsa.1_Frame_Shift_Del_p.P451fs|PRKCH_uc010tsb.1_Frame_Shift_Del_p.P180fs|PRKCH_uc001xfo.2_RNA NM_006255 NP_006246 P24723 KPCL_HUMAN protein kinase C, eta 612 Protein kinase. intracellular signal transduction|platelet activation cytosol|plasma membrane ATP binding|enzyme binding|metal ion binding|protein kinase C activity ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1) 6 OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182) TGAGACATCCTTTTTTTAAGG 0.522 0.44 94 73 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.70 3 7 CASC5 57082 broad.mit.edu 37 15 40916822 40916822 + Frame_Shift_Del DEL A - - rs34749627 SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr15:40916822delA uc010bbs.1 + 11 4599 c.4438delA c.(4438-4440)AAAfs p.K1480fs CASC5_uc010ucq.1_Frame_Shift_Del_p.K1304fs|CASC5_uc001zme.2_Frame_Shift_Del_p.K1454fs|CASC5_uc010bbt.1_Frame_Shift_Del_p.K1454fs NM_170589 NP_733468 Q8NG31 CASC5_HUMAN cancer susceptibility candidate 5 isoform 1 1480 acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm protein binding breast(3)|central_nervous_system(1)|skin(1) 5 all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946) GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211) TCCATTACCTAAAAAAGGACA 0.333 0.42 113 81 IL21R 50615 broad.mit.edu 37 16 27460530 27460530 + Frame_Shift_Del DEL C - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr16:27460530delC uc002doq.1 + 9 1776 c.1543delC c.(1543-1545)CCCfs p.P515fs IL21R_uc002dor.1_Frame_Shift_Del_p.P515fs|IL21R_uc002dos.1_Frame_Shift_Del_p.P515fs|uc002dot.2_RNA NM_181078 NP_851564 Q9HBE5 IL21R_HUMAN interleukin 21 receptor precursor 515 Cytoplasmic (Potential). natural killer cell activation integral to membrane interleukin-21 receptor activity ovary(2)|lung(1)|breast(1) 4 GGACGAAGGACCCCCCCGGAG 0.637 0.18 36 8 RBL2 5934 broad.mit.edu 37 16 53498266 53498266 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr16:53498266delT uc002ehi.3 + 12 1807 c.1689delT c.(1687-1689)CATfs p.H563fs RBL2_uc010vgv.1_Frame_Shift_Del_p.H489fs|RBL2_uc002ehj.2_Frame_Shift_Del_p.H273fs|RBL2_uc010vgw.1_Frame_Shift_Del_p.H347fs NM_005611 NP_005602 Q08999 RBL2_HUMAN retinoblastoma-like 2 (p130) 563 Domain A.|Pocket; binds E1A. cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleolus DNA binding|protein binding ovary(2)|lung(2)|upper_aerodigestive_tract(1) 5 CTCTTTATCATTTTTATAAGG 0.338 0.18 59 13 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 27 226 TP53 7157 broad.mit.edu 37 17 7579470 7579471 + Frame_Shift_Ins INS - G G rs56275308 SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr17:7579470_7579471insG uc002gim.2 - 4 410_411 c.216_217insC c.(214-219)CCCGTGfs p.P72fs TP53_uc002gig.1_Frame_Shift_Ins_p.P72fs|TP53_uc002gih.2_Frame_Shift_Ins_p.P72fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Ins_p.P72fs|TP53_uc010cni.1_Frame_Shift_Ins_p.P72fs|TP53_uc002gij.2_Frame_Shift_Ins_p.P72fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Ins_p.P33fs|TP53_uc010cnk.1_Frame_Shift_Ins_p.P87fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 72_73 Interaction with WWOX.|Interaction with HRMT1L2. V -> M (in sporadic cancers; somatic mutation).|V -> E (in a sporadic cancer; somatic mutation).|V -> L (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.R72fs*51(6)|p.V73L(3)|p.G59fs*23(3)|p.R72C(2)|p.V73fs*76(2)|p.R72H(2)|p.V73M(2)|p.V73fs*9(1)|p.R65fs*38(1)|p.E68fs*76(1)|p.V73fs*50(1)|p.D48fs*55(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.D57_A76del20(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.10 1227 131 NF1 4763 broad.mit.edu 37 17 29592335 29592336 + Frame_Shift_Ins INS - T T SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr17:29592335_29592336insT uc002hgg.2 + 36 5146_5147 c.4813_4814insT c.(4813-4815)ATTfs p.I1605fs NF1_uc002hgh.2_Frame_Shift_Ins_p.I1584fs|NF1_uc002hgi.1_Frame_Shift_Ins_p.I617fs|NF1_uc010cso.2_5'UTR NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 1605 CRAL-TRIO. I -> V (in NF1). actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(3)|p.I1605fs*17(1) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) TGGGAATCCTATTTTTTATTAT 0.327 0.42 23 17 RPS6KB1 6198 broad.mit.edu 37 17 58012655 58012656 + Frame_Shift_Ins INS - A A SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr17:58012655_58012656insA uc002ixy.2 + 10 1075_1076 c.972_973insA c.(970-975)CTTAAAfs p.L324fs RPS6KB1_uc010ddj.1_Frame_Shift_Ins_p.L324fs|RPS6KB1_uc010wom.1_Frame_Shift_Ins_p.L271fs|RPS6KB1_uc010won.1_Frame_Shift_Ins_p.L301fs|RPS6KB1_uc010woo.1_Frame_Shift_Ins_p.L259fs NM_003161 NP_003152 P23443 KS6B1_HUMAN ribosomal protein S6 kinase, 70kDa, polypeptide 324_325 Protein kinase. apoptosis|G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|negative regulation of apoptosis|phosphatidylinositol-mediated signaling|positive regulation of mitotic cell cycle|positive regulation of translational initiation|TOR signaling cascade cell junction|cytoplasm|cytosol|mitochondrial outer membrane|nucleus|nucleus|synapse|synaptosome ATP binding|protein binding|protein kinase activity large_intestine(1) 1 all_cancers(5;1.63e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922) Epithelial(12;3.57e-12)|all cancers(12;6.41e-11) GAGATCTGCTTAAAAAGGTAAG 0.342 0.47 17 15 USP32 84669 broad.mit.edu 37 17 58282966 58282966 + Frame_Shift_Del DEL C - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr17:58282966delC uc002iyo.1 - 26 3377 c.3091delG c.(3091-3093)GACfs p.D1031fs USP32_uc002iyn.1_Frame_Shift_Del_p.D701fs NM_032582 NP_115971 Q8NFA0 UBP32_HUMAN ubiquitin specific protease 32 1031 protein deubiquitination|ubiquitin-dependent protein catabolic process Golgi apparatus|membrane calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity lung(2)|breast(2)|large_intestine(1) 5 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198) CGGGGTAGGTCCCCATTGGTA 0.403 0.47 93 81 LAMA1 284217 broad.mit.edu 37 18 6993723 6993723 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr18:6993723delT uc002knm.2 - 35 5019 c.4925delA c.(4924-4926)AAGfs p.K1642fs LAMA1_uc010wzj.1_Frame_Shift_Del_p.K1118fs NM_005559 NP_005550 P25391 LAMA1_HUMAN laminin, alpha 1 precursor 1642 Domain II and I. axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development extracellular space|laminin-1 complex|laminin-3 complex extracellular matrix structural constituent|receptor binding ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1) 21 Colorectal(10;0.172) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) CCTATTCACCTTTTGGGTACT 0.428 0.43 87 65 LAMA1 284217 broad.mit.edu 37 18 7038885 7038885 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr18:7038885delT uc002knm.2 - 11 1581 c.1487delA c.(1486-1488)AACfs p.N496fs LAMA1_uc010wzj.1_5'UTR NM_005559 NP_005550 P25391 LAMA1_HUMAN laminin, alpha 1 precursor 496 Laminin EGF-like 4. axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development extracellular space|laminin-1 complex|laminin-3 complex extracellular matrix structural constituent|receptor binding ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1) 21 Colorectal(10;0.172) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) GCCCCGGGGGTTTTTTTCCTT 0.532 0.96 1 24 ATP8B1 5205 broad.mit.edu 37 18 55365040 55365040 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr18:55365040delT uc002lgw.2 - 6 614 c.614delA c.(613-615)AATfs p.N205fs uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 205 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) AACAAAATCATTTTTTTTCAG 0.388 0.47 16 14 ALPK2 115701 broad.mit.edu 37 18 56246941 56246941 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr18:56246941delA uc002lhj.3 - 4 1281 c.1067delT c.(1066-1068)TTAfs p.L356fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 356 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 GCTTTCTAATAAAAAAACATG 0.478 0.37 128 75 INSR 3643 broad.mit.edu 37 19 7117126 7117127 + Frame_Shift_Del DEL TG - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr19:7117126_7117127delTG uc002mgd.1 - 22 4198_4199 c.4089_4090delCA c.(4087-4092)CACATGfs p.H1363fs INSR_uc002mge.1_Frame_Shift_Del_p.H1351fs NM_000208 NP_000199 P06213 INSR_HUMAN insulin receptor isoform Long precursor 1363_1364 PIK3R1-binding.|Cytoplasmic (Potential). activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus caveola|endosome membrane|insulin receptor complex|microsome ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1) 12 Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) CCTCCGTTCATGTGTGTGTAAG 0.609 0.34 39 20 NOTCH3 4854 broad.mit.edu 37 19 15288546 15288547 + Frame_Shift_Ins INS - C C SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr19:15288546_15288547insC uc002nan.2 - 24 4268_4269 c.4192_4193insG c.(4192-4194)GACfs p.D1398fs NOTCH3_uc002nao.1_Frame_Shift_Ins_p.D1346fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 1398 Extracellular (Potential).|LNR 1. Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.23 800 233 NOTCH3 4854 broad.mit.edu 37 19 15296358 15296358 + Frame_Shift_Del DEL G - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr19:15296358delG uc002nan.2 - 13 2160 c.2084delC c.(2083-2085)CCGfs p.P695fs NOTCH3_uc002nao.1_Frame_Shift_Del_p.P695fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 695 Extracellular (Potential).|EGF-like 18. Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.39 876 571 NOTCH3 4854 broad.mit.edu 37 19 15308383 15308383 + Frame_Shift_Del DEL G - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr19:15308383delG uc002nan.2 - 2 201 c.125delC c.(124-126)CCTfs p.P42fs NOTCH3_uc002nao.1_Frame_Shift_Del_p.P42fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 42 Extracellular (Potential).|EGF-like 1. Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.13 651 95 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.25 30 10 STK35 140901 broad.mit.edu 37 20 2083471 2083471 + Frame_Shift_Del DEL G - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr20:2083471delG uc010gak.2 + 2 352 c.352delG c.(352-354)GGGfs p.G118fs STK35_uc010zpu.1_5'UTR|STK35_uc002wfw.3_5'Flank NM_080836 NP_543026 Q8TDR2 STK35_HUMAN serine/threonine kinase 35 118 Ala-rich. cytoplasm|nucleolus ATP binding|protein serine/threonine kinase activity ovary(1) 1 0.000 0.28 491 192 TOP1 7150 broad.mit.edu 37 20 39713113 39713114 + Frame_Shift_Ins INS - A A SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr20:39713113_39713114insA uc002xjl.2 + 8 765_766 c.519_520insA c.(517-522)TTGAAAfs p.L173fs TOP1_uc010gge.1_RNA NM_003286 NP_003277 P11387 TOP1_HUMAN DNA topoisomerase I 173_174 Lys-rich. DNA topological change|interspecies interaction between organisms|phosphorylation|programmed cell death|response to drug chromosome|nucleolus|nucleoplasm ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity|protein binding breast(3)|ovary(2)|central_nervous_system(1)|kidney(1) 7 Myeloproliferative disorder(115;0.00878) Irinotecan(DB00762)|Lucanthone(DB04967)|Topotecan(DB01030) ATGGTAAATTGAAAAAACCCAA 0.361 0.39 14 9 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 141 29 TMPRSS2 7113 broad.mit.edu 37 21 42851110 42851110 + Frame_Shift_Del DEL T - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr21:42851110delT uc002yzj.2 - 7 806 c.672delA c.(670-672)AAAfs p.K224fs TMPRSS2_uc010gor.2_Frame_Shift_Del_p.K261fs|TMPRSS2_uc010gos.1_Frame_Shift_Del_p.K224fs NM_005656 NP_005647 O15393 TMPS2_HUMAN transmembrane protease, serine 2 isoform 2 224 Extracellular (Potential).|SRCR. proteolysis cytoplasm|extracellular region|integral to plasma membrane scavenger receptor activity|serine-type endopeptidase activity TMPRSS2/ERG(2499)|TMPRSS2/ETV1(24) prostate(2523)|central_nervous_system(1) 2524 Prostate(19;4.48e-07)|all_epithelial(19;0.031) TGTGGTACAGTTTTTTATAGA 0.403 0.50 55 56 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 170 609 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 70 EP300 2033 broad.mit.edu 37 22 41566525 41566525 + Frame_Shift_Del DEL A - - SNU1040_LARGE_INTESTINE NA SNU1040_LARGE_INTESTINE NA g.chr22:41566525delA uc003azl.3 + 27 4797 c.4402delA c.(4402-4404)AAAfs p.K1468fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1468 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding p.M1470fs*3(3) haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 GGAATGGTACAAAAAAATGCT 0.473 0.35 115 61 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.46 15 13 NRD1 4898 broad.mit.edu 37 1 52306064 52306066 + In_Frame_Del DEL TCT - - rs145326984;rs72496486 SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr1:52306064_52306066delTCT uc001ctc.3 - 2 784_786 c.462_464delAGA c.(460-465)GAAGAT>GAT p.E154del NRD1_uc009vzb.2_Translation_Start_Site|NRD1_uc001ctd.3_In_Frame_Del_p.E154del|NRD1_uc001cte.2_In_Frame_Del_p.E22del|NRD1_uc001ctf.2_In_Frame_Del_p.E154del|NRD1_uc010ong.1_RNA|NRD1_uc009vzc.1_In_Frame_Del_p.E22del|NRD1_uc001ctg.1_5'Flank NM_002525 NP_002516 O43847 NRDC_HUMAN nardilysin isoform a Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity cell surface|cytosol epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding 0 ttcatcatcatcttcttcttctt 0.158 0.70 3 7 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 283 89 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.25 62 21 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.55 5 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.28 48 19 NKD2 85409 broad.mit.edu 37 5 1038447 1038449 + In_Frame_Del DEL CAC - - rs3840989 SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr5:1038447_1038449delCAC uc003jbt.1 + 10 1320_1322 c.1315_1317delCAC c.(1315-1317)CACdel p.H447del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.32 84 40 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.69 4 9 VPS13B 157680 broad.mit.edu 37 8 100729526 100729526 + Frame_Shift_Del DEL T - - SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr8:100729526delT uc003yiv.2 + 37 6768 c.6657delT c.(6655-6657)TGTfs p.C2219fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.C2194fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 2219 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) CTAAGTGGTGTAAACACAGCG 0.418 0.11 348 42 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 22 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.55 290 360 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.74 11 32 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 321 44 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.35 17 9 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.33 32 16 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.66 11 21 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU1041_UPPER_AERODIGESTIVE_TRACT NA SNU1041_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 4 32 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 24 HOXD13 3239 broad.mit.edu 37 2 176957786 176957797 + In_Frame_Del DEL GGCGGCGGCGGC - - rs3832095 SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr2:176957786_176957797delGGCGGCGGCGGC uc002ukf.1 + 1 255_266 c.168_179delGGCGGCGGCGGC c.(166-180)CGGGCGGCGGCGGCG>CGG p.AAAA65del NM_000523 NP_000514 P35453 HXD13_HUMAN homeobox D13 65_68 Poly-Ala. skeletal system development|transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding lung(1) 1 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0526)|READ - Rectum adenocarcinoma(9;0.0678) 0.000 0.25 295 96 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.15 100 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.23 43 13 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.59 119 171 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.23 44 13 RASA1 5921 broad.mit.edu 37 5 86682700 86682700 + Frame_Shift_Del DEL A - - SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr5:86682700delA uc003kiw.2 + 23 3023 c.2905delA c.(2905-2907)ATGfs p.M969fs RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_Frame_Shift_Del_p.M792fs|RASA1_uc011ctv.1_Frame_Shift_Del_p.M802fs|RASA1_uc011ctw.1_Frame_Shift_Del_p.M803fs|RASA1_uc010jaw.2_Frame_Shift_Del_p.M791fs NM_002890 NP_002881 P20936 RASA1_HUMAN RAS p21 protein activator 1 isoform 1 969 cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis cytosol|intrinsic to internal side of plasma membrane glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding upper_aerodigestive_tract(3)|ovary(1)|lung(1) 5 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) 0.000 0.57 60 79 LETM2 137994 broad.mit.edu 37 8 38250402 38250402 + Frame_Shift_Del DEL A - - SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr8:38250402delA uc003xlm.1 + 3 420 c.249delA c.(247-249)CTAfs p.L83fs LETM2_uc003xlk.2_Frame_Shift_Del_p.L130fs|LETM2_uc011lbn.1_5'UTR|LETM2_uc003xll.1_Frame_Shift_Del_p.L83fs|LETM2_uc003xln.1_5'UTR|LETM2_uc003xlo.1_5'UTR NM_144652 NP_653253 Q2VYF4 LETM2_HUMAN leucine zipper-EF-hand containing transmembrane 130 LETM1.|Mitochondrial intermembrane (Potential). integral to membrane|mitochondrial inner membrane 0 all_cancers(2;6.77e-47)|all_epithelial(2;1.01e-50)|all_lung(3;1.25e-23)|Lung NSC(2;2.76e-23)|Colorectal(12;0.000442)|Esophageal squamous(3;0.00202) all_lung(54;0.0657)|Hepatocellular(245;0.152)|Lung NSC(58;0.175) Epithelial(3;1.17e-42)|all cancers(3;5.44e-38)|BRCA - Breast invasive adenocarcinoma(5;5.44e-27)|LUSC - Lung squamous cell carcinoma(2;7.12e-25)|Lung(2;4.49e-22)|COAD - Colon adenocarcinoma(9;0.114) TGGATGAACTAAAATATTATT 0.418 0.36 75 43 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - AA AA rs34108497;rs146125714 SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr8:62550924_62550925insAA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.17 43 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 154 22 PTPN11 5781 broad.mit.edu 37 12 112919931 112919932 + Frame_Shift_Ins INS - AT AT SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr12:112919931_112919932insAT uc001ttx.2 + 10 1526_1527 c.1146_1147insAT c.(1144-1149)GTCATGfs p.V382fs PTPN11_uc001ttw.1_Frame_Shift_Ins_p.V382fs NM_002834 NP_002825 Q06124 PTN11_HUMAN protein tyrosine phosphatase, non-receptor type 382_383 Tyrosine-protein phosphatase. axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway cytosol non-membrane spanning protein tyrosine phosphatase activity|protein binding haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1) 392 AATATGGCGTCATGCGTGTTAG 0.376 0.47 59 53 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.39 11 7 TP53 7157 broad.mit.edu 37 17 7579319 7579329 + Frame_Shift_Del DEL GTCACAGACTT - - rs121912658 SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr17:7579319_7579329delGTCACAGACTT uc002gim.2 - 4 552_562 c.358_368delAAGTCTGTGAC c.(358-369)AAGTCTGTGACTfs p.K120fs TP53_uc002gig.1_Frame_Shift_Del_p.K120fs|TP53_uc002gih.2_Frame_Shift_Del_p.K120fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.K120fs|TP53_uc010cni.1_Frame_Shift_Del_p.K120fs|TP53_uc002gij.2_Frame_Shift_Del_p.K120fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.K81fs|TP53_uc010cnk.1_Frame_Shift_Del_p.K135fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 120_123 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). T -> I (in a sporadic cancer; somatic mutation).|T -> N (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.K120E(3)|p.G59fs*23(3)|p.V122fs*26(2)|p.K120*(2)|p.K120fs*3(2)|p.K120M(2)|p.K120R(2)|p.S121fs*27(1)|p.V122fs*46(1)|p.T118fs*27(1)|p.V122L(1)|p.S121fs*2(1)|p.V73fs*9(1)|p.Y107fs*44(1)|p.S121F(1)|p.S33fs*23(1)|p.P13fs*18(1)|p.T123I(1)|p.T123fs*24(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.H115fs*27(1)|p.K120N(1)|p.K120Q(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.25 33 11 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 92 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 72 160 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU1076_UPPER_AERODIGESTIVE_TRACT NA SNU1076_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.86 5 32 HEPH 9843 broad.mit.edu 37 X 65393494 65393495 + Frame_Shift_Ins INS - C C SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chrX:65393494_65393495insC uc011moz.1 + 4 545_546 c.485_486insC c.(484-486)GGCfs p.G162fs HEPH_uc004dwn.2_Frame_Shift_Ins_p.G162fs|HEPH_uc004dwo.2_5'UTR|HEPH_uc010nkr.2_Frame_Shift_Ins_p.G162fs|HEPH_uc011mpa.1_Frame_Shift_Ins_p.G162fs NM_138737 NP_620074 Q9BQS7 HEPH_HUMAN hephaestin isoform a 159 Extracellular (Potential).|Plastocyanin-like 1. cellular iron ion homeostasis|copper ion transport|transmembrane transport integral to membrane|plasma membrane copper ion binding|oxidoreductase activity lung(5)|ovary(4) 9 CCCCCGGGGGGCAGCCATATCT 0.535 0.21 27 7 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 22 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.51 146 150 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 65 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.33 40 20 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.78 8 29 PPP2CA 5515 broad.mit.edu 37 5 133533464 133533469 + In_Frame_Del DEL TACAGG - - SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr5:133533464_133533469delTACAGG uc003kze.2 - 7 1322_1327 c.924_929delCCTGTA c.(922-930)TTCCTGTAA>TTA p.308_310FL*>L NM_002715 NP_002706 P67775 PP2AA_HUMAN protein phosphatase 2, catalytic subunit, alpha 308_310 ceramide metabolic process|inactivation of MAPK activity|induction of apoptosis|meiosis|negative regulation of cell growth|negative regulation of epithelial to mesenchymal transition|negative regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of protein serine/threonine kinase activity|protein dephosphorylation|regulation of cell adhesion|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling chromosome, centromeric region|cytosol|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction|spindle pole metal ion binding|phosphoprotein phosphatase activity ovary(2)|lung(1)|skin(1) 4 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) Vitamin E(DB00163) AAAATTTCATTACAGGAAGTAGTCTG 0.417 0.42 32 23 MYLK4 340156 broad.mit.edu 37 6 2749462 2749462 + Frame_Shift_Del DEL C - - SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr6:2749462delC uc003mty.3 - 2 364 c.67delG c.(67-69)GCCfs p.A23fs NM_001012418 NP_001012418 Q86YV6 MYLK4_HUMAN myosin light chain kinase family, member 4 23 ATP binding|protein serine/threonine kinase activity breast(3)|ovary(1) 4 Ovarian(93;0.0412) all_hematologic(90;0.0897) TGAAAAAAGGCCATTTTCTCC 0.408 0.51 76 79 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 129 35 SIK2 23235 broad.mit.edu 37 11 111571666 111571667 + Frame_Shift_Ins INS - G G SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr11:111571666_111571667insG uc001plt.2 + 5 653_654 c.535_536insG c.(535-537)AGCfs p.S179fs NM_015191 NP_056006 Q9H0K1 SIK2_HUMAN SNF1-like kinase 2 179 Protein kinase. intracellular protein kinase cascade|regulation of insulin receptor signaling pathway Golgi apparatus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|skin(1) 3 ATGGTGTGGCAGCCCCCCTTAT 0.431 0.22 80 22 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.83 7 35 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.36 47 26 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.25 40 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 33 129 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU1077_ENDOMETRIUM NA SNU1077_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 2 42 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 44 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.60 145 214 BMP2K 55589 broad.mit.edu 37 4 79792137 79792145 + In_Frame_Del DEL CAGCAGCAG - - rs17855588 SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr4:79792137_79792145delCAGCAGCAG uc003hlk.2 + 11 1598_1606 c.1432_1440delCAGCAGCAG c.(1432-1440)CAGCAGCAGdel p.QQQ484del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQ484del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 484_486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 gcaacagcaacagcagcagcagcagcagc 0.177 0.38 20 12 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.43 13 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.30 74 31 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.37 46 27 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.41 217 149 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.54 6 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.71 4 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 17 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.35 823 446 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.24 29 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.11 126 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 32 302 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.33 26 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 245 774 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU1105_CENTRAL_NERVOUS_SYSTEM NA SNU1105_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.99 1 88 MAST2 23139 broad.mit.edu 37 1 46476453 46476453 + Frame_Shift_Del DEL C - - SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr1:46476453delC uc001cov.2 + 10 1313 c.1030delC c.(1030-1032)CCAfs p.P344fs MAST2_uc001cow.2_Frame_Shift_Del_p.P344fs|MAST2_uc001coy.1_Frame_Shift_Del_p.P52fs|MAST2_uc001coz.1_Frame_Shift_Del_p.P229fs|MAST2_uc009vya.2_Frame_Shift_Del_p.P266fs|MAST2_uc001cpa.2_Intron NM_015112 NP_055927 Q6P0Q8 MAST2_HUMAN microtubule associated serine/threonine kinase 344 regulation of interleukin-12 biosynthetic process|spermatid differentiation cytoplasm|cytoskeleton|plasma membrane ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity ovary(5)|lung(3)|stomach(2)|breast(1) 11 Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184) CTCCAACACTCCAGACAGCGT 0.512 0.30 23 10 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.19 225 53 CDKL4 344387 broad.mit.edu 37 2 39414801 39414802 + Frame_Shift_Ins INS - AA AA SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr2:39414801_39414802insAA uc002rrm.2 - 6 701_702 c.701_702insTT c.(700-702)TTCfs p.F234fs CDKL4_uc010fal.1_Frame_Shift_Ins_p.F234fs NM_001009565 NP_001009565 Q5MAI5 CDKL4_HUMAN cyclin-dependent kinase-like 4 234 Protein kinase. cytoplasm ATP binding|cyclin-dependent protein kinase activity ovary(1) 1 all_hematologic(82;0.248) TGATGCCATGGAAAAACCCGTT 0.327 0.34 63 33 MECOM 2122 broad.mit.edu 37 3 168833619 168833619 + Frame_Shift_Del DEL G - - SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr3:168833619delG uc003ffi.3 - 7 1746 c.1477delC c.(1477-1479)CTGfs p.L493fs MECOM_uc010hwk.1_Frame_Shift_Del_p.L516fs|MECOM_uc003ffj.3_Frame_Shift_Del_p.L558fs|MECOM_uc011bpi.1_Frame_Shift_Del_p.L494fs|MECOM_uc003ffn.3_Frame_Shift_Del_p.L493fs|MECOM_uc003ffk.2_Frame_Shift_Del_p.L493fs|MECOM_uc003ffl.2_Frame_Shift_Del_p.L653fs|MECOM_uc011bpj.1_Frame_Shift_Del_p.L681fs|MECOM_uc011bpk.1_Frame_Shift_Del_p.L483fs|MECOM_uc010hwn.2_Frame_Shift_Del_p.L681fs NM_005241 NP_005232 Q03112 EVI1_HUMAN MDS1 and EVI1 complex locus isoform b 493 apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle nuclear speck DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1) 14 TTGTCTTGCAGCCCCACCAGT 0.428 0.20 156 39 PRKCI 5584 broad.mit.edu 37 3 169993017 169993025 + In_Frame_Del DEL TAATTCCAT - - SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr3:169993017_169993025delTAATTCCAT uc003fgs.2 + 8 885_893 c.647_655delTAATTCCAT c.(646-657)GTAATTCCATAT>GAT p.216_219VIPY>D NM_002740 NP_002731 P41743 KPCI_HUMAN protein kinase C, iota 216_219 Regulatory domain. anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport cytosol|endosome|nucleus|polarisome ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding lung(2)|ovary(1)|breast(1)|skin(1) 5 all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169) Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197) GGGTTTTTAGTAATTCCATATAATCCTTC 0.278 0.14 54 9 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.37 12 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.30 57 24 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 11 18 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.83 2 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.16 77 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 1 13 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.59 7 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 42 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 15 43 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 52 365 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU1196_BILIARY_TRACT NA SNU1196_BILIARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 4 43 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 7 52 BCL9 607 broad.mit.edu 37 1 147092543 147092544 + Frame_Shift_Ins INS - GT GT SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr1:147092543_147092544insGT uc001epq.2 + 8 3322_3323 c.2582_2583insGT c.(2581-2583)AACfs p.N861fs BCL9_uc010ozr.1_Frame_Shift_Ins_p.N787fs NM_004326 NP_004317 O00512 BCL9_HUMAN B-cell CLL/lymphoma 9 861 Pro-rich. Wnt receptor signaling pathway nucleus protein binding ovary(2)|large_intestine(2)|breast(1)|skin(1) 6 all_hematologic(923;0.115) CCAGGCATTAACCCTCTGAAGT 0.624 0.44 65 51 TGFBR2 7048 broad.mit.edu 37 3 30713153 30713165 + Frame_Shift_Del DEL TTGTTGCTAGTCA - - SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr3:30713153_30713165delTTGTTGCTAGTCA uc003ceo.2 + 4 860_872 c.478_490delTTGTTGCTAGTCA c.(478-492)TTGTTGCTAGTCATAfs p.L160fs TGFBR2_uc003cen.2_Frame_Shift_Del_p.L185fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 160_164 Extracellular (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 CAATCCTGACTTGTTGCTAGTCATATTTCAAGT 0.479 0.93 4 52 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.24 26 8 BMP2K 55589 broad.mit.edu 37 4 79792137 79792145 + In_Frame_Del DEL CAGCAGCAG - - rs17855588 SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr4:79792137_79792145delCAGCAGCAG uc003hlk.2 + 11 1598_1606 c.1432_1440delCAGCAGCAG c.(1432-1440)CAGCAGCAGdel p.QQQ484del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQ484del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 484_486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 gcaacagcaacagcagcagcagcagcagc 0.177 0.30 37 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.28 104 40 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.27 357 134 APC 324 broad.mit.edu 37 5 112175212 112175216 + Frame_Shift_Del DEL AAAAG - - SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr5:112175212_112175216delAAAAG uc010jby.2 + 16 4301_4305 c.3921_3925delAAAAG c.(3919-3927)ATAAAAGAAfs p.I1307fs APC_uc011cvt.1_Frame_Shift_Del_p.I1289fs|APC_uc003kpz.3_Frame_Shift_Del_p.I1307fs|APC_uc003kpy.3_Frame_Shift_Del_p.I1307fs|APC_uc010jbz.2_Frame_Shift_Del_p.I1024fs|APC_uc010jca.2_Frame_Shift_Del_p.I607fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1307_1309 Ser-rich.|Responsible for down-regulation through a process mediated by direct ubiquitination. E -> G (in Ref. 1; AAA60353/AAA60354). canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.E1309fs*6(51)|p.E1309fs*4(36)|p.E1309*(22)|p.I1307fs*8(15)|p.I1307fs*6(12)|p.K1308*(6)|p.I1307fs*14(3)|p.I1307fs*7(2)|p.I1311fs*4(2)|p.I1307fs*1(2)|p.I1307K(2)|p.?(1)|p.E1309fs*5(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1309K(1)|p.K1308E(1)|p.K1308fs*4(1)|p.K1308fs*6(1)|p.I1307fs*13(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) TAGCAGAAATAAAAGAAAAGATTGG 0.424 0.40 85 57 KCNH2 3757 broad.mit.edu 37 7 150644455 150644456 + In_Frame_Ins INS - CGTCGC CGTCGC SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr7:150644455_150644456insCGTCGC uc003wic.2 - 13 3125_3126 c.3112_3113insGCGACG c.(3112-3114)GTG>GGCGACGTG p.1037_1038insGD KCNH2_uc003wib.2_In_Frame_Ins_p.697_698insGD|KCNH2_uc011kux.1_In_Frame_Ins_p.941_942insGD NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 1037_1038 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) 0.000 0.24 1246 398 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.37 29 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.67 404 812 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.96 1 24 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 138 33 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.38 8 5 TOX3 27324 broad.mit.edu 37 16 52473764 52473765 + In_Frame_Ins INS - ACT ACT SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr16:52473764_52473765insACT uc002egw.2 - 7 1274_1275 c.1103_1104insAGT c.(1102-1104)GTG>GTAGTG p.368_368V>VV TOX3_uc010vgt.1_In_Frame_Ins_p.363_363V>VV|TOX3_uc010vgu.1_In_Frame_Ins_p.368_368V>VV NM_001080430 NP_001073899 O15405 TOX3_HUMAN TOX high mobility group box family member 3 368 apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity 0 GTGATGCTGACACTGTTCCATG 0.520 0.48 85 77 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 26 245 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.31 102 45 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 141 550 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU1197_LARGE_INTESTINE NA SNU1197_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 76 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 26 PTPN22 26191 broad.mit.edu 37 1 114381009 114381010 + Frame_Shift_Ins INS - T T SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr1:114381009_114381010insT uc001eds.2 - 13 1142_1143 c.1012_1013insA c.(1012-1014)ATGfs p.M338fs PTPN22_uc009wgq.2_Frame_Shift_Ins_p.M283fs|PTPN22_uc010owo.1_Frame_Shift_Ins_p.M94fs|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Frame_Shift_Ins_p.M338fs|PTPN22_uc009wgs.2_Frame_Shift_Ins_p.M211fs|PTPN22_uc001edu.2_Frame_Shift_Ins_p.M338fs NM_015967 NP_057051 Q9Y2R2 PTN22_HUMAN protein tyrosine phosphatase, non-receptor type 338 negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation internal side of plasma membrane|nucleus|perinuclear region of cytoplasm kinase binding|protein tyrosine phosphatase activity|SH3 domain binding kidney(2)|lung(1)|skin(1) 4 Lung SC(450;0.184) all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06) Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133) TTGGTTCATCATTTTTGCTGCT 0.376 0.42 121 88 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 265 89 ULK4 54986 broad.mit.edu 37 3 41860984 41860985 + Frame_Shift_Ins INS - T T SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr3:41860984_41860985insT uc003ckv.3 - 19 1979_1980 c.1778_1779insA c.(1777-1779)AAGfs p.K593fs ULK4_uc003ckw.2_Frame_Shift_Ins_p.K593fs NM_017886 NP_060356 Q96C45 ULK4_HUMAN unc-51-like kinase 4 593 ATP binding|protein serine/threonine kinase activity 0 KIRC - Kidney renal clear cell carcinoma(284;0.214) CTCTAGGGTTCTTTTTTTTTTC 0.450 0.12 57 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.39 50 32 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.78 21 73 MSH3 4437 broad.mit.edu 37 5 80063939 80063950 + Splice_Site DEL AGTAAGTACCAG - - SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr5:80063939_80063950delAGTAAGTACCAG uc003kgz.2 + 14 2337 c.2084_splice c.e14+1 p.K695_splice NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) CAAGCTGCCAAGTAAGTACCAGACCCTGAATT 0.377 0.77 13 44 RAD50 10111 broad.mit.edu 37 5 131931460 131931461 + Frame_Shift_Ins INS - T T SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr5:131931460_131931461insT uc003kxi.2 + 13 2552_2553 c.2165_2166insT c.(2164-2166)AAGfs p.K722fs RAD50_uc003kxh.2_Frame_Shift_Ins_p.K583fs NM_005732 NP_005723 Q92878 RAD50_HUMAN RAD50 homolog isoform 1 722 Zinc-hook.|Potential. DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding lung(2)|ovary(1)|skin(1) 4 all_cancers(142;0.0368)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) CTAAAAAAAAAGGAAAAGCGGC 0.431 0.50 60 61 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.25 36 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 1 11 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.66 127 248 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.40 9 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 159 17 TOX3 27324 broad.mit.edu 37 16 52473764 52473765 + In_Frame_Ins INS - ACT ACT SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr16:52473764_52473765insACT uc002egw.2 - 7 1274_1275 c.1103_1104insAGT c.(1102-1104)GTG>GTAGTG p.368_368V>VV TOX3_uc010vgt.1_In_Frame_Ins_p.363_363V>VV|TOX3_uc010vgu.1_In_Frame_Ins_p.368_368V>VV NM_001080430 NP_001073899 O15405 TOX3_HUMAN TOX high mobility group box family member 3 368 apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity 0 GTGATGCTGACACTGTTCCATG 0.520 0.36 95 54 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 2 13 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.69 12 27 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 50 322 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU1214_UPPER_AERODIGESTIVE_TRACT NA SNU1214_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 6 69 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU1272_KIDNEY NA SNU1272_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 49 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU1272_KIDNEY NA SNU1272_KIDNEY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.19 289 68 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU1272_KIDNEY NA SNU1272_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.25 46 15 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU1272_KIDNEY NA SNU1272_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 21 36 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU1272_KIDNEY NA SNU1272_KIDNEY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.35 35 19 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU1272_KIDNEY NA SNU1272_KIDNEY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.37 386 226 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU1272_KIDNEY NA SNU1272_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.11 107 13 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU1272_KIDNEY NA SNU1272_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.30 30 13 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU1272_KIDNEY NA SNU1272_KIDNEY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.13 118 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU1272_KIDNEY NA SNU1272_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 58 372 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU1272_KIDNEY NA SNU1272_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.99 1 69 FAM9A 171482 broad.mit.edu 37 X 8763345 8763346 + In_Frame_Ins INS - CTG CTG SNU16_STOMACH NA SNU16_STOMACH NA g.chrX:8763345_8763346insCTG uc004csg.2 - 7 715_716 c.604_605insCAG c.(604-606)GAA>GCAGAA p.201_202insA NM_174951 NP_777611 Q8IZU1 FAM9A_HUMAN family with sequence similarity 9, member A 201_202 Poly-Ala.|Glu-rich. nucleolus 0 Hepatocellular(5;0.219) tgctgcggcttctgctgctgct 0.144 0.34 27 14 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU16_STOMACH NA SNU16_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.44 39 31 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU16_STOMACH NA SNU16_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.19 487 111 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes SNU16_STOMACH NA SNU16_STOMACH NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.55 15 18 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SNU16_STOMACH NA SNU16_STOMACH NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.53 42 47 FGFR3 2261 broad.mit.edu 37 4 1807392 1807392 + Frame_Shift_Del DEL G - - SNU16_STOMACH NA SNU16_STOMACH NA g.chr4:1807392delG uc003gdr.3 + 12 1897 c.1641delG c.(1639-1641)CAGfs p.Q547fs FGFR3_uc003gdu.2_Frame_Shift_Del_p.Q549fs|FGFR3_uc003gds.3_Frame_Shift_Del_p.Q435fs|FGFR3_uc003gdq.3_Frame_Shift_Del_p.Q548fs NM_000142 NP_000133 P22607 FGFR3_HUMAN fibroblast growth factor receptor 3 isoform 1 547 Protein kinase.|Cytoplasmic (Potential). bone maturation|cell growth|insulin receptor signaling pathway|JAK-STAT cascade|MAPKKK cascade|negative regulation of developmental growth|positive regulation of cell proliferation integral to plasma membrane ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|identical protein binding urinary_tract(2177)|skin(314)|upper_aerodigestive_tract(57)|haematopoietic_and_lymphoid_tissue(24)|prostate(9)|cervix(6)|central_nervous_system(4)|large_intestine(3)|lung(3)|testis(2)|pancreas(1) 2600 Breast(71;0.212)|all_epithelial(65;0.241) all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234) Palifermin(DB00039) 0.000 0.29 200 82 HTT 3064 broad.mit.edu 37 4 3076604 3076609 + In_Frame_Del DEL CAGCAG - - rs10618869 SNU16_STOMACH NA SNU16_STOMACH NA g.chr4:3076604_3076609delCAGCAG uc011bvq.1 + 2 203_208 c.58_63delCAGCAG c.(58-63)CAGCAGdel p.QQ38del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 38_Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagcagc 0.330 0.16 84 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU16_STOMACH NA SNU16_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.74 76 215 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU16_STOMACH NA SNU16_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.45 47 38 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SNU16_STOMACH NA SNU16_STOMACH NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.62 5 8 ICK 22858 broad.mit.edu 37 6 52878488 52878488 + Frame_Shift_Del DEL G - - SNU16_STOMACH NA SNU16_STOMACH NA g.chr6:52878488delG uc003pbh.2 - 10 1614 c.1124delC c.(1123-1125)CCAfs p.P375fs ICK_uc003pbi.2_Frame_Shift_Del_p.P375fs NM_016513 NP_057597 Q9UPZ9 ICK_HUMAN intestinal cell kinase 375 intracellular protein kinase cascade|multicellular organismal development cytosol|nucleus ATP binding|cyclin-dependent protein kinase activity|magnesium ion binding ovary(1)|large_intestine(1)|lung(1)|kidney(1)|central_nervous_system(1) 5 Lung NSC(77;0.103) 0.000 0.33 329 159 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 SNU16_STOMACH NA SNU16_STOMACH NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.17 480 96 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU16_STOMACH NA SNU16_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 3 39 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU16_STOMACH NA SNU16_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.30 43 18 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU16_STOMACH NA SNU16_STOMACH NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.11 85 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU16_STOMACH NA SNU16_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 24 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU16_STOMACH NA SNU16_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.11 181 22 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU16_STOMACH NA SNU16_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.48 818 764 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU16_STOMACH NA SNU16_STOMACH NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 83 870 STXBP2 6813 broad.mit.edu 37 19 7707005 7707006 + Splice_Site DEL GT - - SNU16_STOMACH NA SNU16_STOMACH NA g.chr19:7707005_7707006delGT uc002mha.3 + 8 708 c.663_splice c.e8+1 p.E221_splice STXBP2_uc002mhb.3_Splice_Site_p.E218_splice|STXBP2_uc010dvj.2_Splice_Site|STXBP2_uc010xjr.1_Splice_Site_p.E232_splice|STXBP2_uc010dvk.2_Splice_Site_p.E189_splice|STXBP2_uc002mhc.3_Splice_Site|STXBP2_uc002mhe.1_5'Flank NM_006949 NP_008880 Q15833 STXB2_HUMAN syntaxin binding protein 2 isoform a leukocyte mediated cytotoxicity|neutrophil degranulation|protein transport|regulation of mast cell degranulation|vesicle docking involved in exocytosis azurophil granule|cytolytic granule|cytosol|specific granule|tertiary granule syntaxin-3 binding central_nervous_system(1) 1 0.000 0.97 2 77 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT SNU16_STOMACH NA SNU16_STOMACH NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.15 189 34 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU16_STOMACH NA SNU16_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.79 74 284 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU16_STOMACH NA SNU16_STOMACH NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 66 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU16_STOMACH NA SNU16_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 2 9 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU16_STOMACH NA SNU16_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 4 42 MED15 51586 broad.mit.edu 37 22 20918817 20918819 + In_Frame_Del DEL CAG - - SNU16_STOMACH NA SNU16_STOMACH NA g.chr22:20918817_20918819delCAG uc002zsp.2 + 6 612_614 c.532_534delCAG c.(532-534)CAGdel p.Q188del MED15_uc002zsn.1_In_Frame_Del_p.Q107del|MED15_uc002zso.2_In_Frame_Del_p.Q117del|MED15_uc002zsq.2_In_Frame_Del_p.Q188del|MED15_uc010gso.2_In_Frame_Del_p.Q188del|MED15_uc002zsr.2_In_Frame_Del_p.Q162del|MED15_uc011ahs.1_In_Frame_Del_p.Q162del|MED15_uc011aht.1_In_Frame_Del_p.Q162del|MED15_uc002zss.2_In_Frame_Del_p.Q107del|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 188 Poly-Gln. regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) ggcggcgctacagcagcagcagc 0.148 0.31 95 42 WAS 7454 broad.mit.edu 37 X 48544377 48544378 + Splice_Site INS - T T SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chrX:48544377_48544378insT uc004dkm.3 + 5 562 c.505_splice c.e5+1 p.E169_splice NM_000377 NP_000368 P42768 WASP_HUMAN Wiskott-Aldrich syndrome protein blood coagulation|defense response|epidermis development|immune response|T cell receptor signaling pathway actin cytoskeleton|cytosol identical protein binding|small GTPase regulator activity ovary(1) 1 all_lung(315;1.27e-10) GCCAATGAAGGTGAGTCCTCTA 0.540 0.42 55 40 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 6 61 MCF2 4168 broad.mit.edu 37 X 138669938 138669939 + Frame_Shift_Ins INS - T T SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chrX:138669938_138669939insT uc004fau.2 - 22 2752_2753 c.2458_2459insA c.(2458-2460)AGAfs p.R820fs MCF2_uc004fav.2_Frame_Shift_Ins_p.R836fs|MCF2_uc011mwl.1_Frame_Shift_Ins_p.R797fs|MCF2_uc010nsh.1_Frame_Shift_Ins_p.R820fs|MCF2_uc011mwm.1_Frame_Shift_Ins_p.R781fs|MCF2_uc011mwn.1_Frame_Shift_Ins_p.R965fs|MCF2_uc004faw.2_Frame_Shift_Ins_p.R880fs|MCF2_uc011mwo.1_Frame_Shift_Ins_p.R896fs NM_005369 NP_005360 P10911 MCF2_HUMAN MCF.2 cell line derived transforming sequence 820 apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytoskeleton|cytosol|membrane|membrane fraction protein binding|Rho guanyl-nucleotide exchange factor activity lung(1)|pleura(1) 2 Acute lymphoblastic leukemia(192;0.000127) CTGTTGCTTTCTTTTTTTAACT 0.317 0.31 79 36 F8 2157 broad.mit.edu 37 X 154157686 154157686 + Frame_Shift_Del DEL T - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chrX:154157686delT uc004fmt.2 - 14 4550 c.4379delA c.(4378-4380)AATfs p.N1460fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1460 B. N -> K (in HEMA). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AGAAAGGTTATTTTTTTTGGC 0.413 0.11 249 30 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 295 88 MSH6 2956 broad.mit.edu 37 2 48032085 48032086 + Frame_Shift_Ins INS - A A SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr2:48032085_48032086insA uc002rwd.3 + 6 3627_3628 c.3475_3476insA c.(3475-3477)TACfs p.Y1159fs MSH6_uc010fbj.2_Frame_Shift_Ins_p.Y857fs|MSH6_uc010yoi.1_Frame_Shift_Ins_p.Y1029fs|MSH6_uc010yoj.1_Frame_Shift_Ins_p.Y857fs NM_000179 NP_000170 P52701 MSH6_HUMAN mutS homolog 6 1159 determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes MutSalpha complex ATP binding|DNA-dependent ATPase activity|protein binding large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1) 168 Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) GATGGGTTGTTACGTCCCTGCT 0.431 1.00 0 17 TTN 7273 broad.mit.edu 37 2 179476320 179476320 + Frame_Shift_Del DEL T - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr2:179476320delT uc010zfg.1 - 218 43156 c.42932delA c.(42931-42933)AATfs p.N14311fs uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.N8006fs|TTN_uc010zfi.1_Frame_Shift_Del_p.N7939fs|TTN_uc010zfj.1_Frame_Shift_Del_p.N7814fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 15238 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) ACTTCCACCATTTTTCTCTGG 0.448 0.45 211 171 CNTN6 27255 broad.mit.edu 37 3 1367608 1367608 + Frame_Shift_Del DEL A - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr3:1367608delA uc003boz.2 + 9 1323 c.1056delA c.(1054-1056)TTAfs p.L352fs CNTN6_uc011asj.1_Frame_Shift_Del_p.L280fs|CNTN6_uc003bpa.2_Frame_Shift_Del_p.L352fs NM_014461 NP_055276 Q9UQ52 CNTN6_HUMAN contactin 6 precursor 352 Ig-like C2-type 4. axon guidance|cell adhesion|central nervous system development|Notch signaling pathway anchored to membrane|plasma membrane skin(3)|lung(2)|breast(2)|pancreas(1) 8 all_cancers(2;0.000164)|all_epithelial(2;0.107) Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139) ATACATGGTTAAAAAATGGTG 0.363 0.38 31 19 PBRM1 55193 broad.mit.edu 37 3 52682400 52682400 + Frame_Shift_Del DEL T - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr3:52682400delT uc003des.2 - 7 785 c.773delA c.(772-774)AATfs p.N258fs PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.N258fs|PBRM1_uc003der.2_Frame_Shift_Del_p.N258fs|PBRM1_uc003det.2_Frame_Shift_Del_p.N258fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.N258fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.N258fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.N258fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.N258fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.N258fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.N156fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 258 Bromo 2. chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.46 119 101 TOPBP1 11073 broad.mit.edu 37 3 133329880 133329880 + Frame_Shift_Del DEL T - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr3:133329880delT uc003eps.2 - 25 4273 c.4141delA c.(4141-4143)ATCfs p.I1381fs NM_007027 NP_008958 Q92547 TOPB1_HUMAN topoisomerase (DNA) II binding protein 1 1381 DNA repair|response to ionizing radiation microtubule organizing center|PML body|spindle pole DNA binding|protein C-terminus binding ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1) 7 CTTTGCTGGATTTTTTTTCTC 0.343 0.10 242 26 SKIL 6498 broad.mit.edu 37 3 170078207 170078207 + Frame_Shift_Del DEL A - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr3:170078207delA uc003fgu.2 + 2 800 c.88delA c.(88-90)AAAfs p.K30fs SKIL_uc011bps.1_Frame_Shift_Del_p.K10fs|SKIL_uc003fgv.2_Frame_Shift_Del_p.K30fs|SKIL_uc003fgw.2_Frame_Shift_Del_p.K30fs NM_005414 NP_005405 P12757 SKIL_HUMAN SKI-like isoform 1 30 cell cycle arrest|negative regulation of cell differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of axonogenesis|protein heterotrimerization|protein homotrimerization|regulation of apoptosis|regulation of apoptosis|response to antibiotic|response to growth factor stimulus|skeletal muscle tissue development cytoplasm|PML body chromatin binding|nucleotide binding|protein complex binding|protein domain specific binding|SMAD binding|transcription corepressor activity|transcription repressor activity ovary(2)|skin(1) 3 all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137) Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197) CCCCCCAGCGAAAAAAATGAT 0.438 0.56 62 78 LPP 4026 broad.mit.edu 37 3 188124034 188124035 + Frame_Shift_Ins INS - A A SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr3:188124034_188124035insA uc003frs.1 + 3 372_373 c.126_127insA c.(124-129)CCCAAAfs p.P42fs LPP_uc011bsg.1_Frame_Shift_Ins_p.P42fs|LPP_uc011bsi.1_Frame_Shift_Ins_p.P42fs|LPP_uc003frt.2_Frame_Shift_Ins_p.P42fs NM_005578 NP_005569 Q93052 LPP_HUMAN LIM domain containing preferred translocation 42_43 Pro-rich. cell adhesion cytoplasm|focal adhesion|nucleus protein binding|zinc ion binding HMGA2/LPP(161) soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1) 165 all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088) all_lung(153;0.00139)|Lung NSC(153;0.00202) GBM - Glioblastoma multiforme(93;0.00602) AACAGCCACCCAAAAAGTTTGC 0.520 0.47 88 77 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.44 18 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.28 108 42 LIFR 3977 broad.mit.edu 37 5 38510573 38510573 + Frame_Shift_Del DEL A - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr5:38510573delA uc010ive.1 - 7 1316 c.984delT c.(982-984)TTTfs p.F328fs LIFR_uc003jli.2_Frame_Shift_Del_p.F328fs NM_001127671 NP_001121143 P42702 LIFR_HUMAN leukemia inhibitory factor receptor precursor 328 Extracellular (Potential). positive regulation of cell proliferation extracellular region|integral to plasma membrane ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity ovary(3)|large_intestine(1) 4 all_lung(31;0.00021) TACATCCAGCAAAAATAACGG 0.358 0.43 51 39 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 20 58 PIK3R1 5295 broad.mit.edu 37 5 67522740 67522741 + Frame_Shift_Ins INS - A A SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr5:67522740_67522741insA uc003jva.2 + 2 797_798 c.237_238insA c.(235-240)AGGAAAfs p.R79fs PIK3R1_uc003jvb.2_Frame_Shift_Ins_p.R79fs NM_181523 NP_852664 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 79_80 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1) 101 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) ATATTGGAAGGAAAAAAATCTC 0.490 0.38 53 32 APC 324 broad.mit.edu 37 5 112175651 112175651 + Frame_Shift_Del DEL A - - rs111866410 byFrequency SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr5:112175651delA uc010jby.2 + 16 4740 c.4360delA c.(4360-4362)AAAfs p.K1454fs APC_uc011cvt.1_Frame_Shift_Del_p.K1436fs|APC_uc003kpz.3_Frame_Shift_Del_p.K1454fs|APC_uc003kpy.3_Frame_Shift_Del_p.K1454fs|APC_uc010jbz.2_Frame_Shift_Del_p.K1171fs|APC_uc010jca.2_Frame_Shift_Del_p.K754fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1454 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.K1454E(3)|p.K1454fs*3(1)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.P1453fs*4(1)|p.P1453fs*19(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) AGAAGTACCTAAAAATAAAGC 0.478 0.42 93 67 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.64 4 7 SERPINB1 1992 broad.mit.edu 37 6 2836215 2836216 + Frame_Shift_Ins INS - T T SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr6:2836215_2836216insT uc003mub.2 - 6 653_654 c.609_610insA c.(607-612)AAATTTfs p.K203fs SERPINB1_uc003muc.2_Frame_Shift_Ins_p.K52fs NM_030666 NP_109591 P30740 ILEU_HUMAN serine (or cysteine) proteinase inhibitor, clade 203_204 regulation of proteolysis cytoplasm|extracellular space serine-type endopeptidase inhibitor activity breast(4)|ovary(1) 5 Ovarian(93;0.0412) OV - Ovarian serous cystadenocarcinoma(45;0.0717) CCATATGCAAATTTTTTCTTCT 0.411 0.39 135 86 DNAH8 1769 broad.mit.edu 37 6 38775405 38775406 + Frame_Shift_Ins INS - T T SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr6:38775405_38775406insT uc003ooe.1 + 22 3119_3120 c.2519_2520insT c.(2518-2520)GCTfs p.A840fs NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 GAGGTCTTTGCTTTTTTCTCTC 0.342 0.45 59 49 TTK 7272 broad.mit.edu 37 6 80751896 80751896 + Frame_Shift_Del DEL G - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr6:80751896delG uc003pjc.2 + 22 2625 c.2551delG c.(2551-2553)GAAfs p.E851fs TTK_uc003pjb.3_Frame_Shift_Del_p.E850fs NM_003318 NP_003309 P33981 TTK_HUMAN TTK protein kinase 851 mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation spindle ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1) 11 all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2) BRCA - Breast invasive adenocarcinoma(397;0.0321) CAAGACTTTTGAAAAAAAAAG 0.303 0.47 40 36 ETV1 2115 broad.mit.edu 37 7 13975473 13975473 + Frame_Shift_Del DEL G - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr7:13975473delG uc011jxq.1 - 8 1153 c.414delC c.(412-414)CCCfs p.P138fs ETV1_uc011jxn.1_Frame_Shift_Del_p.P98fs|ETV1_uc011jxo.1_Intron|ETV1_uc011jxp.1_Frame_Shift_Del_p.P80fs|ETV1_uc003ssw.3_Frame_Shift_Del_p.P138fs|ETV1_uc003ssx.2_RNA|ETV1_uc011jxr.1_Frame_Shift_Del_p.P120fs|ETV1_uc011jxs.1_Frame_Shift_Del_p.P120fs|ETV1_uc010ktv.2_Frame_Shift_Del_p.P7fs NM_004956 NP_004947 P50549 ETV1_HUMAN ets variant gene 1 isoform a 138 transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity TMPRSS2/ETV1(24)|EWSR1/ETV1(7) prostate(24)|soft_tissue(4)|bone(3)|lung(2)|central_nervous_system(1)|ovary(1) 35 TGGATGGTGTGGGGGGGTTGG 0.527 0.54 120 143 SRPK2 6733 broad.mit.edu 37 7 104783744 104783745 + Frame_Shift_Ins INS - T T SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr7:104783744_104783745insT uc003vct.2 - 9 1000_1001 c.813_814insA c.(811-816)AAACTGfs p.K271fs SRPK2_uc003vcu.2_Frame_Shift_Ins_p.K271fs|SRPK2_uc003vcv.2_Frame_Shift_Ins_p.K282fs|SRPK2_uc003vcw.1_Frame_Shift_Ins_p.K271fs NM_182691 NP_872633 P78362 SRPK2_HUMAN serine/arginine-rich protein-specific kinase 2 271_272 Protein kinase. angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly cytoplasm|nucleolus 14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1) 6 TTCTTTTTCAGTTTTTTCTTTT 0.361 0.25 115 38 GRM8 2918 broad.mit.edu 37 7 126173278 126173278 + Frame_Shift_Del DEL G - - rs77499554 SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr7:126173278delG uc003vlr.2 - 8 2469 c.2158delC c.(2158-2160)CACfs p.H720fs GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Frame_Shift_Del_p.H720fs|GRM8_uc010lkz.1_RNA NM_000845 NP_000836 O00222 GRM8_HUMAN glutamate receptor, metabotropic 8 isoform a 720 Extracellular (Potential). negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception integral to plasma membrane lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1) 23 Prostate(267;0.186) L-Glutamic Acid(DB00142) 0.000 0.32 750 358 MLL3 58508 broad.mit.edu 37 7 152012386 152012386 + Frame_Shift_Del DEL T - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr7:152012386delT uc003wla.2 - 4 646 c.427delA c.(427-429)AGTfs p.S143fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 143 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) CCTAAGGAACTTTTTTCCCCA 0.378 0.60 165 251 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.74 10 28 SGK3 23678 broad.mit.edu 37 8 67763086 67763086 + Frame_Shift_Del DEL T - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr8:67763086delT uc003xwr.2 + 16 1550 c.1251delT c.(1249-1251)CCTfs p.P417fs SGK3_uc003xwp.2_Frame_Shift_Del_p.P411fs|SGK3_uc003xwt.2_Frame_Shift_Del_p.P417fs|SGK3_uc003xwu.2_Frame_Shift_Del_p.P385fs NM_001033578 NP_001028750 Q96BR1 SGK3_HUMAN serum/glucocorticoid regulated kinase 3 isoform 417 Protein kinase. cell communication|response to stress cytoplasmic membrane-bounded vesicle|early endosome ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity ovary(1)|large_intestine(1)|lung(1)|breast(1) 4 Breast(64;0.186) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206) AGAATCATCCTTTTTTTGAAT 0.308 0.45 71 58 ARFGEF1 10565 broad.mit.edu 37 8 68128856 68128856 + Frame_Shift_Del DEL G - - rs142098461 SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr8:68128856delG uc003xxo.1 - 33 5045 c.4655delC c.(4654-4656)CCAfs p.P1552fs ARFGEF1_uc003xxl.1_Frame_Shift_Del_p.P1006fs|ARFGEF1_uc003xxn.1_Frame_Shift_Del_p.P535fs NM_006421 NP_006412 Q9Y6D6 BIG1_HUMAN brefeldin A-inhibited guanine 1552 exocytosis|regulation of ARF protein signal transduction cytoplasm ARF guanyl-nucleotide exchange factor activity|myosin binding ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1) 8 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206) AGATGGAGGTGGGGGGGCAGT 0.423 0.44 10 8 TG 7038 broad.mit.edu 37 8 133995617 133995617 + Frame_Shift_Del DEL T - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr8:133995617delT uc003ytw.2 + 35 6263 c.6222delT c.(6220-6222)AGTfs p.S2074fs TG_uc010mdw.2_Frame_Shift_Del_p.S833fs|TG_uc011ljb.1_Frame_Shift_Del_p.S443fs|TG_uc011ljc.1_Intron NM_003235 NP_003226 P01266 THYG_HUMAN thyroglobulin precursor 2074 Type IIIB. hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation extracellular space hormone activity ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1) 15 Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155) Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735) BRCA - Breast invasive adenocarcinoma(115;0.000701) KIRC - Kidney renal clear cell carcinoma(542;0.0546) ATGCTCCCAGTTTTTGCCCTT 0.393 0.46 183 153 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 1 10 PTCH1 5727 broad.mit.edu 37 9 98278949 98278951 + In_Frame_Del DEL CTC - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr9:98278949_98278951delCTC uc004avm.3 - 1 297_299 c.152_154delGAG c.(151-156)GGAGAA>GAA p.G51del PTCH1_uc010mrr.2_5'UTR|PTCH1_uc004avo.2_5'UTR|PTCH1_uc010mrv.1_RNA|PTCH1_uc010mrw.1_RNA NM_001083603 NP_001077072 Q13635 PTC1_HUMAN patched isoform L' Error:Variant_position_missing_in_Q13635_after_alignment embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway integral to plasma membrane hedgehog receptor activity skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1) 379 Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136) tctttttcttctcctccgttttc 0.463 0.62 34 56 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 133 21 GUCY1A2 2977 broad.mit.edu 37 11 106810372 106810372 + Frame_Shift_Del DEL A - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr11:106810372delA uc001pjg.1 - 4 1410 c.1020delT c.(1018-1020)CTTfs p.L340fs GUCY1A2_uc010rvo.1_Frame_Shift_Del_p.L340fs|GUCY1A2_uc009yxn.1_Frame_Shift_Del_p.L340fs NM_000855 NP_000846 P33402 GCYA2_HUMAN guanylate cyclase 1, soluble, alpha 2 340 intracellular signal transduction|platelet activation cytoplasm GTP binding|guanylate cyclase activity|heme binding large_intestine(3)|lung(2)|pancreas(2)|ovary(1) 8 all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068) BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476) CCCCCAACTGAAGGACTGACA 0.483 0.51 100 104 LRRK2 120892 broad.mit.edu 37 12 40713869 40713870 + Frame_Shift_Ins INS - A A SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr12:40713869_40713870insA uc001rmg.3 + 34 5028_5029 c.4907_4908insA c.(4906-4908)TCAfs p.S1636fs LRRK2_uc009zjw.2_Frame_Shift_Ins_p.S474fs|LRRK2_uc001rmi.2_Frame_Shift_Ins_p.S469fs NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 1636 activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) AAATTTCTTTCAAAAAAAAGGA 0.351 0.39 100 64 ACVRL1 94 broad.mit.edu 37 12 52314634 52314634 + Frame_Shift_Del DEL A - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr12:52314634delA uc001rzj.2 + 10 1752 c.1469delA c.(1468-1470)CAAfs p.Q490fs ACVRL1_uc001rzk.2_Frame_Shift_Del_p.Q490fs|ACVRL1_uc010snm.1_Frame_Shift_Del_p.Q316fs NM_000020 NP_000011 P37023 ACVL1_HUMAN activin A receptor type II-like 1 precursor 490 Cytoplasmic (Potential).|Protein kinase. blood vessel endothelial cell proliferation involved in sprouting angiogenesis|blood vessel maturation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of endothelial cell migration|negative regulation of focal adhesion assembly|positive regulation of BMP signaling pathway|positive regulation of transcription, DNA-dependent|regulation of blood pressure|regulation of blood vessel endothelial cell migration|regulation of DNA replication|regulation of endothelial cell proliferation|transforming growth factor beta receptor signaling pathway|wound healing, spreading of epidermal cells cell surface|integral to plasma membrane activin binding|activin receptor activity, type I|ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity lung(2) 2 BRCA - Breast invasive adenocarcinoma(357;0.0991) Adenosine triphosphate(DB00171) AAGACACTACAAAAAATTAGC 0.577 0.43 54 41 HSP90B1 7184 broad.mit.edu 37 12 104331534 104331534 + Frame_Shift_Del DEL A - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr12:104331534delA uc001tkb.1 + 6 910 c.805delA c.(805-807)AAAfs p.K269fs HSP90B1_uc010swg.1_Intron|HSP90B1_uc009zui.1_Frame_Shift_Del_p.K269fs NM_003299 NP_003290 P14625 ENPL_HUMAN heat shock protein 90kDa beta, member 1 269 actin rod assembly|anti-apoptosis|cellular response to ATP|ER-associated protein catabolic process|protein folding|protein transport|regulation of phosphoprotein phosphatase activity|response to hypoxia|sequestering of calcium ion cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|melanosome|microsome|midbody|perinuclear region of cytoplasm ATP binding|calcium ion binding|low-density lipoprotein particle receptor binding|protein phosphatase binding|RNA binding|unfolded protein binding|virion binding ovary(2)|skin(1) 3 Rifabutin(DB00615) AAATCTCGTCAAAAAATATTC 0.299 0.46 35 30 SACS 26278 broad.mit.edu 37 13 23907294 23907294 + Frame_Shift_Del DEL T - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr13:23907294delT uc001uon.2 - 10 11310 c.10721delA c.(10720-10722)AATfs p.N3574fs SACS_uc001uoo.2_Frame_Shift_Del_p.N3427fs|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 3574 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) TGTAACATGATTTTTGGGTTT 0.303 0.51 60 62 BRCA2 675 broad.mit.edu 37 13 32912346 32912346 + Frame_Shift_Del DEL A - - rs80359406 SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr13:32912346delA uc001uub.1 + 11 4081 c.3854delA c.(3853-3855)GAAfs p.E1285fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 1285 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) ACTGTAAGTGAAAAAAATAAT 0.264 0.47 73 66 C14orf4 64207 broad.mit.edu 37 14 77493798 77493799 + In_Frame_Ins INS - GCT GCT SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr14:77493798_77493799insGCT uc001xsy.2 - 1 1236_1237 c.337_338insAGC c.(337-339)CAG>CAGCAG p.113_113Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 113 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) ctgctgttgctgctgctgctgc 0.257 0.41 10 7 CIITA 4261 broad.mit.edu 37 16 10989214 10989215 + Frame_Shift_Ins INS - C C SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr16:10989214_10989215insC uc002dai.3 + 2 261_262 c.128_129insC c.(127-129)GACfs p.D43fs CIITA_uc002daj.3_Frame_Shift_Ins_p.D43fs|CIITA_uc002dak.3_Frame_Shift_Ins_p.D43fs|CIITA_uc002dag.2_Frame_Shift_Ins_p.D43fs|CIITA_uc002dah.2_Frame_Shift_Ins_p.D43fs|CIITA_uc010bup.1_Frame_Shift_Ins_p.D43fs NM_000246 NP_000237 P33076 C2TA_HUMAN class II transactivator 43 interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent nucleus activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding central_nervous_system(1) 1 AGCGATGCTGACCCCCTGTGCC 0.579 0.53 105 118 PNMT 5409 broad.mit.edu 37 17 37826414 37826415 + Frame_Shift_Ins INS - G G SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr17:37826414_37826415insG uc002hsi.1 + 3 843_844 c.621_622insG c.(619-624)CCTGGGfs p.P207fs NM_002686 NP_002677 P11086 PNMT_HUMAN phenylethanolamine N-methyltransferase 207_208 catecholamine biosynthetic process|hormone biosynthetic process cytosol phenylethanolamine N-methyltransferase activity ovary(1) 1 all_cancers(6;6.59e-85)|all_epithelial(6;2.89e-103)|Breast(7;1.05e-86)|Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052) UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;3.87e-45)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171) 0.000 0.43 519 387 TOP2A 7153 broad.mit.edu 37 17 38546381 38546381 + Frame_Shift_Del DEL T - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr17:38546381delT uc002huq.2 - 34 4429 c.4303delA c.(4303-4305)AGGfs p.R1435fs NM_001067 NP_001058 P11388 TOP2A_HUMAN DNA topoisomerase II, alpha isozyme 1435 apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1) 7 Breast(137;0.00328) STAD - Stomach adenocarcinoma(5;0.00183) Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385) GGGGCAGCCCTTTTTTTGGCA 0.413 0.44 99 79 PPM1D 8493 broad.mit.edu 37 17 58740623 58740624 + Frame_Shift_Ins INS - A A SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr17:58740623_58740624insA uc002iyt.1 + 6 1750_1751 c.1528_1529insA c.(1528-1530)CAAfs p.Q510fs PPM1D_uc010ddm.1_RNA NM_003620 NP_003611 O15297 PPM1D_HUMAN protein phosphatase 1D 510 negative regulation of cell proliferation|protein dephosphorylation|response to radiation nucleus|protein serine/threonine phosphatase complex metal ion binding|protein binding|protein serine/threonine phosphatase activity upper_aerodigestive_tract(1) 1 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) Epithelial(12;6.75e-12)|all cancers(12;1.96e-10) 0.000 0.41 360 255 P4HB 5034 broad.mit.edu 37 17 79803763 79803764 + Frame_Shift_Ins INS - T T SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr17:79803763_79803764insT uc002kbn.1 - 8 1357_1358 c.1160_1161insA c.(1159-1161)AACfs p.N387fs P4HB_uc002kbl.1_Frame_Shift_Ins_p.N64fs|P4HB_uc002kbm.1_Frame_Shift_Ins_p.N64fs NM_000918 NP_000909 P07237 PDIA1_HUMAN prolyl 4-hydroxylase, beta subunit precursor 387 Thioredoxin 2. cell redox homeostasis|glycerol ether metabolic process|lipid metabolic process|lipoprotein metabolic process|peptidyl-proline hydroxylation to 4-hydroxy-L-proline cell surface|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|extracellular region|melanosome|plasma membrane electron carrier activity|procollagen-proline 4-dioxygenase activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity 0 all_neural(118;0.0878)|Ovarian(332;0.12) BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509) CCACAAAGACGTTTTTTTTCTC 0.559 0.43 69 52 ROCK1 6093 broad.mit.edu 37 18 18690831 18690832 + Frame_Shift_Ins INS - T T SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr18:18690831_18690832insT uc002kte.2 - 1 981_982 c.40_41insA c.(40-42)ATGfs p.M14fs NM_005406 NP_005397 Q13464 ROCK1_HUMAN Rho-associated, coiled-coil containing protein 14 actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction centriole|cytosol|Golgi membrane ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity lung(2)|breast(2)|central_nervous_system(1) 5 Melanoma(1;0.165) 0.000 0.41 410 280 ALPK2 115701 broad.mit.edu 37 18 56246440 56246440 + Frame_Shift_Del DEL T - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr18:56246440delT uc002lhj.3 - 4 1782 c.1568delA c.(1567-1569)AAGfs p.K523fs NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 523 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 CCATAAGTCCTTTCCCCCCAC 0.522 0.94 24 349 LDLR 3949 broad.mit.edu 37 19 11230805 11230805 + Frame_Shift_Del DEL T - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr19:11230805delT uc002mqk.3 + 13 2051 c.1883delT c.(1882-1884)ATTfs p.I628fs LDLR_uc010xlk.1_Frame_Shift_Del_p.I628fs|LDLR_uc010xll.1_Frame_Shift_Del_p.I587fs|LDLR_uc010xlm.1_Frame_Shift_Del_p.I481fs|LDLR_uc010xln.1_Frame_Shift_Del_p.I501fs|LDLR_uc010xlo.1_Frame_Shift_Del_p.I460fs NM_000527 NP_000518 P01130 LDLR_HUMAN low density lipoprotein receptor precursor 628 LDL-receptor class B 6.|Extracellular (Potential). cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity ovary(2)|skin(2) 4 Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524) GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197) Methyl aminolevulinate(DB00992)|Porfimer(DB00707) AACGAAGCCATTTTCAGTGCC 0.488 0.48 169 154 DYRK1B 9149 broad.mit.edu 37 19 40317456 40317456 + Frame_Shift_Del DEL G - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr19:40317456delG uc002omj.2 - 9 1547 c.1267delC c.(1267-1269)CTGfs p.L423fs DYRK1B_uc002omi.2_Frame_Shift_Del_p.L395fs|DYRK1B_uc002omk.2_Frame_Shift_Del_p.L383fs NM_004714 NP_004705 Q9Y463 DYR1B_HUMAN dual-specificity tyrosine-(Y)-phosphorylation 423 Protein kinase. positive regulation of transcription, DNA-dependent nucleus ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|transcription coactivator activity ovary(4)|stomach(1)|central_nervous_system(1)|skin(1) 7 all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06) Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23) 0.000 0.48 742 695 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 220 537 PI4KA 5297 broad.mit.edu 37 22 21153431 21153431 + Frame_Shift_Del DEL G - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr22:21153431delG uc002zsz.3 - 16 2011 c.1780delC c.(1780-1782)CTCfs p.L594fs PI4KA_uc010gsq.1_Frame_Shift_Del_p.L652fs NM_058004 NP_477352 P42356 PI4KA_HUMAN phosphatidylinositol 4-kinase type 3 alpha 594 phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission Golgi-associated vesicle 1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1) 4 all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196) AGCACATCGAGGGGGGAGGGT 0.562 0.43 68 51 MAPK8IP2 23542 broad.mit.edu 37 22 51042380 51042380 + Frame_Shift_Del DEL G - - SNU175_LARGE_INTESTINE NA SNU175_LARGE_INTESTINE NA g.chr22:51042380delG uc003bmx.2 + 5 769 c.652delG c.(652-654)GGGfs p.G218fs MAPK8IP2_uc003bmy.2_Frame_Shift_Del_p.G191fs|MAPK8IP2_uc011asc.1_5'Flank NM_012324 NP_036456 Q13387 JIP2_HUMAN mitogen-activated protein kinase 8 interacting 218 JNK-binding domain (JBD). behavioral fear response|dendrite morphogenesis|MAPKKK cascade|nonassociative learning|positive regulation of anti-apoptosis|regulation of excitatory postsynaptic membrane potential|regulation of JNK cascade|regulation of receptor activity|regulation of synaptic transmission, glutamatergic|signal complex assembly|social behavior cytoplasm|postsynaptic density beta-amyloid binding|kinesin binding|MAP-kinase scaffold activity|protein kinase activator activity|protein kinase binding large_intestine(2)|central_nervous_system(1) 3 all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) OV - Ovarian serous cystadenocarcinoma(4;1.28e-70)|Epithelial(4;3.46e-65)|GBM - Glioblastoma multiforme(4;4.83e-06)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247) 0.000 0.13 350 51 FAM123B 139285 broad.mit.edu 37 X 63410309 63410309 + Frame_Shift_Del DEL G - - SNU1_STOMACH NA SNU1_STOMACH NA g.chrX:63410309delG uc004dvo.2 - 2 3131 c.2858delC c.(2857-2859)CCAfs p.P953fs NM_152424 NP_689637 Q5JTC6 F123B_HUMAN family with sequence similarity 123B 953 Pro-rich. Wnt receptor signaling pathway cytoplasm|nucleus|plasma membrane p.0?(40) kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1) 112 0.000 0.90 23 206 FAM123B 139285 broad.mit.edu 37 X 63412648 63412648 + Frame_Shift_Del DEL A - - SNU1_STOMACH NA SNU1_STOMACH NA g.chrX:63412648delA uc004dvo.2 - 2 792 c.519delT c.(517-519)TTTfs p.F173fs NM_152424 NP_689637 Q5JTC6 F123B_HUMAN family with sequence similarity 123B 173 Wnt receptor signaling pathway cytoplasm|nucleus|plasma membrane p.0?(40)|p.F173fs*36(2) kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1) 112 GGATACTGCTAAAAAAGCCTT 0.562 0.96 4 85 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU1_STOMACH NA SNU1_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.65 15 28 FLNA 2316 broad.mit.edu 37 X 153583264 153583264 + Frame_Shift_Del DEL G - - SNU1_STOMACH NA SNU1_STOMACH NA g.chrX:153583264delG uc004fkk.2 - 31 5395 c.5146delC c.(5146-5148)CAGfs p.Q1716fs FLNA_uc004fki.2_5'Flank|FLNA_uc011mzn.1_5'UTR|FLNA_uc010nuu.1_Frame_Shift_Del_p.Q1708fs NM_001110556 NP_001104026 P21333 FLNA_HUMAN filamin A, alpha isoform 2 1716 Filamin 15. actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering cell cortex|cytosol|extracellular region|nucleus|plasma membrane actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding breast(6) 6 all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176) TTGCCCGGCTGGGGGGCCGTG 0.612 0.91 15 150 F8 2157 broad.mit.edu 37 X 154158195 154158195 + Frame_Shift_Del DEL T - - SNU1_STOMACH NA SNU1_STOMACH NA g.chrX:154158195delT uc004fmt.2 - 14 4041 c.3870delA c.(3868-3870)AAAfs p.K1290fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1290 B. acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) CTTCCTCCCCTTTTTTTGAGA 0.383 0.89 8 64 ARID1A 8289 broad.mit.edu 37 1 27024002 27024002 + Frame_Shift_Del DEL G - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr1:27024002delG uc001bmv.1 + 1 1481 c.1108delG c.(1108-1110)GGGfs p.G370fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.G370fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.G370fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 370 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.Q372fs*19(1)|p.Q372fs*28(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.17 117 24 ARID1A 8289 broad.mit.edu 37 1 27101268 27101268 + Frame_Shift_Del DEL C - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr1:27101268delC uc001bmv.1 + 18 4923 c.4550delC c.(4549-4551)GCCfs p.A1517fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.A1516fs|ARID1A_uc001bmu.1_Intron|ARID1A_uc001bmw.1_Frame_Shift_Del_p.A1134fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.A363fs|ARID1A_uc009vsm.1_Intron|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1517 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) ACGGGCTCTGCCCCCCAGGGC 0.582 0.41 124 87 PLK3 1263 broad.mit.edu 37 1 45268997 45268997 + Frame_Shift_Del DEL C - - rs112574988 SNU1_STOMACH NA SNU1_STOMACH NA g.chr1:45268997delC uc001cmn.2 + 8 1106 c.1006delC c.(1006-1008)CCCfs p.P336fs PLK3_uc001cmo.2_RNA NM_004073 NP_004064 Q9H4B4 PLK3_HUMAN polo-like kinase 3 336 membrane ATP binding|protein binding|protein serine/threonine kinase activity 0 Acute lymphoblastic leukemia(166;0.155) AGACCTGACACCCCCCAACCC 0.577 0.42 37 27 NFIA 4774 broad.mit.edu 37 1 61824898 61824899 + Frame_Shift_Ins INS - C C SNU1_STOMACH NA SNU1_STOMACH NA g.chr1:61824898_61824899insC uc001czw.2 + 6 1382_1383 c.898_899insC c.(898-900)TCCfs p.S300fs NFIA_uc001czy.2_Frame_Shift_Ins_p.S292fs|NFIA_uc010oos.1_Frame_Shift_Ins_p.S345fs|NFIA_uc001czv.2_Frame_Shift_Ins_p.S300fs NM_001134673 NP_001128145 Q12857 NFIA_HUMAN nuclear factor I/A isoform 1 300 DNA replication|viral genome replication cell junction|nucleus DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding pancreas(1)|skin(1) 2 CCAAGGGCGCTCCCCAGGAAGT 0.525 0.34 39 20 RBM15 64783 broad.mit.edu 37 1 110884036 110884038 + In_Frame_Del DEL CTC - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr1:110884036_110884038delCTC uc001dzl.1 + 1 2092_2094 c.2009_2011delCTC c.(2008-2013)TCTCCT>TCT p.P671del RBM15_uc001dzm.1_In_Frame_Del_p.P671del|uc001dzj.2_5'Flank NM_022768 NP_073605 Q96T37 RBM15_HUMAN RNA binding motif protein 15 671 Arg-rich. interspecies interaction between organisms nucleus nucleotide binding|protein binding|RNA binding ovary(3) 3 all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634) BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135) TGCGCTCCTTCTCCTGACCGCAG 0.557 0.46 101 85 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 399 121 MAP3K2 10746 broad.mit.edu 37 2 128079681 128079683 + In_Frame_Del DEL CTT - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr2:128079681_128079683delCTT uc002toj.1 - 11 1049_1051 c.984_986delAAG c.(982-987)AGAAGG>AGG p.328_329RR>R NM_006609 NP_006600 Q9Y2U5 M3K2_HUMAN mitogen-activated protein kinase kinase kinase 328_329 activation of JUN kinase activity|cellular response to mechanical stimulus nucleus ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein kinase binding lung(3)|ovary(2)|large_intestine(1)|central_nervous_system(1) 7 Colorectal(110;0.1) BRCA - Breast invasive adenocarcinoma(221;0.0706) GTCACTTCCCCTTCTTCTTATTC 0.424 0.43 155 116 NFE2L2 4780 broad.mit.edu 37 2 178095913 178095914 + Frame_Shift_Ins INS - T T SNU1_STOMACH NA SNU1_STOMACH NA g.chr2:178095913_178095914insT uc002ulh.3 - 5 1972_1973 c.1417_1418insA c.(1417-1419)ATCfs p.I473fs NFE2L2_uc002ulg.3_Frame_Shift_Ins_p.I457fs|NFE2L2_uc010zfa.1_Frame_Shift_Ins_p.I450fs|NFE2L2_uc002uli.3_Frame_Shift_Ins_p.I457fs NM_006164 NP_006155 Q16236 NF2L2_HUMAN nuclear factor erythroid 2-like 2 isoform 1 473 transcription from RNA polymerase II promoter centrosome|cytosol|nucleus|plasma membrane protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity central_nervous_system(1) 1 Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935) 0.000 0.42 494 363 TTN 7273 broad.mit.edu 37 2 179536771 179536771 + Frame_Shift_Del DEL T - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr2:179536771delT uc010zfg.1 - 150 31475 c.31251delA c.(31249-31251)AAAfs p.K10417fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.K7078fs|TTN_uc010fre.1_Intron|TTN_uc010zfk.1_5'UTR NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 11344 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CCCTATGAACTTTTTCAACTC 0.328 0.48 140 128 INPP5D 3635 broad.mit.edu 37 2 234094532 234094532 + Frame_Shift_Del DEL G - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr2:234094532delG uc010zmo.1 + 20 2472 c.2319delG c.(2317-2319)GAGfs p.E773fs INPP5D_uc010zmp.1_Frame_Shift_Del_p.E772fs NM_001017915 NP_001017915 Q92835 SHIP1_HUMAN SH2 containing inositol phosphatase isoform a 773 apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway cytosol inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding ovary(1)|central_nervous_system(1) 2 Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843) Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185) AAGGAAGTGAGGGGGAGCTGG 0.453 0.45 34 28 TGFBR2 7048 broad.mit.edu 37 3 30691872 30691873 + Frame_Shift_Del DEL AA - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr3:30691872_30691873delAA uc003ceo.2 + 3 756_757 c.374_375delAA c.(373-375)GAAfs p.E125fs TGFBR2_uc003cen.2_Frame_Shift_Del_p.E150fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 125 Extracellular (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 ATTATGAAGGAAAAAAAAAAGC 0.426 0.49 186 176 TGFBR2 7048 broad.mit.edu 37 3 30713896 30713899 + Frame_Shift_Del DEL TCTG - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr3:30713896_30713899delTCTG uc003ceo.2 + 4 1603_1606 c.1221_1224delTCTG c.(1219-1224)ACTCTGfs p.T407fs TGFBR2_uc003cen.2_Frame_Shift_Del_p.T432fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 407_408 Protein kinase.|Cytoplasmic (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 TGGACCCTACTCTGTCTGTGGATG 0.534 0.39 34 22 PBRM1 55193 broad.mit.edu 37 3 52678784 52678784 + Frame_Shift_Del DEL T - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr3:52678784delT uc003des.2 - 8 847 c.835delA c.(835-837)ATAfs p.I279fs PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.I279fs|PBRM1_uc003der.2_Frame_Shift_Del_p.I279fs|PBRM1_uc003det.2_Frame_Shift_Del_p.I279fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.I279fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.I279fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.I279fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.I279fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.I279fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.I177fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 279 chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding p.I279fs*4(2) kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.24 203 65 PRKCI 5584 broad.mit.edu 37 3 169993017 169993025 + In_Frame_Del DEL TAATTCCAT - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr3:169993017_169993025delTAATTCCAT uc003fgs.2 + 8 885_893 c.647_655delTAATTCCAT c.(646-657)GTAATTCCATAT>GAT p.216_219VIPY>D NM_002740 NP_002731 P41743 KPCI_HUMAN protein kinase C, iota 216_219 Regulatory domain. anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport cytosol|endosome|nucleus|polarisome ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding lung(2)|ovary(1)|breast(1)|skin(1) 5 all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169) Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197) GGGTTTTTAGTAATTCCATATAATCCTTC 0.278 0.41 51 35 TNFSF10 8743 broad.mit.edu 37 3 172224591 172224591 + Frame_Shift_Del DEL T - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr3:172224591delT uc003fid.2 - 5 632 c.537delA c.(535-537)AAAfs p.K179fs TNFSF10_uc003fie.2_3'UTR NM_003810 NP_003801 P50591 TNF10_HUMAN tumor necrosis factor (ligand) superfamily, 179 Extracellular (Potential). activation of caspase activity|activation of pro-apoptotic gene products|cell-cell signaling|immune response|induction of apoptosis by extracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|signal transduction extracellular space|integral to plasma membrane|soluble fraction cytokine activity|metal ion binding|tumor necrosis factor receptor binding skin(4)|lung(1) 5 Ovarian(172;0.00197)|Breast(254;0.158) Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235) AGTAAAACCCTTTTTCATGGA 0.388 0.44 316 244 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU1_STOMACH NA SNU1_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.43 104 79 NIPBL 25836 broad.mit.edu 37 5 37008134 37008134 + Frame_Shift_Del DEL T - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr5:37008134delT uc003jkl.3 + 19 4763 c.4264delT c.(4264-4266)TTTfs p.F1422fs NIPBL_uc003jkk.3_Frame_Shift_Del_p.F1422fs NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 1422 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) AATAACACCATTTTTTGTGGA 0.299 0.43 181 136 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU1_STOMACH NA SNU1_STOMACH NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.29 100 40 FER 2241 broad.mit.edu 37 5 108436204 108436204 + Frame_Shift_Del DEL A - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr5:108436204delA uc003kop.1 + 17 2416 c.2032delA c.(2032-2034)AAAfs p.K678fs FER_uc011cvg.1_Frame_Shift_Del_p.K503fs NM_005246 NP_005237 P16591 FER_HUMAN fer (fps/fes related) tyrosine kinase 678 Protein kinase. intracellular signal transduction|peptidyl-tyrosine phosphorylation cytoplasm|nucleus ATP binding|non-membrane spanning protein tyrosine kinase activity lung(2)|stomach(1)|ovary(1)|kidney(1) 5 all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152) OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174) TCTCGAGAGTAAAAACTGTAT 0.333 0.49 44 42 TSSK1B 83942 broad.mit.edu 37 5 112769462 112769462 + Frame_Shift_Del DEL G - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr5:112769462delG uc003kqm.2 - 1 1267 c.1075delC c.(1075-1077)CAAfs p.Q359fs MCC_uc003kql.3_Intron NM_032028 NP_114417 Q9BXA7 TSSK1_HUMAN testis-specific serine kinase 1 359 cell differentiation|multicellular organismal development|spermatogenesis ATP binding|magnesium ion binding|protein serine/threonine kinase activity ovary(2)|skin(2)|stomach(1) 5 all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156) Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449) 0.000 0.20 377 93 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SNU1_STOMACH NA SNU1_STOMACH NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.32 17 8 RUNX2 860 broad.mit.edu 37 6 45390467 45390475 + In_Frame_Del DEL CAGCAGCAG - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr6:45390467_45390475delCAGCAGCAG uc011dvx.1 + 3 406_414 c.196_204delCAGCAGCAG c.(196-204)CAGCAGCAGdel p.QQQ69del RUNX2_uc011dvy.1_In_Frame_Del_p.QQQ69del|RUNX2_uc003oxt.2_In_Frame_Del_p.QQQ55del NM_001024630 NP_001019801 Q13950 RUNX2_HUMAN runt-related transcription factor 2 isoform a 69_71 Poly-Gln. negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent nucleus ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity ovary(2)|skin(1) 3 gcagcagcaacagcagcagcagcagcagg 0.287 0.35 17 9 BAI3 577 broad.mit.edu 37 6 70098782 70098782 + Frame_Shift_Del DEL A - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr6:70098782delA uc003pev.3 + 32 5016 c.4568delA c.(4567-4569)TAAfs p.*1523fs BAI3_uc010kak.2_Frame_Shift_Del_p.*1523fs|BAI3_uc011dxx.1_Frame_Shift_Del_p.*729fs NM_001704 NP_001695 O60242 BAI3_HUMAN brain-specific angiogenesis inhibitor 3 1523 negative regulation of angiogenesis|neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1) 50 all_lung(197;0.212) ACAGAAGTTTAAAAAAATCAA 0.418 0.58 8 11 GRM3 2913 broad.mit.edu 37 7 86394580 86394580 + Frame_Shift_Del DEL T - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr7:86394580delT uc003uid.2 + 2 1218 c.119delT c.(118-120)GTTfs p.V40fs GRM3_uc010lef.2_Frame_Shift_Del_p.V38fs|GRM3_uc010leg.2_Intron|GRM3_uc010leh.2_Intron NM_000840 NP_000831 Q14832 GRM3_HUMAN glutamate receptor, metabotropic 3 precursor 40 Extracellular (Potential). synaptic transmission integral to plasma membrane lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1) 13 Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142) Acamprosate(DB00659)|Nicotine(DB00184) 0.000 0.56 139 175 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU1_STOMACH NA SNU1_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 MLL3 58508 broad.mit.edu 37 7 151874148 151874149 + Frame_Shift_Del DEL TT - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr7:151874148_151874149delTT uc003wla.2 - 38 8608_8609 c.8389_8390delAA c.(8389-8391)AAGfs p.K2797fs MLL3_uc003wkz.2_Frame_Shift_Del_p.K1858fs|MLL3_uc003wky.2_Frame_Shift_Del_p.K306fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 2797 K -> R (in Ref. 1; AAK00583). intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding p.K2797fs*26(18) large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTCTTGTTCCTTTTTTTTTGGT 0.347 0.39 285 179 PCM1 5108 broad.mit.edu 37 8 17796460 17796460 + Frame_Shift_Del DEL A - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr8:17796460delA uc003wyi.3 + 5 976 c.554delA c.(553-555)CAAfs p.Q185fs PCM1_uc011kyh.1_Frame_Shift_Del_p.Q185fs|PCM1_uc003wyj.3_Frame_Shift_Del_p.Q185fs|PCM1_uc003wyg.2_Frame_Shift_Del_p.Q185fs|PCM1_uc003wyh.2_Frame_Shift_Del_p.Q185fs|PCM1_uc010lta.1_Frame_Shift_Del_p.Q185fs NM_006197 NP_006188 Q15154 PCM1_HUMAN pericentriolar material 1 185 centrosome organization|cilium assembly|G2/M transition of mitotic cell cycle|interkinetic nuclear migration|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome centriolar satellite|cytosol|nuclear membrane|pericentriolar material identical protein binding PCM1/JAK2(30) haematopoietic_and_lymphoid_tissue(30)|breast(4)|ovary(2) 36 Colorectal(111;0.0789) GACCTCTTGCAAAACTGTCAG 0.433 0.55 35 42 ARFGEF1 10565 broad.mit.edu 37 8 68117038 68117038 + Frame_Shift_Del DEL T - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr8:68117038delT uc003xxo.1 - 35 5226 c.4836delA c.(4834-4836)AAAfs p.K1612fs ARFGEF1_uc003xxl.1_Frame_Shift_Del_p.K1066fs|ARFGEF1_uc003xxm.1_Frame_Shift_Del_p.K15fs|ARFGEF1_uc003xxn.1_Intron|ARFGEF1_uc003xxp.1_5'Flank NM_006421 NP_006412 Q9Y6D6 BIG1_HUMAN brefeldin A-inhibited guanine 1612 exocytosis|regulation of ARF protein signal transduction cytoplasm ARF guanyl-nucleotide exchange factor activity|myosin binding ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1) 8 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206) CAGCAAACAATTTTTGTTCTG 0.378 0.40 157 106 CSMD3 114788 broad.mit.edu 37 8 113662424 113662425 + Frame_Shift_Ins INS - T T SNU1_STOMACH NA SNU1_STOMACH NA g.chr8:113662424_113662425insT uc003ynu.2 - 19 3317_3318 c.3158_3159insA c.(3157-3159)AACfs p.N1053fs CSMD3_uc003yns.2_Frame_Shift_Ins_p.N325fs|CSMD3_uc003ynt.2_Frame_Shift_Ins_p.N1013fs|CSMD3_uc011lhx.1_Frame_Shift_Ins_p.N949fs NM_198123 NP_937756 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 isoform 1 1053 Extracellular (Potential).|Sushi 5. integral to membrane|plasma membrane ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1) 63 TCCACCAGTGGTTTTTTTCGCA 0.376 0.44 53 41 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU1_STOMACH NA SNU1_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU1_STOMACH NA SNU1_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.34 351 179 PSIP1 11168 broad.mit.edu 37 9 15474027 15474029 + In_Frame_Del DEL CTC - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr9:15474027_15474029delCTC uc003zlv.3 - 9 1166_1168 c.836_838delGAG c.(835-840)GGAGAT>GAT p.G279del PSIP1_uc003zlw.3_In_Frame_Del_p.G279del|PSIP1_uc003zlz.3_In_Frame_Del_p.G279del|PSIP1_uc003zma.3_In_Frame_Del_p.G270del|PSIP1_uc003zly.2_In_Frame_Del_p.G279del NM_033222 NP_150091 O75475 PSIP1_HUMAN PC4 and SFRS1 interacting protein 1 isoform 2 279 initiation of viral infection|interspecies interaction between organisms|nuclear mRNA 5'-splice site recognition|provirus integration|regulation of transcription, DNA-dependent|response to heat|response to oxidative stress|transcription, DNA-dependent cytosol|nuclear heterochromatin|nuclear periphery|nucleoplasm|nucleoplasm|transcriptionally active chromatin activating transcription factor binding|chromatin binding|DNA secondary structure binding|RNA polymerase II transcription coactivator activity breast(1) 1 GBM - Glioblastoma multiforme(50;2.38e-06) TCTTGATCATCTCCTTCTTCTTC 0.276 0.42 220 162 FNBP1 23048 broad.mit.edu 37 9 132689474 132689475 + Frame_Shift_Ins INS - T T SNU1_STOMACH NA SNU1_STOMACH NA g.chr9:132689474_132689475insT uc004byw.1 - 8 1007_1008 c.788_789insA c.(787-789)AATfs p.N263fs FNBP1_uc011mbv.1_Frame_Shift_Ins_p.N263fs|FNBP1_uc011mbw.1_Frame_Shift_Ins_p.N263fs|FNBP1_uc004bza.2_Frame_Shift_Ins_p.N263fs|FNBP1_uc004byz.1_Frame_Shift_Ins_p.N263fs|FNBP1_uc004byx.1_Frame_Shift_Ins_p.N184fs|FNBP1_uc004byy.1_Frame_Shift_Ins_p.N184fs NM_015033 NP_055848 Q96RU3 FNBP1_HUMAN formin binding protein 1 263 Interaction with microtubules (By similarity).|Required for self-association and induction of membrane tubulation.|Self-association, lipid-binding and induction of membrane tubulation. endocytosis cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane identical protein binding|lipid binding 0 Ovarian(14;0.000536) GBM - Glioblastoma multiforme(294;0.0378) CAATACTTACATTTTTCTGATC 0.416 0.51 146 149 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU1_STOMACH NA SNU1_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 224 50 ATM 472 broad.mit.edu 37 11 108151776 108151777 + Frame_Shift_Ins INS - T T rs12788418 SNU1_STOMACH NA SNU1_STOMACH NA g.chr11:108151776_108151777insT uc001pkb.1 + 24 3842_3843 c.3457_3458insT c.(3457-3459)GTTfs p.V1153fs ATM_uc009yxr.1_Frame_Shift_Ins_p.V1153fs NM_000051 NP_000042 Q13315 ATM_HUMAN ataxia telangiectasia mutated isoform 1 1153 cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence cytoplasmic membrane-bounded vesicle|nucleoplasm 1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1) 240 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147) TAGAAAATCTGTTTTACTGACG 0.322 0.45 148 123 ANKK1 255239 broad.mit.edu 37 11 113270644 113270644 + Frame_Shift_Del DEL C - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr11:113270644delC uc001pny.2 + 8 2047 c.1953delC c.(1951-1953)GACfs p.D651fs NM_178510 NP_848605 Q8NFD2 ANKK1_HUMAN ankyrin repeat and kinase domain containing 1 651 ANK 9. ATP binding|protein serine/threonine kinase activity lung(5)|stomach(1)|ovary(1)|breast(1) 8 all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194) BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238) 0.000 0.51 154 163 MLL 4297 broad.mit.edu 37 11 118375057 118375057 + Frame_Shift_Del DEL C - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr11:118375057delC uc001pta.2 + 27 8464 c.8441delC c.(8440-8442)ACCfs p.T2814fs MLL_uc001ptb.2_Frame_Shift_Del_p.T2817fs NM_005933 NP_005924 Q03164 MLL1_HUMAN myeloid/lymphoid or mixed-lineage leukemia 2814 apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter MLL1 complex AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1) 25 all_hematologic(175;0.046) all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244) OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144) CACACAAGTACCCCCTCCGAC 0.448 0.42 266 189 SORL1 6653 broad.mit.edu 37 11 121475904 121475905 + Frame_Shift_Ins INS - A A SNU1_STOMACH NA SNU1_STOMACH NA g.chr11:121475904_121475905insA uc001pxx.2 + 34 4814_4815 c.4734_4735insA c.(4732-4737)CCCAAAfs p.P1578fs SORL1_uc010rzp.1_Frame_Shift_Ins_p.P424fs|SORL1_uc010rzq.1_Frame_Shift_Ins_p.P193fs NM_003105 NP_003096 Q92673 SORL_HUMAN sortilin-related receptor containing LDLR class 1578_1579 Extracellular (Potential).|Fibronectin type-III 1. cholesterol metabolic process|lipid transport|receptor-mediated endocytosis integral to plasma membrane|low-density lipoprotein particle low-density lipoprotein particle binding|transmembrane receptor activity ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1) 15 Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113) BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108) GGATGAGGCCCAAAAAAATGCC 0.436 0.47 188 164 GUCY2C 2984 broad.mit.edu 37 12 14766135 14766135 + Frame_Shift_Del DEL T - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr12:14766135delT uc001rcd.2 - 27 3275 c.3138delA c.(3136-3138)AAAfs p.K1046fs NM_004963 NP_004954 P25092 GUC2C_HUMAN guanylate cyclase 2C precursor 1046 Cytoplasmic (Potential). intracellular signal transduction|receptor guanylyl cyclase signaling pathway integral to membrane ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity ovary(4)|skin(2) 6 CCCGTCTGGGTTTTTGGCTTC 0.428 0.44 326 255 GUCY2C 2984 broad.mit.edu 37 12 14796510 14796510 + Frame_Shift_Del DEL T - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr12:14796510delT uc001rcd.2 - 17 2065 c.1928delA c.(1927-1929)AAGfs p.K643fs NM_004963 NP_004954 P25092 GUC2C_HUMAN guanylate cyclase 2C precursor 643 Cytoplasmic (Potential).|Protein kinase. intracellular signal transduction|receptor guanylyl cyclase signaling pathway integral to membrane ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity ovary(4)|skin(2) 6 TTACAGACCCTTTTTTGGAGG 0.388 0.50 163 160 LRRK2 120892 broad.mit.edu 37 12 40734234 40734234 + Frame_Shift_Del DEL A - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr12:40734234delA uc001rmg.3 + 41 6208 c.6087delA c.(6085-6087)ATAfs p.I2029fs LRRK2_uc009zjw.2_Frame_Shift_Del_p.I867fs|LRRK2_uc001rmi.2_Frame_Shift_Del_p.I862fs NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 2029 Protein kinase. activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) GAATGGGGATAAAAACATCAG 0.458 0.43 149 114 ACVR1B 91 broad.mit.edu 37 12 52345607 52345607 + Frame_Shift_Del DEL G - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr12:52345607delG uc001rzn.2 + 1 122 c.80delG c.(79-81)CGGfs p.R27fs ACVR1B_uc001rzl.2_Frame_Shift_Del_p.R27fs|ACVR1B_uc001rzm.2_Frame_Shift_Del_p.R27fs|ACVR1B_uc010snn.1_Frame_Shift_Del_p.R27fs NM_004302 NP_004293 P36896 ACV1B_HUMAN activin A receptor, type IB isoform a precursor 27 Extracellular (Potential). G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|peptidyl-threonine phosphorylation|positive regulation of activin receptor signaling pathway|positive regulation of erythrocyte differentiation|protein autophosphorylation|transmembrane receptor protein serine/threonine kinase signaling pathway cell surface activin receptor activity, type I|ATP binding|metal ion binding|SMAD binding|transforming growth factor beta receptor activity|ubiquitin protein ligase binding pancreas(4)|breast(2)|ovary(1)|lung(1)|kidney(1) 9 BRCA - Breast invasive adenocarcinoma(357;0.104) Adenosine triphosphate(DB00171) 0.000 0.83 36 179 BRCA2 675 broad.mit.edu 37 13 32906536 32906536 + Frame_Shift_Del DEL T - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr13:32906536delT uc001uub.1 + 10 1148 c.921delT c.(919-921)AGTfs p.S307fs BRCA2_uc001uua.1_Frame_Shift_Del_p.S184fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 307 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) AAGAAGATAGTTTTTCATTAT 0.308 0.49 127 120 CSNK1A1L 122011 broad.mit.edu 37 13 37678404 37678405 + Frame_Shift_Ins INS - T T SNU1_STOMACH NA SNU1_STOMACH NA g.chr13:37678404_37678405insT uc001uwm.1 - 1 1397_1398 c.989_990insA c.(988-990)AACfs p.N330fs NM_145203 NP_660204 Q8N752 KC1AL_HUMAN casein kinase 1, alpha 1-like 330 Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity large_intestine(1) 1 Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109) all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407) CATTATTCTTGTTTTTTTCAGT 0.460 0.39 174 113 DACH1 1602 broad.mit.edu 37 13 72440435 72440443 + In_Frame_Del DEL CTGCTACTA - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr13:72440435_72440443delCTGCTACTA uc010thn.1 - 2 882_890 c.459_467delTAGTAGCAG c.(457-468)AGTAGTAGCAGC>AGC p.153_156SSSS>S DACH1_uc010tho.1_In_Frame_Del_p.153_156SSSS>S|DACH1_uc010thp.1_In_Frame_Del_p.153_156SSSS>S NM_080759 NP_542937 Q9UI36 DACH1_HUMAN dachshund homolog 1 isoform a 153_156 Poly-Ser. multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus DNA binding|nucleotide binding|protein binding breast(1) 1 Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198) GBM - Glioblastoma multiforme(99;0.00032) actgctgctgctgctactactgctgctgc 0.297 0.29 20 8 EDNRB 1910 broad.mit.edu 37 13 78475267 78475267 + Frame_Shift_Del DEL A - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr13:78475267delA uc001vko.2 - 4 1135 c.877delT c.(877-879)TATfs p.Y293fs EDNRB_uc001vkq.1_Frame_Shift_Del_p.Y293fs|uc001vkn.1_Intron|EDNRB_uc010aez.1_Frame_Shift_Del_p.Y293fs|EDNRB_uc001vkp.1_Frame_Shift_Del_p.Y376fs NM_001122659 NP_001116131 P24530 EDNRB_HUMAN endothelin receptor type B isoform 1 precursor 293 Helical; Name=5; (Potential). activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction integral to plasma membrane endothelin-B receptor activity|peptide hormone binding 0 Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037) GBM - Glioblastoma multiforme(99;0.0933) Bosentan(DB00559) ATTAGTGTATAAAAAAATGCA 0.343 0.47 124 112 ARHGEF7 8874 broad.mit.edu 37 13 111953132 111953134 + In_Frame_Del DEL AGA - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr13:111953132_111953134delAGA uc010tjo.1 + 18 1978_1980 c.1926_1928delAGA c.(1924-1929)CCAGAA>CCA p.E645del ARHGEF7_uc001vrv.3_In_Frame_Del_p.E570del|ARHGEF7_uc001vrw.3_In_Frame_Del_p.E570del|ARHGEF7_uc001vrx.3_In_Frame_Del_p.E570del NM_003899 NP_003890 Q14155 ARHG7_HUMAN PAK-interacting exchange factor beta isoform a Error:Variant_position_missing_in_Q14155_after_alignment apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol protein binding|Rho guanyl-nucleotide exchange factor activity ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163) BRCA - Breast invasive adenocarcinoma(86;0.188) TTTTGCTTCCAGAAGAAGAGAAA 0.360 0.51 137 141 OR4E2 26686 broad.mit.edu 37 14 22133746 22133746 + Frame_Shift_Del DEL G - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr14:22133746delG uc010tmd.1 + 1 450 c.450delG c.(448-450)TTGfs p.L150fs NM_001001912 NP_001001912 Q8NGC2 OR4E2_HUMAN olfactory receptor, family 4, subfamily E, 150 Helical; Name=4; (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(2)|pancreas(1)|skin(1) 4 all_cancers(95;0.00113) Acute lymphoblastic leukemia(2;0.0279) GBM - Glioblastoma multiforme(265;0.0137) CTCTCTGGTTGGGGGGTACTG 0.483 0.46 420 357 FANCM 57697 broad.mit.edu 37 14 45668096 45668097 + Frame_Shift_Del DEL AT - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr14:45668096_45668097delAT uc001wwd.3 + 22 6065_6066 c.5966_5967delAT c.(5965-5967)AATfs p.N1989fs FANCM_uc010anf.2_Frame_Shift_Del_p.N1963fs|FANCM_uc001wwe.3_Frame_Shift_Del_p.N1525fs|FANCM_uc010ang.2_Frame_Shift_Del_p.N1238fs NM_020937 NP_065988 Q8IYD8 FANCM_HUMAN Fanconi anemia, complementation group M 1989 Interaction with FAAP24 and EME1. DNA repair Fanconi anaemia nuclear complex ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding ovary(3)|lung(2)|breast(2) 7 ACTGCATTAAATATGTGTCACC 0.302 0.50 132 134 KTN1 3895 broad.mit.edu 37 14 56079224 56079224 + Frame_Shift_Del DEL C - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr14:56079224delC uc001xcb.2 + 3 760 c.458delC c.(457-459)ACCfs p.T153fs KTN1_uc001xce.2_Frame_Shift_Del_p.T153fs|KTN1_uc001xcc.2_Frame_Shift_Del_p.T153fs|KTN1_uc001xcd.2_Frame_Shift_Del_p.T153fs|KTN1_uc010trb.1_Frame_Shift_Del_p.T153fs|KTN1_uc001xcf.1_Frame_Shift_Del_p.T153fs NM_182926 NP_891556 Q86UP2 KTN1_HUMAN kinectin 1 isoform a 153 Lumenal (Potential). microtubule-based movement endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction breast(3)|ovary(2)|lung(1)|central_nervous_system(1) 7 AAACAGCCCACCCCTCCCTCT 0.413 0.39 92 59 KIAA1409 57578 broad.mit.edu 37 14 94121610 94121610 + Frame_Shift_Del DEL G - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr14:94121610delG uc001ybv.1 + 37 6048 c.5965delG c.(5965-5967)GGGfs p.G1989fs KIAA1409_uc001ybs.1_Frame_Shift_Del_p.G1967fs NM_020818 NP_065869 Q9P2D8 UNC79_HUMAN hypothetical protein LOC57578 2144 integral to membrane ovary(10)|skin(4)|large_intestine(3) 17 all_cancers(154;0.0354)|all_epithelial(191;0.216) Epithelial(152;0.188) TTTACCAGCAGGGGGTGCTAT 0.423 0.54 121 140 C15orf55 256646 broad.mit.edu 37 15 34649123 34649123 + Frame_Shift_Del DEL A - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr15:34649123delA uc001zif.2 + 7 2985 c.2830delA c.(2830-2832)AAAfs p.K944fs C15orf55_uc010ucc.1_Frame_Shift_Del_p.K972fs|C15orf55_uc010ucd.1_Frame_Shift_Del_p.K962fs NM_175741 NP_786883 Q86Y26 NUT_HUMAN nuclear protein in testis 944 cytoplasm|nucleus BRD4_ENST00000263377/C15orf55(24)|BRD3/C15orf55(3) midline_organs(25)|ovary(2)|lung(2)|skin(1) 30 all_lung(180;2.78e-08) all cancers(64;4.53e-18)|GBM - Glioblastoma multiforme(113;8.29e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0249) GTCCAAGCCTAAAAACCTTGC 0.512 0.48 126 115 MLLT6 4302 broad.mit.edu 37 17 36881841 36881841 + Frame_Shift_Del DEL A - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr17:36881841delA uc002hqi.3 + 20 3285 c.3272delA c.(3271-3273)GAAfs p.E1091fs MLLT6_uc002hqk.3_Frame_Shift_Del_p.E422fs|MLLT6_uc010cvn.1_5'Flank NM_005937 NP_005928 P55198 AF17_HUMAN myeloid/lymphoid or mixed-lineage leukemia 1091 regulation of transcription, DNA-dependent nucleus protein binding|zinc ion binding breast(3)|prostate(1)|lung(1)|skin(1) 6 Breast(7;4.43e-21) GCCAACCAGGAAAAAGGCTAA 0.607 0.39 45 29 ATP8B1 5205 broad.mit.edu 37 18 55355557 55355557 + Frame_Shift_Del DEL T - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr18:55355557delT uc002lgw.2 - 12 1403 c.1403delA c.(1402-1404)AAGfs p.K468fs uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 468 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) GATACAGCACTTTTTAAAGGT 0.458 0.45 280 229 MAST1 22983 broad.mit.edu 37 19 12985060 12985060 + Frame_Shift_Del DEL G - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr19:12985060delG uc002mvm.2 + 26 4217 c.4089delG c.(4087-4089)CCGfs p.P1363fs NM_014975 NP_055790 Q9Y2H9 MAST1_HUMAN microtubule associated serine/threonine kinase 1363 cytoskeleton organization|intracellular protein kinase cascade cytoplasm|cytoskeleton|plasma membrane ATP binding|magnesium ion binding|protein serine/threonine kinase activity ovary(3)|lung(2)|large_intestine(1)|skin(1) 7 0.000 0.47 321 281 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU1_STOMACH NA SNU1_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.28 39 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU1_STOMACH NA SNU1_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.64 176 316 TSSK2 23617 broad.mit.edu 37 22 19119732 19119732 + Frame_Shift_Del DEL C - - SNU1_STOMACH NA SNU1_STOMACH NA g.chr22:19119732delC uc002zow.2 + 1 1412 c.820delC c.(820-822)CCCfs p.P274fs DGCR14_uc002zot.2_3'UTR|DGCR14_uc002zou.2_3'UTR|DGCR14_uc002zov.2_RNA NM_053006 NP_443732 Q96PF2 TSSK2_HUMAN testis-specific serine kinase 2 274 cell differentiation|multicellular organismal development|spermatogenesis cytoplasm ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity stomach(1) 1 Colorectal(54;0.0993) GTGGCTGCAGCCCCCCAAGCC 0.627 0.45 48 40 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU1_STOMACH NA SNU1_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 7 75 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 31 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.54 112 132 ITGA10 8515 broad.mit.edu 37 1 145541842 145541842 + Frame_Shift_Del DEL C - - SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr1:145541842delC uc001eoa.2 + 29 3441 c.3365delC c.(3364-3366)TCCfs p.S1122fs NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Frame_Shift_Del_p.S991fs|ITGA10_uc009wiw.2_Frame_Shift_Del_p.S979fs|ITGA10_uc010oyw.1_Frame_Shift_Del_p.S1029fs NM_003637 NP_003628 O75578 ITA10_HUMAN integrin, alpha 10 precursor 1122 Extracellular (Potential). cell-matrix adhesion|integrin-mediated signaling pathway integrin complex collagen binding|receptor activity lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1) 8 all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786) ATCCTCATCTCCCTGTGGATC 0.547 0.57 58 78 TTN 7273 broad.mit.edu 37 2 179612891 179612891 + Frame_Shift_Del DEL T - - SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr2:179612891delT uc002unb.2 - 46 14460 c.14236delA c.(14236-14238)ACTfs p.T4746fs TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron NM_133379 NP_596870 Q8WZ42 TITIN_HUMAN titin isoform novex-3 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GAAAGATCAGTTTCTTCTATA 0.373 0.43 64 49 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 1.00 0 11 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.17 35 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.39 54 34 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.59 22 32 PTK7 5754 broad.mit.edu 37 6 43109757 43109758 + Frame_Shift_Ins INS - A A SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr6:43109757_43109758insA uc003oub.1 + 12 2055_2056 c.1857_1858insA c.(1855-1860)CCCAAGfs p.P619fs PTK7_uc003ouc.1_Frame_Shift_Ins_p.P619fs|PTK7_uc003oud.1_Frame_Shift_Ins_p.P579fs|PTK7_uc003oue.1_Frame_Shift_Ins_p.P489fs|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Frame_Shift_Ins_p.P627fs|PTK7_uc010jyj.1_Intron NM_002821 NP_002812 Q13308 PTK7_HUMAN PTK7 protein tyrosine kinase 7 isoform a 619_620 Ig-like C2-type 7.|Extracellular (Potential). actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration cell-cell junction|integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ovary(2)|large_intestine(1) 3 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423) AGGGGGACCCCAAGCCGCTGAT 0.599 0.24 28 9 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 1 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.26 37 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.62 407 662 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.56 11 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 110 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 16 161 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 157 551 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU201_CENTRAL_NERVOUS_SYSTEM NA SNU201_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 2 32 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU213_PANCREAS NA SNU213_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 2 24 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU213_PANCREAS NA SNU213_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.20 234 57 BIRC6 57448 broad.mit.edu 37 2 32639906 32639907 + Frame_Shift_Ins INS - AGAAA AGAAA SNU213_PANCREAS NA SNU213_PANCREAS NA g.chr2:32639906_32639907insAGAAA uc010ezu.2 + 10 1681_1682 c.1547_1548insAGAAA c.(1546-1548)CCAfs p.P516fs NM_016252 NP_057336 Q9NR09 BIRC6_HUMAN baculoviral IAP repeat-containing 6 516 anti-apoptosis|apoptosis intracellular acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1) 14 Acute lymphoblastic leukemia(172;0.155) CTCCAACAGCCAGAAAAACTTC 0.386 0.21 72 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU213_PANCREAS NA SNU213_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.32 67 31 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU213_PANCREAS NA SNU213_PANCREAS NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.49 167 161 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SNU213_PANCREAS NA SNU213_PANCREAS NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.60 4 6 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU213_PANCREAS NA SNU213_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU213_PANCREAS NA SNU213_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.65 143 267 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU213_PANCREAS NA SNU213_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 22 174 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU213_PANCREAS NA SNU213_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.65 12 22 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU213_PANCREAS NA SNU213_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 163 522 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU213_PANCREAS NA SNU213_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 54 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU216_STOMACH NA SNU216_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 2 16 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU216_STOMACH NA SNU216_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.45 126 103 TNN 63923 broad.mit.edu 37 1 175048491 175048498 + Frame_Shift_Del DEL CCACGGGA - - SNU216_STOMACH NA SNU216_STOMACH NA g.chr1:175048491_175048498delCCACGGGA uc001gkl.1 + 3 545_552 c.432_439delCCACGGGA c.(430-441)GGCCACGGGACCfs p.G144fs TNN_uc010pmx.1_Frame_Shift_Del_p.G144fs NM_022093 NP_071376 Q9UQP3 TENN_HUMAN tenascin N precursor 144_147 cell growth|cell migration|signal transduction extracellular space|proteinaceous extracellular matrix large_intestine(5)|ovary(3)|central_nervous_system(1) 9 Breast(1374;0.000962) KIRC - Kidney renal clear cell carcinoma(1967;0.00198) 0.000 1.00 0 265 NEK10 152110 broad.mit.edu 37 3 27326342 27326342 + Frame_Shift_Del DEL T - - SNU216_STOMACH NA SNU216_STOMACH NA g.chr3:27326342delT uc003cdt.1 - 22 2174 c.1900delA c.(1900-1902)ATAfs p.I634fs NEK10_uc003cds.1_Frame_Shift_Del_p.I31fs NM_199347 NP_955379 Q6ZWH5 NEK10_HUMAN NIMA-related kinase 10 isoform 3 634 Protein kinase. ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1) 13 TGTATAAATATTTTCCATAGT 0.353 0.98 1 51 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SNU216_STOMACH NA SNU216_STOMACH NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.36 14 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU216_STOMACH NA SNU216_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.28 52 20 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes SNU216_STOMACH NA SNU216_STOMACH NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.55 159 195 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU216_STOMACH NA SNU216_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.41 29 20 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU216_STOMACH NA SNU216_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.76 4 13 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU216_STOMACH NA SNU216_STOMACH NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.55 29 36 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU216_STOMACH NA SNU216_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 19 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU216_STOMACH NA SNU216_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 193 44 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU216_STOMACH NA SNU216_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.66 16 31 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU216_STOMACH NA SNU216_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 153 400 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU216_STOMACH NA SNU216_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 3 31 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 45 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.33 251 125 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 70 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 45 25 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 19 32 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.31 18 8 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.16 67 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 112 17 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 38 502 SMAD4 4089 broad.mit.edu 37 18 48604793 48604806 + Frame_Shift_Del DEL GTACTTCATACCAT - - SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chr18:48604793_48604806delGTACTTCATACCAT uc010xdp.1 + 12 2153_2166 c.1615_1628delGTACTTCATACCAT c.(1615-1629)GTACTTCATACCATGfs p.V539fs SMAD4_uc002lfb.3_Frame_Shift_Del_p.V384fs NM_005359 NP_005350 Q13485 SMAD4_HUMAN mothers against decapentaplegic homolog 4 539_543 MH2. BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway activin responsive factor complex|centrosome|cytosol I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity p.0?(35)|p.?(2)|p.L536fs*11(1)|p.V539G(1)|p.L540R(1) pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1) 369 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155) CCTAGACGAAGTACTTCATACCATGCCGATTGCA 0.467 0.73 3 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.21 50 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 141 419 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU245_BILIARY_TRACT NA SNU245_BILIARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 70 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 29 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 188 49 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.28 31 12 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.41 22 15 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.22 191 55 MLL3 58508 broad.mit.edu 37 7 151878974 151878974 + Frame_Shift_Del DEL A - - SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr7:151878974delA uc003wla.2 - 36 6190 c.5971delT c.(5971-5973)TCAfs p.S1991fs MLL3_uc003wkz.2_Frame_Shift_Del_p.S1052fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 1991 Pro-rich. intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) GTTTGTTCTGAAACTACAGGA 0.458 0.47 107 96 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.21 27 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 90 13 FOXO1 2308 broad.mit.edu 37 13 41240050 41240051 + In_Frame_Ins INS - GCG GCG SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr13:41240050_41240051insGCG uc001uxl.3 - 1 684_685 c.299_300insCGC c.(298-300)GCG>GCCGCG p.100_100A>AA NM_002015 NP_002006 Q12778 FOXO1_HUMAN forkhead box O1 100 Poly-Ala. anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development cytosol|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding PAX3/FOXO1(749)|PAX7/FOXO1(197) soft_tissue(946)|lung(1)|central_nervous_system(1) 948 Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194) all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815) 0.000 0.40 27 18 EIF2S1 1965 broad.mit.edu 37 14 67831574 67831574 + Frame_Shift_Del DEL G - - SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr14:67831574delG uc001xjg.2 + 2 231 c.90delG c.(88-90)ATGfs p.M30fs NM_004094 NP_004085 P05198 IF2A_HUMAN eukaryotic translation initiation factor 2, 30 S1 motif. cytosol|eukaryotic translation initiation factor 2 complex|polysome|stress granule protein binding|ribosome binding|translation initiation factor activity ovary(1) 1 all cancers(60;0.000683)|OV - Ovarian serous cystadenocarcinoma(108;0.00579)|BRCA - Breast invasive adenocarcinoma(234;0.00937) TTGCTGAAATGGGGGCTTATG 0.279 0.37 86 51 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.50 5 5 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 60 355 DMWD 1762 broad.mit.edu 37 19 46288966 46288966 + Frame_Shift_Del DEL A - - SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr19:46288966delA uc002pdj.1 - 3 1834 c.1788delT c.(1786-1788)CTTfs p.L596fs DMWD_uc002pdk.1_Frame_Shift_Del_p.L596fs|DMWD_uc010eko.1_Frame_Shift_Del_p.L281fs NM_004943 NP_004934 Q09019 DMWD_HUMAN dystrophia myotonica-containing WD repeat motif 596 meiosis 0 Ovarian(192;0.0308)|all_neural(266;0.112) OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236) 0.000 1.00 0 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 133 479 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU283_LARGE_INTESTINE NA SNU283_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 35 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU308_BILIARY_TRACT NA SNU308_BILIARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 53 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SNU308_BILIARY_TRACT NA SNU308_BILIARY_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.26 25 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU308_BILIARY_TRACT NA SNU308_BILIARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.28 111 43 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU308_BILIARY_TRACT NA SNU308_BILIARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 12 24 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes SNU308_BILIARY_TRACT NA SNU308_BILIARY_TRACT NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.52 31 34 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU308_BILIARY_TRACT NA SNU308_BILIARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 133 22 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNU308_BILIARY_TRACT NA SNU308_BILIARY_TRACT NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.29 17 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU308_BILIARY_TRACT NA SNU308_BILIARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.55 17 21 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU308_BILIARY_TRACT NA SNU308_BILIARY_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.29 65 26 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU308_BILIARY_TRACT NA SNU308_BILIARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 37 253 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU308_BILIARY_TRACT NA SNU308_BILIARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 3 46 TNRC6B 23112 broad.mit.edu 37 22 40718944 40718950 + Frame_Shift_Del DEL CACCTGC - - SNU308_BILIARY_TRACT NA SNU308_BILIARY_TRACT NA g.chr22:40718944_40718950delCACCTGC uc011aor.1 + 23 5412_5418 c.5201_5207delCACCTGC c.(5200-5208)ACACCTGCAfs p.T1734fs TNRC6B_uc003aym.2_Frame_Shift_Del_p.T930fs|TNRC6B_uc003ayn.3_Frame_Shift_Del_p.T1624fs NM_001162501 NP_001155973 Q9UPQ9 TNR6B_HUMAN trinucleotide repeat containing 6B isoform 1 1734_1736 gene silencing by RNA|regulation of translation cytoplasmic mRNA processing body nucleotide binding|RNA binding 0 CAGCCCCCTACACCTGCAGCAACCCCA 0.585 0.32 15 7 CDKL5 6792 broad.mit.edu 37 X 18643271 18643273 + In_Frame_Del DEL TCT - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chrX:18643271_18643273delTCT uc004cym.2 + 17 2653_2655 c.2400_2402delTCT c.(2398-2403)GATCTT>GAT p.L802del CDKL5_uc004cyn.2_In_Frame_Del_p.L802del NM_003159 NP_003150 O76039 CDKL5_HUMAN cyclin-dependent kinase-like 5 802 neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation dendrite cytoplasm|dendritic growth cone|nucleus ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1) 6 Hepatocellular(33;0.183) ACAGCCCTGATCTTCTGACGTTG 0.478 1.00 0 40 KDM5C 8242 broad.mit.edu 37 X 53246393 53246393 + Frame_Shift_Del DEL G - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chrX:53246393delG uc004drz.2 - 5 1122 c.589delC c.(589-591)CTAfs p.L197fs KDM5C_uc011moc.1_RNA|KDM5C_uc011mod.1_Frame_Shift_Del_p.L130fs|KDM5C_uc004dsa.2_Frame_Shift_Del_p.L196fs NM_004187 NP_004178 P41229 KDM5C_HUMAN jumonji, AT rich interactive domain 1C isoform 197 chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1) 18 0.000 0.66 34 65 KDM5C 8242 broad.mit.edu 37 X 53250046 53250047 + Frame_Shift_Ins INS - G G SNU324_PANCREAS NA SNU324_PANCREAS NA g.chrX:53250046_53250047insG uc004drz.2 - 2 735_736 c.202_203insC c.(202-204)CGAfs p.R68fs KDM5C_uc011moc.1_RNA|KDM5C_uc011mod.1_Intron|KDM5C_uc004dsa.2_Frame_Shift_Ins_p.R68fs NM_004187 NP_004178 P41229 KDM5C_HUMAN jumonji, AT rich interactive domain 1C isoform 68 chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1) 18 0.000 0.75 71 209 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU324_PANCREAS NA SNU324_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 16 F8 2157 broad.mit.edu 37 X 154157686 154157686 + Frame_Shift_Del DEL T - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chrX:154157686delT uc004fmt.2 - 14 4550 c.4379delA c.(4378-4380)AATfs p.N1460fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1460 B. N -> K (in HEMA). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AGAAAGGTTATTTTTTTTGGC 0.413 0.87 22 141 ARID1A 8289 broad.mit.edu 37 1 27106100 27106100 + Frame_Shift_Del DEL A - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr1:27106100delA uc001bmv.1 + 20 6084 c.5711delA c.(5710-5712)GAAfs p.E1904fs ARID1A_uc001bmu.1_Frame_Shift_Del_p.E1687fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.E750fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.E232fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.E146fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1904 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GGACCTCCAGAAAAACGGATC 0.577 0.41 76 52 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.34 202 105 BCL9 607 broad.mit.edu 37 1 147094076 147094076 + Frame_Shift_Del DEL C - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr1:147094076delC uc001epq.2 + 9 3647 c.2907delC c.(2905-2907)GGCfs p.G969fs BCL9_uc010ozr.1_Frame_Shift_Del_p.G895fs NM_004326 NP_004317 O00512 BCL9_HUMAN B-cell CLL/lymphoma 9 969 Pro-rich. Wnt receptor signaling pathway nucleus protein binding ovary(2)|large_intestine(2)|breast(1)|skin(1) 6 all_hematologic(923;0.115) TTTTAGGTGGCCCCCCACCTC 0.498 0.31 98 45 DDR2 4921 broad.mit.edu 37 1 162724423 162724425 + In_Frame_Del DEL AGA - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr1:162724423_162724425delAGA uc001gcf.2 + 6 660_662 c.195_197delAGA c.(193-198)TCAGAA>TCA p.E67del DDR2_uc001gcg.2_In_Frame_Del_p.E67del NM_001014796 NP_001014796 Q16832 DDR2_HUMAN discoidin domain receptor family, member 2 67 Extracellular (Potential).|F5/8 type C. cell adhesion integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(2)|central_nervous_system(2)|ovary(1)|kidney(1) 6 all_hematologic(112;0.115) BRCA - Breast invasive adenocarcinoma(70;0.113) GGCTGGACTCAGAAGAAGGGGAT 0.532 0.20 76 19 CAMK1G 57172 broad.mit.edu 37 1 209785476 209785492 + Frame_Shift_Del DEL TGCTCCAGCTGCCTGAA - - rs142776782 SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr1:209785476_209785492delTGCTCCAGCTGCCTGAA uc001hhd.2 + 11 1357_1373 c.1255_1271delTGCTCCAGCTGCCTGAA c.(1255-1272)TGCTCCAGCTGCCTGAACfs p.C419fs CAMK1G_uc001hhf.3_Frame_Shift_Del_p.C419fs|CAMK1G_uc001hhe.2_Frame_Shift_Del_p.C419fs NM_020439 NP_065172 Q96NX5 KCC1G_HUMAN calcium/calmodulin-dependent protein kinase IG 419_424 Golgi membrane|plasma membrane ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity breast(1) 1 OV - Ovarian serous cystadenocarcinoma(81;0.0475) CTGTGGCTGCTGCTCCAGCTGCCTGAACATTGGGAGC 0.576 0.24 26 8 CAD 790 broad.mit.edu 37 2 27456981 27456982 + Frame_Shift_Ins INS - C C SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr2:27456981_27456982insC uc002rji.2 + 22 3667_3668 c.3505_3506insC c.(3505-3507)ACCfs p.T1169fs CAD_uc010eyw.2_Frame_Shift_Ins_p.T1106fs NM_004341 NP_004332 P27708 PYR1_HUMAN carbamoylphosphate synthetase 2/aspartate 1169 CPSase B.|ATP-grasp 2.|CPSase (Carbamoyl-phosphate synthase). 'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process cytosol|neuronal cell body|nuclear matrix|terminal button aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1) 10 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) L-Aspartic Acid(DB00128)|L-Glutamine(DB00130) GACGCTGGTGACCCCCCCACAA 0.574 0.33 46 23 ITGB6 3694 broad.mit.edu 37 2 160968601 160968601 + Frame_Shift_Del DEL G - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr2:160968601delG uc002ubh.2 - 13 2107 c.2091delC c.(2089-2091)ATCfs p.I697fs ITGB6_uc010fou.2_Frame_Shift_Del_p.I697fs|ITGB6_uc010zcq.1_Frame_Shift_Del_p.I655fs|ITGB6_uc010fov.1_Frame_Shift_Del_p.I697fs NM_000888 NP_000879 P18564 ITB6_HUMAN integrin, beta 6 precursor 697 Extracellular (Potential). cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|multicellular organismal development integrin complex receptor activity ovary(1)|lung(1)|skin(1) 3 CTTTTTCATTGATGCTGTGAA 0.423 0.45 56 45 LRP2 4036 broad.mit.edu 37 2 169997025 169997025 + Frame_Shift_Del DEL G - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr2:169997025delG uc002ues.2 - 72 13352 c.13139delC c.(13138-13140)CCAfs p.P4380fs NM_004525 NP_004516 P98164 LRP2_HUMAN low density lipoprotein-related protein 2 4380 EGF-like 17.|Extracellular (Potential). hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1) 29 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) 0.000 0.53 127 141 TTN 7273 broad.mit.edu 37 2 179486691 179486691 + Frame_Shift_Del DEL T - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr2:179486691delT uc010zfg.1 - 193 37478 c.37254delA c.(37252-37254)AAAfs p.K12418fs TTN_uc010zfh.1_Frame_Shift_Del_p.K6113fs|TTN_uc010zfi.1_Frame_Shift_Del_p.K6046fs|TTN_uc010zfj.1_Frame_Shift_Del_p.K5921fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 13345 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TGATGTCATATTTTTTGCCCT 0.363 0.51 83 87 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.63 7 12 PLK4 10733 broad.mit.edu 37 4 128807221 128807221 + Frame_Shift_Del DEL T - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr4:128807221delT uc003ifo.2 + 5 941 c.696delT c.(694-696)TCTfs p.S232fs PLK4_uc011cgs.1_Frame_Shift_Del_p.S200fs|PLK4_uc011cgt.1_Frame_Shift_Del_p.S191fs NM_014264 NP_055079 O00444 PLK4_HUMAN polo-like kinase 4 232 Protein kinase. G2/M transition of mitotic cell cycle|positive regulation of centriole replication|trophoblast giant cell differentiation centriole|cleavage furrow|cytosol|nucleolus ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity 0 AAATGCCATCTTTTTTGTCAA 0.378 0.46 85 73 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.31 55 25 RAPGEF2 9693 broad.mit.edu 37 4 160253755 160253755 + Frame_Shift_Del DEL A - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr4:160253755delA uc003iqg.3 + 11 1868 c.1558delA c.(1558-1560)AAAfs p.K520fs NM_014247 NP_055062 Q9Y4G8 RPGF2_HUMAN Rap guanine nucleotide exchange factor 2 520 cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction integral to plasma membrane|intracellular calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity lung(2)|upper_aerodigestive_tract(1)|skin(1) 4 all_hematologic(180;0.24) COAD - Colon adenocarcinoma(41;0.0817) AAAAGTGAACAAAAAAAGTAA 0.418 0.44 54 42 MAP3K1 4214 broad.mit.edu 37 5 56177848 56177849 + In_Frame_Ins INS - CAACAA CAACAA rs147399807;rs34869245 by1000genomes SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr5:56177848_56177849insCAACAA uc003jqw.3 + 14 3322_3323 c.2821_2822insCAACAA c.(2821-2823)TCA>TCAACAACA p.949_950insTT NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949_950 cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) ACCTTCTAGTTcaacaacaaca 0.371 0.22 46 13 NR2F1 7025 broad.mit.edu 37 5 92929417 92929419 + In_Frame_Del DEL TCC - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr5:92929417_92929419delTCC uc003kkj.2 + 3 2828_2830 c.1141_1143delTCC c.(1141-1143)TCCdel p.S383del NM_005654 NP_005645 P10589 COT1_HUMAN nuclear receptor subfamily 2, group F, member 1 383 negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor nucleoplasm ligand-regulated transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding urinary_tract(1)|ovary(1)|lung(1) 3 all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19) UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18) GCGCACCGTGTCCTCCTCCGTCA 0.581 0.43 73 54 ZNF608 57507 broad.mit.edu 37 5 123983516 123983516 + Frame_Shift_Del DEL A - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr5:123983516delA uc003ktq.1 - 4 2684 c.2561delT c.(2560-2562)TTAfs p.L854fs ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Frame_Shift_Del_p.L854fs|ZNF608_uc003ktt.1_Frame_Shift_Del_p.L854fs NM_020747 NP_065798 Q9ULD9 ZN608_HUMAN zinc finger protein 608 854 intracellular zinc ion binding skin(3)|ovary(2)|lung(1) 6 all_cancers(142;0.186)|Prostate(80;0.081) KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221) OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783) ATGATCCTTTAAAAAATGCCC 0.498 0.55 49 60 AFF4 27125 broad.mit.edu 37 5 132227894 132227896 + In_Frame_Del DEL TCT - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr5:132227894_132227896delTCT uc003kyd.2 - 13 3005_3007 c.2597_2599delAGA c.(2596-2601)AAGACC>ACC p.K866del AFF4_uc011cxk.1_In_Frame_Del_p.K544del|AFF4_uc003kye.1_In_Frame_Del_p.K866del NM_014423 NP_055238 Q9UHB7 AFF4_HUMAN ALL1 fused gene from 5q31 866 Ser-rich. transcription from RNA polymerase II promoter mitochondrion|nucleolus protein binding|sequence-specific DNA binding transcription factor activity ovary(2)|kidney(2)|skin(1) 5 all_cancers(142;0.145)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) TTCCCTTCGGTCTTCTTCTGCTT 0.463 0.35 113 62 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.43 42 32 DEK 7913 broad.mit.edu 37 6 18236684 18236684 + Frame_Shift_Del DEL T - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr6:18236684delT uc003ncr.1 - 9 1239 c.1046delA c.(1045-1047)AAGfs p.K349fs DEK_uc011djf.1_Frame_Shift_Del_p.K315fs|DEK_uc011djg.1_RNA NM_003472 NP_003463 P35659 DEK_HUMAN DEK oncogene isoform 1 349 chromatin modification|regulation of transcription from RNA polymerase II promoter|signal transduction|transcription from RNA polymerase II promoter|viral genome replication nucleus DNA binding|histone binding kidney(1) 1 Ovarian(93;0.00769)|Breast(50;0.0495) all_hematologic(90;0.053) OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332) TCTAATTACCTTTTTGCAAAT 0.303 0.42 35 25 HDAC2 3066 broad.mit.edu 37 6 114264518 114264518 + Frame_Shift_Del DEL T - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr6:114264518delT uc003pwd.1 - 12 1657 c.1657delA c.(1657-1659)ACAfs p.T553fs HDAC2_uc003pwc.1_Frame_Shift_Del_p.T429fs|HDAC2_uc003pwe.1_Frame_Shift_Del_p.T429fs NM_001527 NP_001518 Q92769 HDAC2_HUMAN histone deacetylase 2 459 blood coagulation|dendrite development|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|maintenance of chromatin silencing|negative regulation of apoptosis|negative regulation of cell cycle|negative regulation of neuron projection development|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of proteolysis|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter cytoplasm|ESC/E(Z) complex|NuRD complex|Sin3 complex chromatin binding|enzyme binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|sequence-specific DNA binding|transcription factor binding skin(2)|ovary(1)|central_nervous_system(1) 4 all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24) all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832) Vorinostat(DB02546) ATCTGACCTGtttttttgtcc 0.254 0.97 1 31 GRM8 2918 broad.mit.edu 37 7 126544156 126544156 + Frame_Shift_Del DEL T - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr7:126544156delT uc003vlr.2 - 4 1199 c.888delA c.(886-888)AAAfs p.K296fs GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Frame_Shift_Del_p.K296fs|GRM8_uc010lkz.1_RNA|GRM8_uc003vlu.1_Frame_Shift_Del_p.K17fs NM_000845 NP_000836 O00222 GRM8_HUMAN glutamate receptor, metabotropic 8 isoform a 296 Extracellular (Potential). negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception integral to plasma membrane lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1) 23 Prostate(267;0.186) L-Glutamic Acid(DB00142) 0.000 0.61 274 431 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.80 2 8 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.81 3 13 WWP1 11059 broad.mit.edu 37 8 87460442 87460443 + Frame_Shift_Ins INS - A A SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr8:87460442_87460443insA uc003ydt.2 + 19 2344_2345 c.2064_2065insA c.(2062-2067)AGTAAAfs p.S688fs WWP1_uc010mai.2_Frame_Shift_Ins_p.S464fs NM_007013 NP_008944 Q9H0M0 WWP1_HUMAN WW domain containing E3 ubiquitin protein ligase 688_689 HECT. central nervous system development|entry of virus into host cell|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|signal transduction cytoplasm|nucleus|plasma membrane|ubiquitin ligase complex protein binding|ubiquitin-protein ligase activity lung(1)|liver(1) 2 0.000 0.26 39 14 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.30 442 185 CDKN2A 1029 broad.mit.edu 37 9 21971133 21971133 + Frame_Shift_Del DEL G - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr9:21971133delG uc003zpk.2 - 2 437 c.225delC c.(223-225)CCCfs p.P75fs MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Frame_Shift_Del_p.R131fs NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 75 cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.?(13)|p.P75L(2)|p.A76fs*70(2)|p.P75H(1)|p.E61_L94del(1)|p.A76fs*64(1)|p.L65fs*38(1)|p.A68fs*3(1)|p.P75fs*71(1)|p.P75S(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) 0.000 0.15 1400 246 PTCH1 5727 broad.mit.edu 37 9 98270530 98270530 + Frame_Shift_Del DEL C - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr9:98270530delC uc004avk.3 - 1 302 c.114delG c.(112-114)GGGfs p.G38fs PTCH1_uc010mro.2_5'Flank|PTCH1_uc010mrp.2_5'Flank|PTCH1_uc010mrq.2_5'Flank|PTCH1_uc004avl.3_5'Flank|PTCH1_uc010mrr.2_Intron|PTCH1_uc004avm.3_Intron|PTCH1_uc010mrt.1_5'Flank|PTCH1_uc010mru.1_5'Flank|PTCH1_uc004avo.2_Intron|PTCH1_uc010mrv.1_Intron|PTCH1_uc010mrw.1_Intron NM_000264 NP_000255 Q13635 PTC1_HUMAN patched isoform L 38 Cytoplasmic (Potential). embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway integral to plasma membrane hedgehog receptor activity skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1) 379 Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136) 0.000 0.21 186 48 NUP214 8021 broad.mit.edu 37 9 134073597 134073597 + Frame_Shift_Del DEL G - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr9:134073597delG uc004cag.2 + 29 4827 c.4716delG c.(4714-4716)ACGfs p.T1572fs NUP214_uc004cah.2_Frame_Shift_Del_p.T1562fs|NUP214_uc004cai.2_Frame_Shift_Del_p.T1002fs|NUP214_uc010mzg.2_RNA|NUP214_uc011mcg.1_Frame_Shift_Del_p.T398fs|NUP214_uc011mcf.1_Frame_Shift_Del_p.T349fs|NUP214_uc010mzh.1_Frame_Shift_Del_p.T86fs|NUP214_uc010mzi.1_Frame_Shift_Del_p.T86fs NM_005085 NP_005076 P35658 NU214_HUMAN nucleoporin 214kDa 1572 Pro/Ser/Thr-rich.|11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats. carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear pore|nucleoplasm protein binding breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1) 16 all_hematologic(7;0.0028) Myeloproliferative disorder(178;0.204) OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256) CAGCCACCACGGGGGTCCCTG 0.577 0.45 46 38 NLRP10 338322 broad.mit.edu 37 11 7981233 7981233 + Frame_Shift_Del DEL T - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr11:7981233delT uc001mfv.1 - 2 1943 c.1926delA c.(1924-1926)AAAfs p.K642fs NM_176821 NP_789791 Q86W26 NAL10_HUMAN NLR family, pyrin domain containing 10 642 ATP binding lung(4)|ovary(2)|pancreas(1)|kidney(1)|skin(1) 9 Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189) TCCCTCTGCCTTTTCCAGTAG 0.289 0.44 76 59 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.64 4 7 FADD 8772 broad.mit.edu 37 11 70049816 70049817 + Frame_Shift_Ins INS - G G SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr11:70049816_70049817insG uc001opm.2 + 1 548_549 c.251_252insG c.(250-252)GCGfs p.A84fs NM_003824 NP_003815 Q13158 FADD_HUMAN Fas-associated via death domain 84 activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction cytosol death receptor binding|identical protein binding ovary(1)|lung(1)|pancreas(1) 3 Esophageal squamous(2;1.19e-45) LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) 0.000 0.10 605 64 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 82 12 ATM 472 broad.mit.edu 37 11 108216476 108216477 + Frame_Shift_Ins INS - A A SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr11:108216476_108216477insA uc001pkb.1 + 58 8810_8811 c.8425_8426insA c.(8425-8427)CAAfs p.Q2809fs ATM_uc009yxr.1_Frame_Shift_Ins_p.Q2809fs|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron|ATM_uc001pke.1_Frame_Shift_Ins_p.Q1461fs NM_000051 NP_000042 Q13315 ATM_HUMAN ataxia telangiectasia mutated isoform 1 2809 PI3K/PI4K. cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence cytoplasmic membrane-bounded vesicle|nucleoplasm 1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1) 240 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147) AAAGGAGGTGCAAAAAAAGTCT 0.238 0.50 15 15 DRD2 1813 broad.mit.edu 37 11 113283284 113283285 + Frame_Shift_Ins INS - A A SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr11:113283284_113283285insA uc001pnz.2 - 6 1452_1453 c.1131_1132insT c.(1129-1134)ATTGTTfs p.I377fs DRD2_uc010rwv.1_Frame_Shift_Ins_p.I376fs|DRD2_uc001poa.3_Frame_Shift_Ins_p.I377fs|DRD2_uc001pob.3_Frame_Shift_Ins_p.I348fs NM_000795 NP_000786 P14416 DRD2_HUMAN dopamine receptor D2 isoform long 377_378 Helical; Name=6; (By similarity). activation of phospholipase C activity by dopamine receptor signaling pathway|adenohypophysis development|adult walking behavior|arachidonic acid secretion|axonogenesis|behavioral response to cocaine|behavioral response to ethanol|branching morphogenesis of a nerve|cerebral cortex GABAergic interneuron migration|circadian regulation of gene expression|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|intracellular protein kinase cascade|negative regulation of blood pressure|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of dopamine receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|negative regulation of synaptic transmission, glutamatergic|neurological system process involved in regulation of systemic arterial blood pressure|peristalsis|phosphatidylinositol metabolic process|positive regulation of dopamine uptake|positive regulation of growth hormone secretion|positive regulation of neuroblast proliferation|prepulse inhibition|protein localization|regulation of heart rate|regulation of long-term neuronal synaptic plasticity|regulation of potassium ion transport|regulation of sodium ion transport|regulation of synaptic transmission, GABAergic|release of sequestered calcium ion into cytosol|response to amphetamine|response to drug|response to histamine|response to morphine|sensory perception of smell|synapse assembly|temperature homeostasis|visual learning integral to plasma membrane dopamine D2 receptor activity|dopamine receptor activity, coupled via Gi/Go|drug binding|potassium channel regulator activity|protein binding pancreas(1)|skin(1) 2 all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494) BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216) Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Carphenazine(DB01038)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Domperidone(DB01184)|Droperidol(DB00450)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Mesoridazine(DB00933)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Sulpiride(DB00391)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Ziprasidone(DB00246)|Zuclopenthixol(DB01624) TCACCGAGAACAATGGCGAGCA 0.589 0.37 38 22 FLI1 2313 broad.mit.edu 37 11 128638115 128638115 + Frame_Shift_Del DEL C - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr11:128638115delC uc010sbu.1 + 3 674 c.333delC c.(331-333)GGCfs p.G111fs FLI1_uc010sbt.1_Intron|FLI1_uc010sbv.1_Frame_Shift_Del_p.G78fs|FLI1_uc009zci.2_Frame_Shift_Del_p.G45fs|FLI1_uc001qen.2_Frame_Shift_Del_p.G78fs NM_002017 NP_002008 Q01543 FLI1_HUMAN Friend leukemia virus integration 1 111 hemostasis|organ morphogenesis nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity EWSR1/FLI1(2266) bone(2210)|soft_tissue(48)|autonomic_ganglia(4)|central_nervous_system(4)|lung(3)|ovary(2)|pancreas(2) 2273 all_hematologic(175;0.0641) Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182) OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327) AGAAGAATGGCCCCCCTCCTC 0.582 0.38 26 16 DYRK4 8798 broad.mit.edu 37 12 4719362 4719362 + Frame_Shift_Del DEL A - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr12:4719362delA uc001qmx.2 + 11 1217 c.1057delA c.(1057-1059)AAAfs p.K353fs DYRK4_uc009zeh.1_Frame_Shift_Del_p.K468fs|DYRK4_uc001qmy.1_Frame_Shift_Del_p.K353fs|DYRK4_uc001qmz.1_Frame_Shift_Del_p.K67fs|DYRK4_uc001qna.1_5'UTR|DYRK4_uc010ser.1_5'UTR NM_003845 NP_003836 Q9NR20 DYRK4_HUMAN dual-specificity tyrosine-(Y)-phosphorylation 353 Protein kinase. Golgi apparatus ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(2)|skin(1) 3 Colorectal(7;0.103) CAACAGGGGGAAAAAAAGATA 0.398 0.46 41 35 HOXC5 3222 broad.mit.edu 37 12 54428250 54428250 + Frame_Shift_Del DEL A - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr12:54428250delA uc001sew.2 + 2 718 c.643delA c.(643-645)AAAfs p.K215fs HOXC5_uc001set.2_RNA|HOXC4_uc001seu.2_Intron NM_018953 NP_061826 Q00444 HXC5_HUMAN homeobox C5 215 regulation of transcription from RNA polymerase II promoter cell junction|nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 GAAAGATTCCAAAATGAAAAG 0.547 0.50 5 5 FBN1 2200 broad.mit.edu 37 15 48736803 48736803 + Frame_Shift_Del DEL T - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr15:48736803delT uc001zwx.1 - 49 6300 c.5972delA c.(5971-5973)AACfs p.N1991fs FBN1_uc010beo.1_RNA NM_000138 NP_000129 P35555 FBN1_HUMAN fibrillin 1 precursor 1991 EGF-like 34; calcium-binding. heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development basement membrane|extracellular space|microfibril calcium ion binding|extracellular matrix structural constituent|protein binding ovary(2)|large_intestine(1) 3 all_lung(180;0.00279) all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05) CCCATCCAAGTTTTGACAGGT 0.428 0.51 66 69 STK11 6794 broad.mit.edu 37 19 1221314 1221314 + Frame_Shift_Del DEL C - - rs67873004 SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr19:1221314delC uc002lrl.1 + 6 1952 c.837delC c.(835-837)GGCfs p.G279fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 279 Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.P281fs*6(2)|p.?(2)|p.Y246fs*3(1)|p.G279F(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) GCGACTGTGGCCCCCCGCTCT 0.607 0.47 8 7 JAG1 182 broad.mit.edu 37 20 10620204 10620207 + Frame_Shift_Del DEL TGTT - - SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr20:10620204_10620207delTGTT uc002wnw.2 - 26 4112_4115 c.3596_3599delAACA c.(3595-3600)AAACAGfs p.K1199fs NM_000214 NP_000205 P78504 JAG1_HUMAN jagged 1 precursor 1199_1200 Cytoplasmic (Potential). angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation extracellular region|integral to plasma membrane calcium ion binding|growth factor activity|Notch binding|structural molecule activity lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1) 9 TCTGTTGTCCTGTTTGTTTGTCCA 0.564 0.84 6 31 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.13 88 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 118 402 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU324_PANCREAS NA SNU324_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 46 AKAP4 8852 broad.mit.edu 37 X 49958950 49958965 + Frame_Shift_Del DEL ATGTTTACAGGTAGAG - - SNU387_LIVER NA SNU387_LIVER NA g.chrX:49958950_49958965delATGTTTACAGGTAGAG uc004dow.1 - 5 523_538 c.399_414delCTCTACCTGTAAACAT c.(397-414)ACCTCTACCTGTAAACATfs p.T133fs AKAP4_uc004dov.1_Frame_Shift_Del_p.T124fs|AKAP4_uc010njp.1_5'UTR|AKAP4_uc004dou.1_Frame_Shift_Del_p.T124fs NM_003886 NP_003877 Q5JQC9 AKAP4_HUMAN A-kinase anchor protein 4 isoform 1 133_138 cell projection organization|single fertilization|sperm motility cAMP-dependent protein kinase complex|cilium|cytoskeleton|microtubule-based flagellum protein kinase A binding kidney(3)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1) 8 Ovarian(276;0.236) CTCCTACTTTATGTTTACAGGTAGAGGTTGAGGGGC 0.458 0.15 60 11 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU387_LIVER NA SNU387_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 23 ARID1A 8289 broad.mit.edu 37 1 27023909 27023923 + In_Frame_Del DEL GCTGCGGCGGCGGCA - - SNU387_LIVER NA SNU387_LIVER NA g.chr1:27023909_27023923delGCTGCGGCGGCGGCA uc001bmv.1 + 1 1388_1402 c.1015_1029delGCTGCGGCGGCGGCA c.(1015-1029)GCTGCGGCGGCGGCAdel p.AAAAA344del ARID1A_uc001bmt.1_In_Frame_Del_p.AAAAA344del|ARID1A_uc001bmu.1_In_Frame_Del_p.AAAAA344del NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 344_348 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.A339fs*24(1)|p.A344_A348del(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.98 2 117 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU387_LIVER NA SNU387_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.30 165 72 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU387_LIVER NA SNU387_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 77 54 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU387_LIVER NA SNU387_LIVER NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.81 7 29 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU387_LIVER NA SNU387_LIVER NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.78 35 125 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU387_LIVER NA SNU387_LIVER NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 13 RGS22 26166 broad.mit.edu 37 8 101075994 101075995 + Frame_Shift_Del DEL CT - - SNU387_LIVER NA SNU387_LIVER NA g.chr8:101075994_101075995delCT uc003yjb.1 - 8 1196_1197 c.1001_1002delAG c.(1000-1002)AAGfs p.K334fs RGS22_uc003yja.1_Frame_Shift_Del_p.K153fs|RGS22_uc003yjc.1_Frame_Shift_Del_p.K322fs|RGS22_uc011lgz.1_RNA|RGS22_uc010mbo.1_RNA NM_015668 NP_056483 Q8NE09 RGS22_HUMAN regulator of G-protein signaling 22 334 negative regulation of signal transduction cytoplasm|plasma membrane GTPase activator activity|signal transducer activity ovary(3)|skin(2)|breast(1)|central_nervous_system(1) 7 Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169) CTCCAACTGGCTTTCCAACAAT 0.327 0.45 6 5 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU387_LIVER NA SNU387_LIVER NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 163 63 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU387_LIVER NA SNU387_LIVER NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 13 136 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU387_LIVER NA SNU387_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 79 328 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU387_LIVER NA SNU387_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 33 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU398_LIVER NA SNU398_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.04 -1 24 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU398_LIVER NA SNU398_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.16 598 111 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU398_LIVER NA SNU398_LIVER NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.44 10 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU398_LIVER NA SNU398_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.38 95 59 ESR1 2099 broad.mit.edu 37 6 152201836 152201836 + Frame_Shift_Del DEL T - - SNU398_LIVER NA SNU398_LIVER NA g.chr6:152201836delT uc003qom.3 + 5 1060 c.690delT c.(688-690)GATfs p.D230fs ESR1_uc010kin.2_Frame_Shift_Del_p.D230fs|ESR1_uc010kio.2_Frame_Shift_Del_p.D232fs|ESR1_uc010kip.2_Frame_Shift_Del_p.D230fs|ESR1_uc003qon.3_Frame_Shift_Del_p.D230fs|ESR1_uc003qoo.3_Frame_Shift_Del_p.D230fs|ESR1_uc010kiq.2_5'UTR|ESR1_uc010kir.2_Intron|ESR1_uc011eet.1_Intron|ESR1_uc011eeu.1_RNA|ESR1_uc011eev.1_Intron|ESR1_uc011eew.1_Frame_Shift_Del_p.I62fs|ESR1_uc010kis.2_Frame_Shift_Del_p.D11fs|ESR1_uc011eex.1_Frame_Shift_Del_p.D11fs NM_001122742 NP_001116214 P03372 ESR1_HUMAN estrogen receptor alpha isoform 4 230 NR C4-type.|Nuclear receptor.|Mediates interaction with DNTTIP2. positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus chromatin remodeling complex|cytoplasm|nucleoplasm beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding central_nervous_system(2)|ovary(1)|lung(1)|breast(1) 5 Ovarian(120;0.0448) BRCA - Breast invasive adenocarcinoma(37;0.0841) OV - Ovarian serous cystadenocarcinoma(155;4.55e-10) Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539) GCACCATTGATAAAAACAGGA 0.473 0.32 28 13 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU398_LIVER NA SNU398_LIVER NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.85 4 23 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU398_LIVER NA SNU398_LIVER NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 36 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU398_LIVER NA SNU398_LIVER NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.52 119 130 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU398_LIVER NA SNU398_LIVER NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 455 136 SIK2 23235 broad.mit.edu 37 11 111571666 111571667 + Frame_Shift_Ins INS - G G SNU398_LIVER NA SNU398_LIVER NA g.chr11:111571666_111571667insG uc001plt.2 + 5 653_654 c.535_536insG c.(535-537)AGCfs p.S179fs NM_015191 NP_056006 Q9H0K1 SIK2_HUMAN SNF1-like kinase 2 179 Protein kinase. intracellular protein kinase cascade|regulation of insulin receptor signaling pathway Golgi apparatus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|skin(1) 3 ATGGTGTGGCAGCCCCCCTTAT 0.431 0.11 179 23 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - SNU398_LIVER NA SNU398_LIVER NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 1.00 0 21 CSH2 1443 broad.mit.edu 37 17 61950602 61950602 + Frame_Shift_Del DEL A - - SNU398_LIVER NA SNU398_LIVER NA g.chr17:61950602delA uc002jch.2 - 2 223 c.108delT c.(106-108)TTTfs p.F36fs CSH2_uc002jcg.2_Frame_Shift_Del_p.F36fs|CSH2_uc002jci.2_Frame_Shift_Del_p.F36fs|GH2_uc002jcj.2_Intron|CSH2_uc002jck.2_Frame_Shift_Del_p.F36fs NM_020991 NP_066271 P01243 CSH_HUMAN chorionic somatomammotropin hormone 2 isoform 1 36 female pregnancy|signal transduction extracellular region hormone activity|metal ion binding 0 0.000 0.60 34 51 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU398_LIVER NA SNU398_LIVER NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.33 57 28 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU398_LIVER NA SNU398_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.68 169 353 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU398_LIVER NA SNU398_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 75 ATRX 546 broad.mit.edu 37 X 76937241 76937243 + In_Frame_Del DEL CTT - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chrX:76937241_76937243delCTT uc004ecp.3 - 9 3737_3739 c.3505_3507delAAG c.(3505-3507)AAGdel p.K1169del ATRX_uc004ecq.3_In_Frame_Del_p.K1131del|ATRX_uc004eco.3_In_Frame_Del_p.K954del|ATRX_uc004ecr.2_In_Frame_Del_p.K1101del|ATRX_uc010nlx.1_In_Frame_Del_p.K1140del|ATRX_uc010nly.1_In_Frame_Del_p.K1114del NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 1169 Poly-Lys. DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) AAGTTCTTTGCTTCTTCTTTTTA 0.350 0.89 5 42 Unknown 0 broad.mit.edu 37 X 80185320 80185321 + Frame_Shift_Ins INS - A A SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chrX:80185320_80185321insA uc004eec.1 + 1 393_394 c.219_220insA c.(217-222)GGGAAAfs p.G73fs SubName: Full=cDNA FLJ16670 fis, clone THYMU3001133, highly similar to Voltage-dependent anion-selective channel protein 1; SubName: Full=Voltage-dependent anion channel 1, isoform CRA_a; CTAACACTGGGAAAAAAAATGC 0.485 0.79 14 52 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 17 SLC2A1 6513 broad.mit.edu 37 1 43394946 43394946 + Frame_Shift_Del DEL C - - rs80359837 SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr1:43394946delC uc001cik.2 - 7 1432 c.907delG c.(907-909)GTGfs p.V303fs NM_006516 NP_006507 P11166 GTR1_HUMAN solute carrier family 2 (facilitated glucose 303 Extracellular (Potential). V -> L (found in a patient with GLUT1 deficiency syndrome). carbohydrate metabolic process|energy reserve metabolic process|regulation of insulin secretion|water-soluble vitamin metabolic process integral to membrane|melanosome|membrane fraction|midbody D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity central_nervous_system(2)|pancreas(2)|ovary(1) 5 Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0122) Etomidate(DB00292) 0.000 0.59 541 793 CDC7 8317 broad.mit.edu 37 1 91977476 91977476 + Frame_Shift_Del DEL A - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr1:91977476delA uc001doe.2 + 6 733 c.568delA c.(568-570)AAAfs p.K190fs CDC7_uc001dof.2_Frame_Shift_Del_p.K190fs|CDC7_uc010osw.1_Frame_Shift_Del_p.K162fs|CDC7_uc009wdc.2_Frame_Shift_Del_p.K190fs|CDC7_uc009wdd.2_5'Flank NM_003503 NP_003494 O00311 CDC7_HUMAN cell division cycle 7 190 Protein kinase. cell cycle checkpoint|cell division|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|positive regulation of cell proliferation|regulation of S phase cytoplasm|nucleoplasm ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity stomach(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 5 all_lung(203;0.0165)|Lung NSC(277;0.0562) all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124) TAGGCGCCTGAAAAAGTAAGT 0.234 0.52 20 22 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 213 48 RGL1 23179 broad.mit.edu 37 1 183881394 183881395 + Frame_Shift_Ins INS - A A SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr1:183881394_183881395insA uc001gqo.2 + 15 1898_1899 c.1741_1742insA c.(1741-1743)CAAfs p.Q581fs RGL1_uc010pof.1_Frame_Shift_Ins_p.Q386fs|RGL1_uc001gqm.2_Frame_Shift_Ins_p.Q616fs|RGL1_uc010pog.1_Frame_Shift_Ins_p.Q579fs|RGL1_uc010poh.1_Frame_Shift_Ins_p.Q579fs|RGL1_uc010poi.1_Frame_Shift_Ins_p.Q552fs NM_015149 NP_055964 Q9NZL6 RGL1_HUMAN ral guanine nucleotide dissociation 581 Ser-rich. cellular lipid metabolic process|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction intracellular protein binding|Ral guanyl-nucleotide exchange factor activity breast(5)|ovary(4)|lung(2) 11 TGATGAGCCTCAAAAAAAGGTA 0.485 0.64 32 56 TGFB2 7042 broad.mit.edu 37 1 218609370 218609371 + Frame_Shift_Ins INS - A A SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr1:218609370_218609371insA uc001hlm.2 + 5 1466_1467 c.813_814insA c.(811-816)AGGAAAfs p.R271fs TGFB2_uc001hln.2_Frame_Shift_Ins_p.R299fs|TGFB2_uc010pue.1_Intron|TGFB2_uc001hlo.2_Intron NM_003238 NP_003229 P61812 TGFB2_HUMAN transforming growth factor, beta 2 isoform 2 271_272 activation of protein kinase activity|angiogenesis|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cardioblast differentiation|catagen|cell cycle arrest|cell death|cell growth|cell-cell junction organization|cell-cell signaling|collagen fibril organization|dopamine biosynthetic process|embryonic digestive tract development|eye development|glial cell migration|hair follicle morphogenesis|hemopoiesis|menstrual cycle phase|negative regulation of alkaline phosphatase activity|negative regulation of cell growth|negative regulation of epithelial cell proliferation|negative regulation of immune response|negative regulation of macrophage cytokine production|neuron development|neutrophil chemotaxis|odontogenesis|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of cardioblast differentiation|positive regulation of catagen|positive regulation of cell adhesion mediated by integrin|positive regulation of cell cycle|positive regulation of cell division|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of epithelial cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of heart contraction|positive regulation of immune response|positive regulation of integrin biosynthetic process|positive regulation of neuron apoptosis|positive regulation of ossification|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein secretion|positive regulation of stress-activated MAPK cascade|regulation of transforming growth factor-beta2 production|response to hypoxia|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein import into nucleus|somatic stem cell division|transforming growth factor beta receptor signaling pathway axon|extracellular matrix|extracellular space|neuronal cell body|platelet alpha granule lumen beta-amyloid binding|cytokine activity|growth factor activity|protein heterodimerization activity|protein homodimerization activity|receptor signaling protein serine/threonine kinase activity|type II transforming growth factor beta receptor binding 0 all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776) AGTCCACTAGGAAAAAAAACAG 0.431 0.22 101 28 PARP1 142 broad.mit.edu 37 1 226567647 226567647 + Frame_Shift_Del DEL T - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr1:226567647delT uc001hqd.3 - 10 1690 c.1519delA c.(1519-1521)AGCfs p.S507fs NM_001618 NP_001609 P09874 PARP1_HUMAN poly (ADP-ribose) polymerase family, member 1 507 Automodification domain. cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter nuclear envelope|nucleolus|transcription factor complex DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding lung(3)|ovary(2)|breast(2)|skin(2)|upper_aerodigestive_tract(1) 10 Breast(184;0.133) GBM - Glioblastoma multiforme(131;0.0531) TGGCCCTTGCTTTTTTTGGAG 0.607 0.23 101 30 BMPR2 659 broad.mit.edu 37 2 203383628 203383628 + Frame_Shift_Del DEL A - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr2:203383628delA uc002uzf.3 + 6 1853 c.705delA c.(703-705)GCAfs p.A235fs BMPR2_uc010ftr.2_Frame_Shift_Del_p.A235fs NM_001204 NP_001195 Q13873 BMPR2_HUMAN bone morphogenetic protein receptor type II 235 Protein kinase.|Cytoplasmic (Potential). anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway integral to plasma membrane ATP binding|metal ion binding|transforming growth factor beta receptor activity ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1) 9 TTTCCTTTGCAAACCGTCAGA 0.423 0.38 66 40 SPEG 10290 broad.mit.edu 37 2 220349122 220349122 + Frame_Shift_Del DEL C - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr2:220349122delC uc010fwg.2 + 30 6937 c.6937delC c.(6937-6939)CCCfs p.P2313fs NM_005876 NP_005867 Q15772 SPEG_HUMAN SPEG complex locus 2313 Pro-rich. muscle organ development|negative regulation of cell proliferation nucleus ATP binding|protein serine/threonine kinase activity stomach(9)|ovary(4)|central_nervous_system(1) 14 Renal(207;0.0183) Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163) 0.000 0.42 245 174 IRS1 3667 broad.mit.edu 37 2 227662352 227662352 + Frame_Shift_Del DEL G - - rs13306467 SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr2:227662352delG uc002voh.3 - 1 1155 c.1103delC c.(1102-1104)CCGfs p.P368fs NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 368 Ser-rich. fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) 0.000 0.36 272 156 PBRM1 55193 broad.mit.edu 37 3 52623187 52623187 + Frame_Shift_Del DEL T - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr3:52623187delT uc003des.2 - 18 2876 c.2864delA c.(2863-2865)AACfs p.N955fs PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.N955fs|PBRM1_uc003der.2_Frame_Shift_Del_p.N923fs|PBRM1_uc003det.2_Frame_Shift_Del_p.N970fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.N970fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.N955fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.N955fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.N955fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.N954fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.N867fs|PBRM1_uc003dfa.1_Frame_Shift_Del_p.N301fs NM_181042 NP_060635 Q86U86 PB1_HUMAN polybromo 1 isoform 4 955 chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear chromosome chromatin binding|DNA binding|protein binding kidney(136)|breast(4) 140 BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) 0.000 0.48 267 250 PXK 54899 broad.mit.edu 37 3 58395317 58395318 + Frame_Shift_Ins INS - A A SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr3:58395317_58395318insA uc003djz.1 + 15 1466_1467 c.1367_1368insA c.(1366-1368)AGAfs p.R456fs PXK_uc003djx.1_Frame_Shift_Ins_p.R456fs|PXK_uc003djy.1_Frame_Shift_Ins_p.R439fs|PXK_uc003dka.1_Frame_Shift_Ins_p.R456fs|PXK_uc003dkb.1_Frame_Shift_Ins_p.R373fs|PXK_uc003dkc.1_Frame_Shift_Ins_p.R439fs|PXK_uc011bfe.1_Frame_Shift_Ins_p.R423fs|PXK_uc010hnj.1_Frame_Shift_Ins_p.R423fs|PXK_uc003dkd.1_Frame_Shift_Ins_p.R319fs|PXK_uc010hnk.1_Frame_Shift_Ins_p.R230fs NM_017771 NP_060241 Q7Z7A4 PXK_HUMAN PX domain containing serine/threonine kinase 456 Protein kinase. cell communication|inflammatory response|negative regulation of ATPase activity|negative regulation of ion transport|regulation of synaptic transmission centrosome|cytoplasm|nucleus|plasma membrane actin binding|ATP binding|phosphatidylinositol binding|phosphatidylinositol binding|protein C-terminus binding|protein kinase activity ovary(1) 1 BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22) GAGGAGGAAAGAAAAAAAAGAA 0.416 0.40 45 30 GRK4 2868 broad.mit.edu 37 4 3030949 3030949 + Frame_Shift_Del DEL A - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr4:3030949delA uc003ggn.1 + 12 1537 c.1082delA c.(1081-1083)GAAfs p.E361fs GRK4_uc003ggo.1_Frame_Shift_Del_p.E361fs|GRK4_uc003ggp.1_Frame_Shift_Del_p.E329fs|GRK4_uc003ggq.1_Frame_Shift_Del_p.E329fs NM_182982 NP_892027 P32298 GRK4_HUMAN G protein-coupled receptor kinase 4 isoform 361 Protein kinase. cell cortex ATP binding|G-protein coupled receptor kinase activity|signal transducer activity lung(1) 1 UCEC - Uterine corpus endometrioid carcinoma (64;0.168) GTCAATAATGAAAAGTATACG 0.318 0.49 25 24 BMP2K 55589 broad.mit.edu 37 4 79792137 79792145 + In_Frame_Del DEL CAGCAGCAG - - rs17855588 SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr4:79792137_79792145delCAGCAGCAG uc003hlk.2 + 11 1598_1606 c.1432_1440delCAGCAGCAG c.(1432-1440)CAGCAGCAGdel p.QQQ484del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQ484del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 484_486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 gcaacagcaacagcagcagcagcagcagc 0.177 0.22 32 9 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.74 5 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.23 55 16 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.35 154 82 DEK 7913 broad.mit.edu 37 6 18258250 18258250 + Frame_Shift_Del DEL A - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr6:18258250delA uc003ncr.1 - 4 484 c.291delT c.(289-291)TTTfs p.F97fs DEK_uc011djf.1_Frame_Shift_Del_p.F63fs|DEK_uc011djg.1_RNA NM_003472 NP_003463 P35659 DEK_HUMAN DEK oncogene isoform 1 97 chromatin modification|regulation of transcription from RNA polymerase II promoter|signal transduction|transcription from RNA polymerase II promoter|viral genome replication nucleus DNA binding|histone binding kidney(1) 1 Ovarian(93;0.00769)|Breast(50;0.0495) all_hematologic(90;0.053) OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332) 0.000 0.28 347 137 STK38 11329 broad.mit.edu 37 6 36465583 36465583 + Frame_Shift_Del DEL A - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr6:36465583delA uc003omg.2 - 11 1734 c.1146delT c.(1144-1146)TTTfs p.F382fs STK38_uc003omh.2_Frame_Shift_Del_p.F382fs|STK38_uc003omi.2_Frame_Shift_Del_p.F382fs NM_007271 NP_009202 Q15208 STK38_HUMAN serine/threonine kinase 38 382 Protein kinase. intracellular protein kinase cascade|negative regulation of MAP kinase activity cytoplasm|MLL5-L complex ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1) 6 CAACGCCTTCAAAAAAAGAGT 0.368 0.40 30 20 MCHR2 84539 broad.mit.edu 37 6 100382358 100382359 + Frame_Shift_Del DEL AA - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr6:100382358_100382359delAA uc003pqh.1 - 5 937_938 c.622_623delTT c.(622-624)TTCfs p.F208fs MCHR2_uc003pqi.1_Frame_Shift_Del_p.F208fs NM_001040179 NP_001035269 Q969V1 MCHR2_HUMAN melanin-concentrating hormone receptor 2 208 Helical; Name=5; (Potential). integral to membrane|plasma membrane G-protein coupled receptor activity lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|skin(1) 8 all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069) BRCA - Breast invasive adenocarcinoma(108;0.0429) 0.000 0.50 56 56 EGFR 1956 broad.mit.edu 37 7 55268879 55268880 + Splice_Site INS - G G SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr7:55268879_55268880insG uc003tqk.2 + 25 3193 c.2947_splice c.e25-1 p.G983_splice EGFR_uc010kzg.1_Splice_Site_p.G938_splice|EGFR_uc011kco.1_Splice_Site_p.G930_splice NM_005228 NP_005219 P00533 EGFR_HUMAN epidermal growth factor receptor isoform a activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1) 9571 all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318) GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607) Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072) TCTCTGCACCAGGGGGATGAAA 0.510 0.54 19 22 PRKDC 5591 broad.mit.edu 37 8 48869968 48869968 + Frame_Shift_Del DEL A - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr8:48869968delA uc003xqi.2 - 2 235 c.178delT c.(178-180)TCCfs p.S60fs PRKDC_uc003xqj.2_Frame_Shift_Del_p.S60fs|PRKDC_uc011ldh.1_Frame_Shift_Del_p.S60fs NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic 60 cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) AAATCTCTGGAAAAAACTAAA 0.363 0.52 10 11 EXT1 2131 broad.mit.edu 37 8 118832020 118832020 + Frame_Shift_Del DEL G - - rs17439693 byFrequency;by1000genomes SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr8:118832020delG uc003yok.1 - 6 2204 c.1431delC c.(1429-1431)CCCfs p.P477fs NM_000127 NP_000118 Q16394 EXT1_HUMAN exostosin 1 477 Lumenal (Potential). glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development Golgi membrane|integral to endoplasmic reticulum membrane glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity ovary(2)|lung(2) 4 all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173) STAD - Stomach adenocarcinoma(47;0.012) TGAATTTGGAGGGGGGCTTTA 0.517 0.41 13 9 DEPDC6 64798 broad.mit.edu 37 8 121015322 121015322 + Frame_Shift_Del DEL C - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr8:121015322delC uc003yow.3 + 6 1084 c.897delC c.(895-897)AGCfs p.S299fs DEPDC6_uc011lid.1_Frame_Shift_Del_p.S198fs NM_022783 NP_073620 Q8TB45 DPTOR_HUMAN DEP domain containing 6 299 Ser-rich. intracellular signal transduction|negative regulation of cell size|negative regulation of protein kinase activity|negative regulation of TOR signaling cascade|regulation of apoptosis intracellular protein binding 0 Lung NSC(37;9.35e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) STAD - Stomach adenocarcinoma(47;0.00185) 0.000 0.96 47 1072 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 18 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.37 378 220 WNK2 65268 broad.mit.edu 37 9 95947624 95947624 + Frame_Shift_Del DEL C - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr9:95947624delC uc004ati.1 + 1 413 c.413delC c.(412-414)GCCfs p.A138fs WNK2_uc011lud.1_Frame_Shift_Del_p.A138fs|WNK2_uc004atj.2_Frame_Shift_Del_p.A138fs|WNK2_uc010mrc.1_Frame_Shift_Del_p.A138fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 138 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 0.000 0.37 114 67 WNK2 65268 broad.mit.edu 37 9 96018690 96018690 + Frame_Shift_Del DEL C - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr9:96018690delC uc004ati.1 + 9 2144 c.2144delC c.(2143-2145)ACCfs p.T715fs WNK2_uc011lud.1_Frame_Shift_Del_p.T715fs|WNK2_uc004atj.2_Frame_Shift_Del_p.T715fs|WNK2_uc004atk.2_Frame_Shift_Del_p.T352fs|WNK2_uc010mrc.1_Intron NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 715 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 0.000 0.34 1532 783 FANCC 2176 broad.mit.edu 37 9 98003011 98003011 + Frame_Shift_Del DEL T - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr9:98003011delT uc004avh.2 - 4 527 c.265delA c.(265-267)ATTfs p.I89fs FANCC_uc004avi.3_Frame_Shift_Del_p.I89fs|FANCC_uc010mrm.1_RNA|FANCC_uc011lul.1_RNA NM_000136 NP_000127 Q00597 FANCC_HUMAN Fanconi anemia, complementation group C 89 protein complex assembly cytosol|nucleoplasm protein binding kidney(1) 1 Acute lymphoblastic leukemia(62;0.138) CATATTAGAATTTTTTGGCTT 0.279 0.50 14 14 CUBN 8029 broad.mit.edu 37 10 17032408 17032408 + Frame_Shift_Del DEL G - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr10:17032408delG uc001ioo.2 - 29 4327 c.4275delC c.(4273-4275)CCCfs p.P1425fs NM_001081 NP_001072 O60494 CUBN_HUMAN cubilin precursor 1425 CUB 9. cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1) 19 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) TGCTACTCCCGGGGTCCGTCC 0.522 0.52 44 48 MYO3A 53904 broad.mit.edu 37 10 26462760 26462760 + Frame_Shift_Del DEL A - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr10:26462760delA uc001isn.2 + 30 3927 c.3567delA c.(3565-3567)CCAfs p.P1189fs MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron NM_017433 NP_059129 Q8NEV4 MYO3A_HUMAN myosin IIIA 1189 protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception cytoplasm|filamentous actin|filopodium|myosin complex actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 18 ATCAGACTCCAAAAAAAATGA 0.403 0.42 60 43 BTRC 8945 broad.mit.edu 37 10 103310573 103310573 + Frame_Shift_Del DEL C - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr10:103310573delC uc001kta.2 + 14 1887 c.1774delC c.(1774-1776)CCCfs p.P592fs BTRC_uc001ktb.2_Frame_Shift_Del_p.P556fs|BTRC_uc001ktc.2_Frame_Shift_Del_p.P566fs NM_033637 NP_378663 Q9Y297 FBW1A_HUMAN beta-transducin repeat containing protein 592 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|positive regulation of proteolysis|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|viral reproduction|Wnt receptor signaling pathway cytosol|nucleus|SCF ubiquitin ligase complex ovary(1) 1 Colorectal(252;0.234) Epithelial(162;1.05e-08)|all cancers(201;6.59e-07) CCAAGCTGAACCCCCCCGTTC 0.433 0.48 53 49 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 102 14 SORL1 6653 broad.mit.edu 37 11 121495926 121495927 + Frame_Shift_Ins INS - T T SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr11:121495926_121495927insT uc001pxx.2 + 46 6384_6385 c.6304_6305insT c.(6304-6306)CTTfs p.L2102fs SORL1_uc010rzp.1_Frame_Shift_Ins_p.L948fs|SORL1_uc010rzq.1_Frame_Shift_Ins_p.L717fs NM_003105 NP_003096 Q92673 SORL_HUMAN sortilin-related receptor containing LDLR class 2102 Extracellular (Potential).|Fibronectin type-III 6. cholesterol metabolic process|lipid transport|receptor-mediated endocytosis integral to plasma membrane|low-density lipoprotein particle low-density lipoprotein particle binding|transmembrane receptor activity ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1) 15 Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113) BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108) AGCAAGATGCCTTTTTGGCAAC 0.470 0.42 70 51 GUCY2C 2984 broad.mit.edu 37 12 14781607 14781608 + Frame_Shift_Ins INS - T T rs145875994 SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr12:14781607_14781608insT uc001rcd.2 - 20 2358_2359 c.2221_2222insA c.(2221-2223)ATTfs p.I741fs NM_004963 NP_004954 P25092 GUC2C_HUMAN guanylate cyclase 2C precursor 741 Cytoplasmic (Potential).|Protein kinase. intracellular signal transduction|receptor guanylyl cyclase signaling pathway integral to membrane ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity ovary(4)|skin(2) 6 TGTAGTCTCAATTTTTTTGAAA 0.347 0.45 41 33 ACVR1B 91 broad.mit.edu 37 12 52370198 52370200 + In_Frame_Del DEL TCA - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr12:52370198_52370200delTCA uc001rzn.2 + 3 461_463 c.419_421delTCA c.(418-423)CTCATC>CTC p.I144del ACVR1B_uc001rzl.2_In_Frame_Del_p.I144del|ACVR1B_uc001rzm.2_In_Frame_Del_p.I144del|ACVR1B_uc010snn.1_In_Frame_Del_p.I144del NM_004302 NP_004293 P36896 ACV1B_HUMAN activin A receptor, type IB isoform a precursor 144 Helical; (Potential). G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|peptidyl-threonine phosphorylation|positive regulation of activin receptor signaling pathway|positive regulation of erythrocyte differentiation|protein autophosphorylation|transmembrane receptor protein serine/threonine kinase signaling pathway cell surface activin receptor activity, type I|ATP binding|metal ion binding|SMAD binding|transforming growth factor beta receptor activity|ubiquitin protein ligase binding pancreas(4)|breast(2)|ovary(1)|lung(1)|kidney(1) 9 BRCA - Breast invasive adenocarcinoma(357;0.104) Adenosine triphosphate(DB00171) CTCCTGTTCCTCATCATCATCAT 0.537 0.40 34 23 LRP1 4035 broad.mit.edu 37 12 57603940 57603940 + Frame_Shift_Del DEL C - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr12:57603940delC uc001snd.2 + 81 13034 c.12568delC c.(12568-12570)CCCfs p.P4190fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 4190 Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CTCTCCAACGCCCCCCCCAGA 0.637 0.50 8 8 NAV3 89795 broad.mit.edu 37 12 78443808 78443808 + Frame_Shift_Del DEL A - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr12:78443808delA uc001syp.2 + 10 2232 c.2059delA c.(2059-2061)AAAfs p.K687fs NAV3_uc001syo.2_Frame_Shift_Del_p.K687fs|NAV3_uc010sub.1_Frame_Shift_Del_p.K187fs NM_014903 NP_055718 Q8IVL0 NAV3_HUMAN neuron navigator 3 687 Potential. nuclear outer membrane ATP binding|nucleoside-triphosphatase activity large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 17 GAGAACAGTTAAAAACATAGC 0.343 0.33 47 23 DACH1 1602 broad.mit.edu 37 13 72204814 72204815 + In_Frame_Ins INS - AGC AGC SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr13:72204814_72204815insAGC uc010thn.1 - 4 1422_1423 c.999_1000insGCT c.(997-1002)insGCT p.333_334insA DACH1_uc010tho.1_In_Frame_Ins_p.333_334insA|DACH1_uc010thp.1_Intron NM_080759 NP_542937 Q9UI36 DACH1_HUMAN dachshund homolog 1 isoform a 333_334 Interaction with SIX6 and HDAC3 (By similarity). multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus DNA binding|nucleotide binding|protein binding breast(1) 1 Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198) GBM - Glioblastoma multiforme(99;0.00032) gctgcattggtagcagcagcag 0.243 0.17 66 14 TRIP11 9321 broad.mit.edu 37 14 92470377 92470377 + Frame_Shift_Del DEL G - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr14:92470377delG uc001xzy.2 - 11 4731 c.3943delC c.(3943-3945)CAGfs p.Q1315fs TRIP11_uc010auf.1_Frame_Shift_Del_p.Q1051fs NM_004239 NP_004230 Q15643 TRIPB_HUMAN thyroid hormone receptor interactor 11 1315 Potential. transcription from RNA polymerase II promoter cytoskeleton|Golgi apparatus|membrane|nucleus protein binding|transcription coactivator activity ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1) 13 COAD - Colon adenocarcinoma(157;0.223) GAAGACAGCTGGGGTGAAATA 0.413 0.46 71 61 CDC42BPB 9578 broad.mit.edu 37 14 103429465 103429466 + Frame_Shift_Ins INS - T T SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr14:103429465_103429466insT uc001ymi.1 - 20 2985_2986 c.2753_2754insA c.(2752-2754)AACfs p.N918fs CDC42BPB_uc001ymj.1_Frame_Shift_Ins_p.N46fs NM_006035 NP_006026 Q9Y5S2 MRCKB_HUMAN CDC42-binding protein kinase beta 918 Potential. actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction cell leading edge|cell-cell junction|cytoplasm|cytoskeleton ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1) 11 Melanoma(154;0.155) Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199) ATAATTCTCTGTTTTTGGCTTC 0.351 0.39 27 17 CDC42BPB 9578 broad.mit.edu 37 14 103447224 103447224 + Frame_Shift_Del DEL A - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr14:103447224delA uc001ymi.1 - 8 1258 c.1026delT c.(1024-1026)TTTfs p.F342fs NM_006035 NP_006026 Q9Y5S2 MRCKB_HUMAN CDC42-binding protein kinase beta 342 Protein kinase. actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction cell leading edge|cell-cell junction|cytoplasm|cytoskeleton ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1) 11 Melanoma(154;0.155) Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199) TTAGACCTTCAAAAAACGCAT 0.458 0.40 61 41 PAK6 56924 broad.mit.edu 37 15 40565825 40565825 + Frame_Shift_Del DEL C - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr15:40565825delC uc010bbl.2 + 9 2131 c.1691delC c.(1690-1692)ACCfs p.T564fs PAK6_uc010bbm.2_Frame_Shift_Del_p.T564fs|PAK6_uc001zky.3_Frame_Shift_Del_p.T564fs|PAK6_uc010bbn.2_Frame_Shift_Del_p.T564fs|PAK6_uc001zlb.2_Frame_Shift_Del_p.T564fs NM_001128628 NP_001122100 Q9NQU5 PAK6_HUMAN p21-activated kinase 6 564 Protein kinase. ATP binding|protein binding|protein serine/threonine kinase activity lung(5)|large_intestine(1)|ovary(1)|skin(1) 8 all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544) CTGGTGGGAACCCCCTACTGG 0.552 0.64 4 7 UNC13C 440279 broad.mit.edu 37 15 54527275 54527276 + Frame_Shift_Ins INS - A A SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr15:54527275_54527276insA uc002ack.2 + 4 3119_3120 c.3119_3120insA c.(3118-3120)AGAfs p.R1040fs NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 1040 exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) GATCTTCGCAGAAAAAAAACTT 0.366 0.45 45 37 CHRNA5 1138 broad.mit.edu 37 15 78882366 78882366 + Frame_Shift_Del DEL T - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr15:78882366delT uc002bdy.2 + 5 795 c.633delT c.(631-633)GATfs p.D211fs CHRNA5_uc002bdz.2_Intron NM_000745 NP_000736 P30532 ACHA5_HUMAN cholinergic receptor, nicotinic, alpha 5 211 Extracellular (Potential). behavioral response to nicotine cell junction|postsynaptic membrane acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity ovary(1)|central_nervous_system(1)|skin(1) 3 ACAAGAGAGATTTTTTTGATA 0.403 0.46 74 64 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 34 338 PHF23 79142 broad.mit.edu 37 17 7139572 7139572 + Frame_Shift_Del DEL T - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr17:7139572delT uc002gfa.2 - 4 901 c.674delA c.(673-675)AAGfs p.K225fs DVL2_uc002gez.1_5'Flank|DVL2_uc010vtr.1_5'Flank|DVL2_uc010clz.1_5'Flank|PHF23_uc010vtt.1_Frame_Shift_Del_p.K158fs|PHF23_uc010cma.2_Frame_Shift_Del_p.K95fs NM_024297 NP_077273 Q9BUL5 PHF23_HUMAN PHD finger protein 23 225 zinc ion binding 0 0.000 0.47 445 390 TP53 7157 broad.mit.edu 37 17 7579420 7579420 + Frame_Shift_Del DEL G - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr17:7579420delG uc002gim.2 - 4 461 c.267delC c.(265-267)CCCfs p.P89fs TP53_uc002gig.1_Frame_Shift_Del_p.P89fs|TP53_uc002gih.2_Frame_Shift_Del_p.P89fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.P89fs|TP53_uc010cni.1_Frame_Shift_Del_p.P89fs|TP53_uc002gij.2_Frame_Shift_Del_p.P89fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.P50fs|TP53_uc010cnk.1_Frame_Shift_Del_p.P104fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 89 Interaction with WWOX. P -> L (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.A76_S90del15(3)|p.P89S(3)|p.G59fs*23(3)|p.P89fs*60(1)|p.V73fs*9(1)|p.D48fs*55(1)|p.P85fs*58(1)|p.S33fs*23(1)|p.A86fs*33(1)|p.A86fs*32(1)|p.P87fs*54(1)|p.P13fs*18(1)|p.A88fs*52(1)|p.P89L(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.50 496 487 SUZ12 23512 broad.mit.edu 37 17 30315461 30315462 + Frame_Shift_Del DEL AG - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr17:30315461_30315462delAG uc002hgs.2 + 10 1368_1369 c.1146_1147delAG c.(1144-1149)TCAGAGfs p.S382fs SUZ12_uc002hgt.2_Frame_Shift_Del_p.S359fs NM_015355 NP_056170 Q15022 SUZ12_HUMAN joined to JAZF1 382_383 negative regulation of cell differentiation|transcription, DNA-dependent ESC/E(Z) complex histone methyltransferase activity|methylated histone residue binding|zinc ion binding JAZF1/SUZ12(131) soft_tissue(98)|endometrium(33) 131 Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231) CTAGAAATTCAGAGAGTCTCCA 0.401 0.44 35 28 TOP2A 7153 broad.mit.edu 37 17 38546381 38546381 + Frame_Shift_Del DEL T - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr17:38546381delT uc002huq.2 - 34 4429 c.4303delA c.(4303-4305)AGGfs p.R1435fs NM_001067 NP_001058 P11388 TOP2A_HUMAN DNA topoisomerase II, alpha isozyme 1435 apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1) 7 Breast(137;0.00328) STAD - Stomach adenocarcinoma(5;0.00183) Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385) GGGGCAGCCCTTTTTTTGGCA 0.413 0.40 49 32 SMARCE1 6605 broad.mit.edu 37 17 38785153 38785153 + Frame_Shift_Del DEL C - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr17:38785153delC uc002hux.2 - 11 1244 c.1120delG c.(1120-1122)GTCfs p.V374fs SMARCE1_uc010wff.1_3'UTR|SMARCE1_uc010wfg.1_3'UTR|SMARCE1_uc002huy.2_Frame_Shift_Del_p.V339fs|SMARCE1_uc010wfh.1_Frame_Shift_Del_p.V304fs|SMARCE1_uc010wfi.1_Frame_Shift_Del_p.V356fs NM_003079 NP_003070 Q969G3 SMCE1_HUMAN SWI/SNF-related matrix-associated 374 Glu-rich. chromatin modification|negative regulation of transcription, DNA-dependent|nervous system development|nucleosome disassembly|regulation of transcription from RNA polymerase II promoter nBAF complex|npBAF complex|nuclear chromosome|SWI/SNF complex|transcriptional repressor complex chromatin binding|DNA binding|N-acetyltransferase activity|protein binding|protein N-terminus binding|transcription coactivator activity 0 Breast(137;0.000812) 0.000 0.46 727 608 STAT3 6774 broad.mit.edu 37 17 40475061 40475063 + In_Frame_Del DEL CTT - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr17:40475061_40475063delCTT uc002hzl.1 - 20 2087_2089 c.1847_1849delAAG c.(1846-1851)GAAGGA>GGA p.E616del STAT3_uc002hzk.1_In_Frame_Del_p.E616del|STAT3_uc002hzm.1_In_Frame_Del_p.E616del|STAT3_uc010wgh.1_In_Frame_Del_p.E518del|STAT3_uc002hzn.1_In_Frame_Del_p.E616del NM_139276 NP_644805 P40763 STAT3_HUMAN signal transducer and activator of transcription 616 SH2. cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis cytosol|nucleus|plasma membrane calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding ovary(1)|lung(1)|breast(1)|central_nervous_system(1) 4 all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135) BRCA - Breast invasive adenocarcinoma(366;0.139) GTGACGCCTCCTTCTTTGCTGCT 0.562 0.59 54 77 ROCK1 6093 broad.mit.edu 37 18 18539865 18539865 + Frame_Shift_Del DEL T - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr18:18539865delT uc002kte.2 - 29 4389 c.3448delA c.(3448-3450)ATTfs p.I1150fs NM_005406 NP_005397 Q13464 ROCK1_HUMAN Rho-associated, coiled-coil containing protein 1150 PH.|Auto-inhibitory. actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction centriole|cytosol|Golgi membrane ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity lung(2)|breast(2)|central_nervous_system(1) 5 Melanoma(1;0.165) TAGAACAAAATTTTTTTGCTG 0.343 0.56 19 24 PIK3C3 5289 broad.mit.edu 37 18 39573290 39573290 + Frame_Shift_Del DEL C - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr18:39573290delC uc002lap.2 + 7 829 c.771delC c.(769-771)GACfs p.D257fs PIK3C3_uc010xcl.1_Frame_Shift_Del_p.D194fs NM_002647 NP_002638 Q8NEB9 PK3C3_HUMAN catalytic phosphatidylinositol 3-kinase 3 257 cell cycle|cytokinesis|fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway midbody|phosphatidylinositol 3-kinase complex 1-phosphatidylinositol-3-kinase activity|ATP binding|protein binding lung(8)|ovary(1)|breast(1) 10 AAGTTCCTGACCCCCAGATGT 0.294 0.56 24 30 SMAD7 4092 broad.mit.edu 37 18 46474795 46474795 + Frame_Shift_Del DEL G - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr18:46474795delG uc002ldg.2 - 2 913 c.626delC c.(625-627)CCTfs p.P209fs SMAD7_uc010xde.1_5'UTR NM_005904 NP_005895 O15105 SMAD7_HUMAN SMAD family member 7 209 Poly-Pro.|PY-motif.|Important for interaction with SMURF2. Missing: Diminishes interaction with SMURF2. adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding 0 Colorectal(1;0.0518) GGAGTAAGGAGGGGGGGGAGA 0.388 0.76 10 32 ATP8B1 5205 broad.mit.edu 37 18 55351309 55351311 + In_Frame_Del DEL AAG - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr18:55351309_55351311delAAG uc002lgw.2 - 14 1587_1589 c.1587_1589delCTT c.(1585-1590)TTCTTG>TTG p.F529del uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 529 Cytoplasmic (Potential). Missing (in PFIC1). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) AACTGCGAGCAAGAAGAAGAACT 0.448 0.41 60 41 SMARCA4 6597 broad.mit.edu 37 19 11096048 11096048 + Frame_Shift_Del DEL C - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr19:11096048delC uc002mqf.3 + 3 606 c.322delC c.(322-324)CCCfs p.P108fs SMARCA4_uc010dxp.2_Frame_Shift_Del_p.P108fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.P108fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.P108fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.P108fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.P108fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.P108fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.P108fs|SMARCA4_uc002mqe.2_Frame_Shift_Del_p.P108fs NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 108 Necessary for interaction with SS18L1/CREST (By similarity). chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) 0.000 0.46 560 484 CPAMD8 27151 broad.mit.edu 37 19 17081703 17081703 + Frame_Shift_Del DEL G - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr19:17081703delG uc002nfb.2 - 18 2384 c.2352delC c.(2350-2352)CCCfs p.P784fs NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 737 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 0.000 0.50 163 162 JAK3 3718 broad.mit.edu 37 19 17941419 17941420 + Frame_Shift_Ins INS - G G SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr19:17941419_17941420insG uc002nhn.3 - 22 3088_3089 c.2988_2989insC c.(2986-2991)CCCGAAfs p.P996fs JAK3_uc010ebh.2_Intron|JAK3_uc002nho.2_Frame_Shift_Ins_p.P996fs NM_000215 NP_000206 P52333 JAK3_HUMAN Janus kinase 3 996_997 Protein kinase 2. B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis cytoskeleton|cytosol|endomembrane system|membrane ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1) 56 GAGAGGGATTCGGGGGCATACC 0.584 0.34 19 10 DYRK1B 9149 broad.mit.edu 37 19 40316612 40316612 + Frame_Shift_Del DEL G - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr19:40316612delG uc002omj.2 - 11 1913 c.1633delC c.(1633-1635)CAGfs p.Q545fs DYRK1B_uc002omi.2_Frame_Shift_Del_p.Q517fs|DYRK1B_uc002omk.2_Frame_Shift_Del_p.Q505fs NM_004714 NP_004705 Q9Y463 DYR1B_HUMAN dual-specificity tyrosine-(Y)-phosphorylation 545 positive regulation of transcription, DNA-dependent nucleus ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|transcription coactivator activity ovary(4)|stomach(1)|central_nervous_system(1)|skin(1) 7 all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06) Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23) 0.000 0.37 1054 630 LMTK3 114783 broad.mit.edu 37 19 49000676 49000676 + Frame_Shift_Del DEL G - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr19:49000676delG uc002pjk.2 - 12 3737 c.3737delC c.(3736-3738)CCTfs p.P1246fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.53 109 122 LMTK3 114783 broad.mit.edu 37 19 49002150 49002151 + Frame_Shift_Ins INS - G G SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr19:49002150_49002151insG uc002pjk.2 - 12 2262_2263 c.2262_2263insC c.(2260-2265)CCCGCCfs p.P754fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.31 344 156 SBK2 646643 broad.mit.edu 37 19 56041210 56041210 + Frame_Shift_Del DEL G - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr19:56041210delG uc010ygc.1 - 3 937 c.937delC c.(937-939)CGAfs p.R313fs NM_001101401 NP_001094871 P0C263 SBK2_HUMAN SH3-binding domain kinase family, member 2 313 Protein kinase. ATP binding|protein serine/threonine kinase activity 0 CTCCTCCTTCGGGGGTGAGGG 0.761 0.38 10 6 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 71 9 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 142 440 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 48 DDX17 10521 broad.mit.edu 37 22 38897211 38897211 + Frame_Shift_Del DEL T - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr22:38897211delT uc003avy.3 - 2 465 c.362delA c.(361-363)AAGfs p.K121fs DDX17_uc003avx.3_Frame_Shift_Del_p.K121fs|DDX17_uc011anu.1_Frame_Shift_Del_p.K34fs NM_001098504 NP_001091974 Q92841 DDX17_HUMAN DEAD box polypeptide 17 isoform 3 42 RNA processing nucleus ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity skin(3)|upper_aerodigestive_tract(1) 4 Melanoma(58;0.0286) 0.000 0.47 262 234 GTSE1 51512 broad.mit.edu 37 22 46712300 46712300 + Frame_Shift_Del DEL T - - SNU407_LARGE_INTESTINE NA SNU407_LARGE_INTESTINE NA g.chr22:46712300delT uc011aqy.1 + 7 1635 c.1423delT c.(1423-1425)TTTfs p.F475fs GTSE1_uc011aqz.1_Frame_Shift_Del_p.F322fs|GTSE1_uc003bhl.1_Frame_Shift_Del_p.F100fs|GTSE1_uc003bhm.1_Frame_Shift_Del_p.F100fs NM_016426 NP_057510 Q9NYZ3 GTSE1_HUMAN G-2 and S-phase expressed 1 456 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G2 phase of mitotic cell cycle|microtubule-based process cytoplasmic microtubule ovary(1) 1 Ovarian(80;0.00965)|all_neural(38;0.0416) UCEC - Uterine corpus endometrioid carcinoma (28;0.00462) AATTCCTAAGTTTTCTATTGG 0.299 0.41 23 16 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU410_PANCREAS NA SNU410_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 4 35 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 260 54 TTN 7273 broad.mit.edu 37 2 179584324 179584325 + Frame_Shift_Ins INS - T T SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr2:179584324_179584325insT uc010zfg.1 - 79 20386_20387 c.20162_20163insA c.(20161-20163)AACfs p.N6721fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Ins_p.N3382fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 7648 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TGCCAACACTGTTTTTCACTTC 0.396 0.26 222 79 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.24 63 20 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 19 55 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 11 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.82 2 9 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.32 73 35 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 14 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.61 55 86 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.94 1 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 95 10 GRAMD1B 57476 broad.mit.edu 37 11 123480598 123480599 + Frame_Shift_Ins INS - C C rs139670625 by1000genomes SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr11:123480598_123480599insC uc001pyx.2 + 12 1653_1654 c.1324_1325insC c.(1324-1326)ACTfs p.T442fs GRAMD1B_uc001pyw.2_Frame_Shift_Ins_p.T449fs|GRAMD1B_uc010rzw.1_Frame_Shift_Ins_p.T402fs|GRAMD1B_uc010rzx.1_Frame_Shift_Ins_p.T402fs|GRAMD1B_uc009zbe.1_Frame_Shift_Ins_p.T438fs|GRAMD1B_uc001pyy.2_Frame_Shift_Ins_p.T133fs NM_020716 NP_065767 Q3KR37 GRM1B_HUMAN GRAM domain containing 1B 442 integral to membrane ovary(1) 1 Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394) GGCTCCCAAAACTGCCACTGTC 0.500 0.29 39 16 CYP27B1 1594 broad.mit.edu 37 12 58160756 58160768 + Frame_Shift_Del DEL GGCGCCCAACTCG - - SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr12:58160756_58160768delGGCGCCCAACTCG uc001spz.1 - 1 209_221 c.57_69delCGAGTTGGGCGCC c.(55-69)CCCGAGTTGGGCGCCfs p.P19fs CYP27B1_uc001sqa.1_5'UTR|CYP27B1_uc001sqb.1_5'Flank|CYP27B1_uc001sqc.1_5'Flank NM_000785 NP_000776 O15528 CP27B_HUMAN cytochrome P450, family 27, subfamily B, 19_23 bone mineralization|calcium ion homeostasis|calcium ion transport|decidualization|G1 to G0 transition|hormone biosynthetic process|negative regulation of calcidiol 1-monooxygenase activity|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of keratinocyte differentiation|positive regulation of vitamin D 24-hydroxylase activity|positive regulation of vitamin D receptor signaling pathway|regulation of bone mineralization|response to estrogen stimulus|response to interferon-gamma|response to lipopolysaccharide|response to tumor necrosis factor|response to vitamin D|vitamin D biosynthetic process|xenobiotic metabolic process mitochondrial outer membrane calcidiol 1-monooxygenase activity|electron carrier activity|heme binding central_nervous_system(3) 3 all_cancers(7;8.09e-80)|Lung NSC(6;2.26e-27)|all_lung(6;1.99e-25)|all_epithelial(6;3.62e-18)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122) GBM - Glioblastoma multiforme(5;1.97e-113)|all cancers(5;1.54e-78)|BRCA - Breast invasive adenocarcinoma(9;0.0294) Calcidiol(DB00146)|Calcitriol(DB00136)|Ergocalciferol(DB00153) AGCCTAGGGAGGCGCCCAACTCGGGCGCCCAGC 0.629 0.45 23 19 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.34 61 32 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 58 329 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU410_PANCREAS NA SNU410_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 105 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU423_LIVER NA SNU423_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 7 103 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU423_LIVER NA SNU423_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.42 235 173 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SNU423_LIVER NA SNU423_LIVER NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.39 35 22 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU423_LIVER NA SNU423_LIVER NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.41 10 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU423_LIVER NA SNU423_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 84 146 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU423_LIVER NA SNU423_LIVER NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 69 43 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU423_LIVER NA SNU423_LIVER NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.42 102 75 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SNU423_LIVER NA SNU423_LIVER NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.63 7 12 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU423_LIVER NA SNU423_LIVER NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 15 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU423_LIVER NA SNU423_LIVER NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.37 12 7 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU423_LIVER NA SNU423_LIVER NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 49 NCOR2 9612 broad.mit.edu 37 12 124887058 124887059 + In_Frame_Ins INS - GCTGCT GCTGCT rs35831183;rs67031864 SNU423_LIVER NA SNU423_LIVER NA g.chr12:124887058_124887059insGCTGCT uc010tba.1 - 14 1648_1649 c.1531_1532insAGCAGC c.(1531-1533)CCC>CAGCAGCCC p.510_511insQQ NCOR2_uc010tay.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010taz.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbb.1_In_Frame_Ins_p.510_511insQQ|NCOR2_uc010tbc.1_In_Frame_Ins_p.509_510insQQ|NCOR2_uc001ugj.1_In_Frame_Ins_p.510_511insQQ NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 510_511 cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) GCGGGGCATGGgctgctgctgc 0.312 0.26 111 40 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNU423_LIVER NA SNU423_LIVER NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.41 37 26 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT SNU423_LIVER NA SNU423_LIVER NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.11 321 38 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU423_LIVER NA SNU423_LIVER NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.76 59 182 CIC 23152 broad.mit.edu 37 19 42795827 42795828 + Frame_Shift_Ins INS - C C SNU423_LIVER NA SNU423_LIVER NA g.chr19:42795827_42795828insC uc002otf.1 + 11 2856_2857 c.2816_2817insC c.(2815-2817)GGCfs p.G939fs NM_015125 NP_055940 Q96RK0 CIC_HUMAN capicua homolog 939 Pro-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1) 11 Prostate(69;0.00682) GGAGGGGCCGGCCAGCCACTGC 0.693 0.23 23 7 AURKA 6790 broad.mit.edu 37 20 54956539 54956539 + Frame_Shift_Del DEL A - - SNU423_LIVER NA SNU423_LIVER NA g.chr20:54956539delA uc002xxd.1 - 8 1221 c.655delT c.(655-657)TATfs p.Y219fs AURKA_uc002xxe.1_Frame_Shift_Del_p.Y219fs|AURKA_uc002xxf.1_Frame_Shift_Del_p.Y219fs|AURKA_uc002xxg.1_Frame_Shift_Del_p.Y219fs|AURKA_uc002xxh.1_Frame_Shift_Del_p.Y219fs|AURKA_uc002xxi.1_Frame_Shift_Del_p.Y219fs|AURKA_uc002xxj.1_Frame_Shift_Del_p.Y219fs|AURKA_uc002xxk.1_Frame_Shift_Del_p.Y219fs|AURKA_uc010zzd.1_RNA NM_198433 NP_940835 O14965 AURKA_HUMAN serine/threonine protein kinase 6 219 Protein kinase. anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|phosphatidylinositol-mediated signaling|regulation of protein stability|spindle organization cytosol|nucleus|perinuclear region of cytoplasm|spindle microtubule|spindle pole centrosome ATP binding|protein kinase binding|protein serine/threonine kinase activity lung(3)|ovary(2)|breast(1)|large_intestine(1)|skin(1) 8 Colorectal(105;0.202) AGTTCTCTATAAACTGTTCCA 0.378 0.68 47 98 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU423_LIVER NA SNU423_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 33 127 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU423_LIVER NA SNU423_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 132 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU449_LIVER NA SNU449_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 3 38 ARID1A 8289 broad.mit.edu 37 1 27100181 27100182 + In_Frame_Ins INS - GCA GCA SNU449_LIVER NA SNU449_LIVER NA g.chr1:27100181_27100182insGCA uc001bmv.1 + 16 4350_4351 c.3977_3978insGCA c.(3976-3978)CCG>CCGCAG p.1334_1335insQ ARID1A_uc001bmt.1_In_Frame_Ins_p.1333_1334insQ|ARID1A_uc001bmu.1_In_Frame_Ins_p.1334_1335insQ|ARID1A_uc001bmw.1_In_Frame_Ins_p.951_952insQ|ARID1A_uc001bmx.1_In_Frame_Ins_p.180_181insQ|ARID1A_uc009vsm.1_5'UTR|ARID1A_uc009vsn.1_5'Flank NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1334_1335 Gln-rich. androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.Q1334_R1335insQ(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CGCTACCCCCCgcagcagcagc 0.510 0.33 29 14 ARID1A 8289 broad.mit.edu 37 1 27107135 27107136 + Frame_Shift_Ins INS - A A SNU449_LIVER NA SNU449_LIVER NA g.chr1:27107135_27107136insA uc001bmv.1 + 20 7119_7120 c.6746_6747insA c.(6745-6747)TCAfs p.S2249fs ARID1A_uc001bmu.1_Frame_Shift_Ins_p.S2032fs|ARID1A_uc001bmx.1_Frame_Shift_Ins_p.S1095fs|ARID1A_uc009vsm.1_Frame_Shift_Ins_p.S577fs|ARID1A_uc009vsn.1_Frame_Shift_Ins_p.S491fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 2249 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GAGAACCACTCAGAGTTTACTC 0.515 0.95 10 211 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU449_LIVER NA SNU449_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.19 363 87 RIF1 55183 broad.mit.edu 37 2 152320713 152320715 + In_Frame_Del DEL AAG - - SNU449_LIVER NA SNU449_LIVER NA g.chr2:152320713_152320715delAAG uc002txm.2 + 30 4809_4811 c.4679_4681delAAG c.(4678-4683)AAAGAA>AAA p.E1562del RIF1_uc002txl.2_In_Frame_Del_p.E1562del|RIF1_uc002txn.2_In_Frame_Del_p.E1562del|RIF1_uc002txo.2_In_Frame_Del_p.E1562del|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1562 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) TCGGAGGCAAAAGAAGAAGGTTC 0.404 0.62 29 47 MYLK 4638 broad.mit.edu 37 3 123337614 123337616 + In_Frame_Del DEL TCT - - SNU449_LIVER NA SNU449_LIVER NA g.chr3:123337614_123337616delTCT uc003ego.2 - 33 5652_5654 c.5370_5372delAGA c.(5368-5373)GAAGAT>GAT p.E1790del uc003egk.2_Intron|MYLK_uc003egl.2_In_Frame_Del_p.E30del|MYLK_uc003egm.2_Splice_Site_p.D30_splice|MYLK_uc010hrr.2_In_Frame_Del_p.E225del|MYLK_uc011bjv.1_In_Frame_Del_p.E590del|MYLK_uc011bjw.1_Splice_Site_p.D1790_splice|MYLK_uc003egp.2_In_Frame_Del_p.E1721del|MYLK_uc003egq.2_In_Frame_Del_p.E1739del|MYLK_uc003egr.2_In_Frame_Del_p.E1670del|MYLK_uc003egs.2_In_Frame_Del_p.E1614del NM_053025 NP_444253 Q15746 MYLK_HUMAN myosin light chain kinase isoform 1 1790 aorta smooth muscle tissue morphogenesis|muscle contraction cytosol actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity ovary(6)|skin(2)|stomach(1) 9 Lung NSC(201;0.0496) GBM - Glioblastoma multiforme(114;0.0736) TTGGGACACATCTTCTAGAAGAC 0.414 0.41 102 71 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU449_LIVER NA SNU449_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 72 40 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU449_LIVER NA SNU449_LIVER NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.24 75 24 HMMR 3161 broad.mit.edu 37 5 162917425 162917426 + Frame_Shift_Ins INS - A A SNU449_LIVER NA SNU449_LIVER NA g.chr5:162917425_162917426insA uc003lzf.2 + 17 2171_2172 c.1989_1990insA c.(1987-1992)GCTAAAfs p.A663fs HMMR_uc003lzh.2_Frame_Shift_Ins_p.A664fs|HMMR_uc003lzg.2_Frame_Shift_Ins_p.A648fs|HMMR_uc011dem.1_Frame_Shift_Ins_p.A577fs|uc003lzi.2_Intron NM_012484 NP_036616 O75330 HMMR_HUMAN hyaluronan-mediated motility receptor isoform b 663_664 Hyaluronic acid-binding (Potential). cell surface|cytoplasm hyaluronic acid binding 0 Renal(175;0.000281) Medulloblastoma(196;0.00853)|all_neural(177;0.0408) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848) GTCAGCTTGCTAAAAAAAAACA 0.307 0.51 24 25 RIOK1 83732 broad.mit.edu 37 6 7417625 7417626 + Frame_Shift_Del DEL AT - - SNU449_LIVER NA SNU449_LIVER NA g.chr6:7417625_7417626delAT uc003mxn.2 + 17 1832_1833 c.1658_1659delAT c.(1657-1659)CATfs p.H553fs RIOK1_uc003mxo.2_Frame_Shift_Del_p.H312fs NM_031480 NP_113668 Q9BRS2 RIOK1_HUMAN RIO kinase 1 isoform 1 553 ATP binding|protein serine/threonine kinase activity ovary(2)|stomach(1)|skin(1) 4 Ovarian(93;0.0418) ATTCCTAAACATGTGAAAAAAA 0.342 0.36 7 4 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU449_LIVER NA SNU449_LIVER NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 2 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU449_LIVER NA SNU449_LIVER NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 22 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU449_LIVER NA SNU449_LIVER NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 435 51 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU449_LIVER NA SNU449_LIVER NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 203 63 FANCM 57697 broad.mit.edu 37 14 45618077 45618082 + In_Frame_Del DEL AGATAG - - SNU449_LIVER NA SNU449_LIVER NA g.chr14:45618077_45618082delAGATAG uc001wwd.3 + 4 896_901 c.797_802delAGATAG c.(796-804)CAGATAGAG>CAG p.IE267del FANCM_uc001wwc.2_In_Frame_Del_p.IE267del|FANCM_uc010anf.2_In_Frame_Del_p.IE241del NM_020937 NP_065988 Q8IYD8 FANCM_HUMAN Fanconi anemia, complementation group M 267_268 DNA repair Fanconi anaemia nuclear complex ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding ovary(3)|lung(2)|breast(2) 7 CTAATTGGGCAGATAGAGCTTCGTTC 0.330 0.45 86 70 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNU449_LIVER NA SNU449_LIVER NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.50 5 5 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU449_LIVER NA SNU449_LIVER NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 23 198 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU449_LIVER NA SNU449_LIVER NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 43 27 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU449_LIVER NA SNU449_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 44 263 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU449_LIVER NA SNU449_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 5 39 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU466_CENTRAL_NERVOUS_SYSTEM NA SNU466_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 22 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU466_CENTRAL_NERVOUS_SYSTEM NA SNU466_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 244 78 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU466_CENTRAL_NERVOUS_SYSTEM NA SNU466_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.29 61 25 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU466_CENTRAL_NERVOUS_SYSTEM NA SNU466_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.30 57 24 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU466_CENTRAL_NERVOUS_SYSTEM NA SNU466_CENTRAL_NERVOUS_SYSTEM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.36 167 93 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU466_CENTRAL_NERVOUS_SYSTEM NA SNU466_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU466_CENTRAL_NERVOUS_SYSTEM NA SNU466_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU466_CENTRAL_NERVOUS_SYSTEM NA SNU466_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 113 13 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU466_CENTRAL_NERVOUS_SYSTEM NA SNU466_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 3 62 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT SNU466_CENTRAL_NERVOUS_SYSTEM NA SNU466_CENTRAL_NERVOUS_SYSTEM NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.15 299 54 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU466_CENTRAL_NERVOUS_SYSTEM NA SNU466_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.36 27 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU466_CENTRAL_NERVOUS_SYSTEM NA SNU466_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 34 478 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU466_CENTRAL_NERVOUS_SYSTEM NA SNU466_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 68 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 166 66 TGFBR2 7048 broad.mit.edu 37 3 30691871 30691872 + Frame_Shift_Ins INS - A A SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr3:30691871_30691872insA uc003ceo.2 + 3 755_756 c.373_374insA c.(373-375)GAAfs p.E125fs TGFBR2_uc003cen.2_Frame_Shift_Ins_p.E150fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 125 Extracellular (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 CATTATGAAGGAAAAAAAAAAG 0.421 0.71 43 103 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.43 32 24 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.90 1 9 LMTK2 22853 broad.mit.edu 37 7 97784077 97784078 + Frame_Shift_Ins INS - G G SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr7:97784077_97784078insG uc003upd.1 + 5 751_752 c.458_459insG c.(457-459)TTGfs p.L153fs NM_014916 NP_055731 Q8IWU2 LMTK2_HUMAN lemur tyrosine kinase 2 precursor 153 Protein kinase. early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1) 16 all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125) TAGGTTCTCTTGGGAGAGATTT 0.401 0.69 4 9 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.25 61 20 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 1 10 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.65 250 471 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.55 13 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 150 35 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.83 11 54 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.88 2 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 69 306 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU46_UPPER_AERODIGESTIVE_TRACT NA SNU46_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 57 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU475_LIVER NA SNU475_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 67 STK40 83931 broad.mit.edu 37 1 36809835 36809836 + Frame_Shift_Del DEL AT - - SNU475_LIVER NA SNU475_LIVER NA g.chr1:36809835_36809836delAT uc001cak.1 - 9 1176_1177 c.769_770delAT c.(769-771)ATGfs p.M257fs STK40_uc001cal.1_Frame_Shift_Del_p.M262fs|STK40_uc001cam.1_Frame_Shift_Del_p.M257fs|STK40_uc009vva.1_Frame_Shift_Del_p.M257fs|STK40_uc001can.1_Frame_Shift_Del_p.M257fs NM_032017 NP_114406 Q8N2I9 STK40_HUMAN serine/threonine kinase 40 257 Protein kinase. cytoplasm|nucleus ATP binding|protein serine/threonine kinase activity ovary(1) 1 Myeloproliferative disorder(586;0.0393) CAGGGCCCACATGTCACTGGGC 0.624 0.70 72 166 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU475_LIVER NA SNU475_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.39 291 188 MITF 4286 broad.mit.edu 37 3 70014343 70014343 + Frame_Shift_Del DEL A - - SNU475_LIVER NA SNU475_LIVER NA g.chr3:70014343delA uc003dnz.2 + 10 1623 c.1507delA c.(1507-1509)AAAfs p.K503fs MITF_uc011bgb.1_Frame_Shift_Del_p.K451fs|MITF_uc003doa.2_Frame_Shift_Del_p.K502fs|MITF_uc003dob.2_Frame_Shift_Del_p.K487fs|MITF_uc003dod.2_Frame_Shift_Del_p.K478fs|MITF_uc003doe.2_Frame_Shift_Del_p.K396fs|MITF_uc003dof.2_Frame_Shift_Del_p.K402fs NM_198159 NP_937802 O75030 MITF_HUMAN microphthalmia-associated transcription factor 509 melanocyte differentiation|multicellular organismal development|protein complex assembly nucleus|protein complex DNA binding|protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription ovary(2) 2 Lung NSC(201;0.0384)|Prostate(884;0.0526) BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239) CGGAGCTTCCAAAACAAGCAG 0.522 0.50 68 69 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 SNU475_LIVER NA SNU475_LIVER NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.50 5 5 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SNU475_LIVER NA SNU475_LIVER NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 70 19 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU475_LIVER NA SNU475_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 90 113 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU475_LIVER NA SNU475_LIVER NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 30 63 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU475_LIVER NA SNU475_LIVER NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.17 258 54 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU475_LIVER NA SNU475_LIVER NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 2 22 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU475_LIVER NA SNU475_LIVER NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.45 29 24 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU475_LIVER NA SNU475_LIVER NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 67 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU475_LIVER NA SNU475_LIVER NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.64 230 402 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SNU475_LIVER NA SNU475_LIVER NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.93 2 25 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNU475_LIVER NA SNU475_LIVER NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.24 41 13 RPTOR 57521 broad.mit.edu 37 17 78704389 78704390 + Frame_Shift_Ins INS - T T SNU475_LIVER NA SNU475_LIVER NA g.chr17:78704389_78704390insT uc002jyt.1 + 5 1342_1343 c.537_538insT c.(535-540)ATATATfs p.I179fs RPTOR_uc002jys.2_Frame_Shift_Ins_p.I179fs|RPTOR_uc010wuf.1_5'UTR|RPTOR_uc010wug.1_Frame_Shift_Ins_p.I179fs NM_020761 NP_065812 Q8N122 RPTOR_HUMAN raptor isoform 1 179_180 cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade cytosol|lysosome|TORC1 complex protein complex binding lung(4)|urinary_tract(1)|ovary(1) 6 CTCTGTCCATATATGACCTGCA 0.525 0.31 250 113 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU475_LIVER NA SNU475_LIVER NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.34 137 72 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU475_LIVER NA SNU475_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.94 24 402 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU478_BILIARY_TRACT NA SNU478_BILIARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 49 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU478_BILIARY_TRACT NA SNU478_BILIARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.29 240 96 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU478_BILIARY_TRACT NA SNU478_BILIARY_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.52 11 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU478_BILIARY_TRACT NA SNU478_BILIARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.24 68 22 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU478_BILIARY_TRACT NA SNU478_BILIARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 49 24 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU478_BILIARY_TRACT NA SNU478_BILIARY_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.42 23 17 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU478_BILIARY_TRACT NA SNU478_BILIARY_TRACT NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.54 259 298 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU478_BILIARY_TRACT NA SNU478_BILIARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 143 19 TP53 7157 broad.mit.edu 37 17 7577139 7577140 + Frame_Shift_Ins INS - A A rs55832599 SNU478_BILIARY_TRACT NA SNU478_BILIARY_TRACT NA g.chr17:7577139_7577140insA uc002gim.2 - 8 992_993 c.798_799insT c.(796-801)GGACGGfs p.G266fs TP53_uc002gig.1_Intron|TP53_uc002gih.2_Frame_Shift_Ins_p.G266fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Ins_p.G134fs|TP53_uc010cng.1_Frame_Shift_Ins_p.G134fs|TP53_uc002gii.1_Frame_Shift_Ins_p.G134fs|TP53_uc010cnh.1_Frame_Shift_Ins_p.G266fs|TP53_uc010cni.1_Frame_Shift_Ins_p.G266fs|TP53_uc002gij.2_Frame_Shift_Ins_p.G266fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 266_267 |Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). R -> H (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.G266E(45)|p.G266R(42)|p.G266V(31)|p.R267W(20)|p.G266*(12)|p.0?(7)|p.G266fs*79(5)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.G266A(2)|p.G266G(2)|p.G262_S269delGNLLGRNS(2)|p.G266_E271delGRNSFE(2)|p.G266T(1)|p.G266_N268delGRN(1)|p.E258fs*71(1)|p.G266fs*9(1)|p.G262fs*2(1)|p.R267G(1)|p.R267R(1)|p.L265_K305del41(1)|p.L265_R267delLGR(1)|p.G266fs*4(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) AAGCTGTTCCGTCCCAGTAGAT 0.525 1.00 0 12 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU478_BILIARY_TRACT NA SNU478_BILIARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.31 40 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU478_BILIARY_TRACT NA SNU478_BILIARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 39 214 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU478_BILIARY_TRACT NA SNU478_BILIARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.87 15 100 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 29 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 150 58 CDKL4 344387 broad.mit.edu 37 2 39414801 39414802 + Frame_Shift_Ins INS - AA AA SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr2:39414801_39414802insAA uc002rrm.2 - 6 701_702 c.701_702insTT c.(700-702)TTCfs p.F234fs CDKL4_uc010fal.1_Frame_Shift_Ins_p.F234fs NM_001009565 NP_001009565 Q5MAI5 CDKL4_HUMAN cyclin-dependent kinase-like 4 234 Protein kinase. cytoplasm ATP binding|cyclin-dependent protein kinase activity ovary(1) 1 all_hematologic(82;0.248) TGATGCCATGGAAAAACCCGTT 0.327 0.20 57 14 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 1.00 0 13 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.22 64 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.40 12 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.23 54 16 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.62 545 896 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.60 4 6 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 115 13 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 17 219 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.34 25 13 PTGIR 5739 broad.mit.edu 37 19 47124838 47124838 + Frame_Shift_Del DEL A - - SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr19:47124838delA uc002pex.2 - 3 973 c.860delT c.(859-861)CTGfs p.L287fs NM_000960 NP_000951 P43119 PI2R_HUMAN prostaglandin I2 (prostacyclin) receptor (IP) 287 Helical; Name=7; (Potential). cell-cell signaling|G-protein signaling, coupled to cyclic nucleotide second messenger|platelet activation integral to plasma membrane G-protein coupled receptor activity|guanyl-nucleotide exchange factor activity 0 Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212) OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331) Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Epoprostenol(DB01240)|Iloprost(DB01088)|Misoprostol(DB00929) 0.000 1.00 0 13 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.13 111 16 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 153 550 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU489_CENTRAL_NERVOUS_SYSTEM NA SNU489_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 3 21 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU503_LARGE_INTESTINE NA SNU503_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 17 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SNU503_LARGE_INTESTINE NA SNU503_LARGE_INTESTINE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.12 84 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU503_LARGE_INTESTINE NA SNU503_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.32 43 20 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU503_LARGE_INTESTINE NA SNU503_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 18 36 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU503_LARGE_INTESTINE NA SNU503_LARGE_INTESTINE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.67 54 111 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU503_LARGE_INTESTINE NA SNU503_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.92 2 22 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU503_LARGE_INTESTINE NA SNU503_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.58 399 546 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU503_LARGE_INTESTINE NA SNU503_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 73 21 DICER1 23405 broad.mit.edu 37 14 95557586 95557587 + Frame_Shift_Ins INS - A A SNU503_LARGE_INTESTINE NA SNU503_LARGE_INTESTINE NA g.chr14:95557586_95557587insA uc001ydw.2 - 26 5662_5663 c.5480_5481insT c.(5479-5481)CTGfs p.L1827fs DICER1_uc010avh.1_Frame_Shift_Ins_p.L725fs|DICER1_uc001ydv.2_Frame_Shift_Ins_p.L1817fs|DICER1_uc001ydx.2_Frame_Shift_Ins_p.L1827fs NM_030621 NP_085124 Q9UPY3 DICER_HUMAN dicer1 1827 negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference cytosol|RNA-induced silencing complex ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity skin(2)|ovary(1)|pancreas(1)|lung(1) 5 all_cancers(154;0.0621)|all_epithelial(191;0.223) Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215) AGACTGTCTCCAGTGACATCCC 0.431 0.18 146 33 ZNF668 79759 broad.mit.edu 37 16 31073447 31073447 + Frame_Shift_Del DEL G - - SNU503_LARGE_INTESTINE NA SNU503_LARGE_INTESTINE NA g.chr16:31073447delG uc010caf.2 - 3 1159 c.802delC c.(802-804)CAGfs p.Q268fs ZNF668_uc002eao.2_Frame_Shift_Del_p.Q268fs NM_024706 NP_078982 Q96K58 ZN668_HUMAN zinc finger protein 668 268 C2H2-type 8. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(4) 4 0.000 0.28 1027 405 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU503_LARGE_INTESTINE NA SNU503_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.62 12 20 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU503_LARGE_INTESTINE NA SNU503_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 76 234 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU503_LARGE_INTESTINE NA SNU503_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 5 57 MED12 9968 broad.mit.edu 37 X 70360647 70360648 + In_Frame_Ins INS - CAG CAG SNU520_STOMACH NA SNU520_STOMACH NA g.chrX:70360647_70360648insCAG uc004dyy.2 + 42 6406_6407 c.6207_6208insCAG c.(6205-6210)insCAG p.2076_2077insQ MED12_uc004dyz.2_In_Frame_Ins_p.2075_2076insQ|MED12_uc004dza.2_In_Frame_Ins_p.1926_1927insQ|MED12_uc010nla.2_In_Frame_Ins_p.705_706insQ NM_005120 NP_005111 Q93074 MED12_HUMAN mediator complex subunit 12 2076_2077 Gln-rich. androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter mediator complex ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding ovary(1)|breast(1)|central_nervous_system(1)|skin(1) 4 Renal(35;0.156) agcaacagcaacagcagcagca 0.287 0.16 46 9 TAF1 6872 broad.mit.edu 37 X 70608152 70608152 + Frame_Shift_Del DEL A - - SNU520_STOMACH NA SNU520_STOMACH NA g.chrX:70608152delA uc004dzu.3 + 16 2541 c.2490delA c.(2488-2490)ATAfs p.I830fs BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Frame_Shift_Del_p.I851fs|TAF1_uc004dzv.3_Frame_Shift_Del_p.I4fs NM_138923 NP_620278 P21675 TAF1_HUMAN TBP-associated factor 1 isoform 2 830 G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction MLL1 complex|transcription factor TFIID complex ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1) 17 Renal(35;0.156) all_lung(315;0.000321) TGGAAGATATAAAAAAAGCCT 0.423 0.51 63 66 ATRX 546 broad.mit.edu 37 X 76778785 76778787 + In_Frame_Del DEL TCT - - SNU520_STOMACH NA SNU520_STOMACH NA g.chrX:76778785_76778787delTCT uc004ecp.3 - 31 7024_7026 c.6792_6794delAGA c.(6790-6795)GAAGAG>GAG p.2264_2265EE>E ATRX_uc004ecq.3_In_Frame_Del_p.2226_2227EE>E|ATRX_uc004eco.3_In_Frame_Del_p.2049_2050EE>E NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 2264_2265 Poly-Glu. DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) TTCAGTCAACTCTTCTTCTTCTT 0.369 0.41 149 104 Unknown 0 broad.mit.edu 37 X 80185321 80185321 + Frame_Shift_Del DEL A - - SNU520_STOMACH NA SNU520_STOMACH NA g.chrX:80185321delA uc004eec.1 + 1 394 c.220delA c.(220-222)AAAfs p.K74fs SubName: Full=cDNA FLJ16670 fis, clone THYMU3001133, highly similar to Voltage-dependent anion-selective channel protein 1; SubName: Full=Voltage-dependent anion channel 1, isoform CRA_a; TAACACTGGGAAAAAAAATGC 0.483 0.45 101 82 NRK 203447 broad.mit.edu 37 X 105179250 105179251 + Frame_Shift_Ins INS - A A SNU520_STOMACH NA SNU520_STOMACH NA g.chrX:105179250_105179251insA uc004emd.2 + 21 3891_3892 c.3588_3589insA c.(3586-3591)TGTAAAfs p.C1196fs NRK_uc010npc.1_Frame_Shift_Ins_p.C864fs NM_198465 NP_940867 Q7Z2Y5 NRK_HUMAN Nik related kinase 1196_1197 ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1) 14 CTCCTGCATGTAAAAAACCACT 0.391 0.41 97 68 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU520_STOMACH NA SNU520_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 3 50 PIK3CD 5293 broad.mit.edu 37 1 9778839 9778839 + Frame_Shift_Del DEL G - - rs143521812 byFrequency SNU520_STOMACH NA SNU520_STOMACH NA g.chr1:9778839delG uc001aqb.3 + 9 1316 c.1108delG c.(1108-1110)GTGfs p.V370fs PIK3CD_uc010oaf.1_Frame_Shift_Del_p.V370fs|PIK3CD_uc001aqe.3_Frame_Shift_Del_p.V335fs NM_005026 NP_005017 O00329 PK3CD_HUMAN catalytic phosphatidylinositol 3-kinase delta 370 phosphatidylinositol-mediated signaling|protein phosphorylation phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding lung(4)|skin(2)|central_nervous_system(1) 7 all_lung(157;0.222) all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419) CTCGGAGCCCGTGTGGAAGCA 0.617 0.43 13 10 CLSPN 63967 broad.mit.edu 37 1 36208777 36208779 + In_Frame_Del DEL TTC - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr1:36208777_36208779delTTC uc001bzi.2 - 18 3186_3188 c.3106_3108delGAA c.(3106-3108)GAAdel p.E1036del CLSPN_uc009vux.2_In_Frame_Del_p.E972del NM_022111 NP_071394 Q9HAW4 CLSPN_HUMAN claspin 1036 activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation nucleoplasm anaphase-promoting complex binding|DNA binding breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1) 8 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887) 0.000 0.41 708 499 CLSPN 63967 broad.mit.edu 37 1 36226311 36226311 + Frame_Shift_Del DEL T - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr1:36226311delT uc001bzi.2 - 8 1291 c.1211delA c.(1210-1212)AATfs p.N404fs CLSPN_uc009vux.2_Frame_Shift_Del_p.N404fs NM_022111 NP_071394 Q9HAW4 CLSPN_HUMAN claspin 404 activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation nucleoplasm anaphase-promoting complex binding|DNA binding breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1) 8 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887) 0.000 0.43 803 603 HSP90B3P 343477 broad.mit.edu 37 1 92108916 92108916 + Frame_Shift_Del DEL A - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr1:92108916delA uc010osx.1 + 3 943 c.943delA c.(943-945)AAAfs p.K315fs NR_003130 SubName: Full=cDNA FLJ58812, highly similar to Endoplasmin (Heat shock protein 90kDa beta member 1); 0 ACGACTTCTGAAAAAGGGCTG 0.433 0.42 145 104 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 274 73 PTPRC 5788 broad.mit.edu 37 1 198723446 198723449 + Frame_Shift_Del DEL AGAA - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr1:198723446_198723449delAGAA uc001gur.1 + 32 3732_3735 c.3552_3555delAGAA c.(3550-3555)TTAGAAfs p.L1184fs PTPRC_uc001gus.1_Frame_Shift_Del_p.L1136fs|PTPRC_uc001gut.1_Frame_Shift_Del_p.L1023fs NM_002838 NP_002829 P08575 PTPRC_HUMAN protein tyrosine phosphatase, receptor type, C 1184_1185 Tyrosine-protein phosphatase 2.|Cytoplasmic (Potential). axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway focal adhesion|integral to plasma membrane|membrane raft protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1) 12 TAAATCTCTTAGAAAGTGCGGAAA 0.387 0.34 64 33 CAD 790 broad.mit.edu 37 2 27464212 27464213 + Frame_Shift_Del DEL CA - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr2:27464212_27464213delCA uc002rji.2 + 38 5993_5994 c.5831_5832delCA c.(5830-5832)GCAfs p.A1944fs CAD_uc010eyw.2_Frame_Shift_Del_p.A1881fs NM_004341 NP_004332 P27708 PYR1_HUMAN carbamoylphosphate synthetase 2/aspartate 1944 ATCase (Aspartate transcarbamylase). 'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process cytosol|neuronal cell body|nuclear matrix|terminal button aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1) 10 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) L-Aspartic Acid(DB00128)|L-Glutamine(DB00130) TTCAATGTGGCACACACACTGC 0.569 0.56 12 15 BIRC6 57448 broad.mit.edu 37 2 32820101 32820101 + Frame_Shift_Del DEL A - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr2:32820101delA uc010ezu.2 + 68 13636 c.13502delA c.(13501-13503)GAAfs p.E4501fs NM_016252 NP_057336 Q9NR09 BIRC6_HUMAN baculoviral IAP repeat-containing 6 4501 anti-apoptosis|apoptosis intracellular acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1) 14 Acute lymphoblastic leukemia(172;0.155) taaataaCAGAAAAAAAACTG 0.244 0.58 15 21 BCL11A 53335 broad.mit.edu 37 2 60688969 60688969 + Frame_Shift_Del DEL G - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr2:60688969delG uc002sae.1 - 4 1306 c.1078delC c.(1078-1080)CTCfs p.L360fs BCL11A_uc002sab.2_Frame_Shift_Del_p.L360fs|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Frame_Shift_Del_p.L326fs|BCL11A_uc002sad.1_Frame_Shift_Del_p.L208fs|BCL11A_uc002saf.1_Frame_Shift_Del_p.L326fs NM_022893 NP_075044 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A isoform 1 360 Pro-rich. negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|cytoplasm|nucleus|nucleus nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding central_nervous_system(6)|breast(3)|ovary(2)|skin(2) 13 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) 0.000 0.50 620 613 MAP3K2 10746 broad.mit.edu 37 2 128096511 128096511 + Frame_Shift_Del DEL T - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr2:128096511delT uc002toj.1 - 2 185 c.120delA c.(118-120)AAAfs p.K40fs MAP3K2_uc010flz.1_Frame_Shift_Del_p.K40fs NM_006609 NP_006600 Q9Y2U5 M3K2_HUMAN mitogen-activated protein kinase kinase kinase 40 activation of JUN kinase activity|cellular response to mechanical stimulus nucleus ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein kinase binding lung(3)|ovary(2)|large_intestine(1)|central_nervous_system(1) 7 Colorectal(110;0.1) BRCA - Breast invasive adenocarcinoma(221;0.0706) TAAATACCTGTTTTTTTGGTG 0.333 0.49 19 18 RIF1 55183 broad.mit.edu 37 2 152321320 152321320 + Frame_Shift_Del DEL A - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr2:152321320delA uc002txm.2 + 30 5416 c.5286delA c.(5284-5286)ACAfs p.T1762fs RIF1_uc002txl.2_Frame_Shift_Del_p.T1762fs|RIF1_uc002txn.2_Frame_Shift_Del_p.T1762fs|RIF1_uc002txo.2_Frame_Shift_Del_p.T1762fs|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1762 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) TTAGTGAAACAAAAAAGGCAG 0.368 0.41 59 41 TTN 7273 broad.mit.edu 37 2 179597825 179597826 + Frame_Shift_Ins INS - A A SNU520_STOMACH NA SNU520_STOMACH NA g.chr2:179597825_179597826insA uc010zfg.1 - 52 12569_12570 c.12345_12346insT c.(12343-12348)TTTACCfs p.F4115fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Ins_p.F776fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 5042_5043 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AAGGGTTTGGTAAAAAATGGAG 0.460 0.43 136 101 HDAC4 9759 broad.mit.edu 37 2 240002823 240002823 + Frame_Shift_Del DEL G - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr2:240002823delG uc002vyk.3 - 22 3495 c.2703delC c.(2701-2703)CCCfs p.P901fs HDAC4_uc010fyy.2_Frame_Shift_Del_p.P858fs NM_006037 NP_006028 P56524 HDAC4_HUMAN histone deacetylase 4 901 Histone deacetylase. B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent histone deacetylase complex|transcriptional repressor complex activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding breast(3)|skin(2)|ovary(1) 6 all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159) Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04) CGTCTCCCATGGGGGGGTCCA 0.602 0.33 12 6 PDCD1 5133 broad.mit.edu 37 2 242794819 242794819 + Frame_Shift_Del DEL G - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr2:242794819delG uc002wcq.3 - 2 458 c.390delC c.(388-390)CCCfs p.P130fs PDCD1_uc010fzs.2_Frame_Shift_Del_p.P61fs|PDCD1_uc010fzt.2_Intron NM_005018 NP_005009 Q15116 PDCD1_HUMAN programmed cell death 1 precursor 130 Ig-like V-type.|Extracellular (Potential). apoptosis|humoral immune response|multicellular organismal development|T cell costimulation integral to membrane protein tyrosine phosphatase activity|signal transducer activity ovary(1) 1 all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0219) TCTGCGCCTTGGGGGCCAGGG 0.687 0.38 20 12 ULK4 54986 broad.mit.edu 37 3 41860984 41860985 + Frame_Shift_Ins INS - T T SNU520_STOMACH NA SNU520_STOMACH NA g.chr3:41860984_41860985insT uc003ckv.3 - 19 1979_1980 c.1778_1779insA c.(1777-1779)AAGfs p.K593fs ULK4_uc003ckw.2_Frame_Shift_Ins_p.K593fs NM_017886 NP_060356 Q96C45 ULK4_HUMAN unc-51-like kinase 4 593 ATP binding|protein serine/threonine kinase activity 0 KIRC - Kidney renal clear cell carcinoma(284;0.214) CTCTAGGGTTCTTTTTTTTTTC 0.450 0.35 49 26 CXCL9 4283 broad.mit.edu 37 4 76924817 76924817 + Frame_Shift_Del DEL T - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr4:76924817delT uc003hjh.1 - 4 351 c.312delA c.(310-312)AAAfs p.K104fs NM_002416 NP_002407 Q07325 CXCL9_HUMAN small inducible cytokine B9 precursor 104 cell-cell signaling|cellular defense response|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response extracellular space chemokine activity p.K104N(1) ovary(1) 1 Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934) TTTTTTGATGTTTTTTCCCAT 0.338 0.51 91 94 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU520_STOMACH NA SNU520_STOMACH NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.16 41 8 ALPK1 80216 broad.mit.edu 37 4 113360940 113360941 + Frame_Shift_Del DEL AG - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr4:113360940_113360941delAG uc003iap.3 + 14 3729_3730 c.3450_3451delAG c.(3448-3453)ACAGAAfs p.T1150fs ALPK1_uc003ian.3_Frame_Shift_Del_p.T1150fs|ALPK1_uc011cfx.1_Frame_Shift_Del_p.T1072fs|ALPK1_uc003iao.3_RNA|ALPK1_uc010imo.2_Frame_Shift_Del_p.T978fs NM_025144 NP_079420 Q96QP1 ALPK1_HUMAN alpha-kinase 1 1150_1151 Alpha-type protein kinase. ATP binding|protein serine/threonine kinase activity ovary(5) 5 Ovarian(17;0.0446)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.00325) TGGTGAAAACAGAATACAAAGC 0.366 0.49 21 20 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU520_STOMACH NA SNU520_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.33 79 39 INPP4B 8821 broad.mit.edu 37 4 143007332 143007332 + Frame_Shift_Del DEL T - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr4:143007332delT uc003iix.3 - 25 3047 c.2452delA c.(2452-2454)AGAfs p.R818fs INPP4B_uc003iiw.3_Frame_Shift_Del_p.R818fs|INPP4B_uc011chm.1_RNA|INPP4B_uc011chn.1_Frame_Shift_Del_p.R633fs|INPP4B_uc011cho.1_RNA NM_003866 NP_003857 O15327 INP4B_HUMAN inositol polyphosphate-4-phosphatase, type II, 818 signal transduction phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity ovary(1)|lung(1) 2 all_hematologic(180;0.158) ACATTCTTTCTTTTTTTGGAT 0.343 0.47 52 47 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes SNU520_STOMACH NA SNU520_STOMACH NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.48 315 296 NIPBL 25836 broad.mit.edu 37 5 36985083 36985084 + Frame_Shift_Del DEL AA - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr5:36985083_36985084delAA uc003jkl.3 + 10 2300_2301 c.1801_1802delAA c.(1801-1803)AAAfs p.K601fs NIPBL_uc003jkk.3_Frame_Shift_Del_p.K601fs|NIPBL_uc003jkm.1_Frame_Shift_Del_p.K480fs NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 601 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) TGAGACACCTAAAAAAAAGTCT 0.351 0.49 58 56 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU520_STOMACH NA SNU520_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 46 23 ICK 22858 broad.mit.edu 37 6 52878617 52878618 + Frame_Shift_Ins INS - GT GT SNU520_STOMACH NA SNU520_STOMACH NA g.chr6:52878617_52878618insGT uc003pbh.2 - 10 1484_1485 c.994_995insAC c.(994-996)CGAfs p.R332fs ICK_uc003pbi.2_Frame_Shift_Ins_p.R332fs NM_016513 NP_057597 Q9UPZ9 ICK_HUMAN intestinal cell kinase 332 intracellular protein kinase cascade|multicellular organismal development cytosol|nucleus ATP binding|cyclin-dependent protein kinase activity|magnesium ion binding ovary(1)|large_intestine(1)|lung(1)|kidney(1)|central_nervous_system(1) 5 Lung NSC(77;0.103) TGAAGAAATTCGTGTGTGTGGC 0.550 0.41 79 54 MAP3K4 4216 broad.mit.edu 37 6 161519382 161519384 + In_Frame_Del DEL TGT - - rs139506196 SNU520_STOMACH NA SNU520_STOMACH NA g.chr6:161519382_161519384delTGT uc003qtn.2 + 17 3739_3741 c.3597_3599delTGT c.(3595-3600)GCTGTT>GCT p.V1200del MAP3K4_uc010kkc.1_In_Frame_Del_p.V1196del|MAP3K4_uc003qto.2_Intron|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_In_Frame_Del_p.V653del|MAP3K4_uc003qtp.2_Intron|MAP3K4_uc003qtq.2_5'Flank NM_005922 NP_005913 Q9Y6R4 M3K4_HUMAN mitogen-activated protein kinase kinase kinase 4 1200 Poly-Ala. activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity perinuclear region of cytoplasm ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding ovary(3)|lung(3)|skin(2)|stomach(1) 9 Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771) OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05) ctgctgctgctgttgctgcCAGT 0.483 0.31 9 4 NEUROD6 63974 broad.mit.edu 37 7 31378635 31378635 + Frame_Shift_Del DEL T - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr7:31378635delT uc003tch.2 - 2 601 c.248delA c.(247-249)AAGfs p.K83fs NM_022728 NP_073565 Q96NK8 NDF6_HUMAN neurogenic differentiation 6 83 Nuclear localization signal (Potential). cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding ovary(2) 2 CTTTGTTGTCTTTTTTTTCCT 0.398 0.42 7 5 EZH2 2146 broad.mit.edu 37 7 148512120 148512121 + Frame_Shift_Del DEL TA - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr7:148512120_148512121delTA uc003wfd.1 - 14 1708_1709 c.1542_1543delTA c.(1540-1545)TCTAACfs p.S514fs EZH2_uc011kug.1_Intron|EZH2_uc003wfb.1_Frame_Shift_Del_p.S519fs|EZH2_uc003wfc.1_Frame_Shift_Del_p.S475fs|EZH2_uc011kuh.1_Frame_Shift_Del_p.S505fs NM_004456 NP_004447 Q15910 EZH2_HUMAN enhancer of zeste 2 isoform a 514_515 negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent ESC/E(Z) complex DNA binding|histone-lysine N-methyltransferase activity|protein binding haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1) 183 Melanoma(164;0.15) OV - Ovarian serous cystadenocarcinoma(82;0.00239) 0.000 0.16 2357 449 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU520_STOMACH NA SNU520_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.93 2 25 MLL3 58508 broad.mit.edu 37 7 151875096 151875097 + Splice_Site INS - TT TT SNU520_STOMACH NA SNU520_STOMACH NA g.chr7:151875096_151875097insTT uc003wla.2 - 38 7662 c.7443_splice c.e38-1 p.R2481_splice MLL3_uc003wkz.2_Splice_Site_p.R1542_splice|MLL3_uc003wky.2_Splice_Site NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) AAATCCAAATCTTTTaaaaaaa 0.332 0.25 103 35 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.69 18 40 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU520_STOMACH NA SNU520_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 11 FANCG 2189 broad.mit.edu 37 9 35078272 35078273 + In_Frame_Ins INS - GAC GAC SNU520_STOMACH NA SNU520_STOMACH NA g.chr9:35078272_35078273insGAC uc003zwb.1 - 4 867_868 c.375_376insGTC c.(373-378)insGTC p.125_126insV FANCG_uc003zwa.1_5'Flank|FANCG_uc010mkj.1_Intron|FANCG_uc011lot.1_In_Frame_Ins_p.125_126insV NM_004629 NP_004620 O15287 FANCG_HUMAN Fanconi anemia, complementation group G 125_126 cell cycle checkpoint|DNA repair|mitochondrion organization mitochondrion|nucleoplasm damaged DNA binding|protein binding ovary(2)|large_intestine(1)|lung(1) 4 LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778) GAAGCACGAAGGACAGAGTCCC 0.614 0.38 8 5 PIP5K1B 8395 broad.mit.edu 37 9 71509431 71509432 + Frame_Shift_Del DEL AG - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr9:71509431_71509432delAG uc004agu.2 + 8 953_954 c.648_649delAG c.(646-651)AAAGAGfs p.K216fs PIP5K1B_uc011lrq.1_Frame_Shift_Del_p.K216fs|PIP5K1B_uc004agv.2_RNA NM_003558 NP_003549 O14986 PI51B_HUMAN phosphatidylinositol-4-phosphate 5-kinase, type 216_217 PIPK. endomembrane system|membrane|uropod 1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding stomach(1) 1 Lung(182;0.133) CATCCCGTAAAGAGAGAGAGAA 0.426 0.43 177 133 MLLT10 8028 broad.mit.edu 37 10 21962452 21962452 + Frame_Shift_Del DEL G - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr10:21962452delG uc001iqs.2 + 11 1573 c.1225delG c.(1225-1227)GGGfs p.G409fs MLLT10_uc001iqt.2_Frame_Shift_Del_p.G409fs|MLLT10_uc001iqv.2_RNA|MLLT10_uc001iqy.2_Frame_Shift_Del_p.G409fs|MLLT10_uc001ira.2_Intron|MLLT10_uc001irb.2_5'Flank|MLLT10_uc001iqz.2_Frame_Shift_Del_p.G164fs NM_004641 NP_004632 P55197 AF10_HUMAN myeloid/lymphoid or mixed-lineage leukemia 409 DNA-binding. positive regulation of transcription from RNA polymerase II promoter cytoplasm|nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding lung(1)|skin(1) 2 AAGCCAGGAAGGGGGGGTAAA 0.438 0.25 288 96 PTEN 5728 broad.mit.edu 37 10 89717770 89717770 + Frame_Shift_Del DEL A - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr10:89717770delA uc001kfb.2 + 8 1826 c.795delA c.(793-795)CTAfs p.L265fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 265 C2 tensin-type. KMLKKDK->AAGAADA: Reduces the growth suppression activity and cells show anchorage-independent growth. Reduces binding to phospholipid membranes in vitro. Phosphatase activity towards PtdIns(3,4,5)P3 is not affected. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.K267fs*9(4)|p.R55fs*1(4)|p.N212fs*1(2)|p.Y27fs*1(2)|p.M264fs*8(2)|p.G165_*404del(1)|p.?(1)|p.G165_K342del(1)|p.D268fs*30(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) ACAAGATGCTAAAAAAGGTTT 0.348 0.89 22 178 NUMA1 4926 broad.mit.edu 37 11 71746965 71746965 + Frame_Shift_Del DEL C - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr11:71746965delC uc001orl.1 - 3 197 c.25delG c.(25-27)GCTfs p.A9fs NUMA1_uc001ork.1_Frame_Shift_Del_p.A9fs|NUMA1_uc001orm.1_Frame_Shift_Del_p.A9fs|NUMA1_uc009ysx.1_Frame_Shift_Del_p.A9fs|NUMA1_uc001oro.1_Frame_Shift_Del_p.A9fs|NUMA1_uc009ysy.1_Frame_Shift_Del_p.A9fs|NUMA1_uc001orp.2_Frame_Shift_Del_p.A9fs|NUMA1_uc001orq.2_Frame_Shift_Del_p.A9fs NM_006185 NP_006176 Q14980 NUMA1_HUMAN nuclear mitotic apparatus protein 1 9 G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole protein binding|structural molecule activity ovary(3)|lung(2)|skin(2)|central_nervous_system(1) 8 AGGAGTGCAGCCCCCCGGGTG 0.502 0.41 67 47 ATM 472 broad.mit.edu 37 11 108164164 108164164 + Frame_Shift_Del DEL A - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr11:108164164delA uc001pkb.1 + 31 5121 c.4736delA c.(4735-4737)CAAfs p.Q1579fs ATM_uc009yxr.1_Frame_Shift_Del_p.Q1579fs|ATM_uc001pke.1_Frame_Shift_Del_p.Q231fs|ATM_uc001pkf.2_Intron NM_000051 NP_000042 Q13315 ATM_HUMAN ataxia telangiectasia mutated isoform 1 1579 cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence cytoplasmic membrane-bounded vesicle|nucleoplasm 1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1) 240 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147) ATTACTCAGCAAAAAATCAAA 0.303 0.42 80 59 WNT1 7471 broad.mit.edu 37 12 49374348 49374348 + Frame_Shift_Del DEL G - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr12:49374348delG uc001rsu.2 + 3 698 c.500delG c.(499-501)TGGfs p.W167fs NM_005430 NP_005421 P04628 WNT1_HUMAN wingless-type MMTV integration site family, 167 brain segmentation|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|central nervous system morphogenesis|cerebellum formation|dermatome development|diencephalon development|embryonic axis specification|forebrain anterior/posterior pattern formation|fourth ventricle development|hemopoietic stem cell proliferation|hepatocyte differentiation|inner ear morphogenesis|mesoderm morphogenesis|midbrain development|midbrain-hindbrain boundary maturation during brain development|negative regulation of cell-cell adhesion|negative regulation of cell-substrate adhesion|negative regulation of DNA damage checkpoint|negative regulation of fat cell differentiation|neuron fate determination|positive regulation of fibroblast proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of lamellipodium assembly|positive regulation of Notch signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to wounding|signal transduction in response to DNA damage|Spemann organizer formation|T cell differentiation in thymus|Wnt receptor signaling pathway, calcium modulating pathway early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix cytokine activity|frizzled-2 binding|transcription regulatory region DNA binding kidney(1) 1 BRCA - Breast invasive adenocarcinoma(357;0.244) gACTGGCACTGGGGGGGCTGC 0.552 0.33 12 6 UBE3B 89910 broad.mit.edu 37 12 109939222 109939223 + Frame_Shift_Ins INS - G G SNU520_STOMACH NA SNU520_STOMACH NA g.chr12:109939222_109939223insG uc001top.2 + 13 1768_1769 c.1165_1166insG c.(1165-1167)TGGfs p.W389fs UBE3B_uc001toq.2_Frame_Shift_Ins_p.W389fs|UBE3B_uc001too.1_RNA|UBE3B_uc009zvj.1_Frame_Shift_Ins_p.W389fs NM_130466 NP_569733 Q7Z3V4 UBE3B_HUMAN ubiquitin protein ligase E3B 389 protein ubiquitination involved in ubiquitin-dependent protein catabolic process intracellular ubiquitin-protein ligase activity ovary(2)|lung(2) 4 GCAGTTCTTGTGGGGGGTGCCT 0.554 0.37 96 57 EDNRB 1910 broad.mit.edu 37 13 78475267 78475267 + Frame_Shift_Del DEL A - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr13:78475267delA uc001vko.2 - 4 1135 c.877delT c.(877-879)TATfs p.Y293fs EDNRB_uc001vkq.1_Frame_Shift_Del_p.Y293fs|uc001vkn.1_Intron|EDNRB_uc010aez.1_Frame_Shift_Del_p.Y293fs|EDNRB_uc001vkp.1_Frame_Shift_Del_p.Y376fs NM_001122659 NP_001116131 P24530 EDNRB_HUMAN endothelin receptor type B isoform 1 precursor 293 Helical; Name=5; (Potential). activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction integral to plasma membrane endothelin-B receptor activity|peptide hormone binding 0 Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037) GBM - Glioblastoma multiforme(99;0.0933) Bosentan(DB00559) ATTAGTGTATAAAAAAATGCA 0.343 0.43 102 76 KTN1 3895 broad.mit.edu 37 14 56137475 56137475 + Frame_Shift_Del DEL A - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr14:56137475delA uc001xcb.2 + 36 3598 c.3296delA c.(3295-3297)GAAfs p.E1099fs KTN1_uc001xce.2_Frame_Shift_Del_p.E1070fs|KTN1_uc001xcc.2_Frame_Shift_Del_p.E1099fs|KTN1_uc001xcd.2_Frame_Shift_Del_p.E1076fs|KTN1_uc010trb.1_Frame_Shift_Del_p.E1099fs|KTN1_uc001xcf.1_Frame_Shift_Del_p.E1076fs|KTN1_uc010aoq.2_Frame_Shift_Del_p.E365fs|KTN1_uc010trc.1_Frame_Shift_Del_p.E104fs|KTN1_uc001xcg.2_Frame_Shift_Del_p.E60fs NM_182926 NP_891556 Q86UP2 KTN1_HUMAN kinectin 1 isoform a 1099 Lumenal (Potential).|Potential. microtubule-based movement endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction breast(3)|ovary(2)|lung(1)|central_nervous_system(1) 7 CATGGATTTGAAAAAAAGGCA 0.318 0.50 111 109 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU520_STOMACH NA SNU520_STOMACH NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 49 455 CBFA2T3 863 broad.mit.edu 37 16 88967982 88967982 + Frame_Shift_Del DEL G - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr16:88967982delG uc002fmm.1 - 2 420 c.234delC c.(232-234)CCCfs p.P78fs CBFA2T3_uc002fml.1_Frame_Shift_Del_p.P17fs|CBFA2T3_uc010cif.1_Frame_Shift_Del_p.P17fs|CBFA2T3_uc002fmn.1_Frame_Shift_Del_p.P78fs NM_005187 NP_005178 O75081 MTG16_HUMAN myeloid translocation gene on chromosome 16 78 Mediates localization to the nucleus (By similarity).|Pro-rich.|Mediates interaction with PDE7A (in isoform 2).|Required for nucleolar targeting (in isoform 1). cell proliferation|granulocyte differentiation Golgi membrane|nucleolus|nucleoplasm protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding large_intestine(3)|ovary(1) 4 BRCA - Breast invasive adenocarcinoma(80;0.0275) 0.000 0.47 462 413 AATK 9625 broad.mit.edu 37 17 79094046 79094048 + In_Frame_Del DEL CTT - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr17:79094046_79094048delCTT uc010dia.2 - 11 3768_3770 c.3688_3690delAAG c.(3688-3690)AAGdel p.K1230del AATK_uc010dhz.2_RNA NM_001080395 NP_001073864 Q6ZMQ8 LMTK1_HUMAN apoptosis-associated tyrosine kinase 1230 integral to membrane|mitochondrion|perinuclear region of cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1) 9 all_neural(118;0.101) BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524) AGGACACGGCCTTCTTCTTGCGT 0.680 0.56 16 20 HCK 3055 broad.mit.edu 37 20 30674527 30674528 + Frame_Shift_Del DEL CT - - SNU520_STOMACH NA SNU520_STOMACH NA g.chr20:30674527_30674528delCT uc002wxh.2 + 9 1103_1104 c.932_933delCT c.(931-933)ACTfs p.T311fs HCK_uc010gdy.2_Frame_Shift_Del_p.T290fs|HCK_uc002wxi.2_Frame_Shift_Del_p.T289fs NM_002110 NP_002101 P08631 HCK_HUMAN hemopoietic cell kinase isoform p61HCK 311 Protein kinase. interspecies interaction between organisms|mesoderm development|regulation of defense response to virus by virus|viral reproduction caveola|cytosol ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(4)|ovary(2)|central_nervous_system(2)|pancreas(1) 9 UCEC - Uterine corpus endometrioid carcinoma (5;0.0241) GTGATGAAAACTCTGCAGCATG 0.564 0.38 31 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU520_STOMACH NA SNU520_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 280 962 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU520_STOMACH NA SNU520_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 71 CHEK2 11200 broad.mit.edu 37 22 29095888 29095889 + Frame_Shift_Ins INS - C C SNU520_STOMACH NA SNU520_STOMACH NA g.chr22:29095888_29095889insC uc003adu.1 - 9 1017_1018 c.945_946insG c.(943-948)GGGAATfs p.G315fs CHEK2_uc003ads.1_Frame_Shift_Ins_p.G94fs|CHEK2_uc010gvh.1_Frame_Shift_Ins_p.G224fs|CHEK2_uc010gvi.1_Frame_Shift_Ins_p.G315fs|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_RNA|CHEK2_uc010gvk.1_RNA|CHEK2_uc003adt.1_Frame_Shift_Ins_p.G358fs|CHEK2_uc003adv.1_Frame_Shift_Ins_p.G315fs|CHEK2_uc003adw.1_Frame_Shift_Ins_p.G315fs|CHEK2_uc003adx.1_Frame_Shift_Ins_p.G94fs|CHEK2_uc003ady.1_Frame_Shift_Ins_p.G315fs|CHEK2_uc003adz.1_Frame_Shift_Ins_p.G119fs NM_007194 NP_009125 O96017 CHK2_HUMAN protein kinase CHK2 isoform a 315_316 Protein kinase. cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence PML body ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(17)|stomach(1)|ovary(1)|lung(1) 20 AGGCGTTTATTCCCCACCACTT 0.480 0.46 76 65 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU5_STOMACH NA SNU5_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 31 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes SNU5_STOMACH NA SNU5_STOMACH NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.50 6 6 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SNU5_STOMACH NA SNU5_STOMACH NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.36 9 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU5_STOMACH NA SNU5_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 183 234 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU5_STOMACH NA SNU5_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 42 81 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU5_STOMACH NA SNU5_STOMACH NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.53 113 127 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU5_STOMACH NA SNU5_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 11 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU5_STOMACH NA SNU5_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 2 42 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU5_STOMACH NA SNU5_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.62 153 250 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU5_STOMACH NA SNU5_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 403 170 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNU5_STOMACH NA SNU5_STOMACH NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.62 6 10 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes SNU5_STOMACH NA SNU5_STOMACH NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.14 148 24 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU5_STOMACH NA SNU5_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 27 74 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU5_STOMACH NA SNU5_STOMACH NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.28 58 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU5_STOMACH NA SNU5_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 50 278 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU5_STOMACH NA SNU5_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 68 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU601_STOMACH NA SNU601_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 60 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU601_STOMACH NA SNU601_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 227 76 RIF1 55183 broad.mit.edu 37 2 152320713 152320715 + In_Frame_Del DEL AAG - - SNU601_STOMACH NA SNU601_STOMACH NA g.chr2:152320713_152320715delAAG uc002txm.2 + 30 4809_4811 c.4679_4681delAAG c.(4678-4683)AAAGAA>AAA p.E1562del RIF1_uc002txl.2_In_Frame_Del_p.E1562del|RIF1_uc002txn.2_In_Frame_Del_p.E1562del|RIF1_uc002txo.2_In_Frame_Del_p.E1562del|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1562 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) TCGGAGGCAAAAGAAGAAGGTTC 0.404 0.43 45 34 TTN 7273 broad.mit.edu 37 2 179440920 179440922 + In_Frame_Del DEL GTT - - SNU601_STOMACH NA SNU601_STOMACH NA g.chr2:179440920_179440922delGTT uc010zfg.1 - 275 62457_62459 c.62233_62235delAAC c.(62233-62235)AACdel p.N20745del uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.N14440del|TTN_uc010zfi.1_In_Frame_Del_p.N14373del|TTN_uc010zfj.1_In_Frame_Del_p.N14248del|uc002umv.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 21672 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TGATTCTGAAGTTGTATTTTTCT 0.458 0.55 27 33 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU601_STOMACH NA SNU601_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.30 97 42 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU601_STOMACH NA SNU601_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.30 45 19 MAP3K4 4216 broad.mit.edu 37 6 161513056 161513066 + Frame_Shift_Del DEL TGTTCGTTTGA - - SNU601_STOMACH NA SNU601_STOMACH NA g.chr6:161513056_161513066delTGTTCGTTTGA uc003qtn.2 + 13 3292_3302 c.3150_3160delTGTTCGTTTGA c.(3148-3162)GTTGTTCGTTTGATGfs p.V1050fs MAP3K4_uc010kkc.1_Frame_Shift_Del_p.V1050fs|MAP3K4_uc003qto.2_Frame_Shift_Del_p.V1050fs|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_Frame_Shift_Del_p.V503fs|MAP3K4_uc003qtp.2_Frame_Shift_Del_p.V40fs NM_005922 NP_005913 Q9Y6R4 M3K4_HUMAN mitogen-activated protein kinase kinase kinase 4 1050_1054 activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity perinuclear region of cytoplasm ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding ovary(3)|lung(3)|skin(2)|stomach(1) 9 Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771) OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05) ATAAAGAAGTTGTTCGTTTGATGTCTGGGGA 0.336 0.36 74 41 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU601_STOMACH NA SNU601_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.60 6 9 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU601_STOMACH NA SNU601_STOMACH NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.33 52 26 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU601_STOMACH NA SNU601_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.26 20 7 MUC6 4588 broad.mit.edu 37 11 1017496 1017498 + In_Frame_Del DEL TGC - - rs67507057;rs71779662 SNU601_STOMACH NA SNU601_STOMACH NA g.chr11:1017496_1017498delTGC uc001lsw.2 - 31 5354_5356 c.5303_5305delGCA c.(5302-5307)AGCATC>ATC p.S1768del NM_005961 NP_005952 Q6W4X9 MUC6_HUMAN mucin 6, gastric 1768 Thr-rich.|Approximate repeats. maintenance of gastrointestinal epithelium extracellular region extracellular matrix structural constituent ovary(1) 1 all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703) TTGGGGGTGATGCTGGTGGTAGA 0.571 0.38 8 5 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SNU601_STOMACH NA SNU601_STOMACH NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.75 5 15 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SNU601_STOMACH NA SNU601_STOMACH NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.31 25 11 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU601_STOMACH NA SNU601_STOMACH NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 49 492 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU601_STOMACH NA SNU601_STOMACH NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.47 49 44 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU601_STOMACH NA SNU601_STOMACH NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 118 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU601_STOMACH NA SNU601_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.65 134 244 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU601_STOMACH NA SNU601_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 99 FAM48B1 100130302 broad.mit.edu 37 X 24382374 24382376 + In_Frame_Del DEL TGC - - SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chrX:24382374_24382376delTGC uc011mjx.1 + 1 1497_1499 c.1497_1499delTGC c.(1495-1500)ATTGCT>ATT p.A517del NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 ctgctgctattgctgctgctgct 0.202 0.25 42 14 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 36 DPYD 1806 broad.mit.edu 37 1 97847985 97847985 + Frame_Shift_Del DEL A - - SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr1:97847985delA uc001drv.2 - 15 2075 c.1938delT c.(1936-1938)AATfs p.N646fs NM_000110 NP_000101 Q12882 DPYD_HUMAN dihydropyrimidine dehydrogenase isoform 1 646 'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process cytosol 4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity ovary(3)|skin(3)|breast(2) 8 all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994) Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216) Capecitabine(DB01101)|Enfuvirtide(DB00109) AGTCATTTTTATTGTAACTGC 0.264 0.53 38 42 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.16 496 95 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.44 9 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.67 21 42 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.68 75 159 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.39 85 54 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.90 1 9 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.51 18 19 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.14 306 49 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 21 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.71 5 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 30 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039782 + In_Frame_Del DEL CAGCAG - - rs113070757;rs62639301;rs139102413 byFrequency;byFrequency SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr9:2039777_2039782delCAGCAG uc003zhc.2 + 4 766_771 c.667_672delCAGCAG c.(667-672)CAGCAGdel p.QQ237del SMARCA2_uc003zhd.2_In_Frame_Del_p.QQ237del|SMARCA2_uc010mha.2_In_Frame_Del_p.QQ228del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 237_238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagcagc 0.267 0.55 37 46 PCDH15 65217 broad.mit.edu 37 10 55582934 55582935 + Frame_Shift_Ins INS - AGAT AGAT SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr10:55582934_55582935insAGAT uc001jju.1 - 33 4946_4947 c.4551_4552insATCT c.(4549-4554)TCTGATfs p.S1517fs PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Frame_Shift_Ins_p.S1514fs|PCDH15_uc010qhw.1_Frame_Shift_Ins_p.S1477fs|PCDH15_uc010qhx.1_Frame_Shift_Ins_p.S1448fs|PCDH15_uc010qhy.1_Frame_Shift_Ins_p.S1524fs|PCDH15_uc010qhz.1_Frame_Shift_Ins_p.S1519fs|PCDH15_uc010qia.1_Frame_Shift_Ins_p.S1497fs|PCDH15_uc010qib.1_Frame_Shift_Ins_p.S1494fs NM_033056 NP_149045 Q96QU1 PCD15_HUMAN protocadherin 15 isoform CD1-4 precursor 1517_1518 Cytoplasmic (Potential). equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse calcium ion binding pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2) 13 Melanoma(3;0.117)|Lung SC(717;0.238) TCATCCTCATCAGATAGAAATG 0.376 0.41 285 194 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.94 1 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.50 748 759 C14orf4 64207 broad.mit.edu 37 14 77493762 77493764 + In_Frame_Del DEL TGC - - SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr14:77493762_77493764delTGC uc001xsy.2 - 1 1271_1273 c.372_374delGCA c.(370-375)CAGCAA>CAA p.124_125QQ>Q NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 124_125 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) GAgctgttgttgctgctgctgct 0.236 0.10 111 12 RBBP8 5932 broad.mit.edu 37 18 20576385 20576385 + Frame_Shift_Del DEL T - - SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr18:20576385delT uc002ktw.2 + 13 2319 c.1988delT c.(1987-1989)CTTfs p.L663fs RBBP8_uc002kty.2_Frame_Shift_Del_p.L663fs|RBBP8_uc002ktz.2_Frame_Shift_Del_p.L663fs|RBBP8_uc002kua.2_Frame_Shift_Del_p.L663fs|RBBP8_uc010xap.1_5'UTR NM_002894 NP_002885 Q99708 COM1_HUMAN retinoblastoma binding protein 8 isoform a 663 cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter nucleus damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity ovary(1)|lung(1)|skin(1) 3 all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19) OV - Ovarian serous cystadenocarcinoma(1;0.00196) GGAGCAGACCTTTCTCAGTAT 0.318 0.59 66 96 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.78 28 100 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 42 369 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU61_LARGE_INTESTINE NA SNU61_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 5 65 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU620_STOMACH NA SNU620_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 32 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU620_STOMACH NA SNU620_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.47 95 84 TTN 7273 broad.mit.edu 37 2 179433976 179433990 + In_Frame_Del DEL TCCAACAAAGGAGGT - - SNU620_STOMACH NA SNU620_STOMACH NA g.chr2:179433976_179433990delTCCAACAAAGGAGGT uc010zfg.1 - 275 69389_69403 c.69165_69179delACCTCCTTTGTTGGA c.(69163-69180)GAACCTCCTTTGTTGGAT>GAT p.EPPLL23055del uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.EPPLL16750del|TTN_uc010zfi.1_In_Frame_Del_p.EPPLL16683del|TTN_uc010zfj.1_In_Frame_Del_p.EPPLL16558del NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 23982_23986 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GGATCCCCCATCCAACAAAGGAGGTTCCCATGTAA 0.400 0.15 124 22 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SNU620_STOMACH NA SNU620_STOMACH NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.10 69 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU620_STOMACH NA SNU620_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.30 53 23 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU620_STOMACH NA SNU620_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 11 28 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes SNU620_STOMACH NA SNU620_STOMACH NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.72 16 41 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU620_STOMACH NA SNU620_STOMACH NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.83 2 10 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU620_STOMACH NA SNU620_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.94 1 15 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU620_STOMACH NA SNU620_STOMACH NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.45 42 35 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU620_STOMACH NA SNU620_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU620_STOMACH NA SNU620_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.23 657 191 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU620_STOMACH NA SNU620_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 73 13 TP53 7157 broad.mit.edu 37 17 7578546 7578571 + Splice_Site DEL AGGGGAGTACTGTAGGAAGAGGAAGG - - SNU620_STOMACH NA SNU620_STOMACH NA g.chr17:7578546_7578571delAGGGGAGTACTGTAGGAAGAGGAAGG uc002gim.2 - 5 570 c.376_splice c.e5-1 p.Y126_splice TP53_uc002gig.1_Splice_Site_p.Y126_splice|TP53_uc002gih.2_Splice_Site_p.Y126_splice|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'UTR|TP53_uc010cng.1_5'UTR|TP53_uc002gii.1_5'UTR|TP53_uc010cnh.1_Splice_Site_p.Y126_splice|TP53_uc010cni.1_Splice_Site_p.Y126_splice|TP53_uc002gij.2_Splice_Site_p.Y126_splice|TP53_uc010cnj.1_5'UTR|TP53_uc002gin.2_Splice_Site_p.Y33_splice|TP53_uc002gio.2_Splice_Site|TP53_uc010vug.1_Splice_Site_p.Y87_splice NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.?(53)|p.S127F(18)|p.Y126*(11)|p.S127Y(8)|p.0?(7)|p.P128S(7)|p.Y126_K132delYSPALNK(6)|p.Y126N(6)|p.P128fs*42(4)|p.Y126C(4)|p.S127P(3)|p.Y126D(3)|p.P128L(3)|p.Y126_N131delYSPALN(3)|p.S127T(2)|p.Y126S(2)|p.Y126Y(1)|p.S127S(1)|p.S127_Q136del10(1)|p.T125_Y126insX(1)|p.Y33*(1)|p.S127C(1)|p.V73fs*9(1)|p.S127fs*43(1)|p.S127fs*42(1)|p.P128del(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.Y126fs*18(1)|p.S127fs*36(1)|p.P128fs*18(1)|p.P128A(1)|p.P128P(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.77 38 124 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU620_STOMACH NA SNU620_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 98 372 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU620_STOMACH NA SNU620_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 4 49 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU626_CENTRAL_NERVOUS_SYSTEM NA SNU626_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 18 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU626_CENTRAL_NERVOUS_SYSTEM NA SNU626_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.30 241 104 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU626_CENTRAL_NERVOUS_SYSTEM NA SNU626_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.28 66 26 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU626_CENTRAL_NERVOUS_SYSTEM NA SNU626_CENTRAL_NERVOUS_SYSTEM NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.72 10 26 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU626_CENTRAL_NERVOUS_SYSTEM NA SNU626_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU626_CENTRAL_NERVOUS_SYSTEM NA SNU626_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.36 573 318 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU626_CENTRAL_NERVOUS_SYSTEM NA SNU626_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 119 23 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNU626_CENTRAL_NERVOUS_SYSTEM NA SNU626_CENTRAL_NERVOUS_SYSTEM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.62 6 10 TP53 7157 broad.mit.edu 37 17 7579321 7579322 + Frame_Shift_Del DEL CA - - SNU626_CENTRAL_NERVOUS_SYSTEM NA SNU626_CENTRAL_NERVOUS_SYSTEM NA g.chr17:7579321_7579322delCA uc002gim.2 - 4 559_560 c.365_366delTG c.(364-366)GTGfs p.V122fs TP53_uc002gig.1_Frame_Shift_Del_p.V122fs|TP53_uc002gih.2_Frame_Shift_Del_p.V122fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.V122fs|TP53_uc010cni.1_Frame_Shift_Del_p.V122fs|TP53_uc002gij.2_Frame_Shift_Del_p.V122fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.V83fs|TP53_uc010cnk.1_Frame_Shift_Del_p.V137fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 122 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). V -> L (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.G59fs*23(3)|p.V122fs*26(2)|p.V73fs*9(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.V122fs*46(1)|p.Y107fs*44(1)|p.V122L(1)|p.P13fs*18(1)|p.S33fs*23(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.54 510 597 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU626_CENTRAL_NERVOUS_SYSTEM NA SNU626_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 12 30 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU626_CENTRAL_NERVOUS_SYSTEM NA SNU626_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.46 62 52 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU626_CENTRAL_NERVOUS_SYSTEM NA SNU626_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.94 33 483 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU626_CENTRAL_NERVOUS_SYSTEM NA SNU626_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 38 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU668_STOMACH NA SNU668_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU668_STOMACH NA SNU668_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.38 23 14 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU668_STOMACH NA SNU668_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.55 10 12 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SNU668_STOMACH NA SNU668_STOMACH NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.90 1 9 ZNF3 7551 broad.mit.edu 37 7 99669118 99669120 + In_Frame_Del DEL TGG - - SNU668_STOMACH NA SNU668_STOMACH NA g.chr7:99669118_99669120delTGG uc003usq.2 - 6 1294_1296 c.987_989delCCA c.(985-990)CACCAT>CAT p.329_330HH>H ZNF3_uc003usp.2_Intron|ZNF3_uc003usr.2_In_Frame_Del_p.329_330HH>H|ZNF3_uc010lgj.2_In_Frame_Del_p.293_294HH>H|ZNF3_uc003uss.2_In_Frame_Del_p.336_337HH>H|ZNF3_uc003ust.3_In_Frame_Del_p.329_330HH>H NM_032924 NP_116313 P17036 ZNF3_HUMAN zinc finger protein 3 isoform 2 329_330 C2H2-type 5. cell differentiation|leukocyte activation|multicellular organismal development nucleus DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1) 1 Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439) Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029) STAD - Stomach adenocarcinoma(171;0.129) GATTCTCTGATGGTGAATAAGGG 0.502 0.33 10 5 MLL3 58508 broad.mit.edu 37 7 151962168 151962168 + Frame_Shift_Del DEL C - - rs138908625 byFrequency;by1000genomes SNU668_STOMACH NA SNU668_STOMACH NA g.chr7:151962168delC uc003wla.2 - 8 1358 c.1139delG c.(1138-1140)CGTfs p.R380fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 380 PHD-type 1.|RING-type. intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) CCAACCTGCACGTTTTAATGG 0.443 0.21 113 30 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU668_STOMACH NA SNU668_STOMACH NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.42 14 10 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU668_STOMACH NA SNU668_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU668_STOMACH NA SNU668_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 60 11 YAP1 10413 broad.mit.edu 37 11 102100448 102100449 + Frame_Shift_Del DEL AA - - SNU668_STOMACH NA SNU668_STOMACH NA g.chr11:102100448_102100449delAA uc001pgt.2 + 9 1662_1663 c.1292_1293delAA c.(1291-1293)CAAfs p.Q431fs YAP1_uc001pgs.2_Frame_Shift_Del_p.Q381fs|YAP1_uc001pgu.2_Frame_Shift_Del_p.Q415fs|YAP1_uc001pgv.2_Frame_Shift_Del_p.Q377fs|YAP1_uc010ruo.1_Frame_Shift_Del_p.Q253fs|YAP1_uc001pgw.2_Frame_Shift_Del_p.Q255fs|YAP1_uc010rup.1_Frame_Shift_Del_p.Q196fs NM_001130145 NP_001123617 P46937 YAP1_HUMAN Yes-associated protein 1, 65kDa isoform 1 431 Transactivation domain. cell proliferation|cellular response to gamma radiation|contact inhibition|hippo signaling cascade|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent cytoplasm|nucleus protein binding|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding ovary(1)|lung(1)|central_nervous_system(1) 3 all_cancers(8;0.000575)|all_epithelial(12;0.00564) Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936) Lung(13;0.245) BRCA - Breast invasive adenocarcinoma(274;0.0189) ACTATCAACCAAAGCACCCTGC 0.455 1.00 0 16 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU668_STOMACH NA SNU668_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 79 409 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU685_ENDOMETRIUM NA SNU685_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 34 PLK3 1263 broad.mit.edu 37 1 45266826 45266827 + Splice_Site INS - A A SNU685_ENDOMETRIUM NA SNU685_ENDOMETRIUM NA g.chr1:45266826_45266827insA uc001cmn.2 + 3 535 c.435_splice c.e3+2 p.K145_splice PLK3_uc001cmo.2_Splice_Site NM_004073 NP_004064 Q9H4B4 PLK3_HUMAN polo-like kinase 3 membrane ATP binding|protein binding|protein serine/threonine kinase activity 0 Acute lymphoblastic leukemia(166;0.155) AGCCGAAAGGTGAAAGATGGTG 0.396 0.49 43 41 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU685_ENDOMETRIUM NA SNU685_ENDOMETRIUM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 259 102 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SNU685_ENDOMETRIUM NA SNU685_ENDOMETRIUM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 33 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU685_ENDOMETRIUM NA SNU685_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.40 46 31 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes SNU685_ENDOMETRIUM NA SNU685_ENDOMETRIUM NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.58 41 56 TTK 7272 broad.mit.edu 37 6 80749940 80749943 + Frame_Shift_Del DEL AGGA - - SNU685_ENDOMETRIUM NA SNU685_ENDOMETRIUM NA g.chr6:80749940_80749943delAGGA uc003pjc.2 + 20 2409_2412 c.2335_2338delAGGA c.(2335-2340)AGGATAfs p.R779fs TTK_uc003pjb.3_Frame_Shift_Del_p.R778fs NM_003318 NP_003309 P33981 TTK_HUMAN TTK protein kinase 779_780 Protein kinase. mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation spindle ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1) 11 all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2) BRCA - Breast invasive adenocarcinoma(397;0.0321) CCCAAAACAGAGGATATCCATTCC 0.294 0.14 61 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU685_ENDOMETRIUM NA SNU685_ENDOMETRIUM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 129 18 CCNA1 8900 broad.mit.edu 37 13 37006866 37006866 + Frame_Shift_Del DEL G - - SNU685_ENDOMETRIUM NA SNU685_ENDOMETRIUM NA g.chr13:37006866delG uc001uvr.3 + 1 458 c.108delG c.(106-108)CAGfs p.Q36fs CCNA1_uc010teo.1_Intron|CCNA1_uc010abq.2_Intron|CCNA1_uc010abp.2_Intron|CCNA1_uc001uvs.3_Frame_Shift_Del_p.Q36fs|CCNA1_uc010abr.2_RNA NM_003914 NP_003905 P78396 CCNA1_HUMAN cyclin A1 isoform a 36 cell division|G2/M transition of mitotic cell cycle|male meiosis I|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|spermatogenesis cytosol|microtubule cytoskeleton|nucleoplasm protein kinase binding lung(2)|skin(2)|ovary(1) 5 Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242) TCGTCTTCCAGGTAACGTGGG 0.527 0.42 50 36 WDR62 284403 broad.mit.edu 37 19 36562471 36562471 + Frame_Shift_Del DEL C - - SNU685_ENDOMETRIUM NA SNU685_ENDOMETRIUM NA g.chr19:36562471delC uc002odc.2 + 8 987 c.896delC c.(895-897)TCCfs p.S299fs WDR62_uc002odd.2_Frame_Shift_Del_p.S299fs|WDR62_uc002odb.2_Frame_Shift_Del_p.S299fs NM_173636 NP_775907 O43379 WDR62_HUMAN WD repeat domain 62 isoform 2 299 WD 4. cerebral cortex development nucleus 0 Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.06) TCCCTGTCTTCCTGCCTCTGT 0.607 0.82 2 9 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNU685_ENDOMETRIUM NA SNU685_ENDOMETRIUM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.14 87 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU685_ENDOMETRIUM NA SNU685_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 55 173 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU685_ENDOMETRIUM NA SNU685_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 66 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU719_STOMACH NA SNU719_STOMACH NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.83 4 20 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU719_STOMACH NA SNU719_STOMACH NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 224 48 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU719_STOMACH NA SNU719_STOMACH NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.47 16 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU719_STOMACH NA SNU719_STOMACH NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.34 67 35 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU719_STOMACH NA SNU719_STOMACH NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 46 23 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU719_STOMACH NA SNU719_STOMACH NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.32 98 47 STK19 8859 broad.mit.edu 37 6 31948319 31948320 + Frame_Shift_Ins INS - T T SNU719_STOMACH NA SNU719_STOMACH NA g.chr6:31948319_31948320insT uc003nyv.2 + 6 1035_1036 c.907_908insT c.(907-909)GTTfs p.V303fs STK19_uc003nyt.2_Frame_Shift_Ins_p.V256fs|STK19_uc011dox.1_Frame_Shift_Ins_p.V260fs|STK19_uc003nyw.2_Frame_Shift_Ins_p.V299fs|STK19_uc010jtn.1_RNA|C4A_uc011doy.1_5'Flank|C4A_uc011doz.1_5'Flank|C4A_uc011dpa.1_5'Flank NM_032454 NP_115830 P49842 STK19_HUMAN serine/threonine kinase 19 isoform 2 303 nucleus ATP binding|protein binding|protein serine/threonine kinase activity skin(4) 4 CAAGTACTTTGTTAAAGGTATC 0.559 0.51 42 44 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU719_STOMACH NA SNU719_STOMACH NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.79 6 23 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU719_STOMACH NA SNU719_STOMACH NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 10 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU719_STOMACH NA SNU719_STOMACH NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.55 203 253 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU719_STOMACH NA SNU719_STOMACH NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 99 15 NCOR2 9612 broad.mit.edu 37 12 124887059 124887067 + In_Frame_Del DEL GCTGCTGCT - - rs67031864 SNU719_STOMACH NA SNU719_STOMACH NA g.chr12:124887059_124887067delGCTGCTGCT uc010tba.1 - 14 1640_1648 c.1523_1531delAGCAGCAGC c.(1522-1533)CAGCAGCAGCCC>CCC p.QQQ508del NCOR2_uc010tay.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010taz.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010tbb.1_In_Frame_Del_p.QQQ508del|NCOR2_uc010tbc.1_In_Frame_Del_p.QQQ507del|NCOR2_uc001ugj.1_In_Frame_Del_p.QQQ508del NM_001077261 NP_001070729 Q9Y618 NCOR2_HUMAN nuclear receptor co-repressor 2 isoform 2 508_510 Poly-Gln. cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity skin(3)|ovary(1) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) CGGGGCATGGgctgctgctgctgctgctg 0.316 0.43 8 6 Unknown 0 broad.mit.edu 37 19 37240719 37240719 + Frame_Shift_Del DEL A - - SNU719_STOMACH NA SNU719_STOMACH NA g.chr19:37240719delA uc010efc.2 - 5 1382 c.1217delT c.(1216-1218)TTAfs p.L406fs uc010xtm.1_Frame_Shift_Del_p.L374fs Homo sapiens zinc finger protein 850 pseudogene, mRNA (cDNA clone IMAGE:6082150). GTGTCCAATTAACCCTGAGCG 0.403 0.26 28 10 BRSK1 84446 broad.mit.edu 37 19 55814154 55814154 + Frame_Shift_Del DEL A - - SNU719_STOMACH NA SNU719_STOMACH NA g.chr19:55814154delA uc002qkg.2 + 10 1224 c.947delA c.(946-948)GACfs p.D316fs BRSK1_uc002qkf.2_Frame_Shift_Del_p.D332fs|BRSK1_uc002qkh.2_Frame_Shift_Del_p.D11fs NM_032430 NP_115806 Q8TDC3 BRSK1_HUMAN BR serine/threonine kinase 1 316 UBA. establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV cell junction|cytoplasm|nucleus magnesium ion binding|protein serine/threonine kinase activity ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1) 6 Renal(1328;0.245) BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.0474) 0.000 0.33 574 281 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU719_STOMACH NA SNU719_STOMACH NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 81 253 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU719_STOMACH NA SNU719_STOMACH NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 56 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 30 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.63 167 286 STK17B 9262 broad.mit.edu 37 2 197002245 197002247 + In_Frame_Del DEL TGC - - SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr2:197002245_197002247delTGC uc002utk.2 - 8 1367_1369 c.1043_1045delGCA c.(1042-1047)AGCATG>ATG p.S348del STK17B_uc010fsh.2_In_Frame_Del_p.S348del NM_004226 NP_004217 O94768 ST17B_HUMAN serine/threonine kinase 17B 348 apoptosis|induction of apoptosis|intracellular protein kinase cascade nucleus ATP binding|protein serine/threonine kinase activity lung(2) 2 OV - Ovarian serous cystadenocarcinoma(117;0.141) TTGGAAACCATGCTGCTATCCTC 0.404 0.46 100 86 NEK10 152110 broad.mit.edu 37 3 27161265 27161265 + Frame_Shift_Del DEL G - - SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr3:27161265delG uc010hfk.2 - 14 1512 c.1283delC c.(1282-1284)CCAfs p.P428fs NEK10_uc010hfj.2_Frame_Shift_Del_p.P371fs Q6ZWH5 NEK10_HUMAN RecName: Full=Serine/threonine-protein kinase Nek10; EC=2.7.11.1; AltName: Full=NimA-related protein kinase 10; 1116 ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1) 13 AGGGTCATTTGGGGACAGGCT 0.398 0.57 20 26 MAGI1 9223 broad.mit.edu 37 3 65425561 65425572 + In_Frame_Del DEL CTGCTGCTGCTG - - SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr3:65425561_65425572delCTGCTGCTGCTG uc003dmn.2 - 9 1778_1789 c.1252_1263delCAGCAGCAGCAG c.(1252-1263)CAGCAGCAGCAGdel p.QQQQ418del MAGI1_uc003dmm.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc003dmo.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc003dmp.2_In_Frame_Del_p.QQQQ418del|MAGI1_uc010hny.2_In_Frame_Del_p.QQQQ303del NM_001033057 NP_001028229 Q96QZ7 MAGI1_HUMAN membrane associated guanylate kinase, WW and PDZ 418_421 Poly-Gln. cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly tight junction ATP binding|protein C-terminus binding lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1) 6 Lung NSC(201;0.0016) BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133) AACCTTCTGTctgctgctgctgctgctgctgc 0.368 0.58 14 19 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 108 23 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 14 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.44 43 34 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.67 132 272 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 18 44 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.92 1 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 124 34 SIK2 23235 broad.mit.edu 37 11 111571666 111571667 + Frame_Shift_Ins INS - G G SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr11:111571666_111571667insG uc001plt.2 + 5 653_654 c.535_536insG c.(535-537)AGCfs p.S179fs NM_015191 NP_056006 Q9H0K1 SIK2_HUMAN SNF1-like kinase 2 179 Protein kinase. intracellular protein kinase cascade|regulation of insulin receptor signaling pathway Golgi apparatus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(2)|skin(1) 3 ATGGTGTGGCAGCCCCCCTTAT 0.431 0.16 115 22 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.62 6 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 54 885 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.21 467 121 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.71 10 25 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 74 282 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU738_CENTRAL_NERVOUS_SYSTEM NA SNU738_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 99 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU761_LIVER NA SNU761_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 1 18 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU761_LIVER NA SNU761_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 132 28 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU761_LIVER NA SNU761_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.34 33 17 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNU761_LIVER NA SNU761_LIVER NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.73 130 356 PPP3CB 5532 broad.mit.edu 37 10 75198049 75198050 + Frame_Shift_Del DEL GT - - SNU761_LIVER NA SNU761_LIVER NA g.chr10:75198049_75198050delGT uc001jue.2 - 14 1660_1661 c.1525_1526delAC c.(1525-1527)ACCfs p.T509fs PPP3CB_uc001juf.2_Frame_Shift_Del_p.T510fs|PPP3CB_uc001jug.2_Frame_Shift_Del_p.T500fs|PPP3CB_uc010qkj.1_Frame_Shift_Del_p.T137fs NM_021132 NP_066955 P16298 PP2BB_HUMAN protein phosphatase 3, catalytic subunit, beta 509 skin(1) 1 Prostate(51;0.0119) GGCATGTGCGGTGTTCAGAGAA 0.510 0.44 74 57 BTRC 8945 broad.mit.edu 37 10 103294486 103294487 + Frame_Shift_Ins INS - G G SNU761_LIVER NA SNU761_LIVER NA g.chr10:103294486_103294487insG uc001kta.2 + 10 1279_1280 c.1166_1167insG c.(1165-1167)TTGfs p.L389fs BTRC_uc001ktb.2_Frame_Shift_Ins_p.L353fs|BTRC_uc001ktc.2_Frame_Shift_Ins_p.L363fs NM_033637 NP_378663 Q9Y297 FBW1A_HUMAN beta-transducin repeat containing protein 389 WD 3. anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|positive regulation of proteolysis|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|viral reproduction|Wnt receptor signaling pathway cytosol|nucleus|SCF ubiquitin ligase complex ovary(1) 1 Colorectal(252;0.234) Epithelial(162;1.05e-08)|all cancers(201;6.59e-07) GTTCTGCACTTGCGTTTCAATA 0.460 0.47 97 85 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU761_LIVER NA SNU761_LIVER NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.96 16 367 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - SNU761_LIVER NA SNU761_LIVER NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 1.00 0 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU761_LIVER NA SNU761_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 77 279 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU761_LIVER NA SNU761_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 59 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU840_OVARY NA SNU840_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 47 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU840_OVARY NA SNU840_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 284 76 RIF1 55183 broad.mit.edu 37 2 152320713 152320715 + In_Frame_Del DEL AAG - - SNU840_OVARY NA SNU840_OVARY NA g.chr2:152320713_152320715delAAG uc002txm.2 + 30 4809_4811 c.4679_4681delAAG c.(4678-4683)AAAGAA>AAA p.E1562del RIF1_uc002txl.2_In_Frame_Del_p.E1562del|RIF1_uc002txn.2_In_Frame_Del_p.E1562del|RIF1_uc002txo.2_In_Frame_Del_p.E1562del|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1562 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) TCGGAGGCAAAAGAAGAAGGTTC 0.404 0.48 30 28 BMP2K 55589 broad.mit.edu 37 4 79792137 79792145 + In_Frame_Del DEL CAGCAGCAG - - rs17855588 SNU840_OVARY NA SNU840_OVARY NA g.chr4:79792137_79792145delCAGCAGCAG uc003hlk.2 + 11 1598_1606 c.1432_1440delCAGCAGCAG c.(1432-1440)CAGCAGCAGdel p.QQQ484del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.QQQ484del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 484_486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 gcaacagcaacagcagcagcagcagcagc 0.177 0.33 16 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU840_OVARY NA SNU840_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.39 34 22 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU840_OVARY NA SNU840_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.37 46 27 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU840_OVARY NA SNU840_OVARY NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.36 182 101 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SNU840_OVARY NA SNU840_OVARY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.35 56 30 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU840_OVARY NA SNU840_OVARY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SNU840_OVARY NA SNU840_OVARY NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.94 1 17 MEN1 4221 broad.mit.edu 37 11 64577330 64577333 + Frame_Shift_Del DEL AGAC - - SNU840_OVARY NA SNU840_OVARY NA g.chr11:64577330_64577333delAGAC uc001obj.2 - 2 322_325 c.249_252delGTCT c.(247-252)CTGTCTfs p.L83fs MEN1_uc001obk.2_Frame_Shift_Del_p.L83fs|MEN1_uc001obl.2_Frame_Shift_Del_p.L83fs|MEN1_uc001obm.2_Frame_Shift_Del_p.L83fs|MEN1_uc001obn.2_Frame_Shift_Del_p.L83fs|MEN1_uc001obo.2_Frame_Shift_Del_p.L83fs|MEN1_uc001obp.2_Frame_Shift_Del_p.L83fs|MEN1_uc001obq.2_Frame_Shift_Del_p.L83fs|MEN1_uc001obr.2_Frame_Shift_Del_p.L83fs NM_130800 NP_570712 O00255 MEN1_HUMAN menin isoform 1 83_84 DNA repair|histone lysine methylation|MAPKKK cascade|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of JNK cascade|negative regulation of osteoblast differentiation|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of telomerase activity|negative regulation of transcription from RNA polymerase II promoter|osteoblast development|positive regulation of protein binding|positive regulation of transforming growth factor beta receptor signaling pathway|response to gamma radiation|response to UV|transcription, DNA-dependent chromatin|cleavage furrow|cytosol|histone methyltransferase complex|nuclear matrix|soluble fraction double-stranded DNA binding|four-way junction DNA binding|protein binding, bridging|protein N-terminus binding|R-SMAD binding|transcription regulatory region DNA binding|Y-form DNA binding p.I85fs*33(6)|p.I85fs*32(2)|p.L83fs*28(1) parathyroid(105)|pancreas(64)|gastrointestinal_tract_(site_indeterminate)(15)|small_intestine(13)|lung(9)|pituitary(7)|NS(7)|adrenal_gland(5)|soft_tissue(4)|central_nervous_system(4)|thymus(2)|stomach(1)|retroperitoneum(1)|skin(1) 238 0.000 0.48 300 273 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU840_OVARY NA SNU840_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 109 12 PLCG2 5336 broad.mit.edu 37 16 81904462 81904464 + In_Frame_Del DEL AGG - - SNU840_OVARY NA SNU840_OVARY NA g.chr16:81904462_81904464delAGG uc002fgt.2 + 7 722_724 c.570_572delAGG c.(568-573)ATAGGA>ATA p.G191del PLCG2_uc010chg.1_In_Frame_Del_p.G191del NM_002661 NP_002652 P16885 PLCG2_HUMAN phospholipase C, gamma 2 191 intracellular signal transduction|phospholipid catabolic process|platelet activation plasma membrane phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity large_intestine(4)|lung(2)|ovary(1)|skin(1) 8 TACAGGAAATAGGAGCACACAAA 0.345 0.10 128 14 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU840_OVARY NA SNU840_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.84 4 21 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU840_OVARY NA SNU840_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.23 31 9 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU840_OVARY NA SNU840_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 45 368 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU840_OVARY NA SNU840_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 44 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.75 5 15 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.52 164 176 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.33 22 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.37 82 48 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.97 12 424 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 13 34 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.80 2 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.76 4 13 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 1.00 0 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 21 CDKN2A 1029 broad.mit.edu 37 9 21974716 21974717 + Frame_Shift_Ins INS - G G SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr9:21974716_21974717insG uc003zpk.2 - 1 322_323 c.110_111insC c.(109-111)CTGfs p.L37fs MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_Frame_Shift_Ins_p.L37fs|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Intron NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 37 ANK 1. cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.?(23)|p.L32_L37del(6)|p.L37L(2)|p.G35fs*13(1)|p.V28_V51del(1)|p.L37fs*6(1)|p.P38fs*7(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) 0.000 0.95 16 297 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 164 30 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.53 7 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 104 275 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU869_BILIARY_TRACT NA SNU869_BILIARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 55 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU878_LIVER NA SNU878_LIVER NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 30 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU878_LIVER NA SNU878_LIVER NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.38 163 100 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SNU878_LIVER NA SNU878_LIVER NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.33 18 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU878_LIVER NA SNU878_LIVER NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 37 21 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes SNU878_LIVER NA SNU878_LIVER NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.96 8 193 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU878_LIVER NA SNU878_LIVER NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.47 26 23 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNU878_LIVER NA SNU878_LIVER NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.22 214 62 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU878_LIVER NA SNU878_LIVER NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 92 23 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU878_LIVER NA SNU878_LIVER NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.60 23 35 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU878_LIVER NA SNU878_LIVER NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 27 366 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU878_LIVER NA SNU878_LIVER NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 3 51 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU899_UPPER_AERODIGESTIVE_TRACT NA SNU899_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 4 34 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU899_UPPER_AERODIGESTIVE_TRACT NA SNU899_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.12 257 36 CAD 790 broad.mit.edu 37 2 27447911 27447912 + Frame_Shift_Ins INS - T T SNU899_UPPER_AERODIGESTIVE_TRACT NA SNU899_UPPER_AERODIGESTIVE_TRACT NA g.chr2:27447911_27447912insT uc002rji.2 + 11 1582_1583 c.1420_1421insT c.(1420-1422)CTGfs p.L474fs CAD_uc010eyw.2_Frame_Shift_Ins_p.L474fs NM_004341 NP_004332 P27708 PYR1_HUMAN carbamoylphosphate synthetase 2/aspartate 474 CPSase (Carbamoyl-phosphate synthase).|CPSase A. 'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process cytosol|neuronal cell body|nuclear matrix|terminal button aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1) 10 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) L-Aspartic Acid(DB00128)|L-Glutamine(DB00130) TGGTGTGTTACTGACTTTTGGG 0.559 0.46 14 12 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNU899_UPPER_AERODIGESTIVE_TRACT NA SNU899_UPPER_AERODIGESTIVE_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 11 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU899_UPPER_AERODIGESTIVE_TRACT NA SNU899_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.33 62 31 NSD1 64324 broad.mit.edu 37 5 176720888 176720890 + In_Frame_Del DEL CTT - - SNU899_UPPER_AERODIGESTIVE_TRACT NA SNU899_UPPER_AERODIGESTIVE_TRACT NA g.chr5:176720888_176720890delCTT uc003mfr.3 + 23 6657_6659 c.6519_6521delCTT c.(6517-6522)TCCTTC>TCC p.F2174del NSD1_uc003mft.3_In_Frame_Del_p.F1905del|NSD1_uc011dfx.1_In_Frame_Del_p.F1822del NM_022455 NP_071900 Q96L73 NSD1_HUMAN nuclear receptor binding SET domain protein 1 2174 negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|nucleus androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding ovary(2)|kidney(1) 3 all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002) all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198) Kidney(146;0.235) AAGCAGCCTCCTTCTGTGAGATG 0.473 0.88 3 22 CDKN2A 1029 broad.mit.edu 37 9 21971132 21971133 + Frame_Shift_Ins INS - G G SNU899_UPPER_AERODIGESTIVE_TRACT NA SNU899_UPPER_AERODIGESTIVE_TRACT NA g.chr9:21971132_21971133insG uc003zpk.2 - 2 437_438 c.225_226insC c.(223-228)CCCGCCfs p.P75fs MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Frame_Shift_Ins_p.R131fs NM_000077 NP_000068 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A isoform 1 75_76 cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding p.0?(1112)|p.?(13)|p.P75L(2)|p.A76fs*70(2)|p.P75H(1)|p.E61_L94del(1)|p.A76fs*64(1)|p.L65fs*38(1)|p.A68fs*3(1)|p.P75fs*71(1)|p.A76T(1)|p.P75S(1) haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1) 3678 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) 0.000 0.28 2135 848 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 SNU899_UPPER_AERODIGESTIVE_TRACT NA SNU899_UPPER_AERODIGESTIVE_TRACT NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.54 13 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU899_UPPER_AERODIGESTIVE_TRACT NA SNU899_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 154 25 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNU899_UPPER_AERODIGESTIVE_TRACT NA SNU899_UPPER_AERODIGESTIVE_TRACT NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.33 8 4 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU899_UPPER_AERODIGESTIVE_TRACT NA SNU899_UPPER_AERODIGESTIVE_TRACT NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 12 76 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU899_UPPER_AERODIGESTIVE_TRACT NA SNU899_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 102 691 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU899_UPPER_AERODIGESTIVE_TRACT NA SNU899_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 73 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNU8_OVARY NA SNU8_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 36 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNU8_OVARY NA SNU8_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.49 203 194 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNU8_OVARY NA SNU8_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.35 55 30 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNU8_OVARY NA SNU8_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 24 56 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SNU8_OVARY NA SNU8_OVARY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 11 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 SNU8_OVARY NA SNU8_OVARY NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.78 8 29 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNU8_OVARY NA SNU8_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 119 23 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNU8_OVARY NA SNU8_OVARY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 5 49 TP53 7157 broad.mit.edu 37 17 7578504 7578505 + Frame_Shift_Del DEL AG - - SNU8_OVARY NA SNU8_OVARY NA g.chr17:7578504_7578505delAG uc002gim.2 - 5 619_620 c.425_426delCT c.(424-426)CCTfs p.P142fs TP53_uc002gig.1_Frame_Shift_Del_p.P142fs|TP53_uc002gih.2_Frame_Shift_Del_p.P142fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.P10fs|TP53_uc010cng.1_Frame_Shift_Del_p.P10fs|TP53_uc002gii.1_Frame_Shift_Del_p.P10fs|TP53_uc010cnh.1_Frame_Shift_Del_p.P142fs|TP53_uc010cni.1_Frame_Shift_Del_p.P142fs|TP53_uc002gij.2_Frame_Shift_Del_p.P142fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.P49fs|TP53_uc002gio.2_Frame_Shift_Del_p.P10fs|TP53_uc010vug.1_Frame_Shift_Del_p.P103fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 142 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). P -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> R (in a sporadic cancer; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> A (in sporadic cancers; somatic mutation).|P -> H (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.P142L(8)|p.0?(7)|p.P142H(3)|p.P142P(3)|p.P142F(2)|p.P142A(2)|p.P142T(2)|p.P142S(2)|p.P142fs*28(2)|p.L137_W146del10(1)|p.V143fs*29(1)|p.P142_Q144delPVQ(1)|p.K139fs*4(1)|p.A138_V143delAKTCPV(1)|p.N131fs*27(1)|p.A138_P142delAKTCP(1)|p.C141_P142insXX(1)|p.V143_S149del(1)|p.T140fs*28(1)|p.C141fs*5(1)|p.P142del(1)|p.P142fs*7(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) ACAGCTGCACAGGGCAGGTCTT 0.584 1.00 0 22 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT SNU8_OVARY NA SNU8_OVARY NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.10 473 53 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNU8_OVARY NA SNU8_OVARY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.31 40 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNU8_OVARY NA SNU8_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 74 733 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNU8_OVARY NA SNU8_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 45 POLA1 5422 broad.mit.edu 37 X 24830853 24830853 + Frame_Shift_Del DEL A - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chrX:24830853delA uc004dbl.2 + 29 3174 c.3151delA c.(3151-3153)AAAfs p.K1051fs NM_016937 NP_058633 P09884 DPOLA_HUMAN DNA-directed DNA polymerase alpha 1 1051 Poly-Lys. cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding ovary(2)|skin(1) 3 Clofarabine(DB00631)|Fludarabine(DB01073) 0.000 0.52 256 274 KDM6A 7403 broad.mit.edu 37 X 44870215 44870215 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chrX:44870215delT uc004dge.3 + 5 769 c.394delT c.(394-396)TTTfs p.F132fs KDM6A_uc010nhk.2_Frame_Shift_Del_p.F132fs|KDM6A_uc011mkz.1_Frame_Shift_Del_p.F132fs|KDM6A_uc011mla.1_Frame_Shift_Del_p.F132fs|KDM6A_uc011mlb.1_Frame_Shift_Del_p.F132fs|KDM6A_uc011mlc.1_5'UTR NM_021140 NP_066963 O15550 KDM6A_HUMAN ubiquitously transcribed tetratricopeptide 132 TPR 2. histone H3-K4 methylation metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen p.0(2)|p.?(1) kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2) 84 GAATGCTGCCTTTTTATATGG 0.303 0.48 43 40 KDM6A 7403 broad.mit.edu 37 X 44945195 44945196 + Frame_Shift_Ins INS - T T SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chrX:44945195_44945196insT uc004dge.3 + 24 3894_3895 c.3519_3520insT c.(3517-3522)TACTGGfs p.Y1173fs KDM6A_uc011mkz.1_Frame_Shift_Ins_p.Y1225fs|KDM6A_uc011mla.1_Frame_Shift_Ins_p.Y1128fs|KDM6A_uc011mlb.1_Frame_Shift_Ins_p.Y1180fs|KDM6A_uc011mlc.1_Frame_Shift_Ins_p.Y877fs|KDM6A_uc011mld.1_Frame_Shift_Ins_p.Y812fs NM_021140 NP_066963 O15550 KDM6A_HUMAN ubiquitously transcribed tetratricopeptide 1173_1174 JmjC. histone H3-K4 methylation metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen p.W1174fs*6(2) kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2) 84 CTGAAGGTTACTGGGGTGTTCT 0.351 0.43 37 28 PIM2 11040 broad.mit.edu 37 X 48776072 48776073 + Frame_Shift_Ins INS - G G SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chrX:48776072_48776073insG uc004dls.2 - 1 341_342 c.39_40insC c.(37-42)CCCGGGfs p.P13fs NM_006875 NP_006866 Q9P1W9 PIM2_HUMAN serine/threonine protein kinase pim-2 13_14 anti-apoptosis|cell proliferation|male meiosis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|response to virus ATP binding|protein serine/threonine kinase activity lung(3)|stomach(1) 4 0.000 0.40 294 196 WNK3 65267 broad.mit.edu 37 X 54263615 54263616 + Frame_Shift_Del DEL TC - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chrX:54263615_54263616delTC uc004dtd.1 - 20 4681_4682 c.4242_4243delGA c.(4240-4245)GAGATAfs p.E1414fs WNK3_uc004dtc.1_Frame_Shift_Del_p.E1461fs NM_001002838 NP_001002838 Q9BYP7 WNK3_HUMAN WNK lysine deficient protein kinase 3 isoform 2 1414_1415 intracellular protein kinase cascade|positive regulation of establishment of protein localization in plasma membrane|positive regulation of peptidyl-threonine phosphorylation|positive regulation of rubidium ion transmembrane transporter activity|positive regulation of rubidium ion transport|positive regulation of sodium ion transmembrane transporter activity|positive regulation of sodium ion transport|protein autophosphorylation adherens junction|tight junction ATP binding|protein binding|protein serine/threonine kinase activity|rubidium ion transmembrane transporter activity|sodium ion transmembrane transporter activity lung(4)|ovary(3)|kidney(2)|central_nervous_system(2) 11 GCAGTCAATATCTCTCTCTCTT 0.450 0.44 111 86 NRK 203447 broad.mit.edu 37 X 105150564 105150564 + Frame_Shift_Del DEL A - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chrX:105150564delA uc004emd.2 + 11 1306 c.1003delA c.(1003-1005)AAAfs p.K335fs NRK_uc010npc.1_5'UTR NM_198465 NP_940867 Q7Z2Y5 NRK_HUMAN Nik related kinase 335 ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1) 14 TGGAATCATTAAAAAAAGACA 0.303 0.40 25 17 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 33 FAM132A 388581 broad.mit.edu 37 1 1179657 1179658 + Splice_Site INS - G G SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr1:1179657_1179658insG uc001adl.1 - 3 327 c.295_splice c.e3-1 p.R99_splice NM_001014980 NP_001014980 Q5T7M4 F132A_HUMAN family with sequence similarity 132, member A extracellular region 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217) Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.22e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199) GAGATCCCGCTGGGGGGAGAGA 0.678 0.58 5 7 DVL1 1855 broad.mit.edu 37 1 1271642 1271642 + Frame_Shift_Del DEL C - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr1:1271642delC uc001aer.3 - 15 1940 c.1893delG c.(1891-1893)GGGfs p.G631fs DVL1_uc002quu.2_Frame_Shift_Del_p.G373fs|DVL1_uc009vka.2_Frame_Shift_Del_p.G314fs|DVL1_uc001aeu.1_3'UTR NM_004421 NP_004412 O14640 DVL1_HUMAN dishevelled 1 656 canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome frizzled binding|identical protein binding|protein kinase binding|signal transducer activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145) 0.000 0.40 370 244 PAX7 5081 broad.mit.edu 37 1 19062532 19062532 + Frame_Shift_Del DEL A - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr1:19062532delA uc001bay.2 + 8 2160 c.1562delA c.(1561-1563)TAAfs p.*521fs PAX7_uc001baz.2_Frame_Shift_Del_p.*519fs|PAX7_uc010oct.1_Intron NM_002584 NP_002575 P23759 PAX7_HUMAN paired box 7 isoform 1 521 anti-apoptosis nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity PAX7/FOXO1(197) soft_tissue(197)|lung(3)|prostate(1)|ovary(1)|breast(1) 203 Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576) cagttcacctaaaatgacact 0.080 0.39 23 15 UBXN11 91544 broad.mit.edu 37 1 26608854 26608859 + In_Frame_Del DEL CCGGGA - - rs12354016 SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr1:26608854_26608859delCCGGGA uc001blw.2 - 16 1767_1772 c.1494_1499delTCCCGG c.(1492-1500)GGTCCCGGC>GGC p.498_500GPG>G UBXN11_uc001blz.1_In_Frame_Del_p.465_467GPG>G|UBXN11_uc001blv.2_In_Frame_Del_p.460_462GPG>G|UBXN11_uc001bly.2_In_Frame_Del_p.378_380GPG>G|UBXN11_uc001blx.2_In_Frame_Del_p.256_258GPG>G|UBXN11_uc001bma.2_In_Frame_Del_p.465_467GPG>G|UBXN11_uc001bmb.1_In_Frame_Del_p.498_500GPG>G NM_183008 NP_892120 Q5T124 UBX11_HUMAN socius isoform 2 498_500 Pro-rich.|3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|2. Missing. cytoplasm|cytoskeleton ovary(1) 1 gggactggggccgggaccgggaccgg 0.291 0.44 18 14 TIE1 7075 broad.mit.edu 37 1 43783744 43783745 + Splice_Site DEL GT - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr1:43783744_43783745delGT uc001ciu.2 + 17 3001 c.2922_splice c.e17+1 p.Q974_splice TIE1_uc010oke.1_Splice_Site_p.Q929_splice|TIE1_uc009vwq.2_Splice_Site_p.Q930_splice|TIE1_uc010okg.1_Splice_Site_p.Q619_splice NM_005424 NP_005415 P35590 TIE1_HUMAN tyrosine kinase with immunoglobulin-like and mesoderm development integral to plasma membrane ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity lung(3)|stomach(1)|salivary_gland(1)|ovary(1)|skin(1) 7 Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0505) TGAGAAGCAGGTGTGTGTGAGT 0.609 0.29 27 11 PTCH2 8643 broad.mit.edu 37 1 45292627 45292627 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr1:45292627delG uc010olf.1 - 17 2654 c.2642delC c.(2641-2643)CCAfs p.P881fs PTCH2_uc010olg.1_Frame_Shift_Del_p.P579fs NM_003738 NP_003729 Q9Y6C5 PTC2_HUMAN patched 2 881 Extracellular (Potential). protein complex assembly|spermatogenesis integral to plasma membrane hedgehog receptor activity lung(6)|breast(6)|central_nervous_system(3)|skin(2)|ovary(1) 18 Acute lymphoblastic leukemia(166;0.155) TTCAGGAGGTGGGGGGTAGAA 0.622 0.38 48 29 STIL 6491 broad.mit.edu 37 1 47728681 47728681 + Frame_Shift_Del DEL C - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr1:47728681delC uc001crc.1 - 15 2875 c.2720delG c.(2719-2721)GGTfs p.G907fs TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Frame_Shift_Del_p.G861fs|STIL_uc010omo.1_Frame_Shift_Del_p.G890fs|STIL_uc001crd.1_Frame_Shift_Del_p.G908fs|STIL_uc001cre.1_Frame_Shift_Del_p.G907fs|STIL_uc001crf.1_Frame_Shift_Del_p.G520fs|STIL_uc001crg.1_Frame_Shift_Del_p.G843fs NM_003035 NP_003026 Q15468 STIL_HUMAN SCL/TAL1 interrupting locus isoform 2 907 cell proliferation|multicellular organismal development centrosome|cytosol lung(2)|skin(1) 3 Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444) GTTACTGGCACCCCCTGTTGG 0.428 0.46 86 72 JAK1 3716 broad.mit.edu 37 1 65332803 65332803 + Frame_Shift_Del DEL C - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr1:65332803delC uc001dbu.1 - 7 985 c.736delG c.(736-738)GATfs p.D246fs JAK1_uc009wam.1_Frame_Shift_Del_p.D234fs NM_002227 NP_002218 P23458 JAK1_HUMAN janus kinase 1 246 FERM. interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway cytoskeleton|cytosol|endomembrane system|membrane|nucleus ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1) 61 BRCA - Breast invasive adenocarcinoma(111;0.0485) TTTAGGAAATCCTTGAAAACA 0.398 0.53 52 58 RBM15 64783 broad.mit.edu 37 1 110882873 110882873 + Frame_Shift_Del DEL C - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr1:110882873delC uc001dzl.1 + 1 929 c.846delC c.(844-846)CACfs p.H282fs RBM15_uc001dzm.1_Frame_Shift_Del_p.H282fs|uc001dzj.2_5'Flank NM_022768 NP_073605 Q96T37 RBM15_HUMAN RNA binding motif protein 15 282 interspecies interaction between organisms nucleus nucleotide binding|protein binding|RNA binding ovary(3) 3 all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634) BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135) 0.000 0.91 17 176 RNASEL 6041 broad.mit.edu 37 1 182545526 182545527 + Splice_Site INS - A A SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr1:182545526_182545527insA uc001gpj.1 - 5 2073 c.1906_splice c.e5-1 p.I636_splice RNASEL_uc009wxz.1_Splice_Site_p.I636_splice NM_021133 NP_066956 Q05823 RN5A_HUMAN ribonuclease L mRNA processing|response to virus|type I interferon-mediated signaling pathway mitochondrion ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding ovary(4)|stomach(1) 5 TTCATTAATCTAAAAAAACAAA 0.267 0.42 11 8 PIK3C2B 5287 broad.mit.edu 37 1 204426889 204426889 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr1:204426889delG uc001haw.2 - 10 2159 c.1680delC c.(1678-1680)CCCfs p.P560fs PIK3C2B_uc010pqv.1_Frame_Shift_Del_p.P560fs|PIK3C2B_uc001hax.1_Frame_Shift_Del_p.P560fs|PIK3C2B_uc009xbd.1_RNA NM_002646 NP_002637 O00750 P3C2B_HUMAN phosphoinositide-3-kinase, class 2 beta 560 cell communication|phosphatidylinositol-mediated signaling endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1) 7 all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227) GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193) GGGAGGGGCAGGGGGGCAGCT 0.597 0.58 5 7 DSTYK 25778 broad.mit.edu 37 1 205138425 205138425 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr1:205138425delT uc001hbw.2 - 3 1254 c.1190delA c.(1189-1191)AAGfs p.K397fs DSTYK_uc001hbx.2_Frame_Shift_Del_p.K397fs|DSTYK_uc001hby.1_Intron NM_015375 NP_056190 Q6XUX3 DUSTY_HUMAN receptor interacting protein kinase 5 isoform 1 397 Potential. cytoplasm ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(1) 1 CTCATTCTCCTTTTTTCGAGT 0.428 0.42 81 59 ROCK2 9475 broad.mit.edu 37 2 11332603 11332603 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr2:11332603delT uc002rbd.1 - 31 4372 c.3923delA c.(3922-3924)AAGfs p.K1308fs NM_004850 NP_004841 O75116 ROCK2_HUMAN Rho-associated, coiled-coil containing protein 1308 PH.|Phorbol-ester/DAG-type. axon guidance|cytokinesis|intracellular signal transduction cytosol|plasma membrane ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity stomach(2)|skin(2) 4 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162) AATCTCCTCCTTTTTGTCCAT 0.388 0.44 43 34 LRP1B 53353 broad.mit.edu 37 2 141625799 141625799 + Frame_Shift_Del DEL A - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr2:141625799delA uc002tvj.1 - 26 5175 c.4203delT c.(4201-4203)TTTfs p.F1401fs LRP1B_uc010fnl.1_Frame_Shift_Del_p.F583fs NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 1401 Extracellular (Potential).|LDL-receptor class B 11. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) CAATGCGAGGAAAATTTGCAT 0.318 0.43 31 23 TTN 7273 broad.mit.edu 37 2 179457381 179457381 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr2:179457381delG uc010zfg.1 - 250 51871 c.51647delC c.(51646-51648)CCTfs p.P17216fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.P10911fs|TTN_uc010zfi.1_Frame_Shift_Del_p.P10844fs|TTN_uc010zfj.1_Frame_Shift_Del_p.P10719fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 18143 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AATCAACTCAGGGGGTTCTAG 0.373 0.35 62 34 TTN 7273 broad.mit.edu 37 2 179535860 179535860 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr2:179535860delT uc010zfg.1 - 151 31586 c.31362delA c.(31360-31362)AAAfs p.K10454fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.K7115fs|TTN_uc010fre.1_Intron|TTN_uc010zfk.1_5'UTR NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 11381 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TAGTGGGCGGTTTTTTTGGAG 0.368 0.55 26 32 BMPR2 659 broad.mit.edu 37 2 203383716 203383717 + Frame_Shift_Del DEL GA - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr2:203383716_203383717delGA uc002uzf.3 + 6 1941_1942 c.793_794delGA c.(793-795)GAGfs p.E265fs BMPR2_uc010ftr.2_Frame_Shift_Del_p.E265fs NM_001204 NP_001195 Q13873 BMPR2_HUMAN bone morphogenetic protein receptor type II 265 Protein kinase.|Cytoplasmic (Potential). anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway integral to plasma membrane ATP binding|metal ion binding|transforming growth factor beta receptor activity ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1) 9 AGTTGGAGATGAGAGAGTCACT 0.356 0.55 43 52 IDH1 3417 broad.mit.edu 37 2 209116263 209116263 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr2:209116263delT uc002vcs.2 - 3 259 c.13delA c.(13-15)ATCfs p.I5fs IDH1_uc002vct.2_Frame_Shift_Del_p.I5fs|IDH1_uc002vcu.2_Frame_Shift_Del_p.I5fs NM_005896 NP_005887 O75874 IDHC_HUMAN isocitrate dehydrogenase 1 (NADP+), soluble 5 2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle cytosol|peroxisomal matrix isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1) 2868 Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136) CCGCCACTGATTTTTTTGGAC 0.318 0.33 38 19 OXSR1 9943 broad.mit.edu 37 3 38266188 38266189 + Frame_Shift_Ins INS - A A SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr3:38266188_38266189insA uc003chy.2 + 8 1171_1172 c.829_830insA c.(829-831)GAAfs p.E277fs OXSR1_uc010hhb.2_Frame_Shift_Ins_p.E211fs|OXSR1_uc010hha.1_Frame_Shift_Ins_p.E209fs NM_005109 NP_005100 O95747 OXSR1_HUMAN oxidative-stress responsive 1 277 Protein kinase. intracellular protein kinase cascade|response to oxidative stress ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity skin(1) 1 KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738) 0.000 0.46 66 56 SMARCC1 6599 broad.mit.edu 37 3 47677559 47677559 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr3:47677559delT uc003crq.2 - 23 2562 c.2444delA c.(2443-2445)AATfs p.N815fs SMARCC1_uc011bbc.1_RNA|SMARCC1_uc011bbd.1_Frame_Shift_Del_p.N706fs NM_003074 NP_003065 Q92922 SMRC1_HUMAN SWI/SNF-related matrix-associated 815 Glu-rich. chromatin remodeling|nervous system development|transcription, DNA-dependent nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex DNA binding|protein N-terminus binding|transcription coactivator activity skin(2)|lung(1) 3 BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01) 0.000 0.97 5 142 NPRL2 10641 broad.mit.edu 37 3 50385580 50385580 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr3:50385580delG uc003daj.1 - 9 1310 c.907delC c.(907-909)CAGfs p.Q303fs ZMYND10_uc003dag.1_5'Flank|ZMYND10_uc010hll.1_5'Flank|ZMYND10_uc003dah.1_5'Flank|ZMYND10_uc010hlm.1_5'Flank|NPRL2_uc003dai.1_Frame_Shift_Del_p.Q183fs|CYB561D2_uc003dak.2_5'Flank|CYB561D2_uc003dal.2_5'Flank|CYB561D2_uc003dam.2_5'Flank NM_006545 NP_006536 Q8WTW4 NPRL2_HUMAN tumor suppressor candidate 4 303 negative regulation of kinase activity protein binding|protein kinase activity lung(1) 1 TGCAGCTGCTGGGGGTGGCGG 0.582 0.85 4 23 GPR87 53836 broad.mit.edu 37 3 151012163 151012163 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr3:151012163delT uc003eyt.2 - 3 1232 c.871delA c.(871-873)ATCfs p.I291fs MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron NM_023915 NP_076404 Q9BY21 GPR87_HUMAN G protein-coupled receptor 87 291 Extracellular (Potential). integral to membrane|plasma membrane purinergic nucleotide receptor activity, G-protein coupled large_intestine(1) 1 LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517) TAATATAGGATTTTTTGTGCA 0.343 0.53 16 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.32 60 28 ADAM29 11086 broad.mit.edu 37 4 175898285 175898285 + Frame_Shift_Del DEL A - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr4:175898285delA uc003iuc.2 + 5 2279 c.1609delA c.(1609-1611)AAAfs p.K537fs ADAM29_uc003iud.2_Frame_Shift_Del_p.K537fs|ADAM29_uc010irr.2_Frame_Shift_Del_p.K537fs|ADAM29_uc011cki.1_Frame_Shift_Del_p.K537fs NM_014269 NP_055084 Q9UKF5 ADA29_HUMAN ADAM metallopeptidase domain 29 preproprotein 537 Cys-rich.|Extracellular (Potential). proteolysis|spermatogenesis integral to plasma membrane metalloendopeptidase activity|zinc ion binding skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1) 16 Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164) all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286) CTGTGGTATCAAAAATGCTAC 0.398 0.86 6 38 NIPBL 25836 broad.mit.edu 37 5 37064899 37064899 + Frame_Shift_Del DEL A - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr5:37064899delA uc003jkl.3 + 47 8819 c.8320delA c.(8320-8322)AAAfs p.K2774fs NIPBL_uc003jkk.3_3'UTR|NIPBL_uc003jkn.2_3'UTR NM_133433 NP_597677 Q6KC79 NIPBL_HUMAN delangin isoform A 2774 brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis SMC loading complex chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1) 9 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) CATTATTTACAAAAAAATTGC 0.463 0.49 44 43 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.71 63 157 APC 324 broad.mit.edu 37 5 112177434 112177435 + Frame_Shift_Ins INS - A A SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr5:112177434_112177435insA uc010jby.2 + 16 6523_6524 c.6143_6144insA c.(6142-6144)CCAfs p.P2048fs APC_uc011cvt.1_Frame_Shift_Ins_p.P2030fs|APC_uc003kpz.3_Frame_Shift_Ins_p.P2048fs|APC_uc003kpy.3_Frame_Shift_Ins_p.P2048fs|APC_uc010jbz.2_Frame_Shift_Ins_p.P1765fs|APC_uc010jca.2_Frame_Shift_Ins_p.P1348fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 2048 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.?(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) TCCGCAATGCCAAAAAAGAAAA 0.347 0.37 37 22 ARHGAP26 23092 broad.mit.edu 37 5 142513610 142513610 + Frame_Shift_Del DEL C - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr5:142513610delC uc011dbj.1 + 19 1812 c.1777delC c.(1777-1779)CCCfs p.P593fs ARHGAP26_uc003lmt.2_Frame_Shift_Del_p.P593fs|ARHGAP26_uc003lmw.2_Frame_Shift_Del_p.P593fs NM_015071 NP_055886 Q9UNA1 RHG26_HUMAN GTPase regulator associated with the focal 593 Ser-rich. actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction cytoskeleton|cytosol|focal adhesion cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding ovary(1) 1 all_hematologic(541;0.0416) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) TGACTCCAAGCCCCCGTCCTG 0.552 0.24 84 27 CAMK2A 815 broad.mit.edu 37 5 149631370 149631371 + Frame_Shift_Ins INS - G G SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr5:149631370_149631371insG uc003lru.2 - 9 850_851 c.635_636insC c.(634-636)CCGfs p.P212fs CAMK2A_uc003lrt.2_Frame_Shift_Ins_p.P212fs|CAMK2A_uc010jhe.2_Frame_Shift_Ins_p.P192fs|CAMK2A_uc010jhf.1_Frame_Shift_Ins_p.R50fs NM_171825 NP_741960 Q9UQM7 KCC2A_HUMAN calcium/calmodulin-dependent protein kinase II 212 Protein kinase. interferon-gamma-mediated signaling pathway|positive regulation of NF-kappaB transcription factor activity|synaptic transmission cell junction|cytosol|endocytic vesicle membrane|nucleoplasm|presynaptic membrane ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity large_intestine(1) 1 all_hematologic(541;0.224) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) 0.000 0.22 505 140 PRPF4B 8899 broad.mit.edu 37 6 4052975 4052975 + Frame_Shift_Del DEL A - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr6:4052975delA uc003mvv.2 + 11 2425 c.2334delA c.(2332-2334)TTAfs p.L778fs PRPF4B_uc003mvw.2_RNA|C6orf146_uc010jnq.1_Intron|PRPF4B_uc011dhv.1_RNA NM_003913 NP_003904 Q13523 PRP4B_HUMAN serine/threonine-protein kinase PRP4K 778 Protein kinase. catalytic step 2 spliceosome ATP binding|protein binding|protein serine/threonine kinase activity breast(5) 5 Ovarian(93;0.0925) all_hematologic(90;0.0895) GAGAGGTGTTAAAAAAATATG 0.299 0.40 36 24 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.64 23 41 CDC5L 988 broad.mit.edu 37 6 44371563 44371563 + Frame_Shift_Del DEL A - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr6:44371563delA uc003oxl.2 + 6 816 c.557delA c.(556-558)CAAfs p.Q186fs NM_001253 NP_001244 Q99459 CDC5L_HUMAN CDC5-like 186 Potential. cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus DNA binding|RNA binding lung(3)|ovary(1)|kidney(1)|skin(1) 6 all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208) Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536) GCTGCCCTCCAAAAAAGAAGA 0.353 0.42 23 17 TTK 7272 broad.mit.edu 37 6 80751897 80751898 + Frame_Shift_Del DEL AA - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr6:80751897_80751898delAA uc003pjc.2 + 22 2626_2627 c.2552_2553delAA c.(2551-2553)GAAfs p.E851fs TTK_uc003pjb.3_Frame_Shift_Del_p.E850fs NM_003318 NP_003309 P33981 TTK_HUMAN TTK protein kinase 851 mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation spindle ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity p.R838fs*4(3) ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1) 11 all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2) BRCA - Breast invasive adenocarcinoma(397;0.0321) AAGACTTTTGAAAAAAAAAGGG 0.297 0.54 11 13 CYB5R4 51167 broad.mit.edu 37 6 84634230 84634231 + Frame_Shift_Ins INS - A A SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr6:84634230_84634231insA uc003pkf.2 + 10 865_866 c.733_734insA c.(733-735)CAAfs p.Q245fs NM_016230 NP_057314 Q7L1T6 NB5R4_HUMAN cytochrome b5 reductase 4 245 CS. cell development|detection of oxygen|generation of precursor metabolites and energy|glucose homeostasis|insulin secretion|response to antibiotic|superoxide metabolic process endoplasmic reticulum|perinuclear region of cytoplasm cytochrome-b5 reductase activity|heme binding|NAD(P)H oxidase activity breast(2) 2 all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128) BRCA - Breast invasive adenocarcinoma(397;0.0871) GATTGTTCTACAAAAAAAAGAG 0.337 0.30 55 24 AKAP12 9590 broad.mit.edu 37 6 151671000 151671000 + Frame_Shift_Del DEL C - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr6:151671000delC uc011eep.1 + 4 1714 c.1474delC c.(1474-1476)CCCfs p.P492fs AKAP12_uc003qoe.2_Frame_Shift_Del_p.P492fs|AKAP12_uc003qof.2_Frame_Shift_Del_p.P394fs|AKAP12_uc010kim.2_Intron|AKAP12_uc003qog.2_Frame_Shift_Del_p.P387fs NM_005100 NP_005091 Q02952 AKA12_HUMAN A kinase (PRKA) anchor protein 12 isoform 1 492 Involved in PKC-binding (Probable). G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting cell cortex|cytoskeleton|plasma membrane adenylate cyclase binding|protein kinase A binding large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1) 8 Ovarian(120;0.125) BRCA - Breast invasive adenocarcinoma(37;0.175) OV - Ovarian serous cystadenocarcinoma(155;2.98e-11) GCTGTCCAAACCCCCCGAAGG 0.527 0.66 32 61 FGFR1OP 11116 broad.mit.edu 37 6 167417249 167417249 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr6:167417249delT uc003qvj.2 + 4 335 c.250delT c.(250-252)TTTfs p.F84fs CCR6_uc003qvl.2_5'UTR|FGFR1OP_uc011egp.1_Frame_Shift_Del_p.F84fs|FGFR1OP_uc003qvk.2_Frame_Shift_Del_p.F84fs NM_007045 NP_008976 O95684 FR1OP_HUMAN FGFR1 oncogene partner isoform a 84 LisH. G2/M transition of mitotic cell cycle|microtubule anchoring|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell proliferation centrosome|cytosol|nucleus|perinuclear region of cytoplasm protein homodimerization activity|protein kinase binding|protein tyrosine kinase inhibitor activity ovary(1) 1 Breast(66;1.48e-05)|Ovarian(120;0.0607) OV - Ovarian serous cystadenocarcinoma(33;1.73e-19)|BRCA - Breast invasive adenocarcinoma(81;5.1e-06)|GBM - Glioblastoma multiforme(31;0.00231) ATTTCTTCAGTTTTTTAACCT 0.294 0.33 43 21 HECW1 23072 broad.mit.edu 37 7 43436441 43436444 + Frame_Shift_Del DEL CCGT - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr7:43436441_43436444delCCGT uc003tid.1 + 7 1189_1192 c.584_587delCCGT c.(583-588)ACCGTCfs p.T195fs HECW1_uc011kbi.1_Frame_Shift_Del_p.T195fs|HECW1_uc003tie.1_Frame_Shift_Del_p.T227fs NM_015052 NP_055867 Q76N89 HECW1_HUMAN NEDD4-like ubiquitin-protein ligase 1 195_196 C2. protein ubiquitination involved in ubiquitin-dependent protein catabolic process cytoplasm|nucleus ubiquitin-protein ligase activity ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1) 23 GCTGATGAGACCGTCCAAGGACAA 0.422 0.45 71 58 GRM8 2918 broad.mit.edu 37 7 126544156 126544156 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr7:126544156delT uc003vlr.2 - 4 1199 c.888delA c.(886-888)AAAfs p.K296fs GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Frame_Shift_Del_p.K296fs|GRM8_uc010lkz.1_RNA|GRM8_uc003vlu.1_Frame_Shift_Del_p.K17fs NM_000845 NP_000836 O00222 GRM8_HUMAN glutamate receptor, metabotropic 8 isoform a 296 Extracellular (Potential). negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception integral to plasma membrane lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1) 23 Prostate(267;0.186) L-Glutamic Acid(DB00142) 0.000 0.44 381 302 TRIM24 8805 broad.mit.edu 37 7 138265390 138265390 + Frame_Shift_Del DEL A - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr7:138265390delA uc003vuc.2 + 16 2884 c.2669delA c.(2668-2670)GAAfs p.E890fs TRIM24_uc003vub.2_Frame_Shift_Del_p.E856fs NM_015905 NP_056989 O15164 TIF1A_HUMAN transcriptional intermediary factor 1 alpha 890 cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter cytoplasm chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1) 8 CACAACTCAGAAAAAAAGAAA 0.373 0.46 7 6 MLL3 58508 broad.mit.edu 37 7 151874147 151874148 + Frame_Shift_Ins INS - T T SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr7:151874147_151874148insT uc003wla.2 - 38 8609_8610 c.8390_8391insA c.(8389-8391)AAGfs p.K2797fs MLL3_uc003wkz.2_Frame_Shift_Ins_p.K1858fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.K306fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 2797 K -> R (in Ref. 1; AAK00583). intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding p.K2797fs*26(18) large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTTCTTGTTCCTTTTTTTTTGG 0.347 0.40 75 49 DLC1 10395 broad.mit.edu 37 8 12957359 12957359 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr8:12957359delG uc003wwm.2 - 9 2931 c.2487delC c.(2485-2487)CCCfs p.P829fs DLC1_uc003wwk.1_Frame_Shift_Del_p.P392fs|DLC1_uc003wwl.1_Frame_Shift_Del_p.P426fs|DLC1_uc011kxx.1_Frame_Shift_Del_p.P318fs NM_182643 NP_872584 Q96QB1 RHG07_HUMAN deleted in liver cancer 1 isoform 1 829 actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction caveola|cytosol|focal adhesion|nucleus Rho GTPase activator activity|SH2 domain binding ovary(3)|pancreas(2)|lung(1)|kidney(1) 7 TATTCCCCGAGGGGGAGAAAC 0.577 0.91 5 48 WHSC1L1 54904 broad.mit.edu 37 8 38146945 38146945 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr8:38146945delT uc003xli.2 - 18 3715 c.3197delA c.(3196-3198)AACfs p.N1066fs WHSC1L1_uc011lbm.1_Frame_Shift_Del_p.N1066fs|WHSC1L1_uc010lwe.2_Frame_Shift_Del_p.N1017fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 1066 Potential. cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TTTTCTTGAGTTTTTTTCAAT 0.373 0.37 69 40 ADAM32 203102 broad.mit.edu 37 8 39007371 39007371 + Frame_Shift_Del DEL C - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr8:39007371delC uc003xmt.3 + 5 583 c.338delC c.(337-339)ACGfs p.T113fs ADAM32_uc011lch.1_Frame_Shift_Del_p.T120fs|ADAM32_uc003xmu.3_Frame_Shift_Del_p.T113fs NM_145004 NP_659441 Q8TC27 ADA32_HUMAN a disintegrin and metalloprotease domain 32 113 proteolysis integral to membrane metalloendopeptidase activity|zinc ion binding ovary(1)|lung(1)|kidney(1) 3 all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503) LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146) ACACTCAGCACGTGCTCTGGA 0.373 0.43 67 50 VPS13B 157680 broad.mit.edu 37 8 100830957 100830957 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr8:100830957delT uc003yiv.2 + 47 8648 c.8537delT c.(8536-8538)CTTfs p.L2846fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.L2821fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 2846 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TTCAGCCCTCTTTTTATCATG 0.363 0.41 19 13 POU5F1B 5462 broad.mit.edu 37 8 128428179 128428179 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr8:128428179delG uc003ysf.2 + 1 323 c.68delG c.(67-69)TGGfs p.W23fs uc003ysc.1_Intron|uc003ysd.1_Intron|LOC727677_uc003yse.1_Intron NM_001159542 NP_001153014 Q06416 P5F1B_HUMAN POU class 5 homeobox 1B 23 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 GATGGGCCATGGGGGGCGGAG 0.706 0.90 1 9 TG 7038 broad.mit.edu 37 8 133894751 133894752 + Frame_Shift_Ins INS - G G SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr8:133894751_133894752insG uc003ytw.2 + 7 824_825 c.783_784insG c.(781-786)ATTTTTfs p.I261fs NM_003235 NP_003226 P01266 THYG_HUMAN thyroglobulin precursor 261_262 Thyroglobulin type-1 3. hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation extracellular space hormone activity ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1) 15 Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155) Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735) BRCA - Breast invasive adenocarcinoma(115;0.000701) KIRC - Kidney renal clear cell carcinoma(542;0.0546) ATGACACCATTTTTGCTGGCCT 0.470 0.43 55 42 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 1 12 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.62 253 405 BRD3 8019 broad.mit.edu 37 9 136918529 136918530 + Frame_Shift_Del DEL GG - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr9:136918529_136918530delGG uc004cew.2 - 2 258_259 c.70_71delCC c.(70-72)CCGfs p.P24fs BRD3_uc004cex.2_Frame_Shift_Del_p.P24fs NM_007371 NP_031397 Q15059 BRD3_HUMAN bromodomain containing protein 3 24 nucleus protein binding p.P24fs*24(1) BRD3/C15orf55(3) stomach(4)|midline_organs(3)|kidney(1) 8 OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07) GGAGACCTCCGGGGGGGGTGGG 0.658 0.53 8 9 MYST4 23522 broad.mit.edu 37 10 76744938 76744938 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr10:76744938delT uc001jwn.1 + 12 2967 c.2474delT c.(2473-2475)CTTfs p.L825fs MYST4_uc001jwm.1_Frame_Shift_Del_p.L533fs|MYST4_uc001jwo.1_Frame_Shift_Del_p.L533fs|MYST4_uc001jwp.1_Frame_Shift_Del_p.L642fs NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 825 Catalytic.|Interaction with BRPF1. histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) GAGCCATTCCTTTTTTATGTC 0.378 0.42 64 47 EIF3A 8661 broad.mit.edu 37 10 120809481 120809482 + Frame_Shift_Del DEL CT - - rs149195320 SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr10:120809481_120809482delCT uc001ldu.2 - 17 2635_2636 c.2489_2490delAG c.(2488-2490)GAGfs p.E830fs EIF3A_uc010qsu.1_Frame_Shift_Del_p.E796fs|EIF3A_uc009xzg.1_5'UTR NM_003750 NP_003741 Q14152 EIF3A_HUMAN eukaryotic translation initiation factor 3, 830 Interaction with EIF3B.|Glu-rich. formation of translation initiation complex cytosol|eukaryotic translation initiation factor 3 complex protein binding|structural molecule activity|translation initiation factor activity 0 Lung NSC(174;0.094)|all_lung(145;0.123) all cancers(201;0.0236) GTTCGGCGCGCTCTCTCTCTTC 0.490 0.53 18 20 NLRP6 171389 broad.mit.edu 37 11 280371 280371 + Frame_Shift_Del DEL A - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr11:280371delA uc010qvs.1 + 4 637 c.637delA c.(637-639)AAAfs p.K213fs NLRP6_uc010qvt.1_Frame_Shift_Del_p.K213fs NM_138329 NP_612202 P59044 NALP6_HUMAN NLR family, pyrin domain containing 6 213 NACHT. cytoplasm ATP binding upper_aerodigestive_tract(1)|skin(1) 2 all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122) 0.000 0.20 581 145 CCKBR 887 broad.mit.edu 37 11 6292451 6292451 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr11:6292451delT uc001mcp.2 + 5 1215 c.1022delT c.(1021-1023)CTTfs p.L341fs CCKBR_uc001mcq.2_Frame_Shift_Del_p.L269fs|CCKBR_uc001mcr.2_Frame_Shift_Del_p.L341fs|CCKBR_uc001mcs.2_Frame_Shift_Del_p.L410fs|CCKBR_uc001mct.1_RNA NM_176875 NP_795344 P32239 GASR_HUMAN cholecystokinin B receptor 341 Helical; Name=6; (Potential). activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception 1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding lung(5)|ovary(2)|breast(1) 8 Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029) Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139) Pentagastrin(DB00183) 0.000 0.32 709 334 SCYL1 57410 broad.mit.edu 37 11 65305963 65305964 + Frame_Shift_Del DEL GA - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr11:65305963_65305964delGA uc001oea.1 + 18 2430_2431 c.2353_2354delGA c.(2353-2355)GAGfs p.E785fs SCYL1_uc009yqk.2_3'UTR|SCYL1_uc001oeb.1_Frame_Shift_Del_p.E768fs|SCYL1_uc001oec.1_Frame_Shift_Del_p.G772fs|SCYL1_uc001oed.1_Frame_Shift_Del_p.E642fs|SCYL1_uc001oee.1_Frame_Shift_Del_p.G410fs NM_020680 NP_065731 Q96KG9 NTKL_HUMAN SCY1-like 1 isoform A 785 Potential. regulation of transcription, DNA-dependent|retrograde vesicle-mediated transport, Golgi to ER|transcription, DNA-dependent cis-Golgi network|COPI vesicle coat|ER-Golgi intermediate compartment|microtubule organizing center|nucleus ATP binding|DNA binding|protein tyrosine kinase activity skin(1) 1 0.000 0.38 479 291 THRSP 7069 broad.mit.edu 37 11 77775063 77775063 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr11:77775063delG uc001oyx.2 + 1 157 c.136delG c.(136-138)GGGfs p.G46fs NM_003251 NP_003242 Q92748 THRSP_HUMAN thyroid hormone-responsive protein 46 lipid biosynthetic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|nucleus breast(1) 1 all_cancers(14;2.23e-19)|all_epithelial(13;7.49e-22)|Breast(9;6.38e-17)|Ovarian(111;0.152) OV - Ovarian serous cystadenocarcinoma(8;2.15e-25) 0.000 0.50 173 172 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 158 26 LTBR 4055 broad.mit.edu 37 12 6499902 6499902 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr12:6499902delG uc001qny.1 + 10 1275 c.1107delG c.(1105-1107)CTGfs p.L369fs LTBR_uc010sfc.1_Frame_Shift_Del_p.L350fs|LTBR_uc001qnz.1_Frame_Shift_Del_p.L364fs NM_002342 NP_002333 P36941 TNR3_HUMAN lymphotoxin beta receptor precursor 369 Cytoplasmic (Potential). apoptosis|cellular response to mechanical stimulus|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade integral to membrane protein binding|receptor activity lung(2) 2 GACCAGTACTGGGGGGACCAC 0.597 0.40 59 40 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.31 33 15 CDX2 1045 broad.mit.edu 37 13 28539006 28539006 + Splice_Site DEL C - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr13:28539006delC uc001urv.2 - 2 861 c.687_splice c.e2+1 p.Q229_splice NM_001265 NP_001256 Q99626 CDX2_HUMAN caudal type homeobox 2 organ morphogenesis|transcription from RNA polymerase II promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity lung(1) 1 all_cancers(110;0.191)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155) Lung SC(185;0.0156) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199) GCGGTCCCCACCTGCCTCTCA 0.617 0.30 61 26 CHD8 57680 broad.mit.edu 37 14 21861813 21861813 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr14:21861813delG uc001was.1 - 32 5398 c.5304delC c.(5302-5304)CCCfs p.P1768fs CHD8_uc001war.1_Frame_Shift_Del_p.P1664fs|SNORD9_uc001wat.1_5'Flank NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 2047 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) TAGTATCAGAGGGGGATACTC 0.552 0.49 70 66 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.44 9 7 TRIP11 9321 broad.mit.edu 37 14 92472698 92472698 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr14:92472698delT uc001xzy.2 - 11 2410 c.1622delA c.(1621-1623)AAGfs p.K541fs TRIP11_uc010auf.1_Frame_Shift_Del_p.K277fs NM_004239 NP_004230 Q15643 TRIPB_HUMAN thyroid hormone receptor interactor 11 541 Potential. transcription from RNA polymerase II promoter cytoskeleton|Golgi apparatus|membrane|nucleus protein binding|transcription coactivator activity ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1) 13 COAD - Colon adenocarcinoma(157;0.223) ATGAACTCTCTTTTTTTCATC 0.303 0.48 48 44 CHRNB4 1143 broad.mit.edu 37 15 78922277 78922277 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr15:78922277delT uc002bed.1 - 5 482 c.370delA c.(370-372)ACCfs p.T124fs CHRNB4_uc002bee.1_Intron|CHRNB4_uc010blh.1_5'UTR NM_000750 NP_000741 P30926 ACHB4_HUMAN cholinergic receptor, nicotinic, beta 4 124 Extracellular (Potential). regulation of neurotransmitter secretion|synaptic transmission involved in micturition|synaptic transmission, cholinergic cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity 0 0.000 0.42 238 172 CHD9 80205 broad.mit.edu 37 16 53340227 53340228 + Frame_Shift_Ins INS - T T SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr16:53340227_53340228insT uc002ehb.2 + 31 6862_6863 c.6698_6699insT c.(6697-6699)AGTfs p.S2233fs CHD9_uc002egy.2_Frame_Shift_Ins_p.S2233fs|CHD9_uc002ehc.2_Frame_Shift_Ins_p.S2234fs|CHD9_uc002ehf.2_Frame_Shift_Ins_p.S1347fs|CHD9_uc010cbw.2_Frame_Shift_Ins_p.S299fs|CHD9_uc002ehg.1_Frame_Shift_Ins_p.S240fs NM_025134 NP_079410 Q3L8U1 CHD9_HUMAN chromodomain helicase DNA binding protein 9 2233 cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleoplasm ATP binding|DNA binding|helicase activity|protein binding lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1) 7 all_cancers(37;0.0212) ACTCAGGATAGTTTTCAGATGA 0.401 0.37 50 29 FANCA 2175 broad.mit.edu 37 16 89831345 89831346 + Frame_Shift_Del DEL AG - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr16:89831345_89831346delAG uc002fou.1 - 28 2772_2773 c.2730_2731delCT c.(2728-2733)CTCTGGfs p.L910fs FANCA_uc010vpn.1_Frame_Shift_Del_p.L910fs|FANCA_uc010vpo.1_Frame_Shift_Del_p.L39fs NM_000135 NP_000126 O15360 FANCA_HUMAN Fanconi anemia, complementation group A isoform 910_911 DNA repair|protein complex assembly cytoplasm|nucleoplasm protein binding ovary(2)|breast(2)|central_nervous_system(1)|skin(1) 6 Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194) BRCA - Breast invasive adenocarcinoma(80;0.028) CTGTGTGTCCAGAGAGAGAGGG 0.559 0.46 19 16 MYH10 4628 broad.mit.edu 37 17 8380303 8380305 + In_Frame_Del DEL CTT - - rs139898919 byFrequency SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr17:8380303_8380305delCTT uc002gll.2 - 40 5771_5773 c.5675_5677delAAG c.(5674-5679)GAAGCG>GCG p.E1892del MYH10_uc002glm.2_In_Frame_Del_p.E1923del|MYH10_uc010cnx.2_In_Frame_Del_p.E1901del NM_005964 NP_005955 P35580 MYH10_HUMAN myosin, heavy polypeptide 10, non-muscle 1892 Potential. actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape cell cortex|cleavage furrow|midbody|myosin complex|stress fiber actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity ovary(2) 2 GCACGCGTCGCTTCTTCTTCTGC 0.571 0.29 37 15 CDK12 51755 broad.mit.edu 37 17 37672018 37672019 + Frame_Shift_Ins INS - T T SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr17:37672018_37672019insT uc010cvv.2 + 9 3389_3390 c.2803_2804insT c.(2803-2805)ATTfs p.I935fs CDK12_uc010wef.1_Frame_Shift_Ins_p.I934fs|CDK12_uc002hrw.3_Frame_Shift_Ins_p.I935fs NM_016507 NP_057591 Q9NYV4 CDK12_HUMAN Cdc2-related kinase, arginine/serine-rich 935 Protein kinase. mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1) 19 AAAGAAGCCTATTTTTCAAGCC 0.406 0.46 53 45 RNF43 54894 broad.mit.edu 37 17 56438165 56438168 + Frame_Shift_Del DEL CAGA - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr17:56438165_56438168delCAGA uc002iwf.2 - 6 2781_2784 c.825_828delTCTG c.(823-828)TGTCTGfs p.C275fs RNF43_uc010wnv.1_Frame_Shift_Del_p.C234fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.C275fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.C275fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.C148fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 275_276 RING-type; atypical.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.40 530 348 GRB2 2885 broad.mit.edu 37 17 73316467 73316467 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr17:73316467delG uc002jnx.3 - 6 993 c.636delC c.(634-636)CCCfs p.P212fs GRB2_uc002jny.3_Frame_Shift_Del_p.P171fs NM_002086 NP_002077 P62993 GRB2_HUMAN growth factor receptor-bound protein 2 isoform 212 SH3 2. axon guidance|blood coagulation|cell junction assembly|cell-cell signaling|cellular response to ionizing radiation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|receptor internalization|signal transduction in response to DNA damage|T cell costimulation cytosol|Golgi apparatus epidermal growth factor receptor binding|insulin receptor substrate binding|SH3/SH2 adaptor activity ovary(3) 3 all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222) all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185) Pegademase bovine(DB00061) TCCGGTTCACGGGGGTGACAT 0.453 0.43 47 35 ROCK1 6093 broad.mit.edu 37 18 18588126 18588127 + Frame_Shift_Del DEL TG - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr18:18588126_18588127delTG uc002kte.2 - 14 2380_2381 c.1439_1440delCA c.(1438-1440)ACAfs p.T480fs NM_005406 NP_005397 Q13464 ROCK1_HUMAN Rho-associated, coiled-coil containing protein 480 Interaction with FHOD1.|Potential.|REM. actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction centriole|cytosol|Golgi membrane ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity lung(2)|breast(2)|central_nervous_system(1) 5 Melanoma(1;0.165) TCTGAGACACTGTAGATTCTAG 0.327 0.50 29 29 RIOK3 8780 broad.mit.edu 37 18 21059376 21059376 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr18:21059376delT uc002kui.3 + 12 2057 c.1440delT c.(1438-1440)GATfs p.D480fs RIOK3_uc010dls.2_Frame_Shift_Del_p.D477fs|RIOK3_uc010xas.1_Frame_Shift_Del_p.D464fs|RIOK3_uc010xat.1_Frame_Shift_Del_p.D224fs NM_003831 NP_003822 O14730 RIOK3_HUMAN sudD suppressor of bimD6 homolog 480 Protein kinase. chromosome segregation ATP binding|protein binding|protein serine/threonine kinase activity ovary(2)|central_nervous_system(1) 3 all_cancers(21;0.000106)|all_epithelial(16;6.74e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0202)|Ovarian(20;0.127) ATGAAGCTGATTTTTTAGCTG 0.413 0.55 24 29 SMAD2 4087 broad.mit.edu 37 18 45374949 45374952 + Frame_Shift_Del DEL AGTG - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr18:45374949_45374952delAGTG uc002lcy.2 - 8 1139_1142 c.891_894delCACT c.(889-894)CTCACTfs p.L297fs SMAD2_uc002lcz.2_Frame_Shift_Del_p.L297fs|SMAD2_uc010xdc.1_Frame_Shift_Del_p.L267fs|SMAD2_uc010xdd.1_Frame_Shift_Del_p.L267fs NM_005901 NP_005892 Q15796 SMAD2_HUMAN Sma- and Mad-related protein 2 isoform 1 297_298 MH2. anterior/posterior pattern formation|cell fate commitment|common-partner SMAD protein phosphorylation|intracellular signal transduction|mesoderm formation|negative regulation of transcription, DNA-dependent|palate development|paraxial mesoderm morphogenesis|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|regulation of binding|regulation of transforming growth factor beta receptor signaling pathway|response to cholesterol|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|zygotic specification of dorsal/ventral axis activin responsive factor complex|cytosol activating transcription factor binding|co-SMAD binding|double-stranded DNA binding|I-SMAD binding|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding large_intestine(3)|lung(1)|central_nervous_system(1) 5 AGCCATCTACAGTGAGTGAGGGCT 0.422 0.42 58 42 ATP8B1 5205 broad.mit.edu 37 18 55328515 55328517 + In_Frame_Del DEL GCA - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr18:55328515_55328517delGCA uc002lgw.2 - 21 2596_2598 c.2596_2598delTGC c.(2596-2598)TGCdel p.C866del uc002lgu.1_Intron|uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 866 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) GGGTGACGCGGCAGCAGATGACT 0.567 0.36 80 45 VAV1 7409 broad.mit.edu 37 19 6832176 6832178 + In_Frame_Del DEL GAA - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr19:6832176_6832178delGAA uc002mfu.1 + 15 1570_1572 c.1473_1475delGAA c.(1471-1476)TTGAAG>TTG p.K494del VAV1_uc010xjh.1_In_Frame_Del_p.K462del|VAV1_uc010dva.1_In_Frame_Del_p.K494del|VAV1_uc002mfv.1_In_Frame_Del_p.K439del NM_005428 NP_005419 P15498 VAV_HUMAN vav 1 guanine nucleotide exchange factor 494 PH. apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation cytosol|plasma membrane metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1) 16 CAAGAGAATTGAAGAAGAAGTGG 0.438 0.40 34 23 NOTCH3 4854 broad.mit.edu 37 19 15272238 15272238 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr19:15272238delG uc002nan.2 - 33 6277 c.6201delC c.(6199-6201)CCCfs p.P2067fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 2067 Cytoplasmic (Potential). Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) 0.000 0.49 293 280 NOTCH3 4854 broad.mit.edu 37 19 15290919 15290919 + Frame_Shift_Del DEL C - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr19:15290919delC uc002nan.2 - 20 3367 c.3291delG c.(3289-3291)GGGfs p.G1097fs NOTCH3_uc002nao.1_Frame_Shift_Del_p.G1045fs NM_000435 NP_000426 Q9UM47 NOTC3_HUMAN Notch homolog 3 precursor 1097 Extracellular (Potential).|EGF-like 28. Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1) 21 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) CACGGCAGGTCCCCCCATGCT 0.652 0.41 10 7 DYRK1B 9149 broad.mit.edu 37 19 40316612 40316612 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr19:40316612delG uc002omj.2 - 11 1913 c.1633delC c.(1633-1635)CAGfs p.Q545fs DYRK1B_uc002omi.2_Frame_Shift_Del_p.Q517fs|DYRK1B_uc002omk.2_Frame_Shift_Del_p.Q505fs NM_004714 NP_004705 Q9Y463 DYR1B_HUMAN dual-specificity tyrosine-(Y)-phosphorylation 545 positive regulation of transcription, DNA-dependent nucleus ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|transcription coactivator activity ovary(4)|stomach(1)|central_nervous_system(1)|skin(1) 7 all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06) Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23) 0.000 0.35 837 442 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.34 35 18 CD79A 973 broad.mit.edu 37 19 42383610 42383610 + Frame_Shift_Del DEL C - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr19:42383610delC uc002orv.2 + 3 570 c.385delC c.(385-387)CCCfs p.P129fs CD79A_uc002oru.2_Frame_Shift_Del_p.P91fs NM_001783 NP_001774 P11912 CD79A_HUMAN CD79A antigen isoform 1 precursor 129 Extracellular (Potential). B cell differentiation|B cell proliferation|B cell receptor signaling pathway B cell receptor complex|external side of plasma membrane|integral to membrane|membrane raft|multivesicular body transmembrane receptor activity ovary(2)|pancreas(1) 3 0.000 0.43 230 173 LMTK3 114783 broad.mit.edu 37 19 49002059 49002060 + Frame_Shift_Del DEL GG - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr19:49002059_49002060delGG uc002pjk.2 - 12 2353_2354 c.2353_2354delCC c.(2353-2355)CCGfs p.P785fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.23 373 113 BRSK1 84446 broad.mit.edu 37 19 55813012 55813013 + Frame_Shift_Ins INS - A A SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr19:55813012_55813013insA uc002qkg.2 + 8 1088_1089 c.811_812insA c.(811-813)GAAfs p.E271fs BRSK1_uc002qkf.2_Frame_Shift_Ins_p.E287fs|BRSK1_uc002qkh.2_5'Flank NM_032430 NP_115806 Q8TDC3 BRSK1_HUMAN BR serine/threonine kinase 1 271 Protein kinase. establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV cell junction|cytoplasm|nucleus magnesium ion binding|protein serine/threonine kinase activity ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1) 6 Renal(1328;0.245) BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.0474) AGTGGAGCCCGAAAAAAGGCTC 0.584 0.47 21 19 HCK 3055 broad.mit.edu 37 20 30661595 30661595 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr20:30661595delG uc002wxh.2 + 4 474 c.303delG c.(301-303)AAGfs p.K101fs HCK_uc010gdy.2_Frame_Shift_Del_p.K80fs|HCK_uc002wxi.2_Frame_Shift_Del_p.K79fs NM_002110 NP_002101 P08631 HCK_HUMAN hemopoietic cell kinase isoform p61HCK 101 SH3. interspecies interaction between organisms|mesoderm development|regulation of defense response to virus by virus|viral reproduction caveola|cytosol ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(4)|ovary(2)|central_nervous_system(2)|pancreas(1) 9 UCEC - Uterine corpus endometrioid carcinoma (5;0.0241) 0.000 0.51 411 434 TP53RK 112858 broad.mit.edu 37 20 45315440 45315440 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr20:45315440delT uc002xsk.2 - 2 937 c.714delA c.(712-714)AAAfs p.K238fs SLC13A3_uc002xsg.1_5'Flank|SLC13A3_uc010gho.1_5'Flank|TP53RK_uc002xsj.2_3'UTR NM_033550 NP_291028 Q96S44 PRPK_HUMAN p53-related protein kinase 238 Protein kinase. lipopolysaccharide biosynthetic process membrane|nucleus ATP binding|p53 binding|protein serine/threonine kinase activity|protein tyrosine kinase activity 0 Myeloproliferative disorder(115;0.0122) CTTCATCTAATTTTTTTAGCA 0.448 0.43 65 50 SS18L1 26039 broad.mit.edu 37 20 60740566 60740566 + Frame_Shift_Del DEL G - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr20:60740566delG uc002ycb.2 + 8 967 c.912delG c.(910-912)GAGfs p.E304fs SS18L1_uc011aaa.1_Frame_Shift_Del_p.E304fs|SS18L1_uc002ybz.1_RNA|SS18L1_uc002yca.1_RNA|SS18L1_uc002ycc.1_RNA NM_198935 NP_945173 O75177 CREST_HUMAN SS18-like protein 1 304 Gln-rich.|MFD domain (By similarity). chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent condensed chromosome kinetochore ovary(2) 2 Breast(26;3.97e-09) BRCA - Breast invasive adenocarcinoma(19;1.92e-08) 0.000 0.91 16 162 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 76 345 SMARCB1 6598 broad.mit.edu 37 22 24134057 24134057 + Frame_Shift_Del DEL A - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr22:24134057delA uc002zyb.2 + 2 415 c.208delA c.(208-210)AAAfs p.K70fs SMARCB1_uc002zyg.2_Frame_Shift_Del_p.K70fs|SMARCB1_uc011ajb.1_Intron|SMARCB1_uc002zya.2_Frame_Shift_Del_p.K70fs|SMARCB1_uc002zyc.2_Intron|SMARCB1_uc002zyd.2_Intron|SMARCB1_uc002zye.1_Frame_Shift_Del_p.K33fs|SMARCB1_uc002zyf.1_Intron|SMARCB1_uc010gue.1_Intron NM_003073 NP_003064 Q12824 SNF5_HUMAN SWI/SNF related, matrix associated, actin 70 cell cycle|chromatin remodeling|DNA integration|interspecies interaction between organisms|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|retroviral genome replication|transcription, DNA-dependent nBAF complex|npBAF complex|nucleolus|nucleoplasm|SWI/SNF complex p53 binding p.?(2) soft_tissue(193)|central_nervous_system(172)|haematopoietic_and_lymphoid_tissue(23)|meninges(5)|skin(5)|bone(4)|ovary(2)|endometrium(1)|lung(1)|pancreas(1) 407 Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05) GTCACATGGTAAAAAAACAAA 0.443 0.28 26 10 ADRBK2 157 broad.mit.edu 37 22 26114297 26114297 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr22:26114297delT uc003abx.3 + 19 1887 c.1740delT c.(1738-1740)TATfs p.Y580fs ADRBK2_uc003aby.3_RNA NM_005160 NP_005151 P35626 ARBK2_HUMAN beta-adrenergic receptor kinase 2 580 PH. ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity lung(3)|ovary(2)|stomach(1)|central_nervous_system(1) 7 Adenosine triphosphate(DB00171) AGCGTCGCTATTTTTACCTCT 0.483 0.42 29 21 MN1 4330 broad.mit.edu 37 22 28193952 28193953 + Frame_Shift_Del DEL CA - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr22:28193952_28193953delCA uc003adj.2 - 1 3534_3535 c.2579_2580delTG c.(2578-2580)CTGfs p.L860fs NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 860 binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 0.000 0.41 467 322 ZNRF3 84133 broad.mit.edu 37 22 29440843 29440844 + Frame_Shift_Ins INS - T T SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr22:29440843_29440844insT uc003aeg.2 + 5 574_575 c.409_410insT c.(409-411)CTTfs p.L137fs ZNRF3_uc003aeh.1_Frame_Shift_Ins_p.L137fs NM_032173 NP_115549 Q9ULT6 ZNRF3_HUMAN zinc and ring finger 3 237 Helical; (Potential). integral to membrane zinc ion binding ovary(1) 1 0.000 0.44 133 103 DDX17 10521 broad.mit.edu 37 22 38897211 38897211 + Frame_Shift_Del DEL T - - SNUC2A_LARGE_INTESTINE NA SNUC2A_LARGE_INTESTINE NA g.chr22:38897211delT uc003avy.3 - 2 465 c.362delA c.(361-363)AAGfs p.K121fs DDX17_uc003avx.3_Frame_Shift_Del_p.K121fs|DDX17_uc011anu.1_Frame_Shift_Del_p.K34fs NM_001098504 NP_001091974 Q92841 DDX17_HUMAN DEAD box polypeptide 17 isoform 3 42 RNA processing nucleus ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity skin(3)|upper_aerodigestive_tract(1) 4 Melanoma(58;0.0286) 0.000 0.11 456 56 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 21 TNFRSF9 3604 broad.mit.edu 37 1 7998254 7998254 + Frame_Shift_Del DEL T - - rs9657965 byFrequency;by1000genomes SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr1:7998254delT uc001aot.2 - 4 473 c.345delA c.(343-345)AAAfs p.K115fs NM_001561 NP_001552 Q07011 TNR9_HUMAN tumor necrosis factor receptor superfamily, 115 Extracellular (Potential).|TNFR-Cys 3. induction of apoptosis|negative regulation of cell proliferation integral to plasma membrane binding|receptor activity large_intestine(1)|lung(1)|ovary(1)|skin(1) 4 Ovarian(185;0.0634)|all_lung(157;0.151) all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649) CAAACGTACCTTTTTTTGTCA 0.413 0.91 5 53 SPEN 23013 broad.mit.edu 37 1 16260558 16260558 + Frame_Shift_Del DEL A - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr1:16260558delA uc001axk.1 + 11 8027 c.7823delA c.(7822-7824)GAAfs p.E2608fs SPEN_uc010obp.1_Frame_Shift_Del_p.E2567fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 2608 RID. interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) GCTGACAAGGAAAAGGTGGCT 0.453 0.46 27 23 PLK3 1263 broad.mit.edu 37 1 45270026 45270026 + Frame_Shift_Del DEL C - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr1:45270026delC uc001cmn.2 + 12 1458 c.1358delC c.(1357-1359)GCCfs p.A453fs PLK3_uc001cmo.2_RNA NM_004073 NP_004064 Q9H4B4 PLK3_HUMAN polo-like kinase 3 453 membrane ATP binding|protein binding|protein serine/threonine kinase activity 0 Acute lymphoblastic leukemia(166;0.155) CAGAACCCGGCCCCCCTGGCC 0.617 0.52 21 23 TRIM33 51592 broad.mit.edu 37 1 115053498 115053499 + Frame_Shift_Ins INS - C C rs6691166 by1000genomes SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr1:115053498_115053499insC uc001eew.2 - 1 283_284 c.199_200insG c.(199-201)GTGfs p.V67fs TRIM33_uc001eex.2_Frame_Shift_Ins_p.V67fs NM_015906 NP_056990 Q9UPN9 TRI33_HUMAN tripartite motif-containing 33 protein isoform 67 Necessary for E3 ubiquitin-protein ligase activity and repression of SMAD4 signaling and transcriptional repression. negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent nucleus co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 11 all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184) all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05) Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133) 0.000 0.12 225 31 ARNT 405 broad.mit.edu 37 1 150789282 150789283 + Frame_Shift_Ins INS - G G SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr1:150789282_150789283insG uc001evr.1 - 18 1926_1927 c.1783_1784insC c.(1783-1785)CGGfs p.R595fs ARNT_uc010pck.1_Frame_Shift_Ins_p.R84fs|ARNT_uc001evs.1_Frame_Shift_Ins_p.R580fs|ARNT_uc009wmb.1_Frame_Shift_Ins_p.R581fs|ARNT_uc009wmc.1_Frame_Shift_Ins_p.R595fs|ARNT_uc009wmd.1_Frame_Shift_Ins_p.R580fs NM_001668 NP_001659 P27540 ARNT_HUMAN aryl hydrocarbon receptor nuclear translocator 595 positive regulation of hormone biosynthetic process|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|response to hypoxia aryl hydrocarbon receptor binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity skin(4)|lung(3)|central_nervous_system(1)|kidney(1) 9 all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211) CTCTGCCGGCCGGGGGGTAGGA 0.525 0.39 37 24 NTRK1 4914 broad.mit.edu 37 1 156849088 156849093 + In_Frame_Del DEL GGGACT - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr1:156849088_156849093delGGGACT uc001fqh.1 + 15 2036_2041 c.1980_1985delGGGACT c.(1978-1986)CAGGGACTG>CAG p.GL661del NTRK1_uc001fqf.1_In_Frame_Del_p.GL625del|NTRK1_uc009wsi.1_In_Frame_Del_p.GL360del|NTRK1_uc001fqi.1_In_Frame_Del_p.GL655del|NTRK1_uc009wsk.1_In_Frame_Del_p.GL658del NM_002529 NP_002520 P04629 NTRK1_HUMAN neurotrophic tyrosine kinase, receptor, type 1 661_662 Cytoplasmic (Potential).|Protein kinase. activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction endosome|integral to plasma membrane ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity lung(9)|ovary(6)|stomach(1)|central_nervous_system(1) 17 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) Imatinib(DB00619) TAGTGGGCCAGGGACTGGTGGTCAAG 0.587 0.58 8 11 TPR 7175 broad.mit.edu 37 1 186330039 186330040 + Splice_Site INS - A A SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr1:186330039_186330040insA uc001grv.2 - 10 1256 c.959_splice c.e10-1 p.A320_splice TPR_uc010pop.1_Splice_Site_p.A396_splice NM_003292 NP_003283 P12270 TPR_HUMAN nuclear pore complex-associated protein TPR carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm ATP binding|protein binding|serine-tRNA ligase activity ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1) 7 Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157) Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553) CTTTGTTGGCTAAAAAACAATT 0.322 0.37 48 28 OBSCN 84033 broad.mit.edu 37 1 228503566 228503566 + Frame_Shift_Del DEL G - - rs79023478 byFrequency;by1000genomes SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr1:228503566delG uc009xez.1 + 50 13075 c.13031delG c.(13030-13032)CGGfs p.R4344fs OBSCN_uc001hsn.2_Frame_Shift_Del_p.R4344fs NM_001098623 NP_001092093 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and 4344 Ig-like 45. apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|M band|Z disc ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1) 28 Prostate(94;0.0405) 0.000 0.40 164 110 SOX11 6664 broad.mit.edu 37 2 5833526 5833528 + In_Frame_Del DEL GAC - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr2:5833526_5833528delGAC uc002qyj.2 + 1 728_730 c.673_675delGAC c.(673-675)GACdel p.D233del NM_003108 NP_003099 P35716 SOX11_HUMAN SRY-box 11 233 Poly-Asp. cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis cytoplasm|nucleolus enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding central_nervous_system(3) 3 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) OV - Ovarian serous cystadenocarcinoma(76;0.132) 0.000 0.43 192 143 MYCN 4613 broad.mit.edu 37 2 16082314 16082314 + Frame_Shift_Del DEL C - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr2:16082314delC uc002rci.2 + 2 428 c.128delC c.(127-129)ACCfs p.T43fs MYCNOS_uc002rch.1_5'Flank|MYCN_uc010yjr.1_Frame_Shift_Del_p.T35fs NM_005378 NP_005369 P04198 MYCN_HUMAN v-myc myelocytomatosis viral related oncogene, 43 regulation of transcription from RNA polymerase II promoter chromatin|nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity central_nervous_system(2)|ovary(1)|lung(1)|skin(1) 5 all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197) GBM - Glioblastoma multiforme(3;0.000332) 0.000 0.37 73 42 NRBP1 29959 broad.mit.edu 37 2 27658018 27658018 + Frame_Shift_Del DEL C - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr2:27658018delC uc002rko.2 + 8 1417 c.585delC c.(583-585)GACfs p.D195fs NRBP1_uc002rkq.2_Frame_Shift_Del_p.D195fs|NRBP1_uc002rkp.2_Frame_Shift_Del_p.D195fs|NRBP1_uc002rkr.2_5'Flank NM_013392 NP_037524 Q9UHY1 NRBP_HUMAN nuclear receptor binding protein 195 Protein kinase. ER to Golgi vesicle-mediated transport|gene expression|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor cell cortex|endomembrane system|lamellipodium|membrane|nucleoplasm ATP binding|protein homodimerization activity|protein kinase activity ovary(2)|lung(1) 3 Acute lymphoblastic leukemia(172;0.155) ACTCCTGTGACCCCCCCATCA 0.587 0.37 62 37 BIRC6 57448 broad.mit.edu 37 2 32800345 32800347 + In_Frame_Del DEL GAA - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr2:32800345_32800347delGAA uc010ezu.2 + 66 13401_13403 c.13267_13269delGAA c.(13267-13269)GAAdel p.E4425del NM_016252 NP_057336 Q9NR09 BIRC6_HUMAN baculoviral IAP repeat-containing 6 4425 anti-apoptosis|apoptosis intracellular acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1) 14 Acute lymphoblastic leukemia(172;0.155) CGGTGAAGAGGAAGAAGAACAGT 0.453 0.41 88 60 VRK2 7444 broad.mit.edu 37 2 58386493 58386495 + In_Frame_Del DEL AGG - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr2:58386493_58386495delAGG uc002rzo.2 + 16 1937_1939 c.1192_1194delAGG c.(1192-1194)AGGdel p.R400del VRK2_uc010fcb.2_3'UTR|VRK2_uc002rzs.2_3'UTR|VRK2_uc002rzr.2_3'UTR|VRK2_uc010fcc.2_In_Frame_Del_p.R282del|VRK2_uc002rzv.2_In_Frame_Del_p.R400del|VRK2_uc010fcd.2_In_Frame_Del_p.R377del|VRK2_uc002rzp.2_In_Frame_Del_p.R400del|VRK2_uc010ypg.1_In_Frame_Del_p.R400del|VRK2_uc002rzq.2_3'UTR|VRK2_uc002rzu.2_3'UTR|VRK2_uc002rzt.2_In_Frame_Del_p.R282del|FANCL_uc002rzw.3_3'UTR|FANCL_uc002rzx.3_3'UTR|FANCL_uc010fce.2_3'UTR NM_001130482 NP_001123954 Q86Y07 VRK2_HUMAN vaccinia related kinase 2 isoform 2 400 integral to membrane ATP binding|protein binding|protein serine/threonine kinase activity ovary(1) 1 GGAAAGCACAAGGAGAAGACAGA 0.310 0.37 38 22 TTN 7273 broad.mit.edu 37 2 179583429 179583429 + Frame_Shift_Del DEL A - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr2:179583429delA uc010zfg.1 - 81 20990 c.20766delT c.(20764-20766)TTTfs p.F6922fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.F3583fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 7849 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AACCTTTCACAAAAAGATGTG 0.383 0.43 69 53 CNTN6 27255 broad.mit.edu 37 3 1262422 1262422 + Frame_Shift_Del DEL T - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr3:1262422delT uc003boz.2 + 3 374 c.107delT c.(106-108)ATTfs p.I36fs CNTN6_uc010hbo.2_Frame_Shift_Del_p.I31fs|CNTN6_uc011asj.1_5'UTR|CNTN6_uc003bpa.2_Frame_Shift_Del_p.I36fs NM_014461 NP_055276 Q9UQ52 CNTN6_HUMAN contactin 6 precursor 36 Ig-like C2-type 1. axon guidance|cell adhesion|central nervous system development|Notch signaling pathway anchored to membrane|plasma membrane skin(3)|lung(2)|breast(2)|pancreas(1) 8 all_cancers(2;0.000164)|all_epithelial(2;0.107) Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139) CATGATGTCATTTTTCCTTTG 0.398 0.49 39 38 RHOA 387 broad.mit.edu 37 3 49405885 49405885 + Frame_Shift_Del DEL A - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr3:49405885delA uc003cwu.2 - 3 529 c.253delT c.(253-255)TCCfs p.S85fs RHOA_uc010hku.2_Frame_Shift_Del_p.S4fs NM_001664 NP_001655 P61586 RHOA_HUMAN ras homolog gene family, member A precursor 85 axon guidance|interspecies interaction between organisms|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of axonogenesis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of neuron differentiation|positive regulation of NF-kappaB import into nucleus|positive regulation of stress fiber assembly|regulation of cell migration|regulation of small GTPase mediated signal transduction|Rho protein signal transduction|spindle assembly involved in mitosis cytoskeleton|cytosol|plasma membrane GTP binding|GTPase activity|myosin binding ovary(2) 2 BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258) Atorvastatin(DB01076)|Simvastatin(DB00641) CTGTCGATGGAAAAACACATC 0.512 0.39 48 31 SEMA3B 7869 broad.mit.edu 37 3 50311902 50311902 + Frame_Shift_Del DEL G - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr3:50311902delG uc003cyu.2 + 13 1488 c.1246delG c.(1246-1248)GGGfs p.G416fs SEMA3B_uc003cyt.2_Frame_Shift_Del_p.G415fs|SEMA3B_uc003cyv.2_Frame_Shift_Del_p.G303fs|SEMA3B_uc003cyw.2_Frame_Shift_Del_p.G139fs|SEMA3B_uc010hli.2_Frame_Shift_Del_p.G308fs|SEMA3B_uc003cyx.2_Frame_Shift_Del_p.G302fs|SEMA3B_uc003cyy.2_Frame_Shift_Del_p.G73fs|SEMA3B_uc011bdo.1_Frame_Shift_Del_p.G73fs NM_004636 NP_004627 Q13214 SEM3B_HUMAN semaphorin 3B isoform 1 precursor 416 Sema. axon guidance|cell-cell signaling endoplasmic reticulum|extracellular region|membrane receptor activity lung(2)|central_nervous_system(2)|kidney(1)|skin(1) 6 BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605) CCTGCCCACTGGGGGGCGCCC 0.562 0.53 47 52 EPHA6 285220 broad.mit.edu 37 3 96706303 96706304 + Frame_Shift_Ins INS - C C SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr3:96706303_96706304insC uc010how.1 + 3 623_624 c.580_581insC c.(580-582)ATTfs p.I194fs EPHA6_uc003drp.1_Frame_Shift_Ins_p.I194fs NM_001080448 NP_001073917 Q9UF33 EPHA6_HUMAN EPH receptor A6 isoform a 99 Ephrin-binding.|Extracellular (Potential). integral to plasma membrane ATP binding|ephrin receptor activity stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1) 16 AGCTCAGAAAATTTATGTGGAA 0.391 0.51 42 43 IL1RAP 3556 broad.mit.edu 37 3 190345194 190345194 + Frame_Shift_Del DEL A - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr3:190345194delA uc003fsm.1 + 8 1064 c.858delA c.(856-858)GGAfs p.G286fs IL1RAP_uc003fsk.2_Frame_Shift_Del_p.G286fs|IL1RAP_uc003fsl.2_Frame_Shift_Del_p.G286fs|IL1RAP_uc010hzf.2_Frame_Shift_Del_p.G145fs|IL1RAP_uc010hzg.1_Frame_Shift_Del_p.G286fs|IL1RAP_uc003fsn.1_RNA|IL1RAP_uc003fso.1_Frame_Shift_Del_p.G286fs|IL1RAP_uc003fsp.1_RNA|IL1RAP_uc003fsq.2_Frame_Shift_Del_p.G286fs NM_002182 NP_002173 Q9NPH3 IL1AP_HUMAN interleukin 1 receptor accessory protein isoform 286 Extracellular (Potential).|Ig-like C2-type 3. inflammatory response|innate immune response|protein complex assembly extracellular region|integral to plasma membrane ovary(1) 1 all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21) Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06) GBM - Glioblastoma multiforme(93;0.00851) CCATTGATGGAAAAAAACCTG 0.388 0.45 34 28 TNK2 10188 broad.mit.edu 37 3 195597005 195597006 + Frame_Shift_Ins INS - G G SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr3:195597005_195597006insG uc003fvu.1 - 11 2065_2066 c.1522_1523insC c.(1522-1524)CAGfs p.Q508fs TNK2_uc003fvq.1_5'Flank|TNK2_uc003fvr.1_Frame_Shift_Ins_p.Q18fs|TNK2_uc003fvs.1_Frame_Shift_Ins_p.Q540fs|TNK2_uc003fvt.1_Frame_Shift_Ins_p.Q571fs|TNK2_uc010hzw.1_RNA|TNK2_uc003fvv.1_Frame_Shift_Ins_p.Q338fs NM_005781 NP_005772 Q07912 ACK1_HUMAN tyrosine kinase, non-receptor, 2 isoform 1 508 Missing (in Ref. 4; AAH08884). positive regulation of peptidyl-tyrosine phosphorylation|protein ubiquitination|small GTPase mediated signal transduction adherens junction|cytoplasmic vesicle membrane|endosome|nucleus ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1) 10 all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206) Lung NSC(153;0.191) Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05) GBM - Glioblastoma multiforme(46;0.000757) Adenosine triphosphate(DB00171) TCCTAGATGCTGGGGGGGCCGG 0.614 0.28 28 11 TNK2 10188 broad.mit.edu 37 3 195597045 195597046 + Frame_Shift_Ins INS - G G SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr3:195597045_195597046insG uc003fvu.1 - 11 2025_2026 c.1482_1483insC c.(1480-1485)CCCGACfs p.P494fs TNK2_uc003fvq.1_5'Flank|TNK2_uc003fvr.1_Frame_Shift_Ins_p.P4fs|TNK2_uc003fvs.1_Frame_Shift_Ins_p.P526fs|TNK2_uc003fvt.1_Frame_Shift_Ins_p.P557fs|TNK2_uc010hzw.1_RNA|TNK2_uc003fvv.1_Frame_Shift_Ins_p.P324fs NM_005781 NP_005772 Q07912 ACK1_HUMAN tyrosine kinase, non-receptor, 2 isoform 1 494_495 Missing (in Ref. 4; AAH08884). positive regulation of peptidyl-tyrosine phosphorylation|protein ubiquitination|small GTPase mediated signal transduction adherens junction|cytoplasmic vesicle membrane|endosome|nucleus ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1) 10 all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206) Lung NSC(153;0.191) Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05) GBM - Glioblastoma multiforme(46;0.000757) Adenosine triphosphate(DB00171) CTCAGGAGGTCGGGGGGGTCCA 0.619 0.38 28 17 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.26 20 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.26 64 22 FBXW7 55294 broad.mit.edu 37 4 153249360 153249361 + Frame_Shift_Ins INS - T T SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr4:153249360_153249361insT uc003ims.2 - 9 1566_1567 c.1417_1418insA c.(1417-1419)AGAfs p.R473fs FBXW7_uc011cii.1_Frame_Shift_Ins_p.R473fs|FBXW7_uc003imt.2_Frame_Shift_Ins_p.R473fs|FBXW7_uc011cih.1_Frame_Shift_Ins_p.R297fs|FBXW7_uc003imq.2_Frame_Shift_Ins_p.R393fs|FBXW7_uc003imr.2_Frame_Shift_Ins_p.R355fs NM_033632 NP_361014 Q969H0 FBXW7_HUMAN F-box and WD repeat domain containing 7 isoform 473 WD 3. interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex protein binding|protein binding p.R473fs*4(3)|p.R473fs*25(2) haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1) 308 all_hematologic(180;0.093) Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067) TTTCCCTTACCTTTTTTCATGA 0.416 0.45 88 71 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.71 15 36 COL4A3BP 10087 broad.mit.edu 37 5 74696124 74696125 + Splice_Site INS - A A SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr5:74696124_74696125insA uc011csu.1 - 10 1440 c.1018_splice c.e10-1 p.S340_splice COL4A3BP_uc003kds.2_Splice_Site_p.S340_splice|COL4A3BP_uc003kdt.2_Splice_Site_p.S468_splice|COL4A3BP_uc003kdu.2_Splice_Site_p.S340_splice NM_005713 NP_005704 Q9Y5P4 C43BP_HUMAN alpha 3 type IV collagen binding protein isoform ER to Golgi ceramide transport|immune response cytosol|endoplasmic reticulum membrane|Golgi apparatus ceramide binding|phosphatidylinositol-4-phosphate binding|protein binding|protein kinase activity skin(1) 1 all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174) OV - Ovarian serous cystadenocarcinoma(47;1e-53) ACTCTGTGACTAAAAAAACATA 0.371 0.43 29 22 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.62 45 75 CHD1 1105 broad.mit.edu 37 5 98235340 98235340 + Frame_Shift_Del DEL T - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr5:98235340delT uc003knf.2 - 7 1077 c.929delA c.(928-930)AACfs p.N310fs NM_001270 NP_001261 O14646 CHD1_HUMAN chromodomain helicase DNA binding protein 1 310 Chromo 1. regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117) COAD - Colon adenocarcinoma(37;0.0717) Epirubicin(DB00445) TGGTTCTTTGTTTTTTTCAAA 0.413 0.48 83 78 APC 324 broad.mit.edu 37 5 112173690 112173690 + Frame_Shift_Del DEL T - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr5:112173690delT uc010jby.2 + 16 2779 c.2399delT c.(2398-2400)GTTfs p.V800fs APC_uc011cvt.1_Frame_Shift_Del_p.V782fs|APC_uc003kpz.3_Frame_Shift_Del_p.V800fs|APC_uc003kpy.3_Frame_Shift_Del_p.V800fs|APC_uc010jbz.2_Frame_Shift_Del_p.V517fs|APC_uc010jca.2_Frame_Shift_Del_p.V100fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 800 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.?(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) GGTGATTATGTTTTTGACACC 0.373 0.42 75 54 APC 324 broad.mit.edu 37 5 112175952 112175952 + Frame_Shift_Del DEL A - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr5:112175952delA uc010jby.2 + 16 5041 c.4661delA c.(4660-4662)GAAfs p.E1554fs APC_uc011cvt.1_Frame_Shift_Del_p.E1536fs|APC_uc003kpz.3_Frame_Shift_Del_p.E1554fs|APC_uc003kpy.3_Frame_Shift_Del_p.E1554fs|APC_uc010jbz.2_Frame_Shift_Del_p.E1271fs|APC_uc010jca.2_Frame_Shift_Del_p.E854fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1554 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.T1556fs*3(35)|p.E1554fs*5(2)|p.E1554*(2)|p.?(1)|p.T1556fs*9(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1554fs*11(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) AAAGAGGCAGAAAAAACTATT 0.338 0.38 28 17 VDAC1 7416 broad.mit.edu 37 5 133316638 133316639 + Frame_Shift_Ins INS - T T SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr5:133316638_133316639insT uc003kyp.1 - 6 431_432 c.332_333insA c.(331-333)AATfs p.N111fs VDAC1_uc003kyq.1_Frame_Shift_Ins_p.N111fs|VDAC1_uc003kyr.1_Frame_Shift_Ins_p.N111fs NM_003374 NP_003365 P21796 VDAC1_HUMAN voltage-dependent anion channel 1 111 Beta stranded. apoptosis|interspecies interaction between organisms mitochondrial nucleoid|mitochondrial outer membrane|plasma membrane|pore complex porin activity|protein binding|voltage-gated anion channel activity 0 KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02) Dihydroxyaluminium(DB01375) TGATTTTAGCATTTTTTTTCCT 0.406 0.34 54 28 NUP153 9972 broad.mit.edu 37 6 17675498 17675499 + Frame_Shift_Ins INS - T T rs140571428 byFrequency SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr6:17675498_17675499insT uc003ncd.1 - 4 884_885 c.684_685insA c.(682-687)AAACCAfs p.K228fs NUP153_uc011dje.1_Frame_Shift_Ins_p.K228fs|NUP153_uc010jpl.1_Frame_Shift_Ins_p.K228fs NM_005124 NP_005115 P49790 NU153_HUMAN nucleoporin 153kDa 228_229 carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm DNA binding|protein binding|transporter activity|zinc ion binding lung(4)|ovary(2)|breast(2)|skin(1) 9 Breast(50;0.0259)|Ovarian(93;0.0584) all_hematologic(90;0.125) all cancers(50;0.0981)|Epithelial(50;0.112) TTGAATGCTGGTTTTTTTGAGC 0.411 0.40 58 38 PHF3 23469 broad.mit.edu 37 6 64415953 64415953 + Frame_Shift_Del DEL A - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr6:64415953delA uc003pep.1 + 11 3428 c.3402delA c.(3400-3402)CCAfs p.P1134fs PHF3_uc010kah.1_Frame_Shift_Del_p.P948fs|PHF3_uc003pen.2_Frame_Shift_Del_p.P1046fs|PHF3_uc011dxs.1_Frame_Shift_Del_p.P403fs NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 1134 multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) ATCTTTCTCCAAAAAAAGTAA 0.358 0.46 46 39 TTK 7272 broad.mit.edu 37 6 80741193 80741195 + In_Frame_Del DEL TCT - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr6:80741193_80741195delTCT uc003pjc.2 + 14 1605_1607 c.1531_1533delTCT c.(1531-1533)TCTdel p.S513del TTK_uc003pjb.3_In_Frame_Del_p.S512del NM_003318 NP_003309 P33981 TTK_HUMAN TTK protein kinase 513 mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation spindle ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1) 11 all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2) BRCA - Breast invasive adenocarcinoma(397;0.0321) GGTTTTAGCATCTTCTTCAGCAA 0.296 0.39 22 14 LRGUK 136332 broad.mit.edu 37 7 133906656 133906656 + Frame_Shift_Del DEL A - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr7:133906656delA uc003vrm.1 + 16 1985 c.1969delA c.(1969-1971)AAAfs p.K657fs NM_144648 NP_653249 Q96M69 LRGUK_HUMAN leucine-rich repeats and guanylate kinase domain 657 ATP binding|kinase activity lung(2)|skin(2)|kidney(1) 5 ACTTTCAGCCAAAAAAACACC 0.388 0.36 39 22 EPHB6 2051 broad.mit.edu 37 7 142562052 142562054 + In_Frame_Del DEL CCT - - rs67146761;rs8177142 SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr7:142562052_142562054delCCT uc011kst.1 + 7 1281_1283 c.494_496delCCT c.(493-498)CCCTCC>CCC p.S176del EPHB6_uc011ksu.1_In_Frame_Del_p.S176del|EPHB6_uc003wbs.2_5'UTR|EPHB6_uc003wbt.2_Intron|EPHB6_uc003wbu.2_5'UTR|EPHB6_uc003wbv.2_5'Flank NM_004445 NP_004436 O15197 EPHB6_HUMAN ephrin receptor EphB6 precursor 176 Extracellular (Potential).|Poly-Ser. extracellular region|integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1) 19 Melanoma(164;0.059) GAGAGCTTTCcctcctcctcctc 0.522 0.12 77 11 KCNH2 3757 broad.mit.edu 37 7 150656679 150656679 + Frame_Shift_Del DEL G - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr7:150656679delG uc003wic.2 - 3 466 c.453delC c.(451-453)CCCfs p.P151fs KCNH2_uc011kux.1_Frame_Shift_Del_p.P55fs|KCNH2_uc003wie.2_Frame_Shift_Del_p.P151fs NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 151 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) GCCAGCTGGTGGGGGGGCCCC 0.587 0.40 15 10 NOS3 4846 broad.mit.edu 37 7 150698398 150698398 + Frame_Shift_Del DEL G - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr7:150698398delG uc003wif.2 + 11 1609 c.1313delG c.(1312-1314)AGGfs p.R438fs NOS3_uc011kuy.1_Frame_Shift_Del_p.R232fs|NOS3_uc011kuz.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kva.1_Frame_Shift_Del_p.R438fs|NOS3_uc011kvb.1_Frame_Shift_Del_p.R438fs NM_000603 NP_000594 P29474 NOS3_HUMAN nitric oxide synthase 3 isoform 1 438 Interaction with NOSIP. anti-apoptosis|arginine catabolic process|blood vessel remodeling|endothelial cell migration|mitochondrion organization|negative regulation of muscle hyperplasia|negative regulation of platelet activation|nitric oxide biosynthetic process|platelet activation|positive regulation of angiogenesis|positive regulation of guanylate cyclase activity|positive regulation of vasodilation|regulation of blood vessel size|regulation of nitric-oxide synthase activity|regulation of systemic arterial blood pressure by endothelin|response to fluid shear stress|response to heat|smooth muscle hyperplasia caveola|cytoskeleton|cytosol|Golgi membrane actin monomer binding|arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding central_nervous_system(5)|large_intestine(2)|skin(1) 8 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) L-Arginine(DB00125)|L-Citrulline(DB00155)|Rosuvastatin(DB01098)|Tetrahydrobiopterin(DB00360) 0.000 0.48 338 307 MLL3 58508 broad.mit.edu 37 7 151874148 151874149 + Frame_Shift_Del DEL TT - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr7:151874148_151874149delTT uc003wla.2 - 38 8608_8609 c.8389_8390delAA c.(8389-8391)AAGfs p.K2797fs MLL3_uc003wkz.2_Frame_Shift_Del_p.K1858fs|MLL3_uc003wky.2_Frame_Shift_Del_p.K306fs NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 2797 K -> R (in Ref. 1; AAK00583). intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding p.K2797fs*26(18) large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) TTCTTGTTCCTTTTTTTTTGGT 0.347 0.40 105 71 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.81 4 17 TRPS1 7227 broad.mit.edu 37 8 116426519 116426519 + Frame_Shift_Del DEL T - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr8:116426519delT uc003ynz.2 - 6 4037 c.3578delA c.(3577-3579)AATfs p.N1193fs TRPS1_uc011lhy.1_Frame_Shift_Del_p.N1197fs|TRPS1_uc003yny.2_Frame_Shift_Del_p.N1206fs|TRPS1_uc010mcy.2_Frame_Shift_Del_p.N1193fs NM_014112 NP_054831 Q9UHF7 TRPS1_HUMAN zinc finger transcription factor TRPS1 1193 Transcriptional repressor domain (By similarity). negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) GGGACCTTCATTTTTTACATT 0.418 0.37 73 43 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.20 368 94 SMARCA2 6595 broad.mit.edu 37 9 2039816 2039818 + In_Frame_Del DEL CAA - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr9:2039816_2039818delCAA uc003zhc.2 + 4 805_807 c.706_708delCAA c.(706-708)CAAdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.26 225 80 IFNA4 3441 broad.mit.edu 37 9 21187074 21187077 + Frame_Shift_Del DEL AAAG - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr9:21187074_21187077delAAAG uc003zon.2 - 1 522_525 c.454_457delCTTT c.(454-459)CTTTATfs p.L152fs NM_021068 NP_066546 P05014 IFNA4_HUMAN interferon, alpha 4 precursor 152_153 blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway extracellular space cytokine activity|interferon-alpha/beta receptor binding ovary(1)|skin(1) 2 GBM - Glioblastoma multiforme(5;2.69e-202)|Lung(24;2.26e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13) TCTGTTAGATAAAGAGTGATTCTT 0.451 0.33 41 20 CTSL1 1514 broad.mit.edu 37 9 90343256 90343256 + Frame_Shift_Del DEL C - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr9:90343256delC uc004aph.2 + 4 691 c.341delC c.(340-342)GCCfs p.A114fs CTSL1_uc004api.2_Frame_Shift_Del_p.A114fs|CTSL1_uc004apj.2_Frame_Shift_Del_p.A59fs|CTSL1_uc010mqh.2_Intron|CTSL1_uc004apk.2_Frame_Shift_Del_p.A114fs|CTSL1_uc004apl.2_Frame_Shift_Del_p.A114fs NM_001912 NP_001903 P07711 CATL1_HUMAN cathepsin L1 preproprotein 114 macrophage apoptosis|proteolysis extracellular region|lysosome|nucleus cysteine-type endopeptidase activity|histone binding ovary(3) 3 Glucagon recombinant(DB00040) TTTTATGAGGCCCCCAGATCT 0.502 0.50 26 26 GRIN3A 116443 broad.mit.edu 37 9 104500075 104500075 + Frame_Shift_Del DEL G - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr9:104500075delG uc004bbp.1 - 1 788 c.187delC c.(187-189)CGCfs p.R63fs GRIN3A_uc004bbq.1_Frame_Shift_Del_p.R63fs NM_133445 NP_597702 Q8TCU5 NMD3A_HUMAN glutamate receptor, ionotropic, 63 Extracellular (Potential). response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1) 7 Acute lymphoblastic leukemia(62;0.0568) Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740) 0.000 0.35 79 43 MUSK 4593 broad.mit.edu 37 9 113459694 113459694 + Frame_Shift_Del DEL A - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr9:113459694delA uc004bey.2 + 5 674 c.576delA c.(574-576)GCAfs p.A192fs MUSK_uc004bex.2_Frame_Shift_Del_p.A192fs NM_005592 NP_005583 O15146 MUSK_HUMAN skeletal muscle receptor tyrosine kinase 192 Ig-like 2.|Extracellular (Potential). transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(3)|ovary(2)|central_nervous_system(1) 6 GATGTGTGGCAAAAAACAGCC 0.483 0.45 73 60 MASTL 84930 broad.mit.edu 37 10 27459254 27459254 + Frame_Shift_Del DEL A - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr10:27459254delA uc001itm.2 + 8 2005 c.1366delA c.(1366-1368)AAAfs p.K456fs MASTL_uc001itl.2_Frame_Shift_Del_p.K456fs|MASTL_uc009xkw.1_Frame_Shift_Del_p.K456fs|MASTL_uc009xkx.1_RNA NM_032844 NP_116233 Q96GX5 GWL_HUMAN microtubule associated serine/threonine 456 Protein kinase. cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus centrosome|cleavage furrow|nucleus ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity stomach(1)|ovary(1)|lung(1) 3 CAGTCCTTGTAAAAAAATTAT 0.338 0.42 53 38 ERCC6 2074 broad.mit.edu 37 10 50679168 50679169 + Splice_Site INS - A A SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr10:50679168_50679169insA uc001jhs.3 - 17 3079 c.2925_splice c.e17-1 p.R975_splice ERCC6_uc009xod.2_Splice_Site_p.R135_splice|ERCC6_uc010qgr.1_Splice_Site_p.R345_splice|ERCC6_uc001jhr.3_Splice_Site_p.R343_splice NM_000124 NP_000115 Q03468 ERCC6_HUMAN excision repair cross-complementing rodent base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair nucleolus|soluble fraction|transcription elongation factor complex ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1) 16 AAGATTTGTCTAAAAAAATAAA 0.327 0.44 37 29 PTEN 5728 broad.mit.edu 37 10 89720712 89720712 + Frame_Shift_Del DEL A - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr10:89720712delA uc001kfb.2 + 9 1894 c.863delA c.(862-864)GAAfs p.E288fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 288 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.E288fs*3(6)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.E288*(2)|p.G165_*404del(1)|p.S287fs*1(1)|p.G165_K342del(1)|p.E288fs*8(1)|p.S287fs*8(1)|p.W274_F341del(1)|p.E288K(1)|p.E288fs*9(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) GAAACCTCAGAAAAAGTAGAA 0.299 0.44 81 64 FGFR2 2263 broad.mit.edu 37 10 123263368 123263369 + Frame_Shift_Ins INS - G G SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr10:123263368_123263369insG uc010qtk.1 - 11 2021_2022 c.1374_1375insC c.(1372-1377)CCCATGfs p.P458fs FGFR2_uc010qtg.1_Frame_Shift_Ins_p.P346fs|FGFR2_uc010qth.1_Frame_Shift_Ins_p.P343fs|FGFR2_uc010qti.1_Frame_Shift_Ins_p.P369fs|FGFR2_uc010qtj.1_Frame_Shift_Ins_p.P459fs|FGFR2_uc010qtl.1_Frame_Shift_Ins_p.P342fs|FGFR2_uc010qtm.1_Frame_Shift_Ins_p.P341fs|FGFR2_uc001lfl.3_Frame_Shift_Ins_p.P459fs|FGFR2_uc001lfm.2_Frame_Shift_Ins_p.P370fs|FGFR2_uc001lfg.3_Frame_Shift_Ins_p.P66fs NM_000141 NP_000132 P21802 FGFR2_HUMAN fibroblast growth factor receptor 2 isoform 1 458_459 Cytoplasmic (Potential). angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1) 96 Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107) STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722) all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845) Palifermin(DB00039) CCTGCCAGCATGGGGGTGTCTG 0.530 0.37 56 33 NUP98 4928 broad.mit.edu 37 11 3733905 3733907 + In_Frame_Del DEL CTC - - rs146002237 SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr11:3733905_3733907delCTC uc001lyh.2 - 20 2920_2922 c.2629_2631delGAG c.(2629-2631)GAGdel p.E877del NUP98_uc001lyi.2_In_Frame_Del_p.E877del|NUP98_uc001lyj.1_In_Frame_Del_p.E877del|NUP98_uc001lyk.1_In_Frame_Del_p.E894del NM_016320 NP_057404 P52948 NUP98_HUMAN nucleoporin 98kD isoform 1 894 Poly-Glu. carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex protein binding|structural constituent of nuclear pore|transporter activity breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1) 12 Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227) BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199) TAGACGGATGCTCCTCCTCCTCT 0.458 0.51 41 43 NR1H3 10062 broad.mit.edu 37 11 47282887 47282887 + Frame_Shift_Del DEL C - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr11:47282887delC uc009ylm.2 + 5 816 c.595delC c.(595-597)CCCfs p.P199fs NR1H3_uc009yll.1_Frame_Shift_Del_p.P205fs|NR1H3_uc010rhk.1_Frame_Shift_Del_p.P205fs|NR1H3_uc001nek.2_Frame_Shift_Del_p.P154fs|NR1H3_uc001nej.2_Frame_Shift_Del_p.P199fs|NR1H3_uc001nel.2_Frame_Shift_Del_p.P154fs|NR1H3_uc001nen.3_Frame_Shift_Del_p.P199fs|NR1H3_uc001nem.2_Frame_Shift_Del_p.P199fs|NR1H3_uc001nep.2_Frame_Shift_Del_p.P108fs NM_005693 NP_005684 Q13133 NR1H3_HUMAN nuclear receptor subfamily 1, group H, member 3 199 apoptotic cell clearance|cellular response to lipopolysaccharide|cholesterol homeostasis|negative regulation of cholesterol storage|negative regulation of inflammatory response|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of macrophage activation|negative regulation of pancreatic juice secretion|negative regulation of pinocytosis|negative regulation of secretion of lysosomal enzymes|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of cholesterol homeostasis|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of receptor biosynthetic process|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of circadian rhythm|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to progesterone stimulus|triglyceride homeostasis nuclear chromatin|nucleoplasm cholesterol binding|steroid hormone receptor activity|sterol response element binding|transcription coactivator activity|zinc ion binding ovary(2)|lung(1) 3 GGCTTCCTCACCCCCCCAAAT 0.592 0.57 19 25 MAML2 84441 broad.mit.edu 37 11 96075011 96075011 + Frame_Shift_Del DEL C - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr11:96075011delC uc001pfw.1 - 1 1334 c.49delG c.(49-51)GCCfs p.A17fs NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 17 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) GCCCCAGAGGCCCCCCCTAGC 0.677 0.44 15 12 NPAT 4863 broad.mit.edu 37 11 108057280 108057280 + Frame_Shift_Del DEL T - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr11:108057280delT uc001pjz.3 - 8 757 c.655delA c.(655-657)AGTfs p.S219fs NPAT_uc001pka.2_Frame_Shift_Del_p.S14fs NM_002519 NP_002510 Q14207 NPAT_HUMAN nuclear protein, ataxia-telangiectasia locus 219 Interaction with MIZF. positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle Cajal body protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity ovary(2) 2 all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116) AAAGTGGTACTTTTTCTCTGA 0.313 0.43 54 41 PLEKHA5 54477 broad.mit.edu 37 12 19427574 19427575 + Frame_Shift_Ins INS - A A rs12369271 SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr12:19427574_19427575insA uc001reb.2 + 10 1038_1039 c.952_953insA c.(952-954)GAAfs p.E318fs PLEKHA5_uc010sie.1_Frame_Shift_Ins_p.E324fs|PLEKHA5_uc001rea.2_Frame_Shift_Ins_p.E318fs|PLEKHA5_uc009zin.2_Frame_Shift_Ins_p.E76fs|PLEKHA5_uc010sif.1_Frame_Shift_Ins_p.E210fs|PLEKHA5_uc010sig.1_Frame_Shift_Ins_p.E210fs|PLEKHA5_uc010sih.1_Frame_Shift_Ins_p.E210fs|PLEKHA5_uc001rec.1_Frame_Shift_Ins_p.E6fs NM_019012 NP_061885 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A 318 1-phosphatidylinositol binding|protein binding ovary(1)|kidney(1)|skin(1) 3 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) CAAAATTGAAGAAAAAAAGGCA 0.332 0.48 66 60 LRRK2 120892 broad.mit.edu 37 12 40713869 40713870 + Frame_Shift_Ins INS - A A SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr12:40713869_40713870insA uc001rmg.3 + 34 5028_5029 c.4907_4908insA c.(4906-4908)TCAfs p.S1636fs LRRK2_uc009zjw.2_Frame_Shift_Ins_p.S474fs|LRRK2_uc001rmi.2_Frame_Shift_Ins_p.S469fs NM_198578 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 1636 activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1) 24 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) AAATTTCTTTCAAAAAAAAGGA 0.351 0.48 45 42 AMHR2 269 broad.mit.edu 37 12 53819645 53819645 + Frame_Shift_Del DEL G - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr12:53819645delG uc001scx.1 + 6 872 c.794delG c.(793-795)CGGfs p.R265fs AMHR2_uc009zmy.1_Frame_Shift_Del_p.R265fs NM_020547 NP_065434 Q16671 AMHR2_HUMAN anti-Mullerian hormone receptor, type II isoform 265 Cytoplasmic (Potential).|Protein kinase. Mullerian duct regression ATP binding|hormone binding|metal ion binding ovary(1)|skin(1) 2 Adenosine triphosphate(DB00171) ACTGCCAGCCGGGGGGGTCCT 0.512 0.47 31 28 MDM2 4193 broad.mit.edu 37 12 69233090 69233090 + Frame_Shift_Del DEL C - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr12:69233090delC uc001sui.2 + 11 1242 c.955delC c.(955-957)CCCfs p.P319fs MDM2_uc009zri.2_Frame_Shift_Del_p.P274fs|MDM2_uc009zqx.2_Frame_Shift_Del_p.P264fs|MDM2_uc009zqw.2_Intron|MDM2_uc001suk.2_Intron|MDM2_uc001sun.3_Frame_Shift_Del_p.P138fs|MDM2_uc009zqz.2_Frame_Shift_Del_p.P266fs|MDM2_uc009zra.2_Frame_Shift_Del_p.P117fs|MDM2_uc001sum.1_Intron|MDM2_uc009zrd.2_Frame_Shift_Del_p.P3fs|MDM2_uc009zrc.2_Frame_Shift_Del_p.P3fs|MDM2_uc009zre.2_Frame_Shift_Del_p.P60fs|MDM2_uc009zrf.2_Frame_Shift_Del_p.P3fs|MDM2_uc001suo.2_Frame_Shift_Del_p.P113fs|MDM2_uc009zrg.2_Frame_Shift_Del_p.P35fs|MDM2_uc009zrh.2_Frame_Shift_Del_p.P87fs NM_002392 NP_002383 Q00987 MDM2_HUMAN mouse double minute 2 homolog isoform MDM2 313 RanBP2-type.|Necessary for interaction with USP2.|Region II. cellular response to hypoxia|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|establishment of protein localization|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein complex assembly|protein destabilization|protein localization to nucleus|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to antibiotic|synaptic transmission cytosol|endocytic vesicle membrane|insoluble fraction|nucleolus|nucleoplasm|plasma membrane|protein complex enzyme binding|identical protein binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding lung(2)|central_nervous_system(1) 3 all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684) all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143) TGAAATGAATCCCCCCCTTCC 0.428 0.58 60 83 NAV3 89795 broad.mit.edu 37 12 78401034 78401035 + Frame_Shift_Ins INS - AAAGC AAAGC SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr12:78401034_78401035insAAAGC uc001syp.2 + 8 1889_1890 c.1716_1717insAAAGC c.(1714-1719)GAGAAAfs p.E572fs NAV3_uc001syo.2_Frame_Shift_Ins_p.E572fs NM_014903 NP_055718 Q8IVL0 NAV3_HUMAN neuron navigator 3 572_573 nuclear outer membrane ATP binding|nucleoside-triphosphatase activity large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 17 TAACCATGGAGAAAGCAAGTGC 0.505 0.32 75 35 SACS 26278 broad.mit.edu 37 13 23905485 23905486 + Frame_Shift_Ins INS - A A SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr13:23905485_23905486insA uc001uon.2 - 10 13118_13119 c.12529_12530insT c.(12529-12531)TACfs p.Y4177fs SACS_uc001uoo.2_Frame_Shift_Ins_p.Y4030fs|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 4177 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) TTCTCCCGGGTAAAAAACATTC 0.416 0.47 99 88 SACS 26278 broad.mit.edu 37 13 23912669 23912669 + Frame_Shift_Del DEL A - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr13:23912669delA uc001uon.2 - 10 5935 c.5346delT c.(5344-5346)TTTfs p.F1782fs SACS_uc001uoo.2_Frame_Shift_Del_p.F1635fs|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 1782 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) CTGGACCTCTAAAAAGTGGCG 0.423 0.45 66 55 LCP1 3936 broad.mit.edu 37 13 46733797 46733797 + Frame_Shift_Del DEL T - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr13:46733797delT uc001vaz.3 - 2 127 c.1delA c.(1-3)ATGfs p.M1fs LCP1_uc001vba.3_Frame_Shift_Del_p.M1fs NM_002298 NP_002289 P13796 PLSL_HUMAN L-plastin 1 regulation of intracellular protein transport|T cell activation involved in immune response cell junction|cytosol|ruffle membrane calcium ion binding lung(4)|ovary(3) 7 Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262) KIRC - Kidney renal clear cell carcinoma(16;0.234) GBM - Glioblastoma multiforme(144;5.39e-05) CCTCTGGCCATTTTTTATTGC 0.398 0.80 3 12 DACH1 1602 broad.mit.edu 37 13 72440403 72440403 + Frame_Shift_Del DEL G - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr13:72440403delG uc010thn.1 - 2 922 c.499delC c.(499-501)CTCfs p.L167fs DACH1_uc010tho.1_Frame_Shift_Del_p.L167fs|DACH1_uc010thp.1_Frame_Shift_Del_p.L167fs NM_080759 NP_542937 Q9UI36 DACH1_HUMAN dachshund homolog 1 isoform a 167 multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus DNA binding|nucleotide binding|protein binding breast(1) 1 Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198) GBM - Glioblastoma multiforme(99;0.00032) TTCCCGGGGAGGGGGCCGCAg 0.348 0.41 13 9 FANCM 57697 broad.mit.edu 37 14 45658040 45658040 + Frame_Shift_Del DEL T - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr14:45658040delT uc001wwd.3 + 20 4914 c.4815delT c.(4813-4815)AGTfs p.S1605fs FANCM_uc010anf.2_Frame_Shift_Del_p.S1579fs|FANCM_uc001wwe.3_Frame_Shift_Del_p.S1141fs|FANCM_uc010ang.2_Frame_Shift_Del_p.S819fs NM_020937 NP_065988 Q8IYD8 FANCM_HUMAN Fanconi anemia, complementation group M 1605 DNA repair Fanconi anaemia nuclear complex ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding ovary(3)|lung(2)|breast(2) 7 TAGAGGATAGTTTTTGTGTTG 0.289 0.49 57 55 RAB15 376267 broad.mit.edu 37 14 65417871 65417872 + Splice_Site INS - GA GA SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr14:65417871_65417872insGA uc001xhz.2 - 4 328 c.247_splice c.e4-1 p.G83_splice FNTB_uc010tsl.1_Intron|FNTB_uc010tsm.1_Intron|RAB15_uc010aqk.2_Splice_Site NM_198686 NP_941959 P59190 RAB15_HUMAN RAB15, member RAS onocogene family protein transport|small GTPase mediated signal transduction plasma membrane GTP binding ovary(1) 1 all cancers(60;0.00136)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.0102) AAATATCCCCTGAGAGAGAGAG 0.510 0.34 46 24 TCF12 6938 broad.mit.edu 37 15 57545545 57545548 + Frame_Shift_Del DEL TGCC - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr15:57545545_57545548delTGCC uc002aec.2 + 15 1558_1561 c.1274_1277delTGCC c.(1273-1278)TTGCCTfs p.L425fs TCF12_uc010ugm.1_Frame_Shift_Del_p.L477fs|TCF12_uc010ugn.1_Frame_Shift_Del_p.L445fs|TCF12_uc002aea.2_Frame_Shift_Del_p.L449fs|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Frame_Shift_Del_p.L449fs|TCF12_uc002aed.2_Frame_Shift_Del_p.L425fs|TCF12_uc002aee.2_Frame_Shift_Del_p.L255fs|TCF12_uc010bft.2_Frame_Shift_Del_p.L279fs|TCF12_uc010ugo.1_Frame_Shift_Del_p.L189fs|TCF12_uc010ugp.1_Frame_Shift_Del_p.L83fs|TCF12_uc010ugq.1_Frame_Shift_Del_p.L59fs|TCF12_uc010ugr.1_Frame_Shift_Del_p.L38fs NM_207038 NP_996921 Q99081 HTF4_HUMAN transcription factor 12 isoform b 425_426 immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity central_nervous_system(5)|ovary(2)|lung(1) 8 Colorectal(260;0.0907) all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239) TCCACCAGTTTGCCTGCTGGTCAC 0.461 0.52 35 38 AXIN1 8312 broad.mit.edu 37 16 347093 347093 + Frame_Shift_Del DEL C - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr16:347093delC uc002cgp.1 - 7 2095 c.1918delG c.(1918-1920)GAAfs p.E640fs AXIN1_uc002cgq.1_Frame_Shift_Del_p.E640fs NM_003502 NP_003493 O15169 AXIN1_HUMAN axin 1 isoform a 640 Interaction with RNF111.|Interaction with PPP2CA. activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding breast(1)|liver(1) 2 all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187) ATCTCCTTTTCCCCCTCAATG 0.647 0.47 60 53 CHD9 80205 broad.mit.edu 37 16 53243678 53243679 + Frame_Shift_Ins INS - A A SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr16:53243678_53243679insA uc002ehb.2 + 2 1901_1902 c.1737_1738insA c.(1735-1740)AGCAAAfs p.S579fs CHD9_uc002egy.2_Frame_Shift_Ins_p.S579fs|CHD9_uc002egz.1_Frame_Shift_Ins_p.S579fs|CHD9_uc002eha.1_Frame_Shift_Ins_p.S579fs|CHD9_uc002ehc.2_Frame_Shift_Ins_p.S579fs|CHD9_uc002ehd.2_Frame_Shift_Ins_p.S105fs NM_025134 NP_079410 Q3L8U1 CHD9_HUMAN chromodomain helicase DNA binding protein 9 579_580 Lys-rich. cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleoplasm ATP binding|DNA binding|helicase activity|protein binding lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1) 7 all_cancers(37;0.0212) ACAAAGACAGCAAAAAAACAAA 0.332 0.47 8 7 NLRP1 22861 broad.mit.edu 37 17 5462267 5462268 + Frame_Shift_Ins INS - T T SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr17:5462267_5462268insT uc002gci.2 - 4 2303_2304 c.1748_1749insA c.(1747-1749)AAGfs p.K583fs NLRP1_uc002gcg.1_Frame_Shift_Ins_p.K583fs|NLRP1_uc002gck.2_Frame_Shift_Ins_p.K583fs|NLRP1_uc002gcj.2_Frame_Shift_Ins_p.K583fs|NLRP1_uc002gcl.2_Frame_Shift_Ins_p.K583fs|NLRP1_uc002gch.3_Frame_Shift_Ins_p.K583fs|NLRP1_uc010clh.2_Frame_Shift_Ins_p.K583fs NM_033004 NP_127497 Q9C000 NALP1_HUMAN NLR family, pyrin domain containing 1 isoform 1 583 NACHT. defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide cytoplasm|NALP1 inflammasome complex|nucleus ATP binding|caspase activator activity|enzyme binding|protein domain specific binding lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1) 9 Colorectal(1115;3.48e-05) TGAAAAGGGTCTTTTTTTGCCA 0.535 0.39 56 36 MLLT6 4302 broad.mit.edu 37 17 36871867 36871869 + In_Frame_Del DEL CTC - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr17:36871867_36871869delCTC uc002hqi.3 + 9 835_837 c.822_824delCTC c.(820-825)GTCTCC>GTC p.S277del MLLT6_uc010cvm.1_In_Frame_Del_p.S277del|MLLT6_uc002hqj.2_5'UTR|MLLT6_uc002hqk.3_5'Flank NM_005937 NP_005928 P55198 AF17_HUMAN myeloid/lymphoid or mixed-lineage leukemia 277 Poly-Ser. regulation of transcription, DNA-dependent nucleus protein binding|zinc ion binding breast(3)|prostate(1)|lung(1)|skin(1) 6 Breast(7;4.43e-21) TCCTTCAGGTCTCCTCCTCGGCT 0.591 0.31 20 9 MLLT6 4302 broad.mit.edu 37 17 36872036 36872038 + In_Frame_Del DEL TCC - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr17:36872036_36872038delTCC uc002hqi.3 + 9 1004_1006 c.991_993delTCC c.(991-993)TCCdel p.S338del MLLT6_uc010cvm.1_In_Frame_Del_p.S338del|MLLT6_uc002hqj.2_5'UTR|MLLT6_uc002hqk.3_5'Flank NM_005937 NP_005928 P55198 AF17_HUMAN myeloid/lymphoid or mixed-lineage leukemia 338 Poly-Ser. regulation of transcription, DNA-dependent nucleus protein binding|zinc ion binding breast(3)|prostate(1)|lung(1)|skin(1) 6 Breast(7;4.43e-21) ctcctcttcttcctcctcctctt 0.438 0.44 44 34 CDK12 51755 broad.mit.edu 37 17 37627292 37627294 + In_Frame_Del DEL AAG - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr17:37627292_37627294delAAG uc010cvv.2 + 2 1793_1795 c.1207_1209delAAG c.(1207-1209)AAGdel p.K404del CDK12_uc010wef.1_In_Frame_Del_p.K403del|CDK12_uc002hrw.3_In_Frame_Del_p.K404del NM_016507 NP_057591 Q9NYV4 CDK12_HUMAN Cdc2-related kinase, arginine/serine-rich 404 mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1) 19 CAGTAGGAAAAAGAAGGAAAGAG 0.458 0.37 58 34 CDK12 51755 broad.mit.edu 37 17 37627361 37627361 + Frame_Shift_Del DEL T - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr17:37627361delT uc010cvv.2 + 2 1862 c.1276delT c.(1276-1278)TTTfs p.F426fs CDK12_uc010wef.1_Frame_Shift_Del_p.F425fs|CDK12_uc002hrw.3_Frame_Shift_Del_p.F426fs NM_016507 NP_057591 Q9NYV4 CDK12_HUMAN Cdc2-related kinase, arginine/serine-rich 426 mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1) 19 TTCACCTGTATTTTTGCCTAG 0.443 0.27 51 19 CSF3 1440 broad.mit.edu 37 17 38171944 38171944 + Frame_Shift_Del DEL C - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr17:38171944delC uc002htp.2 + 2 81 c.41delC c.(40-42)GCCfs p.A14fs CSF3_uc002hto.2_Frame_Shift_Del_p.A14fs|CSF3_uc002htq.2_Frame_Shift_Del_p.A10fs|CSF3_uc010wep.1_Frame_Shift_Del_p.A10fs NM_000759 NP_000750 P09919 CSF3_HUMAN colony stimulating factor 3 isoform a precursor 14 cytokine-mediated signaling pathway|granulocyte differentiation|immune response|positive regulation of cell proliferation extracellular space cytokine activity|enzyme binding|granulocyte colony-stimulating factor receptor binding|growth factor activity ovary(1) 1 Colorectal(19;0.000442) Myeloproliferative disorder(1115;0.0255) Filgrastim(DB00099)|Pegfilgrastim(DB00019) CTGTCCCCAGCCCTGCAGCTG 0.647 0.58 5 7 BRIP1 83990 broad.mit.edu 37 17 59878817 59878817 + Frame_Shift_Del DEL A - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr17:59878817delA uc002izk.1 - 8 1078 c.937delT c.(937-939)TATfs p.Y313fs NM_032043 NP_114432 Q9BX63 FANCJ_HUMAN BRCA1 interacting protein C-terminal helicase 1 313 Helicase ATP-binding. DNA damage checkpoint|double-strand break repair|regulation of transcription from RNA polymerase II promoter cytoplasm|nucleus ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding ovary(1) 1 ACTCCATGATAAAAATAGCAG 0.358 0.54 63 73 JUND 3727 broad.mit.edu 37 19 18392043 18392043 + Frame_Shift_Del DEL G - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr19:18392043delG uc002nip.2 - 1 390 c.252delC c.(250-252)CCCfs p.P84fs hsa-mir-3188|MI0014232_5'Flank NM_005354 NP_005345 P17535 JUND_HUMAN jun D proto-oncogene 84 regulation of transcription from RNA polymerase II promoter chromatin|nucleus protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding 0 0.000 0.33 249 122 AXL 558 broad.mit.edu 37 19 41743896 41743896 + Frame_Shift_Del DEL C - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr19:41743896delC uc010ehj.2 + 7 1021 c.831delC c.(829-831)GACfs p.D277fs CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Frame_Shift_Del_p.D277fs|AXL_uc010ehk.2_Frame_Shift_Del_p.D277fs NM_021913 NP_068713 P30530 UFO_HUMAN AXL receptor tyrosine kinase isoform 1 277 Extracellular (Potential).|Fibronectin type-III 1. integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1) 13 GAGAACCAGACCCCCCAGAGG 0.622 0.31 11 5 DMPK 1760 broad.mit.edu 37 19 46283130 46283130 + Frame_Shift_Del DEL G - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr19:46283130delG uc002pdd.1 - 1 732 c.188delC c.(187-189)CCAfs p.P63fs DMPK_uc010xxs.1_5'Flank|DMPK_uc002pde.1_Frame_Shift_Del_p.P63fs|DMPK_uc002pdf.1_Intron|DMPK_uc002pdg.1_Intron|DMPK_uc002pdh.1_Intron|DMPK_uc002pdi.1_Intron|DMPK_uc010xxt.1_Intron|DMPK_uc010xxu.1_Frame_Shift_Del_p.P63fs NM_001081563 NP_001075032 Q09013 DMPK_HUMAN myotonic dystrophy protein kinase isoform 1 63 regulation of heart contraction ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity lung(3) 3 Ovarian(192;0.0308)|all_neural(266;0.112) OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24) GGGCTCCGCTGGGGGGGTGGT 0.617 0.37 19 11 LMTK3 114783 broad.mit.edu 37 19 49002136 49002136 + Frame_Shift_Del DEL G - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr19:49002136delG uc002pjk.2 - 12 2277 c.2277delC c.(2275-2277)CCCfs p.P759fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.39 176 112 SGK2 10110 broad.mit.edu 37 20 42198075 42198075 + Frame_Shift_Del DEL C - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr20:42198075delC uc002xkv.2 + 5 678 c.459delC c.(457-459)CACfs p.H153fs SGK2_uc002xkt.2_RNA|SGK2_uc002xkr.2_Frame_Shift_Del_p.H93fs|SGK2_uc010ggm.2_Frame_Shift_Del_p.H93fs|SGK2_uc002xks.2_Frame_Shift_Del_p.H92fs|SGK2_uc002xku.2_Frame_Shift_Del_p.H93fs|SGK2_uc002xkq.1_Frame_Shift_Del_p.H93fs NM_016276 NP_057360 Q9HBY8 SGK2_HUMAN serum/glucocorticoid regulated kinase 2 isoform 153 Protein kinase. intracellular protein kinase cascade|response to oxidative stress ATP binding|potassium channel regulator activity|protein serine/threonine kinase activity|sodium channel regulator activity lung(3)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1) 6 Myeloproliferative disorder(115;0.00452) COAD - Colon adenocarcinoma(18;0.0031) ACGTGCGGCACCCCTTCCTCG 0.597 0.45 6 5 GNAS 2778 broad.mit.edu 37 20 57429881 57429881 + Frame_Shift_Del DEL G - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr20:57429881delG uc002xzw.2 + 1 1846 c.1561delG c.(1561-1563)GGGfs p.G521fs GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_RNA NM_080425 NP_536350 P63092 GNAS2_HUMAN GNAS complex locus XLas Error:Variant_position_missing_in_P63092_after_alignment activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1) 292 all_lung(29;0.0104) BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109) 0.000 0.37 83 48 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.11 89 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 120 354 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.88 7 49 NF2 4771 broad.mit.edu 37 22 30050663 30050664 + Frame_Shift_Del DEL CA - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr22:30050663_30050664delCA uc003age.3 + 5 908_909 c.465_466delCA c.(463-468)CCCAGTfs p.P155fs NF2_uc003afy.3_Frame_Shift_Del_p.P155fs|NF2_uc003afz.3_Frame_Shift_Del_p.P72fs|NF2_uc003agf.3_Frame_Shift_Del_p.P155fs|NF2_uc003agb.3_Frame_Shift_Del_p.P78fs|NF2_uc003agc.3_Frame_Shift_Del_p.P117fs|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Frame_Shift_Del_p.P155fs|NF2_uc003aga.3_Frame_Shift_Del_p.P113fs|NF2_uc003agh.3_Frame_Shift_Del_p.P114fs|NF2_uc003agi.3_Frame_Shift_Del_p.P72fs|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Frame_Shift_Del_p.P117fs NM_000268 NP_000259 P35240 MERL_HUMAN neurofibromin 2 isoform 1 155_156 FERM. actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane cytoskeletal protein binding|protein binding p.D152fs*18(2)|p.Y150fs*46(1)|p.?(1)|p.L127_D382del(1)|p.A145_L163del(1)|p.L140_P252del(1) meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1) 728 ACTACGACCCCAGTGTTCACAA 0.441 0.52 39 43 TNRC6B 23112 broad.mit.edu 37 22 40661866 40661866 + Frame_Shift_Del DEL C - - SNUC4_LARGE_INTESTINE NA SNUC4_LARGE_INTESTINE NA g.chr22:40661866delC uc011aor.1 + 5 1843 c.1632delC c.(1630-1632)CACfs p.H544fs TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Frame_Shift_Del_p.H544fs|TNRC6B_uc003ayo.2_Frame_Shift_Del_p.H348fs NM_001162501 NP_001155973 Q9UPQ9 TNR6B_HUMAN trinucleotide repeat containing 6B isoform 1 544 gene silencing by RNA|regulation of translation cytoplasmic mRNA processing body nucleotide binding|RNA binding 0 AAAAGGGCCACCCCCTCCCTG 0.522 0.46 31 26 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 27 F8 2157 broad.mit.edu 37 X 154157686 154157686 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chrX:154157686delT uc004fmt.2 - 14 4550 c.4379delA c.(4378-4380)AATfs p.N1460fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1460 B. N -> K (in HEMA). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AGAAAGGTTATTTTTTTTGGC 0.413 0.88 31 233 ARID1A 8289 broad.mit.edu 37 1 27088682 27088682 + Frame_Shift_Del DEL C - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr1:27088682delC uc001bmv.1 + 7 2664 c.2291delC c.(2290-2292)TCCfs p.S764fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.S764fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.S764fs|ARID1A_uc001bmw.1_Frame_Shift_Del_p.S381fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 764 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.Q766fs*67(1)|p.Q766fs*51(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CAGTACAGTTCCCCCCAGCCC 0.522 0.40 29 19 TNNI3K 51086 broad.mit.edu 37 1 74797186 74797186 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr1:74797186delT uc001dgf.1 + 6 548 c.497delT c.(496-498)GTTfs p.V166fs TNNI3K_uc001dgc.1_Frame_Shift_Del_p.V267fs|TNNI3K_uc001dgd.2_Frame_Shift_Del_p.V267fs|TNNI3K_uc001dge.1_Frame_Shift_Del_p.V267fs NM_015978 NP_057062 Q59H18 TNI3K_HUMAN TNNI3 interacting kinase isoform b 166 ANK 4. cytoplasm|nucleus ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1) 10 CAAGATGCAGTTTTTTTCACT 0.398 0.49 104 98 ARHGAP29 9411 broad.mit.edu 37 1 94645419 94645419 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr1:94645419delT uc001dqj.3 - 20 2711 c.2342delA c.(2341-2343)AAGfs p.K781fs ARHGAP29_uc009wdq.1_RNA|ARHGAP29_uc001dqk.2_Frame_Shift_Del_p.K347fs NM_004815 NP_004806 Q52LW3 RHG29_HUMAN PTPL1-associated RhoGAP 1 781 Rho-GAP. Rho protein signal transduction cytosol metal ion binding|Rho GTPase activator activity breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1) 11 all_lung(203;0.000732)|Lung NSC(277;0.00328) all cancers(265;0.0187)|Epithelial(280;0.159) AAGACTATTCTTTTTTGTCTC 0.318 0.50 71 70 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 261 83 SHC1 6464 broad.mit.edu 37 1 154941251 154941253 + In_Frame_Del DEL CTC - - rs76505256 byFrequency SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr1:154941251_154941253delCTC uc001ffv.2 - 3 845_847 c.624_626delGAG c.(622-627)AGGAGA>AGA p.208_209RR>R SHC1_uc001ffz.1_5'Flank|SHC1_uc001ffw.2_In_Frame_Del_p.208_209RR>R|SHC1_uc001ffx.2_In_Frame_Del_p.98_99RR>R|SHC1_uc001ffy.2_In_Frame_Del_p.98_99RR>R NM_183001 NP_892113 P29353 SHC1_HUMAN SHC-transforming protein 1 isoform 1 208_209 PID. activation of MAPK activity|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|positive regulation of DNA replication|Ras protein signal transduction|regulation of epidermal growth factor receptor activity|regulation of growth cytosol|mitochondrial matrix|Shc-EGFR complex epidermal growth factor receptor binding|insulin receptor binding|insulin-like growth factor receptor binding|phospholipid binding|protein binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(1)|skin(1) 2 all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245) BRCA - Breast invasive adenocarcinoma(34;0.00034) AAGTACCTTTCTCCTCCTTGTCG 0.640 0.42 53 38 RIF1 55183 broad.mit.edu 37 2 152321320 152321320 + Frame_Shift_Del DEL A - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr2:152321320delA uc002txm.2 + 30 5416 c.5286delA c.(5284-5286)ACAfs p.T1762fs RIF1_uc002txl.2_Frame_Shift_Del_p.T1762fs|RIF1_uc002txn.2_Frame_Shift_Del_p.T1762fs|RIF1_uc002txo.2_Frame_Shift_Del_p.T1762fs|RIF1_uc002txp.2_RNA NM_018151 NP_060621 Q5UIP0 RIF1_HUMAN RAP1 interacting factor 1 1762 cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1) 15 BRCA - Breast invasive adenocarcinoma(221;0.0429) TTAGTGAAACAAAAAAGGCAG 0.368 0.48 47 43 CHN1 1123 broad.mit.edu 37 2 175742640 175742640 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr2:175742640delT uc002uji.2 - 6 1007 c.477delA c.(475-477)AAAfs p.K159fs CHN1_uc010zeq.1_Frame_Shift_Del_p.K159fs|CHN1_uc002ujj.2_Intron NM_001822 NP_001813 P15882 CHIN_HUMAN chimerin (chimaerin) 1 isoform a 159 regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction cytosol GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity ovary(2)|skin(1) 3 OV - Ovarian serous cystadenocarcinoma(117;0.226) CTGGCATATGTTTTTTGTATG 0.423 0.45 161 134 HOXD11 3237 broad.mit.edu 37 2 176972823 176972824 + Frame_Shift_Ins INS - C C SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr2:176972823_176972824insC uc002uki.2 + 1 740_741 c.740_741insC c.(739-741)GGCfs p.G247fs HOXD11_uc010fqx.2_Intron NM_021192 NP_067015 P31277 HXD11_HUMAN homeobox D11 247 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678) 0.000 0.50 11 11 TTN 7273 broad.mit.edu 37 2 179473392 179473392 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr2:179473392delT uc010zfg.1 - 223 44866 c.44642delA c.(44641-44643)AACfs p.N14881fs uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.N8576fs|TTN_uc010zfi.1_Frame_Shift_Del_p.N8509fs|TTN_uc010zfj.1_Frame_Shift_Del_p.N8384fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 15808 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CCCAAATCTGTTTTCAGCTCT 0.393 0.52 100 107 PDCD1 5133 broad.mit.edu 37 2 242795104 242795104 + Frame_Shift_Del DEL G - - rs41444844 byFrequency SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr2:242795104delG uc002wcq.3 - 2 173 c.105delC c.(103-105)CCCfs p.P35fs PDCD1_uc010fzs.2_5'UTR|PDCD1_uc010fzt.2_RNA NM_005018 NP_005009 Q15116 PDCD1_HUMAN programmed cell death 1 precursor 35 Ig-like V-type.|Extracellular (Potential). apoptosis|humoral immune response|multicellular organismal development|T cell costimulation integral to membrane protein tyrosine phosphatase activity|signal transducer activity ovary(1) 1 all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0219) 0.000 0.49 573 549 TOP2B 7155 broad.mit.edu 37 3 25648715 25648715 + Frame_Shift_Del DEL C - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr3:25648715delC uc003cdj.2 - 31 4230 c.4230delG c.(4228-4230)GGGfs p.G1410fs TOP2B_uc011awm.1_Frame_Shift_Del_p.G267fs|TOP2B_uc010hff.1_Frame_Shift_Del_p.G276fs NM_001068 NP_001059 Q02880 TOP2B_HUMAN DNA topoisomerase II, beta isozyme 1415 DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|resolution of meiotic recombination intermediates|sister chromatid segregation cytosol|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex|WINAC complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity breast(2)|ovary(1)|lung(1)|skin(1) 5 CTTTATCTAACCCATCTGAAG 0.289 0.50 103 103 CTDSPL 10217 broad.mit.edu 37 3 38022357 38022357 + Frame_Shift_Del DEL A - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr3:38022357delA uc003chg.2 + 8 852 c.830delA c.(829-831)TAGfs p.*277fs CTDSPL_uc003chh.2_Frame_Shift_Del_p.*266fs|CTDSPL_uc003chi.2_RNA NM_001008392 NP_001008393 O15194 CTDSL_HUMAN small CTD phosphatase 3 isoform 1 277 nucleus metal ion binding|phosphoprotein phosphatase activity 0 Melanoma(1037;0.0122) KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902) TGCAATAGGTAGCCCTGGCCT 0.617 0.62 6 10 NEK4 6787 broad.mit.edu 37 3 52780152 52780152 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr3:52780152delT uc003dfq.3 - 10 1941 c.1752delA c.(1750-1752)AAAfs p.K584fs NEK4_uc011bej.1_Frame_Shift_Del_p.K495fs|NEK4_uc003dfr.2_Frame_Shift_Del_p.K538fs NM_003157 NP_003148 P51957 NEK4_HUMAN NIMA-related kinase 4 584 cell division|mitosis nucleus ATP binding|metal ion binding|protein serine/threonine kinase activity large_intestine(1) 1 BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513) TTTCAGCCTCTTTTTGTGTTG 0.413 0.47 122 108 EIF4G1 1981 broad.mit.edu 37 3 184039677 184039678 + Frame_Shift_Ins INS - A A SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr3:184039677_184039678insA uc003fnp.2 + 10 1503_1504 c.1305_1306insA c.(1303-1308)CCCACCfs p.P435fs EIF4G1_uc003fno.1_Frame_Shift_Ins_p.P376fs|EIF4G1_uc010hxw.1_Frame_Shift_Ins_p.P271fs|EIF4G1_uc003fnt.2_Frame_Shift_Ins_p.P146fs|EIF4G1_uc003fnq.2_Frame_Shift_Ins_p.P348fs|EIF4G1_uc003fnr.2_Frame_Shift_Ins_p.P271fs|EIF4G1_uc010hxx.2_Frame_Shift_Ins_p.P442fs|EIF4G1_uc003fns.2_Frame_Shift_Ins_p.P395fs|EIF4G1_uc010hxy.2_Frame_Shift_Ins_p.P442fs|EIF4G1_uc003fnv.3_Frame_Shift_Ins_p.P435fs|EIF4G1_uc003fnu.3_Frame_Shift_Ins_p.P435fs|EIF4G1_uc003fnw.2_Frame_Shift_Ins_p.P442fs|EIF4G1_uc003fnx.2_Frame_Shift_Ins_p.P239fs|EIF4G1_uc003fny.3_Frame_Shift_Ins_p.P239fs NM_198241 NP_937884 Q04637 IF4G1_HUMAN eukaryotic translation initiation factor 4 435_436 insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation cytosol|eukaryotic translation initiation factor 4F complex protein binding|translation initiation factor activity lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1) 7 all_cancers(143;1.06e-10)|Ovarian(172;0.0339) Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22) TGGCGCCCCCCACCATCCCCTC 0.505 0.67 9 18 FGFR3 2261 broad.mit.edu 37 4 1806180 1806181 + Frame_Shift_Ins INS - C C SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr4:1806180_1806181insC uc003gdr.3 + 9 1455_1456 c.1199_1200insC c.(1198-1200)AGCfs p.S400fs FGFR3_uc003gdu.2_Frame_Shift_Ins_p.S402fs|FGFR3_uc003gds.3_Intron|FGFR3_uc003gdq.3_Frame_Shift_Ins_p.S400fs NM_000142 NP_000133 P22607 FGFR3_HUMAN fibroblast growth factor receptor 3 isoform 1 400 Cytoplasmic (Potential). bone maturation|cell growth|insulin receptor signaling pathway|JAK-STAT cascade|MAPKKK cascade|negative regulation of developmental growth|positive regulation of cell proliferation integral to plasma membrane ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|identical protein binding urinary_tract(2177)|skin(314)|upper_aerodigestive_tract(57)|haematopoietic_and_lymphoid_tissue(24)|prostate(9)|cervix(6)|central_nervous_system(4)|large_intestine(3)|lung(3)|testis(2)|pancreas(1) 2600 Breast(71;0.212)|all_epithelial(65;0.241) all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234) Palifermin(DB00039) CGCCTGCGCAGCCCCCCCAAGA 0.629 0.31 38 17 CDKL2 8999 broad.mit.edu 37 4 76522337 76522337 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr4:76522337delT uc003hiq.2 - 9 1629 c.1104delA c.(1102-1104)AAAfs p.K368fs CDKL2_uc011cbp.1_Frame_Shift_Del_p.K368fs NM_003948 NP_003939 Q92772 CDKL2_HUMAN cyclin-dependent kinase-like 2 368 sex differentiation|signal transduction cytoplasm|nucleus ATP binding|cyclin-dependent protein kinase activity ovary(2)|stomach(2)|breast(2)|skin(1) 7 Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122) CTCTATTGCCTTTTTCAGCTT 0.373 0.47 109 97 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.35 70 37 FBXW7 55294 broad.mit.edu 37 4 153244156 153244156 + Frame_Shift_Del DEL C - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr4:153244156delC uc003ims.2 - 12 2150 c.2001delG c.(1999-2001)GGGfs p.G667fs FBXW7_uc011cii.1_Frame_Shift_Del_p.G667fs|FBXW7_uc003imt.2_Frame_Shift_Del_p.G667fs|FBXW7_uc011cih.1_Frame_Shift_Del_p.G491fs|FBXW7_uc003imq.2_Frame_Shift_Del_p.G587fs|FBXW7_uc003imr.2_Frame_Shift_Del_p.G549fs NM_033632 NP_361014 Q969H0 FBXW7_HUMAN F-box and WD repeat domain containing 7 isoform 667 interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex protein binding|protein binding p.S668fs*26(1)|p.S668fs*39(1) haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1) 308 all_hematologic(180;0.093) Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067) CTCCCCCACTCCCCCCACTCT 0.488 0.88 21 160 LIFR 3977 broad.mit.edu 37 5 38506172 38506172 + Frame_Shift_Del DEL A - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr5:38506172delA uc010ive.1 - 9 1458 c.1126delT c.(1126-1128)TCAfs p.S376fs LIFR_uc003jli.2_Frame_Shift_Del_p.S376fs NM_001127671 NP_001121143 P42702 LIFR_HUMAN leukemia inhibitory factor receptor precursor 376 Fibronectin type-III 2.|Extracellular (Potential). positive regulation of cell proliferation extracellular region|integral to plasma membrane ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity ovary(3)|large_intestine(1) 4 all_lung(31;0.00021) TATTTTCCTGAAAAACTGTTA 0.259 0.44 40 32 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.40 39 26 APC 324 broad.mit.edu 37 5 112176660 112176661 + Frame_Shift_Ins INS - A A SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr5:112176660_112176661insA uc010jby.2 + 16 5749_5750 c.5369_5370insA c.(5368-5370)AGAfs p.R1790fs APC_uc011cvt.1_Frame_Shift_Ins_p.R1772fs|APC_uc003kpz.3_Frame_Shift_Ins_p.R1790fs|APC_uc003kpy.3_Frame_Shift_Ins_p.R1790fs|APC_uc010jbz.2_Frame_Shift_Ins_p.R1507fs|APC_uc010jca.2_Frame_Shift_Ins_p.R1090fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1790 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.N1792fs*7(1)|p.K1192fs*3(1)|p.?(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) ACACGTGTAAGAAAAAATGCAG 0.317 0.49 71 68 FBN2 2201 broad.mit.edu 37 5 127710323 127710324 + Frame_Shift_Del DEL AC - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr5:127710323_127710324delAC uc003kuu.2 - 15 2531_2532 c.2092_2093delGT c.(2092-2094)GTTfs p.V698fs FBN2_uc003kuv.2_Frame_Shift_Del_p.V665fs NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 698 EGF-like 10; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) TCACTTACCAACACACACACGT 0.406 0.38 67 41 CDC25C 995 broad.mit.edu 37 5 137627690 137627690 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr5:137627690delT uc003lcp.1 - 8 1002 c.731delA c.(730-732)AAGfs p.K244fs CDC25C_uc003lcq.1_Frame_Shift_Del_p.K171fs|CDC25C_uc003lcr.1_Frame_Shift_Del_p.K244fs|CDC25C_uc011cyp.1_Frame_Shift_Del_p.K261fs|CDC25C_uc003lcs.1_Frame_Shift_Del_p.K322fs NM_001790 NP_001781 P30307 MPIP3_HUMAN cell division cycle 25C isoform a 244 cell cycle checkpoint|cell division|cell proliferation|DNA replication|G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis|traversing start control point of mitotic cell cycle cytosol|nucleoplasm protein tyrosine phosphatase activity|WW domain binding lung(3) 3 KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592) AGAAAAATACTTTTTTTTAAC 0.388 0.55 71 86 PHF3 23469 broad.mit.edu 37 6 64395813 64395814 + Splice_Site DEL GT - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr6:64395813_64395814delGT uc003pep.1 + 3 2215 c.2189_splice c.e3+1 p.R730_splice PHF3_uc010kaf.1_Splice_Site_p.R730_splice|PHF3_uc003pem.2_Splice_Site_p.R683_splice|PHF3_uc010kag.1_Splice_Site_p.R642_splice|PHF3_uc010kah.1_Splice_Site_p.R544_splice|PHF3_uc003pen.2_Splice_Site_p.R642_splice|PHF3_uc011dxs.1_Intron|PHF3_uc003peo.2_Frame_Shift_Del_p.R730fs NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) ATGGCAACAGGTGTGTGTGTAT 0.376 0.35 15 8 LATS1 9113 broad.mit.edu 37 6 150005515 150005515 + Frame_Shift_Del DEL G - - rs56149740 SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr6:150005515delG uc003qmu.1 - 4 1258 c.710delC c.(709-711)CCAfs p.P237fs LATS1_uc010kif.1_Frame_Shift_Del_p.P132fs|LATS1_uc003qmv.1_Frame_Shift_Del_p.P237fs|LATS1_uc003qmw.2_Frame_Shift_Del_p.P237fs|LATS1_uc010kig.1_Frame_Shift_Del_p.P132fs NM_004690 NP_004681 O95835 LATS1_HUMAN LATS homolog 1 237 cell division|cytoplasmic sequestering of protein|G2/M transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|positive regulation of peptidyl-serine phosphorylation|regulation of actin filament polymerization|sister chromatid segregation microtubule organizing center|spindle pole ATP binding|magnesium ion binding|protein kinase binding|protein serine/threonine kinase activity lung(5)|central_nervous_system(1) 6 Ovarian(120;0.0164) OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116) AGGTGGTGGTGGGGGGTTCAC 0.532 0.45 41 34 MLLT4 4301 broad.mit.edu 37 6 168325729 168325729 + Frame_Shift_Del DEL A - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr6:168325729delA uc003qwd.2 + 22 3175 c.3033delA c.(3031-3033)CTAfs p.L1011fs MLLT4_uc003qwb.1_Frame_Shift_Del_p.L996fs|MLLT4_uc003qwc.1_Frame_Shift_Del_p.L1012fs|MLLT4_uc003qwg.1_Frame_Shift_Del_p.L321fs NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 1012 PDZ. adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) CTGTGACCCTAAAAAAGCAGA 0.423 0.47 81 71 PDK4 5166 broad.mit.edu 37 7 95223039 95223039 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr7:95223039delT uc003uoa.2 - 3 636 c.316delA c.(316-318)AGCfs p.S106fs PDK4_uc003unz.2_5'Flank NM_002612 NP_002603 Q16654 PDK4_HUMAN pyruvate dehydrogenase kinase 4 precursor 106 glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate mitochondrial matrix ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity 0 all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151) STAD - Stomach adenocarcinoma(171;0.0151) TCATCTGGGCTTTTCTCATGG 0.333 0.56 60 76 EPHB6 2051 broad.mit.edu 37 7 142562075 142562077 + In_Frame_Del DEL TCT - - rs74716339;rs79875204;rs78315767 SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr7:142562075_142562077delTCT uc011kst.1 + 7 1304_1306 c.517_519delTCT c.(517-519)TCTdel p.S176del EPHB6_uc011ksu.1_In_Frame_Del_p.S176del|EPHB6_uc003wbs.2_5'UTR|EPHB6_uc003wbt.2_Intron|EPHB6_uc003wbu.2_5'UTR|EPHB6_uc003wbv.2_5'Flank NM_004445 NP_004436 O15197 EPHB6_HUMAN ephrin receptor EphB6 precursor 176 Extracellular (Potential).|Poly-Ser. extracellular region|integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1) 19 Melanoma(164;0.059) ctcctcctcctcttcttcctcTG 0.517 0.26 64 22 PBK 55872 broad.mit.edu 37 8 27690581 27690581 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr8:27690581delT uc003xgi.2 - 2 251 c.50delA c.(49-51)AAGfs p.K17fs PBK_uc011lap.1_Frame_Shift_Del_p.K17fs NM_018492 NP_060962 Q96KB5 TOPK_HUMAN PDZ binding kinase 17 mitosis ATP binding|protein binding|protein serine/threonine kinase activity 0 Ovarian(32;0.000953) UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141) ACCAGATTTCTTTTTTTCTGA 0.318 0.52 37 40 ERLIN2 11160 broad.mit.edu 37 8 37597958 37597959 + Frame_Shift_Del DEL TG - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr8:37597958_37597959delTG uc003xke.3 + 3 298_299 c.183_184delTG c.(181-186)TCTGTGfs p.S61fs ERLIN2_uc003xkc.3_Frame_Shift_Del_p.S61fs|ERLIN2_uc003xkd.2_Frame_Shift_Del_p.S61fs|ERLIN2_uc003xkf.3_Frame_Shift_Del_p.S61fs|ERLIN2_uc003xkg.2_Frame_Shift_Del_p.S61fs NM_007175 NP_009106 O94905 ERLN2_HUMAN ER lipid raft associated 2 isoform 1 61_62 Lumenal (Potential). ER-associated protein catabolic process endoplasmic reticulum membrane|integral to membrane|plasma membrane protein binding 0 Lung NSC(58;0.174) BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10) CATATAAGTCTGTGCAGGTATG 0.500 0.41 30 21 CSMD3 114788 broad.mit.edu 37 8 113326156 113326157 + Frame_Shift_Ins INS - T T SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr8:113326156_113326157insT uc003ynu.2 - 49 7833_7834 c.7674_7675insA c.(7672-7677)AAAGGCfs p.K2558fs CSMD3_uc003yns.2_Frame_Shift_Ins_p.K1760fs|CSMD3_uc003ynt.2_Frame_Shift_Ins_p.K2518fs|CSMD3_uc011lhx.1_Frame_Shift_Ins_p.K2454fs|CSMD3_uc003ynw.1_Frame_Shift_Ins_p.K269fs NM_198123 NP_937756 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 isoform 1 2558_2559 CUB 14.|Extracellular (Potential). integral to membrane|plasma membrane ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1) 63 ATCCGGAAGCCTTTTTTGTTAT 0.307 0.43 76 58 COL14A1 7373 broad.mit.edu 37 8 121240955 121240956 + Frame_Shift_Ins INS - T T SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr8:121240955_121240956insT uc003yox.2 + 18 2409_2410 c.2144_2145insT c.(2143-2145)AGTfs p.S715fs COL14A1_uc003yoy.2_Frame_Shift_Ins_p.S393fs NM_021110 NP_066933 Q05707 COEA1_HUMAN collagen, type XIV, alpha 1 precursor 715 cell-cell adhesion|collagen fibril organization collagen type XIV|extracellular space collagen binding|extracellular matrix structural constituent|protein binding, bridging ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1) 12 Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503) TTAGTTGACAGTTTTTGGACAG 0.267 0.50 69 69 MAPK15 225689 broad.mit.edu 37 8 144804319 144804319 + Frame_Shift_Del DEL G - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr8:144804319delG uc003yzj.2 + 14 1574 c.1533delG c.(1531-1533)CAGfs p.Q511fs NM_139021 NP_620590 Q8TD08 MK15_HUMAN mitogen-activated protein kinase 15 511 protein autophosphorylation extracellular region ATP binding|MAP kinase activity|SH3 domain binding lung(2) 2 all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146) 0.000 0.51 713 731 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.43 487 365 PRKACG 5568 broad.mit.edu 37 9 71628914 71628914 + Frame_Shift_Del DEL C - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr9:71628914delC uc004agy.2 - 1 126 c.95delG c.(94-96)GGAfs p.G32fs NM_002732 NP_002723 P22612 KAPCG_HUMAN protein kinase, cAMP-dependent, catalytic, 32 activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|gluconeogenesis|intracellular protein kinase cascade|male gonad development|nerve growth factor receptor signaling pathway|regulation of insulin secretion|spermatogenesis|transmembrane transport|triglyceride catabolic process|water transport cytosol|nucleoplasm ATP binding|cAMP-dependent protein kinase activity ovary(1)|pancreas(1)|skin(1) 3 AGCGGGGTTTCCCCATCTGTA 0.597 0.49 112 106 SYK 6850 broad.mit.edu 37 9 93650847 93650847 + Frame_Shift_Del DEL G - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr9:93650847delG uc004aqz.2 + 13 1978 c.1773delG c.(1771-1773)ATGfs p.M591fs SYK_uc004ara.2_Frame_Shift_Del_p.M568fs|SYK_uc004arb.2_Frame_Shift_Del_p.M568fs|SYK_uc004arc.2_Frame_Shift_Del_p.M591fs|SYK_uc011ltr.1_RNA|SYK_uc011lts.1_RNA|SYK_uc011ltt.1_RNA NM_003177 NP_003168 P43405 KSYK_HUMAN spleen tyrosine kinase isoform 1 591 Protein kinase. cell proliferation|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|neutrophil chemotaxis|organ morphogenesis|platelet activation|protein complex assembly cytosol|T cell receptor complex ATP binding|integrin binding|non-membrane spanning protein tyrosine kinase activity lung(2)|stomach(1)|ovary(1)|skin(1) 5 GAGAGCGGATGGGGTGCCCTG 0.443 0.37 78 45 WNK2 65268 broad.mit.edu 37 9 96021418 96021419 + Frame_Shift_Ins INS - C C SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr9:96021418_96021419insC uc004ati.1 + 11 2588_2589 c.2588_2589insC c.(2587-2589)CACfs p.H863fs WNK2_uc011lud.1_Frame_Shift_Ins_p.H863fs|WNK2_uc004atj.2_Frame_Shift_Ins_p.H863fs|WNK2_uc004atk.2_Frame_Shift_Ins_p.H500fs|WNK2_uc010mrc.1_Frame_Shift_Ins_p.H811fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 863 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 AAGCTGCCCCACCCCCCTGGGG 0.698 0.32 26 12 FANCC 2176 broad.mit.edu 37 9 98003011 98003011 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr9:98003011delT uc004avh.2 - 4 527 c.265delA c.(265-267)ATTfs p.I89fs FANCC_uc004avi.3_Frame_Shift_Del_p.I89fs|FANCC_uc010mrm.1_RNA|FANCC_uc011lul.1_RNA NM_000136 NP_000127 Q00597 FANCC_HUMAN Fanconi anemia, complementation group C 89 protein complex assembly cytosol|nucleoplasm protein binding kidney(1) 1 Acute lymphoblastic leukemia(62;0.138) CATATTAGAATTTTTTGGCTT 0.279 0.49 25 24 MYO3A 53904 broad.mit.edu 37 10 26462760 26462760 + Frame_Shift_Del DEL A - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr10:26462760delA uc001isn.2 + 30 3927 c.3567delA c.(3565-3567)CCAfs p.P1189fs MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron NM_017433 NP_059129 Q8NEV4 MYO3A_HUMAN myosin IIIA 1189 protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception cytoplasm|filamentous actin|filopodium|myosin complex actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 18 ATCAGACTCCAAAAAAAATGA 0.403 0.45 90 75 CCKBR 887 broad.mit.edu 37 11 6292451 6292451 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr11:6292451delT uc001mcp.2 + 5 1215 c.1022delT c.(1021-1023)CTTfs p.L341fs CCKBR_uc001mcq.2_Frame_Shift_Del_p.L269fs|CCKBR_uc001mcr.2_Frame_Shift_Del_p.L341fs|CCKBR_uc001mcs.2_Frame_Shift_Del_p.L410fs|CCKBR_uc001mct.1_RNA NM_176875 NP_795344 P32239 GASR_HUMAN cholecystokinin B receptor 341 Helical; Name=6; (Potential). activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception 1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding lung(5)|ovary(2)|breast(1) 8 Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029) Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139) Pentagastrin(DB00183) 0.000 0.28 1067 405 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.64 8 14 NUMA1 4926 broad.mit.edu 37 11 71716313 71716313 + Frame_Shift_Del DEL G - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr11:71716313delG uc001orl.1 - 23 5967 c.5795delC c.(5794-5796)CCAfs p.P1932fs IL18BP_uc009ysu.1_Intron|NUMA1_uc001orj.2_Frame_Shift_Del_p.P114fs|NUMA1_uc009ysw.1_Frame_Shift_Del_p.P1499fs|NUMA1_uc001ork.1_Frame_Shift_Del_p.P796fs|NUMA1_uc001orm.1_Frame_Shift_Del_p.P1918fs NM_006185 NP_006176 Q14980 NUMA1_HUMAN nuclear mitotic apparatus protein 1 1932 G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole protein binding|structural molecule activity ovary(3)|lung(2)|skin(2)|central_nervous_system(1) 8 CTTCAGATGTGGGGGGCACAC 0.607 0.46 69 58 ANKK1 255239 broad.mit.edu 37 11 113265743 113265743 + Frame_Shift_Del DEL C - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr11:113265743delC uc001pny.2 + 3 667 c.573delC c.(571-573)ATCfs p.I191fs NM_178510 NP_848605 Q8NFD2 ANKK1_HUMAN ankyrin repeat and kinase domain containing 1 191 Protein kinase. ATP binding|protein serine/threonine kinase activity lung(5)|stomach(1)|ovary(1)|breast(1) 8 all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194) BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238) TCAGCTACATCCCCCCTGAGA 0.572 0.60 18 27 SORL1 6653 broad.mit.edu 37 11 121416050 121416051 + Frame_Shift_Ins INS - C C SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr11:121416050_121416051insC uc001pxx.2 + 14 2043_2044 c.1963_1964insC c.(1963-1965)ACCfs p.T655fs NM_003105 NP_003096 Q92673 SORL_HUMAN sortilin-related receptor containing LDLR class 655 Extracellular (Potential). cholesterol metabolic process|lipid transport|receptor-mediated endocytosis integral to plasma membrane|low-density lipoprotein particle low-density lipoprotein particle binding|transmembrane receptor activity ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1) 15 Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113) BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108) CAAACGGCGGACCCCCCATGCC 0.545 0.34 84 44 ERBB3 2065 broad.mit.edu 37 12 56493620 56493621 + Splice_Site DEL AG - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr12:56493620_56493621delAG uc001sjh.2 + 25 3131 c.2938_splice c.e25-1 p.R980_splice ERBB3_uc009zoj.2_Intron|ERBB3_uc010sqb.1_Splice_Site_p.R337_splice|ERBB3_uc010sqc.1_Splice_Site_p.R921_splice|ERBB3_uc009zok.2_Splice_Site_p.R245_splice|ERBB3_uc001sjk.2_Splice_Site_p.R221_splice|ERBB3_uc001sjl.2_Splice_Site_p.R100_splice NM_001982 NP_001973 P21860 ERBB3_HUMAN erbB-3 isoform 1 precursor cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1) 8 OV - Ovarian serous cystadenocarcinoma(18;0.112) CTATCGATATAGAGAGAGAGTG 0.505 0.62 8 13 XPO4 64328 broad.mit.edu 37 13 21436900 21436901 + Frame_Shift_Del DEL CT - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr13:21436900_21436901delCT uc001unq.3 - 3 308_309 c.272_273delAG c.(271-273)GAGfs p.E91fs XPO4_uc010tcr.1_Frame_Shift_Del_p.E17fs NM_022459 NP_071904 Q9C0E2 XPO4_HUMAN exportin 4 91 protein transport cytoplasm|nucleus protein binding large_intestine(1)|ovary(1)|kidney(1) 3 all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244) all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548) TTCGCAGAGACTCGATGCTACC 0.431 0.42 80 59 NKX2-1 7080 broad.mit.edu 37 14 36988309 36988309 + Frame_Shift_Del DEL C - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr14:36988309delC uc001wtt.2 - 1 595 c.254delG c.(253-255)GGCfs p.G85fs SFTA3_uc001wts.2_Intron|NKX2-1_uc001wtu.2_Frame_Shift_Del_p.G115fs|NKX2-1_uc001wtv.2_Frame_Shift_Del_p.G85fs|uc001wtw.1_5'Flank NM_003317 NP_003308 P43699 NKX21_HUMAN thyroid transcription factor 1 isoform 2 85 epithelial tube branching involved in lung morphogenesis|globus pallidus development|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|thyroid gland development protein binding|transcription regulatory region DNA binding skin(1) 1 all_cancers(3;4.47e-51)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.165) Lung(8;1.8e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.014)|all cancers(34;0.0366)|LUSC - Lung squamous cell carcinoma(13;0.132) GBM - Glioblastoma multiforme(112;0.0171) 0.000 0.49 141 138 PRKCH 5583 broad.mit.edu 37 14 61952228 61952229 + Frame_Shift_Ins INS - T T SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr14:61952228_61952229insT uc001xfn.2 + 10 1592_1593 c.1287_1288insT c.(1285-1290)CTGTTTfs p.L429fs PRKCH_uc010tsa.1_Frame_Shift_Ins_p.L268fs|PRKCH_uc010tsb.1_5'UTR NM_006255 NP_006246 P24723 KPCL_HUMAN protein kinase C, eta 429_430 Protein kinase. intracellular signal transduction|platelet activation cytosol|plasma membrane ATP binding|enzyme binding|metal ion binding|protein kinase C activity ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1) 6 OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182) AGGATCGTCTGTTTTTTGTGAT 0.460 0.40 78 51 ADAM10 102 broad.mit.edu 37 15 58920068 58920069 + Frame_Shift_Del DEL TG - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr15:58920068_58920069delTG uc002afd.1 - 10 1634_1635 c.1190_1191delCA c.(1189-1191)ACAfs p.T397fs ADAM10_uc010bgc.1_RNA|ADAM10_uc010ugz.1_Frame_Shift_Del_p.T96fs|ADAM10_uc002afe.1_Intron NM_001110 NP_001101 O14672 ADA10_HUMAN ADAM metallopeptidase domain 10 precursor 397 Peptidase M12B.|Extracellular (Potential). cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding skin(2) 2 GBM - Glioblastoma multiforme(80;0.202) GTGTGCACTCTGTTCCAGAATC 0.347 0.96 5 130 PML 5371 broad.mit.edu 37 15 74315374 74315375 + Frame_Shift_Del DEL CG - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr15:74315374_74315375delCG uc002awv.2 + 3 948_949 c.808_809delCG c.(808-810)CGCfs p.R270fs PML_uc002awm.2_Frame_Shift_Del_p.R270fs|PML_uc002awl.2_Frame_Shift_Del_p.R270fs|PML_uc002awj.1_Frame_Shift_Del_p.R270fs|PML_uc002awk.2_Frame_Shift_Del_p.R270fs|PML_uc002awn.2_Frame_Shift_Del_p.R270fs|PML_uc002awo.2_Frame_Shift_Del_p.R270fs|PML_uc002awp.2_Frame_Shift_Del_p.R270fs|PML_uc002awq.2_Frame_Shift_Del_p.R270fs|PML_uc002awr.2_Frame_Shift_Del_p.R270fs|PML_uc002aws.2_Frame_Shift_Del_p.R270fs|PML_uc002awt.2_Frame_Shift_Del_p.R270fs|PML_uc002awu.2_Frame_Shift_Del_p.R270fs|PML_uc010ule.1_Intron|PML_uc002aww.1_Frame_Shift_Del_p.R185fs|PML_uc002awx.2_Frame_Shift_Del_p.R28fs|PML_uc002awy.2_5'Flank NM_033238 NP_150241 P29590 PML_HUMAN promyelocytic leukemia protein isoform 1 270 cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding central_nervous_system(2)|kidney(2)|breast(1) 5 CCAGCTGGGCCGCGCGCGTGCC 0.713 0.80 2 8 NTRK3 4916 broad.mit.edu 37 15 88799219 88799219 + Frame_Shift_Del DEL G - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr15:88799219delG uc002bme.1 - 2 328 c.166delC c.(166-168)CTCfs p.L56fs NTRK3_uc002bmh.2_Frame_Shift_Del_p.L56fs|NTRK3_uc002bmf.1_Frame_Shift_Del_p.L56fs|NTRK3_uc010bnh.1_Frame_Shift_Del_p.L56fs|NTRK3_uc002bmg.2_Frame_Shift_Del_p.L56fs NM_001012338 NP_001012338 Q16288 NTRK3_HUMAN neurotrophic tyrosine kinase, receptor, type 3 56 Extracellular (Potential). transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ETV6/NTRK3(234) soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1) 281 BRCA - Breast invasive adenocarcinoma(143;0.211) CCTTCCAGGAGGGGGAAGAGG 0.562 0.45 48 39 FANCI 55215 broad.mit.edu 37 15 89843605 89843606 + In_Frame_Ins INS - GGCAAT GGCAAT rs151267266 SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr15:89843605_89843606insGGCAAT uc010bnp.1 + 26 2968_2969 c.2878_2879insGGCAAT c.(2878-2880)CGG>CGGCAATGG p.960_961insQW FANCI_uc002bnm.1_In_Frame_Ins_p.900_901insQW|FANCI_uc002bnn.1_RNA|FANCI_uc002bnp.1_In_Frame_Ins_p.721_722insQW|FANCI_uc002bnq.1_In_Frame_Ins_p.373_374insQW NM_001113378 NP_001106849 Q9NVI1 FANCI_HUMAN Fanconi anemia, complementation group I isoform 960_961 cell cycle|DNA repair nucleoplasm protein binding ovary(2) 2 Lung NSC(78;0.0472)|all_lung(78;0.089) ATTCCAGATCCGGCAATTTCAG 0.480 0.53 45 50 BCAR1 9564 broad.mit.edu 37 16 75268820 75268821 + Frame_Shift_Ins INS - C C SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr16:75268820_75268821insC uc002fdv.2 - 5 2099_2100 c.1976_1977insG c.(1975-1977)GGCfs p.G659fs BCAR1_uc002fdt.2_Frame_Shift_Ins_p.G112fs|BCAR1_uc002fdu.2_Frame_Shift_Ins_p.G449fs|BCAR1_uc010cgu.2_Frame_Shift_Ins_p.G648fs|BCAR1_uc010vna.1_Frame_Shift_Ins_p.G657fs|BCAR1_uc010vnb.1_Frame_Shift_Ins_p.G705fs|BCAR1_uc002fdw.2_Frame_Shift_Ins_p.G659fs|BCAR1_uc010vnc.1_Frame_Shift_Ins_p.G511fs|BCAR1_uc010vnd.1_Frame_Shift_Ins_p.G677fs|BCAR1_uc002fdx.2_Frame_Shift_Ins_p.G677fs NM_014567 NP_055382 P56945 BCAR1_HUMAN breast cancer anti-estrogen resistance 1 659 actin filament organization|B cell receptor signaling pathway|blood coagulation|cell adhesion|cell division|cell migration|cell proliferation|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|integrin-mediated signaling pathway|nerve growth factor receptor signaling pathway|platelet-derived growth factor receptor signaling pathway|positive regulation of cell migration|regulation of apoptosis|regulation of cell growth|T cell receptor signaling pathway cytosol|focal adhesion|membrane fraction|ruffle protein kinase binding|protein phosphatase binding|SH3 domain binding|signal transducer activity central_nervous_system(5)|breast(2)|prostate(1) 8 BRCA - Breast invasive adenocarcinoma(221;0.169) 0.000 0.40 554 377 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 44 593 ORMDL3 94103 broad.mit.edu 37 17 38079413 38079414 + Frame_Shift_Ins INS - C C SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr17:38079413_38079414insC uc002htj.1 - 3 417_418 c.277_278insG c.(277-279)GTCfs p.V93fs ORMDL3_uc002hti.1_RNA|ORMDL3_uc002htk.1_Frame_Shift_Ins_p.V93fs NM_139280 NP_644809 Q8N138 ORML3_HUMAN ORM1-like 3 93 Lumenal (Potential). ceramide metabolic process integral to membrane|SPOTS complex protein binding 0 Colorectal(19;0.000442) Lung(15;0.0234) CGTGAACTGGACCCCATAATCC 0.594 0.31 11 5 WNK4 65266 broad.mit.edu 37 17 40939870 40939870 + Frame_Shift_Del DEL G - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr17:40939870delG uc002ibj.2 + 8 1837 c.1816delG c.(1816-1818)GGGfs p.G606fs WNK4_uc010wgx.1_Frame_Shift_Del_p.G270fs|WNK4_uc002ibk.1_Frame_Shift_Del_p.G378fs|WNK4_uc010wgy.1_Intron NM_032387 NP_115763 Q96J92 WNK4_HUMAN WNK lysine deficient protein kinase 4 606 intracellular protein kinase cascade tight junction ATP binding|protein serine/threonine kinase activity ovary(3)|skin(3)|stomach(1) 7 Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.0749) TCAGCCCCCTGGGGGGGTGCC 0.637 0.34 47 24 VEZF1 7716 broad.mit.edu 37 17 56056605 56056610 + In_Frame_Del DEL TGCTGC - - rs61731354;rs73995411;rs145983359 byFrequency;by1000genomes;byFrequency SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr17:56056605_56056610delTGCTGC uc002ivf.1 - 5 1184_1189 c.1041_1046delGCAGCA c.(1039-1047)CAGCAGCAA>CAA p.347_349QQQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.197_199QQQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 347_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgctgct 0.311 0.27 19 7 RNF43 54894 broad.mit.edu 37 17 56435160 56435160 + Frame_Shift_Del DEL A - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr17:56435160delA uc002iwf.2 - 8 3933 c.1977delT c.(1975-1977)GGTfs p.G659fs RNF43_uc010wnv.1_Frame_Shift_Del_p.G618fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.G659fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.G659fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.G532fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 659 Pro-rich.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.12 573 80 RNF43 54894 broad.mit.edu 37 17 56435161 56435161 + Frame_Shift_Del DEL C - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr17:56435161delC uc002iwf.2 - 8 3932 c.1976delG c.(1975-1977)GGTfs p.G659fs RNF43_uc010wnv.1_Frame_Shift_Del_p.G618fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.G659fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.G659fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.G532fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 659 Pro-rich.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.70 105 240 MAP2K7 5609 broad.mit.edu 37 19 7974971 7974973 + In_Frame_Del DEL AGG - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr19:7974971_7974973delAGG uc002mit.2 + 3 355_357 c.290_292delAGG c.(289-294)CAGGAG>CAG p.E98del MAP2K7_uc002miv.2_In_Frame_Del_p.E98del|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_In_Frame_Del_p.E98del|MAP2K7_uc010dvv.2_5'UTR NM_145185 NP_660186 O14733 MP2K7_HUMAN mitogen-activated protein kinase kinase 7 98 activation of JUN kinase activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleus ATP binding|JUN kinase kinase activity|magnesium ion binding|protein binding|protein kinase binding|protein phosphatase binding|protein serine/threonine kinase activity|protein tyrosine kinase activity large_intestine(7)|central_nervous_system(2)|ovary(1)|lung(1) 11 Etoposide(DB00773) 0.000 0.98 28 1400 JUNB 3726 broad.mit.edu 37 19 12902925 12902925 + Frame_Shift_Del DEL G - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr19:12902925delG uc002mvc.2 + 1 616 c.340delG c.(340-342)GGGfs p.G114fs JUNB_uc002mvb.2_RNA NM_002229 NP_002220 P17275 JUNB_HUMAN jun B proto-oncogene 114 chromatin|nucleus protein dimerization activity|transcription coactivator activity|transcription corepressor activity lung(2)|central_nervous_system(1) 3 TTACCCCCGCGGGGGTGGCAG 0.667 0.87 2 13 LYL1 4066 broad.mit.edu 37 19 13211824 13211824 + Frame_Shift_Del DEL G - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr19:13211824delG uc002mwi.2 - 2 523 c.162delC c.(160-162)CCCfs p.P54fs NM_005583 NP_005574 P12980 LYL1_HUMAN lymphoblastic leukemia derived sequence 1 54 B cell differentiation|blood vessel maturation|definitive hemopoiesis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding 0 OV - Ovarian serous cystadenocarcinoma(19;6.08e-22) 0.000 0.53 900 1001 PRKACA 5566 broad.mit.edu 37 19 14218178 14218178 + Frame_Shift_Del DEL T - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr19:14218178delT uc002myc.2 - 2 290 c.90delA c.(88-90)AAAfs p.K30fs PRKACA_uc002myb.2_Frame_Shift_Del_p.K22fs|PRKACA_uc010xnm.1_Translation_Start_Site|PRKACA_uc002myd.2_Translation_Start_Site NM_002730 NP_002721 P17612 KAPCA_HUMAN cAMP-dependent protein kinase catalytic subunit 30 activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|G2/M transition of mitotic cell cycle|gluconeogenesis|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|regulation of insulin secretion|transmembrane transport|triglyceride catabolic process|water transport cAMP-dependent protein kinase complex|centrosome|cytosol|nucleoplasm|plasma membrane ATP binding|cAMP-dependent protein kinase activity|cAMP-dependent protein kinase inhibitor activity|protein kinase binding lung(1) 1 GACTTTCCCATTTTTTAAGAA 0.552 0.50 20 20 BRD4 23476 broad.mit.edu 37 19 15376247 15376248 + Frame_Shift_Ins INS - G G SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr19:15376247_15376248insG uc002nar.2 - 5 988_989 c.766_767insC c.(766-768)CAGfs p.Q256fs BRD4_uc002nas.2_Frame_Shift_Ins_p.Q256fs|BRD4_uc002nat.3_Frame_Shift_Ins_p.Q256fs|BRD4_uc002nau.3_Frame_Shift_Ins_p.Q256fs NM_058243 NP_490597 O60885 BRD4_HUMAN bromodomain-containing protein 4 isoform long 256 interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle condensed nuclear chromosome|cytoplasm protein binding ovary(2) 2 OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18) 0.000 0.22 485 134 CD79A 973 broad.mit.edu 37 19 42383610 42383610 + Frame_Shift_Del DEL C - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr19:42383610delC uc002orv.2 + 3 570 c.385delC c.(385-387)CCCfs p.P129fs CD79A_uc002oru.2_Frame_Shift_Del_p.P91fs NM_001783 NP_001774 P11912 CD79A_HUMAN CD79A antigen isoform 1 precursor 129 Extracellular (Potential). B cell differentiation|B cell proliferation|B cell receptor signaling pathway B cell receptor complex|external side of plasma membrane|integral to membrane|membrane raft|multivesicular body transmembrane receptor activity ovary(2)|pancreas(1) 3 0.000 0.40 410 268 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 144 505 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 6 82 MED15 51586 broad.mit.edu 37 22 20918817 20918819 + In_Frame_Del DEL CAG - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr22:20918817_20918819delCAG uc002zsp.2 + 6 612_614 c.532_534delCAG c.(532-534)CAGdel p.Q188del MED15_uc002zsn.1_In_Frame_Del_p.Q107del|MED15_uc002zso.2_In_Frame_Del_p.Q117del|MED15_uc002zsq.2_In_Frame_Del_p.Q188del|MED15_uc010gso.2_In_Frame_Del_p.Q188del|MED15_uc002zsr.2_In_Frame_Del_p.Q162del|MED15_uc011ahs.1_In_Frame_Del_p.Q162del|MED15_uc011aht.1_In_Frame_Del_p.Q162del|MED15_uc002zss.2_In_Frame_Del_p.Q107del|MED15_uc011ahu.1_5'Flank NM_001003891 NP_001003891 Q96RN5 MED15_HUMAN mediator complex subunit 15 isoform a 188 Poly-Gln. regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding skin(1) 1 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) ggcggcgctacagcagcagcagc 0.148 0.32 17 8 PI4KA 5297 broad.mit.edu 37 22 21159300 21159300 + Frame_Shift_Del DEL C - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr22:21159300delC uc002zsz.3 - 11 1379 c.1148delG c.(1147-1149)TGTfs p.C383fs PI4KA_uc010gsq.1_Frame_Shift_Del_p.C441fs NM_058004 NP_477352 P42356 PI4KA_HUMAN phosphatidylinositol 4-kinase type 3 alpha 383 phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission Golgi-associated vesicle 1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1) 4 all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196) GAGGTCCACACAGGCAGCATT 0.582 0.43 55 41 PI4KA 5297 broad.mit.edu 37 22 21172812 21172812 + Frame_Shift_Del DEL G - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr22:21172812delG uc002zsz.3 - 7 872 c.641delC c.(640-642)CCTfs p.P214fs PI4KA_uc010gsq.1_Frame_Shift_Del_p.P272fs NM_058004 NP_477352 P42356 PI4KA_HUMAN phosphatidylinositol 4-kinase type 3 alpha 214 phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission Golgi-associated vesicle 1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1) 4 all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196) GGAACTGGGAGGGGGCATGCC 0.488 0.39 27 17 TNRC6B 23112 broad.mit.edu 37 22 40658035 40658035 + Frame_Shift_Del DEL A - - SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr22:40658035delA uc011aor.1 + 4 526 c.315delA c.(313-315)CTAfs p.L105fs TNRC6B_uc003aym.2_Frame_Shift_Del_p.L141fs|TNRC6B_uc003ayn.3_Frame_Shift_Del_p.L105fs|TNRC6B_uc003ayo.2_5'Flank NM_001162501 NP_001155973 Q9UPQ9 TNR6B_HUMAN trinucleotide repeat containing 6B isoform 1 105 gene silencing by RNA|regulation of translation cytoplasmic mRNA processing body nucleotide binding|RNA binding 0 0.000 0.71 570 1395 EP300 2033 broad.mit.edu 37 22 41553195 41553196 + Frame_Shift_Ins INS - C C SNUC5_LARGE_INTESTINE NA SNUC5_LARGE_INTESTINE NA g.chr22:41553195_41553196insC uc003azl.3 + 18 3679_3680 c.3284_3285insC c.(3283-3285)AGCfs p.S1095fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1095 Bromo. apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 ATTGTGAAGAGCCCCATGGATC 0.391 0.61 91 142 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SQ1_LUNG NA SQ1_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 4 99 MAMLD1 10046 broad.mit.edu 37 X 149639324 149639325 + In_Frame_Ins INS - CAG CAG SQ1_LUNG NA SQ1_LUNG NA g.chrX:149639324_149639325insCAG uc004fee.1 + 3 1555_1556 c.1479_1480insCAG c.(1477-1482)insCAG p.502_503insQ MAMLD1_uc011mxt.1_In_Frame_Ins_p.464_465insQ|MAMLD1_uc011mxu.1_In_Frame_Ins_p.477_478insQ|MAMLD1_uc011mxv.1_In_Frame_Ins_p.477_478insQ|MAMLD1_uc011mxw.1_In_Frame_Ins_p.429_430insQ NM_005491 NP_005482 Q13495 MAMD1_HUMAN mastermind-like domain containing 1 502_503 male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus 0 Acute lymphoblastic leukemia(192;6.56e-05) TAAGCcagcaacagcagcagca 0.441 0.59 13 19 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SQ1_LUNG NA SQ1_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.46 194 165 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SQ1_LUNG NA SQ1_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.50 40 40 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SQ1_LUNG NA SQ1_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 177 292 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SQ1_LUNG NA SQ1_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.40 29 19 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SQ1_LUNG NA SQ1_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.92 1 12 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SQ1_LUNG NA SQ1_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.99 1 68 SCYL1 57410 broad.mit.edu 37 11 65305310 65305312 + In_Frame_Del DEL GAC - - SQ1_LUNG NA SQ1_LUNG NA g.chr11:65305310_65305312delGAC uc001oea.1 + 15 2067_2069 c.1990_1992delGAC c.(1990-1992)GACdel p.D665del SCYL1_uc009yqk.2_In_Frame_Del_p.D665del|SCYL1_uc001oeb.1_In_Frame_Del_p.D648del|SCYL1_uc001oec.1_In_Frame_Del_p.D665del|SCYL1_uc001oed.1_In_Frame_Del_p.D522del|SCYL1_uc001oee.1_In_Frame_Del_p.D309del NM_020680 NP_065731 Q96KG9 NTKL_HUMAN SCY1-like 1 isoform A 665 regulation of transcription, DNA-dependent|retrograde vesicle-mediated transport, Golgi to ER|transcription, DNA-dependent cis-Golgi network|COPI vesicle coat|ER-Golgi intermediate compartment|microtubule organizing center|nucleus ATP binding|DNA binding|protein tyrosine kinase activity skin(1) 1 0.000 0.25 1046 348 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SQ1_LUNG NA SQ1_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.57 96 129 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SQ1_LUNG NA SQ1_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.71 28 68 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SQ1_LUNG NA SQ1_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 2 25 TAF15 8148 broad.mit.edu 37 17 34149739 34149741 + In_Frame_Del DEL ATG - - SQ1_LUNG NA SQ1_LUNG NA g.chr17:34149739_34149741delATG uc002hkd.2 + 6 472_474 c.386_388delATG c.(385-390)TATGAT>TAT p.D130del TAF15_uc010ctw.1_RNA|TAF15_uc002hkc.2_In_Frame_Del_p.D127del NM_139215 NP_631961 Q92804 RBP56_HUMAN TBP-associated factor 15 isoform 1 130 Gln/Gly/Ser/Tyr-rich. positive regulation of transcription, DNA-dependent cytoplasm|nucleus DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding TAF15/NR4A3(33) bone(33)|lung(1)|skin(1) 35 Ovarian(249;0.17) UCEC - Uterine corpus endometrioid carcinoma (308;0.0193) CAAGGCTCATATGATGAGCAGTC 0.433 0.94 8 118 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SQ1_LUNG NA SQ1_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.32 160 75 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SQ1_LUNG NA SQ1_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 57 519 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SQ1_LUNG NA SQ1_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 78 MAPK8IP2 23542 broad.mit.edu 37 22 51043281 51043282 + Frame_Shift_Ins INS - G G SQ1_LUNG NA SQ1_LUNG NA g.chr22:51043281_51043282insG uc003bmx.2 + 6 1671_1672 c.1554_1555insG c.(1552-1557)CACACGfs p.H518fs MAPK8IP2_uc003bmy.2_Frame_Shift_Ins_p.H491fs|MAPK8IP2_uc011asc.1_5'Flank NM_012324 NP_036456 Q13387 JIP2_HUMAN mitogen-activated protein kinase 8 interacting 518_519 behavioral fear response|dendrite morphogenesis|MAPKKK cascade|nonassociative learning|positive regulation of anti-apoptosis|regulation of excitatory postsynaptic membrane potential|regulation of JNK cascade|regulation of receptor activity|regulation of synaptic transmission, glutamatergic|signal complex assembly|social behavior cytoplasm|postsynaptic density beta-amyloid binding|kinesin binding|MAP-kinase scaffold activity|protein kinase activator activity|protein kinase binding large_intestine(2)|central_nervous_system(1) 3 all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) OV - Ovarian serous cystadenocarcinoma(4;1.28e-70)|Epithelial(4;3.46e-65)|GBM - Glioblastoma multiforme(4;4.83e-06)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247) 0.000 0.97 11 389 FAM48B1 100130302 broad.mit.edu 37 X 24382374 24382400 + In_Frame_Del DEL TGCTGCTGCTGCTGCTGCTGCTGCTGC - - rs10560780;rs2525863 SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:24382374_24382400delTGCTGCTGCTGCTGCTGCTGCTGCTGC uc011mjx.1 + 1 1497_1523 c.1497_1523delTGCTGCTGCTGCTGCTGCTGCTGCTGC c.(1495-1524)ATTGCTGCTGCTGCTGCTGCTGCTGCTGCT>ATT p.AAAAAAAAA509del NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 ctgctgctattgctgctgctgctgctgctgctgctgctgctgctgct 0.181 0.53 8 9 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 4 46 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.61 66 105 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 13 31 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.35 26 14 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 1127 271 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.40 70 46 JUNB 3726 broad.mit.edu 37 19 12903092 12903093 + Frame_Shift_Ins INS - G G SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:12903092_12903093insG uc002mvc.2 + 1 783_784 c.507_508insG c.(505-510)CCCGGGfs p.P169fs JUNB_uc002mvb.2_RNA NM_002229 NP_002220 P17275 JUNB_HUMAN jun B proto-oncogene 169_170 chromatin|nucleus protein dimerization activity|transcription coactivator activity|transcription corepressor activity lung(2)|central_nervous_system(1) 3 cggctgggcccgggggcgTCTA 0.564 0.13 53 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.75 40 118 GSK3A 2931 broad.mit.edu 37 19 42746510 42746510 + Frame_Shift_Del DEL G - - SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:42746510delG uc002otb.1 - 1 227 c.108delC c.(106-108)CCCfs p.P36fs GSK3A_uc002ota.1_5'Flank|GSK3A_uc002otc.2_RNA NM_019884 NP_063937 P49840 GSK3A_HUMAN glycogen synthase kinase 3 alpha 36 Gly-rich. insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of insulin receptor signaling pathway|negative regulation of transferase activity|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process beta-catenin destruction complex|cytosol ATP binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|tau-protein kinase activity ovary(2)|lung(2) 4 Prostate(69;0.00682) 0.000 0.27 281 105 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.22 439 124 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 8 126 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 5 73 ARID1A 8289 broad.mit.edu 37 1 27024002 27024002 + Frame_Shift_Del DEL G - - ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:27024002delG uc001bmv.1 + 1 1481 c.1108delG c.(1108-1110)GGGfs p.G370fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.G370fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.G370fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 370 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.Q372fs*19(1)|p.Q372fs*28(1) ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.16 142 28 TNNI3K 51086 broad.mit.edu 37 1 74929124 74929144 + Splice_Site DEL GCGGCTGCGGCAGCAGACATG - - rs145840620;rs140963906;rs138685516 ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:74929124_74929144delGCGGCTGCGGCAGCAGACATG uc001dgf.1 + 21 2063 c.2012_splice c.e21-1 p.A671_splice TNNI3K_uc001dgd.2_Splice_Site_p.A772_splice|TNNI3K_uc001dge.1_Splice_Site_p.A772_splice NM_015978 NP_057062 Q59H18 TNI3K_HUMAN TNNI3 interacting kinase isoform b cytoplasm|nucleus ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1) 10 TTGGTTTGCAGCGGCTGCGGCAGCAGACATGGCTTACCACC 0.439 0.14 169 28 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.13 625 95 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.46 26 22 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.29 27 11 SPRY1 10252 broad.mit.edu 37 4 124323228 124323231 + Frame_Shift_Del DEL TGAT - - ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:124323228_124323231delTGAT uc003ifa.2 + 2 670_673 c.482_485delTGAT c.(481-486)CTGATTfs p.L161fs SPRY1_uc003ifb.2_Frame_Shift_Del_p.L161fs NM_199327 NP_955359 O43609 SPY1_HUMAN sprouty homolog 1, antagonist of FGF signaling 161_162 epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway cytosol|lamellipodium|plasma membrane skin(2)|ovary(1) 3 0.000 0.27 1465 529 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 75 105 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 43 73 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.86 2 12 ATXN1 6310 broad.mit.edu 37 6 16327915 16327916 + In_Frame_Ins INS - TGC TGC rs11969612 by1000genomes ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:16327915_16327916insTGC uc003nbt.2 - 8 1597_1598 c.626_627insGCA c.(625-627)CAT>CAGCAT p.208_209insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.208_209insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 208_209 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) gctgatgctgatgctgctgctg 0.381 0.15 139 24 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.40 25 17 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 27 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.36 7 4 GLI1 2735 broad.mit.edu 37 12 57857549 57857563 + In_Frame_Del DEL GGGGGCCCCCAGTGT - - ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:57857549_57857563delGGGGGCCCCCAGTGT uc001snx.2 + 2 153_167 c.75_89delGGGGGCCCCCAGTGT c.(73-90)CAGGGGGCCCCCAGTGTG>CAG p.GAPSV26del GLI1_uc009zpp.2_Intron|GLI1_uc009zpq.2_Intron|GLI1_uc009zpr.1_Intron NM_005269 NP_005260 P08151 GLI1_HUMAN GLI family zinc finger 1 isoform 1 26_30 epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter cytosol|nucleus transcription regulatory region DNA binding|zinc ion binding skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1) 15 GBM - Glioblastoma multiforme(3;3.99e-32) TCCCCAGTCAGGGGGCCCCCAGTGTGGGGACAGAA 0.605 0.34 105 54 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.31 124 55 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.16 52 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.46 161 136 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 65 380 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 116 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SU8686_PANCREAS NA SU8686_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.25 142 48 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SU8686_PANCREAS NA SU8686_PANCREAS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.37 52 30 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SU8686_PANCREAS NA SU8686_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 47 47 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SU8686_PANCREAS NA SU8686_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.18 53 12 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SU8686_PANCREAS NA SU8686_PANCREAS NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.53 117 133 MAP3K4 4216 broad.mit.edu 37 6 161522922 161522923 + Splice_Site DEL AG - - SU8686_PANCREAS NA SU8686_PANCREAS NA g.chr6:161522922_161522923delAG uc003qtn.2 + 18 3817 c.3675_splice c.e18-1 p.R1225_splice MAP3K4_uc010kkc.1_Splice_Site_p.R1221_splice|MAP3K4_uc003qto.2_Splice_Site_p.R1175_splice|MAP3K4_uc011efz.1_Splice_Site|MAP3K4_uc011ega.1_Splice_Site_p.R678_splice|MAP3K4_uc003qtp.2_Splice_Site_p.R161_splice|MAP3K4_uc003qtq.2_5'UTR NM_005922 NP_005913 Q9Y6R4 M3K4_HUMAN mitogen-activated protein kinase kinase kinase 4 activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity perinuclear region of cytoplasm ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding ovary(3)|lung(3)|skin(2)|stomach(1) 9 Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771) OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05) ATATTAAAACAGGGGTTCCAGC 0.356 0.68 10 21 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SU8686_PANCREAS NA SU8686_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 540 61 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 SU8686_PANCREAS NA SU8686_PANCREAS NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.59 9 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SU8686_PANCREAS NA SU8686_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 201 71 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SU8686_PANCREAS NA SU8686_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 24 299 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SU8686_PANCREAS NA SU8686_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.64 83 146 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SU8686_PANCREAS NA SU8686_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 148 456 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SU8686_PANCREAS NA SU8686_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 3 36 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.83 6 29 BCL11A 53335 broad.mit.edu 37 2 60688554 60688562 + In_Frame_Del DEL TCCTCTTCT - - SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:60688554_60688562delTCCTCTTCT uc002sae.1 - 4 1713_1721 c.1485_1493delAGAAGAGGA c.(1483-1494)GAAGAAGAGGAG>GAG p.495_498EEEE>E BCL11A_uc002sab.2_In_Frame_Del_p.495_498EEEE>E|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_In_Frame_Del_p.164_167EEEE>E|BCL11A_uc010ypj.1_In_Frame_Del_p.461_464EEEE>E|BCL11A_uc002sad.1_In_Frame_Del_p.343_346EEEE>E|BCL11A_uc002saf.1_In_Frame_Del_p.461_464EEEE>E NM_022893 NP_075044 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A isoform 1 495_498 Glu-rich. negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|cytoplasm|nucleus|nucleus nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding p.E494_E497del(1) central_nervous_system(6)|breast(3)|ovary(2)|skin(2) 13 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) ctcctcttcctcctcttcttcctcttcct 0.435 0.37 17 10 FN1 2335 broad.mit.edu 37 2 216295510 216295511 + Frame_Shift_Ins INS - GG GG SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:216295510_216295511insGG uc002vfa.2 - 5 878_879 c.612_613insCC c.(610-615)CCCTACfs p.P204fs FN1_uc002vfb.2_Frame_Shift_Ins_p.P204fs|FN1_uc002vfc.2_Frame_Shift_Ins_p.P204fs|FN1_uc002vfd.2_Frame_Shift_Ins_p.P204fs|FN1_uc002vfe.2_Frame_Shift_Ins_p.P204fs|FN1_uc002vff.2_Frame_Shift_Ins_p.P204fs|FN1_uc002vfg.2_Frame_Shift_Ins_p.P204fs|FN1_uc002vfh.2_Frame_Shift_Ins_p.P204fs|FN1_uc002vfi.2_Frame_Shift_Ins_p.P204fs|FN1_uc002vfj.2_Frame_Shift_Ins_p.P204fs|FN1_uc002vfl.2_Frame_Shift_Ins_p.P204fs NM_212482 NP_997647 P02751 FINC_HUMAN fibronectin 1 isoform 1 preproprotein 204_205 Fibrin- and heparin-binding 1.|Fibronectin type-I 4. acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix collagen binding|extracellular matrix structural constituent|heparin binding central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1) 13 Renal(323;0.127) Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) CAGCCTTGGTAGGGCTTCTCCC 0.441 0.44 83 64 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 64 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 51 92 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.36 14 8 POU3F2 5454 broad.mit.edu 37 6 99283172 99283173 + In_Frame_Ins INS - CAG CAG SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:99283172_99283173insCAG uc003ppe.2 + 1 593_594 c.423_424insCAG c.(421-426)insCAG p.149_150insQ NM_005604 NP_005595 P20265 PO3F2_HUMAN POU domain, class 3, transcription factor 2 149_150 positive regulation of cell proliferation identical protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197) BRCA - Breast invasive adenocarcinoma(108;0.0355) aacagcagcaacagcagcagca 0.465 0.22 25 7 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 17 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.28 348 137 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 291 139 SMOC1 64093 broad.mit.edu 37 14 70477519 70477519 + Frame_Shift_Del DEL C - - SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:70477519delC uc001xls.1 + 8 966 c.713delC c.(712-714)GCCfs p.A238fs SMOC1_uc001xlt.1_Frame_Shift_Del_p.A238fs NM_022137 NP_071420 Q9H4F8 SMOC1_HUMAN secreted modular calcium-binding protein 1 238 Thyroglobulin type-1 2. cell differentiation|eye development|limb development|regulation of osteoblast differentiation|signal transduction basement membrane calcium ion binding upper_aerodigestive_tract(1)|pancreas(1) 2 all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028) 0.000 0.43 8 6 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.18 75 17 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.50 49 49 MYLK2 85366 broad.mit.edu 37 20 30418850 30418850 + Frame_Shift_Del DEL G - - SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:30418850delG uc002wwq.2 + 10 1432 c.1330delG c.(1330-1332)GGGfs p.G444fs MYLK2_uc002wws.2_Frame_Shift_Del_p.G61fs|MYLK2_uc010gdw.1_RNA NM_033118 NP_149109 Q9H1R3 MYLK2_HUMAN skeletal myosin light chain kinase 444 Protein kinase. cardiac muscle tissue morphogenesis|regulation of muscle filament sliding ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity lung(2)|skin(2)|ovary(1)|central_nervous_system(1) 6 Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347) GGTGAACTTTGGGACCCCAGA 0.552 0.35 35 19 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 71 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 150 389 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 53 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 36 FANCL 55120 broad.mit.edu 37 2 58387283 58387284 + Frame_Shift_Del DEL CT - - rs145260146 SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:58387283_58387284delCT uc002rzw.3 - 13 1118_1119 c.1051_1052delAG c.(1051-1053)AGTfs p.S351fs FANCL_uc002rzx.3_Frame_Shift_Del_p.S356fs|FANCL_uc010fce.2_Frame_Shift_Del_p.S323fs|FANCL_uc010fcf.1_Frame_Shift_Del_p.S292fs NM_018062 NP_060532 Q9NW38 FANCL_HUMAN Fanconi anemia, complementation group L isoform 351 RING-type. DNA repair cytoplasm|nucleoplasm ubiquitin-protein ligase activity|zinc ion binding ovary(2) 2 GATGTTAAAACTCTGTCTACTA 0.337 0.59 25 36 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.36 9 5 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.24 103 33 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.39 20 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 61 106 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 31 70 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.31 42 19 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.14 389 62 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 271 110 LGR5 8549 broad.mit.edu 37 12 71977816 71977816 + Frame_Shift_Del DEL G - - rs145066798 SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:71977816delG uc001swl.2 + 18 2074 c.2026delG c.(2026-2028)GCTfs p.A676fs LGR5_uc001swm.2_Frame_Shift_Del_p.A652fs|LGR5_uc001swn.1_Intron NM_003667 NP_003658 O75473 LGR5_HUMAN leucine-rich repeat-containing G protein-coupled 676 Cytoplasmic (Potential). integral to plasma membrane protein-hormone receptor activity lung(4)|skin(3)|ovary(1)|pancreas(1) 9 TGAAACGAAAGCTCCATTTTC 0.488 0.55 57 69 NTRK3 4916 broad.mit.edu 37 15 88669499 88669500 + Splice_Site DEL TA - - SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:88669499_88669500delTA uc002bme.1 - 12 1558 c.1396_splice c.e12+1 p.G466_splice NTRK3_uc002bmh.2_Splice_Site_p.G458_splice|NTRK3_uc002bmf.1_Splice_Site_p.G466_splice|NTRK3_uc010upl.1_Splice_Site_p.G368_splice|NTRK3_uc010bnh.1_Splice_Site_p.G458_splice|NTRK3_uc002bmg.2_Splice_Site_p.G466_splice NM_001012338 NP_001012338 Q16288 NTRK3_HUMAN neurotrophic tyrosine kinase, receptor, type 3 transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ETV6/NTRK3(234) soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1) 281 BRCA - Breast invasive adenocarcinoma(143;0.211) ACTCCCACCTTACCCTTCATTC 0.455 0.17 48 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 52 609 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 1.00 0 11 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.22 147 41 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.14 60 10 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 213 556 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 5 72 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 3 32 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.34 21 11 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.32 21 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.36 14 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.67 95 194 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 15 32 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.93 1 13 PKHD1 5314 broad.mit.edu 37 6 51612725 51612725 + Frame_Shift_Del DEL T - - SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:51612725delT uc003pah.1 - 58 9965 c.9689delA c.(9688-9690)GATfs p.D3230fs PKHD1_uc010jzn.1_Frame_Shift_Del_p.D1213fs|PKHD1_uc003pai.2_Frame_Shift_Del_p.D3230fs NM_138694 NP_619639 P08F94 PKHD1_HUMAN fibrocystin isoform 1 3230 Extracellular (Potential). cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body protein binding|receptor activity lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1) 44 Lung NSC(77;0.0605) GGGAGCTCTATCTGTTGATGT 0.488 0.48 76 69 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 25 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 3 49 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 572 64 CDK20 23552 broad.mit.edu 37 9 90582524 90582527 + Frame_Shift_Del DEL AGAT - - SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:90582524_90582527delAGAT uc004apr.2 - 8 1197_1200 c.891_894delATCT c.(889-894)CCATCTfs p.P297fs CDK20_uc004aps.2_Frame_Shift_Del_p.P276fs|CDK20_uc004apt.2_Frame_Shift_Del_p.P289fs|CDK20_uc004apu.2_Frame_Shift_Del_p.H235fs NM_001039803 NP_001034892 Q8IZL9 CDK20_HUMAN cell cycle related kinase isoform 3 297_298 cell division|multicellular organismal development cilium|mitochondrion|nucleus ATP binding|cyclin-dependent protein kinase activity skin(1) 1 TCGGCAGCTCAGATGGATGGGCAG 0.608 0.50 60 61 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 863 423 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.36 25 14 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.23 63 19 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 21 258 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 1.00 0 15 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.40 114 76 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 56 261 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 5 88 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 52 F8 2157 broad.mit.edu 37 X 154157686 154157686 + Frame_Shift_Del DEL T - - SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:154157686delT uc004fmt.2 - 14 4550 c.4379delA c.(4378-4380)AATfs p.N1460fs NM_000132 NP_000123 P00451 FA8_HUMAN coagulation factor VIII isoform a precursor 1460 B. N -> K (in HEMA). acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1) 11 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AGAAAGGTTATTTTTTTTGGC 0.413 0.38 186 116 TPRXL 348825 broad.mit.edu 37 3 14106033 14106038 + In_Frame_Del DEL TAGCTC - - rs139011213 by1000genomes SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14106033_14106038delTAGCTC uc011avd.1 + 3 812_817 c.357_362delTAGCTC c.(355-363)AGTAGCTCC>AGC p.119_121SSS>S TPRXL_uc003byh.1_In_Frame_Del_p.119_121SSS>S|TPRXL_uc003byg.2_In_Frame_Del_p.119_121SSS>S NR_002223 RecName: Full=Putative protein TPRXL; 0 gccccagcagtagctccagcagcagc 0.000 0.36 7 4 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 117 32 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.55 14 17 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.52 88 96 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 34 62 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.17 499 101 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.75 3 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.89 2 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 341 112 ITPR2 3709 broad.mit.edu 37 12 26553063 26553073 + Frame_Shift_Del DEL CTTTCGATGGC - - SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:26553063_26553073delCTTTCGATGGC uc001rhg.2 - 53 7935_7945 c.7518_7528delGCCATCGAAAG c.(7516-7530)AGGCCATCGAAAGATfs p.R2506fs ITPR2_uc009zjg.1_Frame_Shift_Del_p.R657fs NM_002223 NP_002214 Q14571 ITPR2_HUMAN inositol 1,4,5-triphosphate receptor, type 2 2506_2510 Extracellular (Potential). activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 14 Colorectal(261;0.0847) TGGCTTACATCTTTCGATGGCCTTCTTAGCA 0.408 0.19 206 47 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.41 10 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 26 303 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.10 79 9 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.52 35 38 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.20 73 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 148 362 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 31 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.34 194 100 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 9 4 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.38 8 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.42 49 35 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 23 43 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.30 266 116 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.62 6 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.22 165 46 CREBBP 1387 broad.mit.edu 37 16 3832849 3832849 + Frame_Shift_Del DEL A - - SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:3832849delA uc002cvv.2 - 6 1613 c.1409delT c.(1408-1410)TTAfs p.L470fs CREBBP_uc002cvw.2_Frame_Shift_Del_p.L432fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 470 cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding p.L470*(1)|p.L470fs*1(1) haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) TGGGTTACTTAAAGAAGTGGC 0.527 0.52 32 34 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 14 127 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 342 913 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 29 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.79 6 23 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 219 48 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.29 17 7 SKIL 6498 broad.mit.edu 37 3 170078673 170078673 + Frame_Shift_Del DEL C - - SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:170078673delC uc003fgu.2 + 2 1266 c.554delC c.(553-555)ACAfs p.T185fs SKIL_uc011bps.1_Frame_Shift_Del_p.T165fs|SKIL_uc003fgv.2_Frame_Shift_Del_p.T185fs|SKIL_uc003fgw.2_Frame_Shift_Del_p.T185fs NM_005414 NP_005405 P12757 SKIL_HUMAN SKI-like isoform 1 185 cell cycle arrest|negative regulation of cell differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of axonogenesis|protein heterotrimerization|protein homotrimerization|regulation of apoptosis|regulation of apoptosis|response to antibiotic|response to growth factor stimulus|skeletal muscle tissue development cytoplasm|PML body chromatin binding|nucleotide binding|protein complex binding|protein domain specific binding|SMAD binding|transcription corepressor activity|transcription repressor activity ovary(2)|skin(1) 3 all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137) Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197) CAAATAAATACAGTGTGTGAT 0.388 0.49 38 36 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.68 7 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 34 48 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.82 6 28 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.34 125 63 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.51 17 18 SGK1 6446 broad.mit.edu 37 6 134495666 134495667 + Frame_Shift_Ins INS - T T SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:134495666_134495667insT uc003qen.3 - 2 223_224 c.134_135insA c.(133-135)AACfs p.N45fs SGK1_uc003qeo.3_Frame_Shift_Ins_p.N140fs|SGK1_uc011ect.1_Frame_Shift_Ins_p.N35fs|SGK1_uc011ecu.1_Frame_Shift_Ins_p.N45fs|SGK1_uc011ecv.1_Frame_Shift_Ins_p.N59fs|SGK1_uc011ecw.1_Frame_Shift_Ins_p.N73fs NM_005627 NP_005618 O00141 SGK1_HUMAN serum/glucocorticoid regulated kinase 1 isoform 45 Necessary for localization to the cytoplasm. apoptosis|response to stress|sodium ion transport endoplasmic reticulum|nucleus|plasma membrane ATP binding|protein binding|protein serine/threonine kinase activity skin(3)|stomach(1)|lung(1)|central_nervous_system(1) 6 Colorectal(23;0.221) OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847) ATGCATAGGAGTTATTGGCAAT 0.416 0.26 59 21 BRAF 673 broad.mit.edu 37 7 140453138 140453139 + In_Frame_Ins INS - GTA GTA rs121913374;rs121913375 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:140453138_140453139insGTA uc003vwc.3 - 15 1857_1858 c.1796_1797insTAC c.(1795-1797)ACA>ACTACA p.599_599T>TT NM_004333 NP_004324 P15056 BRAF_HUMAN B-Raf 599 Protein kinase. T -> R (in CFC syndrome). activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission cytosol|nucleus|plasma membrane ATP binding|metal ion binding p.A598_T599insV(6)|p.T599I(5)|p.T599_V600insTT(3)|p.T599_R603>I(2)|p.T599_V600>IAL(2)|p.T599T(2)|p.T599_V600insT(2)|p.V600R(1)|p.T599_V600insV(1)|p.T599_V600insDFGLAT(1)|p.D594_T599del(1) KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2) thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1) 18290 Melanoma(164;0.00956) Sorafenib(DB00398) GAGATTTCACTGTAGCTAGACC 0.361 0.75 33 100 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 1 9 NOS3 4846 broad.mit.edu 37 7 150693562 150693572 + Frame_Shift_Del DEL CCCCCGGCCCC - - SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:150693562_150693572delCCCCCGGCCCC uc003wif.2 + 4 637_647 c.341_351delCCCCCGGCCCC c.(340-351)TCCCCCGGCCCCfs p.S114fs NOS3_uc011kuy.1_Intron|NOS3_uc011kuz.1_Frame_Shift_Del_p.S114fs|NOS3_uc011kva.1_Frame_Shift_Del_p.S114fs|NOS3_uc011kvb.1_Frame_Shift_Del_p.S114fs NM_000603 NP_000594 P29474 NOS3_HUMAN nitric oxide synthase 3 isoform 1 114_117 Interaction with NOSIP. anti-apoptosis|arginine catabolic process|blood vessel remodeling|endothelial cell migration|mitochondrion organization|negative regulation of muscle hyperplasia|negative regulation of platelet activation|nitric oxide biosynthetic process|platelet activation|positive regulation of angiogenesis|positive regulation of guanylate cyclase activity|positive regulation of vasodilation|regulation of blood vessel size|regulation of nitric-oxide synthase activity|regulation of systemic arterial blood pressure by endothelin|response to fluid shear stress|response to heat|smooth muscle hyperplasia caveola|cytoskeleton|cytosol|Golgi membrane actin monomer binding|arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding central_nervous_system(5)|large_intestine(2)|skin(1) 8 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) L-Arginine(DB00125)|L-Citrulline(DB00155)|Rosuvastatin(DB01098)|Tetrahydrobiopterin(DB00360) ggccggccctcccccggccccccggccccTG 0.507 0.89 6 51 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.41 13 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 18 FAS 355 broad.mit.edu 37 10 90773879 90773883 + Frame_Shift_Del DEL TTGAC - - SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:90773879_90773883delTTGAC uc001kfr.2 + 9 1026_1030 c.680_684delTTGAC c.(679-684)GTTGACfs p.V227fs FAS_uc010qna.1_RNA|FAS_uc001kfs.2_Frame_Shift_Del_p.L219fs|FAS_uc001kft.2_Frame_Shift_Del_p.V206fs|FAS_uc010qnb.1_RNA|FAS_uc010qnc.1_RNA|FAS_uc001kfw.2_3'UTR|FAS_uc010qnd.1_RNA|FAS_uc010qne.1_RNA|FAS_uc009xtp.2_RNA NM_000043 NP_000034 P25445 TNR6_HUMAN tumor necrosis factor receptor superfamily, 227_228 Interaction with HIPK3 (By similarity).|Cytoplasmic (Potential). activation of caspase activity|activation of pro-apoptotic gene products|anti-apoptosis|cellular response to mechanical stimulus|positive regulation of necrotic cell death cytosol|extracellular region|integral to membrane|soluble fraction identical protein binding|kinase binding upper_aerodigestive_tract(1)|breast(1) 2 Colorectal(252;0.0161) Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193) TTTTCAGATGTTGACTTGAGTAAAT 0.302 0.39 27 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 177 87 PABPN1 8106 broad.mit.edu 37 14 23777257 23777258 + Frame_Shift_Ins INS - C C SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:23777257_23777258insC uc001wjh.3 + 3 469_470 c.281_282insC c.(280-282)GGCfs p.G94fs BCL2L2_uc001wjg.3_Frame_Shift_Ins_p.G94fs|BCL2L2_uc001wji.3_Frame_Shift_Ins_p.G94fs NM_004643 NP_004634 Q86U42 PABP2_HUMAN poly(A) binding protein, nuclear 1 Error:Variant_position_missing_in_Q86U42_after_alignment modification by virus of host mRNA processing|mRNA 3'-end processing|muscle contraction|nuclear mRNA splicing, via spliceosome|poly(A)+ mRNA export from nucleus|termination of RNA polymerase II transcription|viral infectious cycle cytoplasm|nucleoplasm|ribonucleoprotein complex nucleotide binding|protein binding|RNA binding ovary(2) 2 all_cancers(95;6.69e-06) GBM - Glioblastoma multiforme(265;0.00643) CCCAACTGGGGCCGCCTTGTAG 0.574 0.15 55 10 SOCS1 8651 broad.mit.edu 37 16 11349141 11349159 + Frame_Shift_Del DEL CCGGTAATCGGCGTGCGAA - - SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:11349141_11349159delCCGGTAATCGGCGTGCGAA uc002dar.1 - 2 331_349 c.177_195delTTCGCACGCCGATTACCGG c.(175-195)CGTTCGCACGCCGATTACCGGfs p.R59fs C16orf75_uc002daq.1_Intron NM_003745 NP_003736 O15524 SOCS1_HUMAN suppressor of cytokine signaling 1 59_65 Kinase inhibitory region (KIR). interferon-gamma-mediated signaling pathway|JAK-STAT cascade|negative regulation of insulin receptor signaling pathway|negative regulation of tyrosine phosphorylation of Stat3 protein|regulation of growth|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway cytosol insulin-like growth factor receptor binding|protein kinase binding|protein kinase inhibitor activity p.Y64fs*49(1)|p.R65fs*48(1)|p.S60fs*19(1)|p.R65R(1)|p.Y64fs*1(1)|p.Y64fs*12(1)|p.Y64N(1)|p.D63_Q108del(1) haematopoietic_and_lymphoid_tissue(64)|lung(3)|breast(1)|central_nervous_system(1) 69 0.000 0.10 403 43 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.41 32 22 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.27 65 24 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 166 377 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 2 40 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.02 -1 65 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 637 186 LRP1B 53353 broad.mit.edu 37 2 141986801 141986801 + Frame_Shift_Del DEL T - - SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr2:141986801delT uc002tvj.1 - 6 1773 c.801delA c.(799-801)GCAfs p.A267fs LRP1B_uc010fnl.1_Intron NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 267 Extracellular (Potential).|LDL-receptor class B 1. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) TTAATCCTCCTGCTTTTGTTA 0.294 1.00 0 127 TTN 7273 broad.mit.edu 37 2 179437975 179437983 + In_Frame_Del DEL AACTCATAT - - SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr2:179437975_179437983delAACTCATAT uc010zfg.1 - 275 65396_65404 c.65172_65180delATATGAGTT c.(65170-65181)GAATATGAGTTC>GAC p.21724_21727EYEF>D uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.15419_15422EYEF>D|TTN_uc010zfi.1_In_Frame_Del_p.15352_15355EYEF>D|TTN_uc010zfj.1_In_Frame_Del_p.15227_15230EYEF>D NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 22651_22654 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATAATCCTGAACTCATATTCATGTCCTT 0.421 0.13 607 89 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.45 27 22 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.12 224 32 HTT 3064 broad.mit.edu 37 4 3076672 3076673 + In_Frame_Ins INS - CCGCCGCCG CCGCCGCCG rs76533208 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr4:3076672_3076673insCCGCCGCCG uc011bvq.1 + 2 271_272 c.126_127insCCGCCGCCG c.(124-129)insCCGCCGCCG p.51_52insPPP NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 49_50 establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) aacagccgccaccgccgccgcc 0.084 0.38 61 38 BMP2K 55589 broad.mit.edu 37 4 79792082 79792083 + In_Frame_Ins INS - CAG CAG rs5859654;rs35071794 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr4:79792082_79792083insCAG uc003hlk.2 + 11 1543_1544 c.1377_1378insCAG c.(1375-1380)insCAG p.486_487insQ BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Ins_p.486_487insQ|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486_487 Gln/His-rich. nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 GTCATCCTCACcagcagcagca 0.262 0.26 243 87 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.47 34 30 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.69 109 247 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.31 90 40 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.67 5 10 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.10 246 26 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 19 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 39 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) agcagcagcaacagcagcagca 0.267 0.44 79 61 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.48 896 830 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.52 94 100 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.31 245 112 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 27 314 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SUIT2_PANCREAS NA SUIT2_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 6 183 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 39 ROCK2 9475 broad.mit.edu 37 2 11334379 11334385 + Splice_Site DEL TACTCTA - - rs55839233 SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:11334379_11334385delTACTCTA uc002rbd.1 - 29 4057 c.3608_splice c.e29+1 p.D1203_splice NM_004850 NP_004841 O75116 ROCK2_HUMAN Rho-associated, coiled-coil containing protein axon guidance|cytokinesis|intracellular signal transduction cytosol|plasma membrane ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity stomach(2)|skin(2) 4 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162) CAAAAACACTTACTCTATATCTAAAAC 0.285 0.41 19 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 96 113 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 41 83 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.91 1 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.49 58 56 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 38 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.92 1 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 381 84 CHD9 80205 broad.mit.edu 37 16 53338483 53338488 + In_Frame_Del DEL TCTTCA - - SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:53338483_53338488delTCTTCA uc002ehb.2 + 30 6729_6734 c.6565_6570delTCTTCA c.(6565-6570)TCTTCAdel p.SS2191del CHD9_uc002egy.2_In_Frame_Del_p.SS2191del|CHD9_uc002ehc.2_In_Frame_Del_p.SS2191del|CHD9_uc002ehf.2_In_Frame_Del_p.SS1305del|CHD9_uc010cbw.2_Intron|CHD9_uc002ehg.1_In_Frame_Del_p.SS197del NM_025134 NP_079410 Q3L8U1 CHD9_HUMAN chromodomain helicase DNA binding protein 9 2191_2192 Ser-rich. cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleoplasm ATP binding|DNA binding|helicase activity|protein binding lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1) 7 all_cancers(37;0.0212) ctcctcctcctcttcatcttcATCAG 0.194 0.31 92 41 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 8 57 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.68 22 47 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 108 326 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 10 95 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.74 14 39 RGL1 23179 broad.mit.edu 37 1 183881394 183881395 + Frame_Shift_Ins INS - A A SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:183881394_183881395insA uc001gqo.2 + 15 1898_1899 c.1741_1742insA c.(1741-1743)CAAfs p.Q581fs RGL1_uc010pof.1_Frame_Shift_Ins_p.Q386fs|RGL1_uc001gqm.2_Frame_Shift_Ins_p.Q616fs|RGL1_uc010pog.1_Frame_Shift_Ins_p.Q579fs|RGL1_uc010poh.1_Frame_Shift_Ins_p.Q579fs|RGL1_uc010poi.1_Frame_Shift_Ins_p.Q552fs NM_015149 NP_055964 Q9NZL6 RGL1_HUMAN ral guanine nucleotide dissociation 581 Ser-rich. cellular lipid metabolic process|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction intracellular protein binding|Ral guanyl-nucleotide exchange factor activity breast(5)|ovary(4)|lung(2) 11 TGATGAGCCTCAAAAAAAGGTA 0.485 0.20 74 19 IRS1 3667 broad.mit.edu 37 2 227661395 227661396 + In_Frame_Ins INS - TGC TGC rs138975702 by1000genomes SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:227661395_227661396insTGC uc002voh.3 - 1 2111_2112 c.2059_2060insGCA c.(2059-2061)AAC>AGCAAC p.686_687insS NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 686_687 fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) AGGGACGGCGTtgctgctgctg 0.550 0.20 270 66 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.23 40 12 ALPK1 80216 broad.mit.edu 37 4 113353696 113353697 + Frame_Shift_Ins INS - T T SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:113353696_113353697insT uc003iap.3 + 11 3272_3273 c.2993_2994insT c.(2992-2994)AATfs p.N998fs ALPK1_uc003ian.3_Frame_Shift_Ins_p.N998fs|ALPK1_uc011cfx.1_Frame_Shift_Ins_p.N920fs|ALPK1_uc003iao.3_Intron|ALPK1_uc010imo.2_Frame_Shift_Ins_p.N826fs NM_025144 NP_079420 Q96QP1 ALPK1_HUMAN alpha-kinase 1 998 ATP binding|protein serine/threonine kinase activity ovary(5) 5 Ovarian(17;0.0446)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.00325) 0.000 0.91 9 86 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 50 74 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 17 47 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.18 103 22 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.29 22 9 TTBK1 84630 broad.mit.edu 37 6 43252917 43252918 + Frame_Shift_Del DEL AG - - SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:43252917_43252918delAG uc003ouq.1 + 15 4048_4049 c.3769_3770delAG c.(3769-3771)AGAfs p.R1257fs NM_032538 NP_115927 Q5TCY1 TTBK1_HUMAN tau tubulin kinase 1 1257 Pro-rich. cell junction|cytoplasm|nucleus ATP binding|protein binding|protein serine/threonine kinase activity lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1) 9 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399) 0.000 0.20 176 44 PHIP 55023 broad.mit.edu 37 6 79650450 79650450 + Frame_Shift_Del DEL T - - SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:79650450delT uc003pir.2 - 40 5652 c.5426delA c.(5425-5427)AAGfs p.K1809fs PHIP_uc003piq.2_Frame_Shift_Del_p.K833fs|PHIP_uc011dyp.1_Frame_Shift_Del_p.K1808fs|IRAK1BP1_uc010kbg.1_Intron|PHIP_uc003pio.3_Frame_Shift_Del_p.K695fs NM_017934 NP_060404 Q8WWQ0 PHIP_HUMAN pleckstrin homology domain interacting protein 1809 insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis nucleus insulin receptor binding large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1) 6 all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219) BRCA - Breast invasive adenocarcinoma(397;0.231) TTCAGTCAACTTTCGGACTCG 0.363 0.47 110 97 TBX18 9096 broad.mit.edu 37 6 85446744 85446744 + Frame_Shift_Del DEL G - - SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:85446744delG uc003pkl.1 - 8 1483 c.1483delC c.(1483-1485)CAGfs p.Q495fs TBX18_uc010kbq.1_Intron NM_001080508 NP_001073977 O95935 TBX18_HUMAN T-box 18 495 multicellular organismal development nucleus DNA binding|sequence-specific DNA binding transcription factor activity ovary(2)|pancreas(2)|lung(1) 5 all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858) BRCA - Breast invasive adenocarcinoma(108;0.0267) TACTGGAGCTGGGGGGACATT 0.537 0.33 8 4 MYB 4602 broad.mit.edu 37 6 135520172 135520173 + Frame_Shift_Ins INS - A A SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:135520172_135520173insA uc003qfc.2 + 10 1529_1530 c.1330_1331insA c.(1330-1332)CAAfs p.Q444fs MYB_uc003qfh.2_Frame_Shift_Ins_p.Q565fs|MYB_uc003qfi.2_Frame_Shift_Ins_p.Q549fs|MYB_uc010kgi.2_Frame_Shift_Ins_p.Q444fs|MYB_uc003qfq.2_Frame_Shift_Ins_p.Q562fs|MYB_uc010kgj.2_Frame_Shift_Ins_p.Q409fs|MYB_uc003qfo.2_Frame_Shift_Ins_p.Q359fs|MYB_uc003qfu.2_Frame_Shift_Ins_p.Q441fs|MYB_uc003qfl.2_RNA|MYB_uc003qfv.2_RNA|MYB_uc003qfz.2_RNA|MYB_uc003qfx.2_RNA|MYB_uc003qga.2_RNA|MYB_uc003qgb.2_RNA|MYB_uc010kgk.2_RNA|MYB_uc003qfd.2_RNA|MYB_uc003qfe.2_RNA|MYB_uc003qfg.2_RNA|MYB_uc003qff.2_RNA|MYB_uc003qfj.2_RNA|MYB_uc003qfm.2_RNA|MYB_uc003qfp.2_RNA|MYB_uc003qfn.2_RNA|MYB_uc003qfk.2_RNA|MYB_uc003qfr.2_RNA|MYB_uc003qfs.2_Frame_Shift_Ins_p.Q70fs|MYB_uc003qft.2_RNA|MYB_uc003qfw.2_Frame_Shift_Ins_p.Q256fs|MYB_uc003qfy.2_RNA|MYB_uc003qgc.2_RNA|MYB_uc003qfb.1_Frame_Shift_Ins_p.Q444fs NM_005375 NP_005366 P10242 MYB_HUMAN v-myb myeloblastosis viral oncogene homolog 444 Negative regulatory domain (By similarity). blood coagulation|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of histone H3-K4 methylation|positive regulation of histone H3-K9 methylation|positive regulation of T-helper cell differentiation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear matrix DNA binding|protein binding lung(1) 1 all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221) Lung NSC(302;3.08e-05)|Ovarian(999;0.208) OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117) TGTGAAAACTCAAAAGGAAAAT 0.342 0.89 6 48 TNFAIP3 7128 broad.mit.edu 37 6 138192638 138192639 + Frame_Shift_Ins INS - TTGTGGCGCT TTGTGGCGCT SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:138192638_138192639insTTGTGGCGCT uc003qhr.2 + 2 340_341 c.274_275insTTGTGGCGCT c.(274-276)CTTfs p.L92fs TNFAIP3_uc003qhs.2_Frame_Shift_Ins_p.L92fs NM_006290 NP_006281 P21580 TNAP3_HUMAN tumor necrosis factor, alpha-induced protein 3 92 TRAF-binding.|OTU. anti-apoptosis|apoptosis|B-1 B cell homeostasis|negative regulation of B cell activation|negative regulation of bone resorption|negative regulation of CD40 signaling pathway|negative regulation of endothelial cell apoptosis|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of inflammatory response|negative regulation of interleukin-2 production|negative regulation of interleukin-6 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of osteoclast proliferation|negative regulation of protein ubiquitination|negative regulation of smooth muscle cell proliferation|negative regulation of toll-like receptor 2 signaling pathway|negative regulation of toll-like receptor 3 signaling pathway|negative regulation of tumor necrosis factor production|negative regulation of type I interferon production|positive regulation of protein catabolic process|protein K48-linked ubiquitination|protein K63-linked deubiquitination|protein oligomerization|regulation of defense response to virus by host|regulation of germinal center formation|regulation of vascular wound healing|tolerance induction to lipopolysaccharide centrosome|cytosol|nucleus caspase inhibitor activity|DNA binding|protease binding|protein self-association|ubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-protein ligase activity|ubiquitin-specific protease activity|zinc ion binding p.0?(22)|p.V93fs*3(1) haematopoietic_and_lymphoid_tissue(133)|lung(3)|ovary(1) 137 Breast(32;0.135)|Colorectal(23;0.24) GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468) AGTCCGGAAGCTTGTGGCGCTG 0.500 0.44 22 17 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 2 16 PAXIP1 22976 broad.mit.edu 37 7 154760266 154760267 + In_Frame_Ins INS - CTG CTG rs141168451 by1000genomes SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:154760266_154760267insCTG uc003wlp.2 - 7 1687_1688 c.1644_1645insCAG c.(1642-1647)insCAG p.548_549insQ PAXIP1_uc003wlq.1_In_Frame_Ins_p.514_515insQ|PAXIP1_uc011kvs.1_In_Frame_Ins_p.512_513insQ|PAXIP1_uc003wlr.1_In_Frame_Ins_p.457_458insQ NM_007349 NP_031375 Q6ZW49 PAXI1_HUMAN PAX interacting protein 1 548_549 Gln-rich. DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent histone methyltransferase complex|nuclear matrix lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_neural(206;0.119) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.0296) UCEC - Uterine corpus endometrioid carcinoma (81;0.178) TGACTTTGCATctgctgctgct 0.233 0.27 289 108 PRKDC 5591 broad.mit.edu 37 8 48805817 48805818 + Splice_Site INS - A A rs33914855;rs67588121 SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:48805817_48805818insA uc003xqi.2 - 32 3787 c.3730_splice c.e32-1 p.L1244_splice PRKDC_uc003xqj.2_Splice_Site_p.L1244_splice|PRKDC_uc011ldh.1_Intron NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) GGCCCCCGAAGTACAAGAGGGT 0.594 0.32 251 117 LYN 4067 broad.mit.edu 37 8 56863054 56863054 + Frame_Shift_Del DEL A - - SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:56863054delA uc003xsk.3 + 5 603 c.321delA c.(319-321)ACAfs p.T107fs LYN_uc003xsl.3_Frame_Shift_Del_p.T86fs NM_002350 NP_002341 P07948 LYN_HUMAN Yamaguchi sarcoma viral (v-yes-1) oncogene 107 SH3. erythrocyte differentiation|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of cellular component movement|positive regulation of stress-activated protein kinase signaling cascade|positive regulation of tyrosine phosphorylation of STAT protein|response to DNA damage stimulus|T cell costimulation cytosol|Golgi apparatus|membrane raft|nucleus|perinuclear region of cytoplasm ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|receptor signaling protein tyrosine kinase activity ovary(1)|breast(1)|central_nervous_system(1) 3 all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772) Epithelial(17;0.000834)|all cancers(17;0.00598) CCCTTTTAACAAAAAAAGAAG 0.338 0.26 51 18 NACAP1 83955 broad.mit.edu 37 8 102381498 102381498 + Frame_Shift_Del DEL T - - SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:102381498delT uc003ykc.1 + 1 378 c.361delT c.(361-363)TTTfs p.F121fs NACAP1_uc010mbs.1_RNA NR_002182 SubName: Full=NACAP1 protein; 0 ACCTACATGGTTTTTGGGGAA 0.418 0.48 102 93 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 3 69 RPS6KB2 6199 broad.mit.edu 37 11 67200594 67200595 + Splice_Site INS - A A SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:67200594_67200595insA uc001old.2 + 9 790 c.708_splice c.e9-2 p.M236_splice RPS6KB2_uc001olf.2_Splice_Site_p.M36_splice|RPS6KB2_uc001olg.2_Splice_Site_p.M236_splice|RPS6KB2_uc009yrq.2_Splice_Site_p.M36_splice|RPS6KB2_uc001ole.2_Splice_Site|RPS6KB2_uc001olh.2_Splice_Site|RPS6KB2_uc009yrr.2_Splice_Site_p.M67_splice NM_003952 NP_003943 Q9UBS0 KS6B2_HUMAN ribosomal protein S6 kinase, 70kDa, polypeptide nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of translational initiation|translation nucleoplasm ATP binding|protein serine/threonine kinase activity ovary(2)|central_nervous_system(2)|stomach(1)|lung(1)|salivary_gland(1) 7 BRCA - Breast invasive adenocarcinoma(15;3.26e-06) ACCTGGACCCCAGGGCCCCTGA 0.649 0.14 55 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 713 255 NCAPD3 23310 broad.mit.edu 37 11 134078847 134078848 + Splice_Site INS - A A SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:134078847_134078848insA uc001qhd.1 - 7 1401 c.795_splice c.e7-1 p.R265_splice NCAPD3_uc010scm.1_Splice_Site|NCAPD3_uc009zda.1_Splice_Site NM_015261 NP_056076 P42695 CNDD3_HUMAN non-SMC condensin II complex, subunit D3 cell division|mitotic chromosome condensation nuclear centromeric heterochromatin|nuclear condensin complex methylated histone residue binding ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1) 5 all_hematologic(175;0.127) all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227) TTAAGAGCTCTAAAAAAAAAAG 0.337 0.15 41 7 LOC100130776 100130776 broad.mit.edu 37 12 58121116 58121116 + Frame_Shift_Del DEL C - - SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:58121116delC uc001sps.3 + 2 508 c.341delC c.(340-342)TCCfs p.S114fs AGAP2_uc001spo.1_5'Flank|AGAP2_uc001spq.2_Intron|AGAP2_uc001spp.2_Intron|AGAP2_uc001spr.2_Intron NR_027032 SubName: Full=cDNA FLJ59598; SubName: Full=HCG2014417, isoform CRA_a; 0 CAGCAACCCTCCCCCCGCTCT 0.657 0.46 131 113 ULK1 8408 broad.mit.edu 37 12 132400479 132400485 + Frame_Shift_Del DEL CTGCCGC - - SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132400479_132400485delCTGCCGC uc001uje.2 + 19 1921_1927 c.1653_1659delCTGCCGC c.(1651-1659)GGCTGCCGCfs p.G551fs NM_003565 NP_003556 O75385 ULK1_HUMAN Unc-51-like kinase 1 551_553 autophagy|protein localization|regulation of autophagy autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex ATP binding|protein complex binding|protein serine/threonine kinase activity ovary(1)|lung(1)|central_nervous_system(1)|skin(1) 4 all_neural(191;0.0982)|Medulloblastoma(191;0.163) OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07) CCGGGCTGGGCTGCCGCCTGCACAGCG 0.700 0.22 40 11 CHD8 57680 broad.mit.edu 37 14 21873556 21873556 + Frame_Shift_Del DEL T - - SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:21873556delT uc001was.1 - 16 2376 c.2282delA c.(2281-2283)AACfs p.N761fs CHD8_uc001war.1_Frame_Shift_Del_p.N657fs|CHD8_uc001wav.1_Frame_Shift_Del_p.N203fs NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 1040 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) GGGTGCCAAGTTTTTTTCAAC 0.378 0.29 131 54 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.22 283 79 NDRG3 57446 broad.mit.edu 37 20 35293663 35293663 + Frame_Shift_Del DEL T - - SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:35293663delT uc002xfw.2 - 11 816 c.734delA c.(733-735)AATfs p.N245fs NDRG3_uc002xfx.2_Frame_Shift_Del_p.N233fs|NDRG3_uc010zvq.1_Frame_Shift_Del_p.N150fs|NDRG3_uc010zvr.1_Frame_Shift_Del_p.N133fs NM_032013 NP_114402 Q9UGV2 NDRG3_HUMAN N-myc downstream regulated gene 3 isoform a 245 cell differentiation|negative regulation of cell growth|spermatogenesis cytoplasm ovary(1) 1 Myeloproliferative disorder(115;0.00878) 0.000 0.45 356 292 ZNF217 7764 broad.mit.edu 37 20 52198814 52198814 + Frame_Shift_Del DEL G - - SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:52198814delG uc002xwq.3 - 1 823 c.552delC c.(550-552)GCCfs p.A184fs ZNF217_uc010gij.1_Frame_Shift_Del_p.A176fs NM_006526 NP_006517 O75362 ZN217_HUMAN zinc finger protein 217 184 negative regulation of transcription, DNA-dependent histone deacetylase complex protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding skin(2)|ovary(1)|large_intestine(1)|lung(1)|breast(1) 6 all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398) BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198) GTTTGCTTCTGGCCCCCGATT 0.493 0.42 221 162 SS18L1 26039 broad.mit.edu 37 20 60740566 60740566 + Frame_Shift_Del DEL G - - SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:60740566delG uc002ycb.2 + 8 967 c.912delG c.(910-912)GAGfs p.E304fs SS18L1_uc011aaa.1_Frame_Shift_Del_p.E304fs|SS18L1_uc002ybz.1_RNA|SS18L1_uc002yca.1_RNA|SS18L1_uc002ycc.1_RNA NM_198935 NP_945173 O75177 CREST_HUMAN SS18-like protein 1 304 Gln-rich.|MFD domain (By similarity). chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent condensed chromosome kinetochore ovary(2) 2 Breast(26;3.97e-09) BRCA - Breast invasive adenocarcinoma(19;1.92e-08) 0.000 0.36 214 120 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 61 150 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.85 9 52 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 2 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 42 48 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 12 28 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.19 461 108 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 69 34 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.56 7 9 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 19 213 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.69 11 25 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 142 448 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN "glutamate receptor, ionotrophic, AMPA 3 isoform" glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.5 1 0 37 DVL1 1855 broad.mit.edu 37 1 1271770 1271771 + Frame_Shift_Ins INS - C C rs1061334 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:1271770_1271771insC uc001aer.3 - 15 1811_1812 c.1764_1765insG c.(1762-1767)GGGAGCfs p.G588fs DVL1_uc002quu.2_Frame_Shift_Ins_p.G330fs|DVL1_uc009vka.2_Frame_Shift_Ins_p.G271fs|DVL1_uc001aeu.1_3'UTR NM_004421 NP_004412 O14640 DVL1_HUMAN dishevelled 1 613_614 canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome frizzled binding|identical protein binding|protein kinase binding|signal transducer activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145) 0.000 0.16 672 130 PTCH2 8643 broad.mit.edu 37 1 45295309 45295310 + Frame_Shift_Ins INS - T T SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:45295309_45295310insT uc010olf.1 - 8 1071_1072 c.1059_1060insA c.(1057-1062)CAAGCCfs p.Q353fs PTCH2_uc010olg.1_Frame_Shift_Ins_p.Q52fs NM_003738 NP_003729 Q9Y6C5 PTC2_HUMAN patched 2 353_354 Extracellular (Potential). protein complex assembly|spermatogenesis integral to plasma membrane hedgehog receptor activity lung(6)|breast(6)|central_nervous_system(3)|skin(2)|ovary(1) 18 Acute lymphoblastic leukemia(166;0.155) CGCTGCCAGGCTTGTAGCACTG 0.599 0.17 106 22 STIL 6491 broad.mit.edu 37 1 47746107 47746109 + In_Frame_Del DEL AAC - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:47746107_47746109delAAC uc001crc.1 - 12 2176_2178 c.2021_2023delGTT c.(2020-2025)TGTTCT>TCT p.C674del TAL1_uc001crb.1_Intron|STIL_uc010omn.1_In_Frame_Del_p.C627del|STIL_uc010omo.1_In_Frame_Del_p.C674del|STIL_uc001crd.1_In_Frame_Del_p.C674del|STIL_uc001cre.1_In_Frame_Del_p.C674del|STIL_uc001crf.1_In_Frame_Del_p.C287del|STIL_uc001crg.1_In_Frame_Del_p.C627del NM_003035 NP_003026 Q15468 STIL_HUMAN SCL/TAL1 interrupting locus isoform 2 674 PIN1-binding (By similarity). cell proliferation|multicellular organismal development centrosome|cytosol lung(2)|skin(1) 3 Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444) CTGTGGGGAGAACAACTGCCCAT 0.483 0.42 133 98 SHC1 6464 broad.mit.edu 37 1 154942540 154942541 + Frame_Shift_Ins INS - T T SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:154942540_154942541insT uc001ffv.2 - 1 683_684 c.462_463insA c.(460-465)AAAGTCfs p.K154fs SHC1_uc001ffz.1_5'Flank|SHC1_uc001ffw.2_Frame_Shift_Ins_p.K154fs|SHC1_uc001ffx.2_Frame_Shift_Ins_p.K44fs|SHC1_uc001ffy.2_Frame_Shift_Ins_p.K44fs NM_183001 NP_892113 P29353 SHC1_HUMAN SHC-transforming protein 1 isoform 1 154_155 activation of MAPK activity|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|positive regulation of DNA replication|Ras protein signal transduction|regulation of epidermal growth factor receptor activity|regulation of growth cytosol|mitochondrial matrix|Shc-EGFR complex epidermal growth factor receptor binding|insulin receptor binding|insulin-like growth factor receptor binding|phospholipid binding|protein binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(1)|skin(1) 2 all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245) BRCA - Breast invasive adenocarcinoma(34;0.00034) GGTCCCATGACTTTGTCGTTGG 0.624 0.12 93 13 ABL2 27 broad.mit.edu 37 1 179077894 179077894 + Frame_Shift_Del DEL T - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:179077894delT uc001gmj.3 - 12 2795 c.2508delA c.(2506-2508)AAAfs p.K836fs ABL2_uc010pnf.1_Frame_Shift_Del_p.K733fs|ABL2_uc010png.1_Frame_Shift_Del_p.K712fs|ABL2_uc010pnh.1_Frame_Shift_Del_p.K815fs|ABL2_uc001gmg.3_Frame_Shift_Del_p.K718fs|ABL2_uc001gmi.3_Frame_Shift_Del_p.K821fs|ABL2_uc001gmh.3_Frame_Shift_Del_p.K800fs|ABL2_uc010pne.1_Frame_Shift_Del_p.K697fs NM_007314 NP_009298 P42684 ABL2_HUMAN arg tyrosine kinase isoform b 836 F-actin-binding (By similarity). axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction cytoskeleton|cytosol ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(8)|breast(3)|ovary(2)|central_nervous_system(1) 14 Adenosine triphosphate(DB00171)|Dasatinib(DB01254) TTTCCTCTGATTTTTTTGGAA 0.522 0.19 295 69 PTGS2 5743 broad.mit.edu 37 1 186645847 186645848 + Splice_Site INS - A A SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:186645847_186645848insA uc001gsb.2 - 7 861 c.724_splice c.e7-1 p.I242_splice PTGS2_uc009wyo.2_Splice_Site_p.I89_splice NM_000963 NP_000954 P35354 PGH2_HUMAN prostaglandin-endoperoxide synthase 2 precursor cellular component movement|cyclooxygenase pathway|hormone biosynthetic process|positive regulation of brown fat cell differentiation|positive regulation of cell migration involved in sprouting angiogenesis|positive regulation of fever generation|positive regulation of fibroblast growth factor production|positive regulation of nitric oxide biosynthetic process|positive regulation of platelet-derived growth factor production|positive regulation of prostaglandin biosynthetic process|positive regulation of transforming growth factor-beta production|positive regulation vascular endothelial growth factor production|regulation of blood pressure|response to oxidative stress|xenobiotic metabolic process endoplasmic reticulum lumen|endoplasmic reticulum membrane|microsome|neuron projection|nucleus "enzyme binding|heme binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peroxidase activity|prostaglandin-endoperoxide synthase activity" ovary(1)|central_nervous_system(1) 2 Acetaminophen(DB00316)|Aspirin(DB00945)|Balsalazide(DB01014)|Bromfenac(DB00963)|Carprofen(DB00821)|Celecoxib(DB00482)|Ciclopirox(DB01188)|Diclofenac(DB00586)|Diflunisal(DB00861)|Epoprostenol(DB01240)|Etodolac(DB00749)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|gamma-Homolinolenic acid(DB00154)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lumiracoxib(DB01283)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Rofecoxib(DB00533)|Salicyclic acid(DB00936)|Salsalate(DB01399)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Valdecoxib(DB00580) ATCAATTATCtaaaaaaataaa 0.347 0.29 91 37 MSH6 2956 broad.mit.edu 37 2 48030691 48030692 + Frame_Shift_Ins INS - T T rs63749812;rs2020910 byFrequency;by1000genomes SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:48030691_48030692insT uc002rwd.3 + 5 3457_3458 c.3305_3306insT c.(3304-3306)ACTfs p.T1102fs MSH6_uc010fbj.2_Frame_Shift_Ins_p.T800fs|MSH6_uc010yoi.1_Frame_Shift_Ins_p.T972fs|MSH6_uc010yoj.1_Frame_Shift_Ins_p.T800fs NM_000179 NP_000170 P52701 MSH6_HUMAN mutS homolog 6 1102 "determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes" MutSalpha complex ATP binding|DNA-dependent ATPase activity|protein binding large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1) 168 Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) ATTACGAAGACTTTTTTTGGAG 0.455 0.12 427 59 IL1B 3553 broad.mit.edu 37 2 113590307 113590308 + Frame_Shift_Ins INS - T T SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:113590307_113590308insT uc002tii.1 - 5 484_485 c.397_398insA c.(397-399)AGCfs p.S133fs IL1B_uc002tih.1_Frame_Shift_Ins_p.S102fs NM_000576 NP_000567 P01584 IL1B_HUMAN "interleukin 1, beta proprotein" 133 activation of MAPK activity|anti-apoptosis|apoptosis|cell-cell signaling|cellular response to drug|cellular response to mechanical stimulus|cytokine-mediated signaling pathway|embryo implantation|fever generation|negative regulation of adiponectin secretion|negative regulation of cell proliferation|negative regulation of glucose transport|negative regulation of insulin receptor signaling pathway|negative regulation of lipid catabolic process|negative regulation of MAP kinase activity|positive regulation of angiogenesis|positive regulation of calcidiol 1-monooxygenase activity|positive regulation of cell adhesion molecule production|positive regulation of cell division|positive regulation of fever generation|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of heterotypic cell-cell adhesion|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of interferon-gamma production|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of lipid catabolic process|positive regulation of membrane protein ectodomain proteolysis|positive regulation of mitosis|positive regulation of monocyte chemotactic protein-1 production|positive regulation of myosin light chain kinase activity|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric oxide biosynthetic process|positive regulation of prostaglandin secretion|positive regulation of protein export from nucleus|positive regulation of T cell proliferation|positive regulation vascular endothelial growth factor production|regulation of insulin secretion|sequestering of triglyceride|smooth muscle adaptation cytosol|extracellular space cytokine activity|growth factor activity|interleukin-1 receptor binding|protein domain specific binding lung(3)|breast(1) 4 Anakinra(DB00026)|Minocycline(DB01017)|Procaterol(DB01366) CATCACCAAGCTTTTTTGCTGT 0.495 0.13 378 56 ACVR1C 130399 broad.mit.edu 37 2 158406875 158406876 + Frame_Shift_Ins INS - A A SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:158406875_158406876insA uc002tzk.3 - 4 816_817 c.573_574insT c.(571-576)ATTGCAfs p.I191fs ACVR1C_uc002tzl.3_Frame_Shift_Ins_p.I111fs|ACVR1C_uc010fof.2_Intron|ACVR1C_uc010foe.2_Frame_Shift_Ins_p.I141fs NM_145259 NP_660302 Q8NER5 ACV1C_HUMAN "activin A receptor, type IC isoform 1" 191_192 Cytoplasmic (Potential).|GS. apoptosis|cell differentiation|regulation of apoptosis activin receptor complex "activin receptor activity, type I|ATP binding|transforming growth factor beta receptor activity" lung(3)|ovary(2)|skin(2) 7 ATCGTCCTTGCAATTGTCCTTT 0.386 0.14 263 42 STK25 10494 broad.mit.edu 37 2 242437714 242437714 + Frame_Shift_Del DEL G - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:242437714delG uc002wbm.2 - 8 1239 c.968delC c.(967-969)CCTfs p.P323fs STK25_uc002wbk.2_Frame_Shift_Del_p.P142fs|STK25_uc002wbl.2_3'UTR|STK25_uc002wbn.2_Frame_Shift_Del_p.P323fs|STK25_uc002wbo.2_Frame_Shift_Del_p.P246fs|STK25_uc010zos.1_Frame_Shift_Del_p.P229fs|STK25_uc010zot.1_Frame_Shift_Del_p.P249fs|STK25_uc002wbp.2_Frame_Shift_Del_p.P323fs|STK25_uc010fzo.2_Frame_Shift_Del_p.P246fs|STK25_uc010zou.1_Frame_Shift_Del_p.P229fs|STK25_uc010zov.1_Frame_Shift_Del_p.P229fs NM_006374 NP_006365 O00506 STK25_HUMAN serine/threonine kinase 25 323 response to oxidative stress|signal transduction Golgi apparatus ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity 0 all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2) Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839) CCGGATGGTAGGGGGGAACGT 0.652 0.4 73 48 TPRXL 348825 broad.mit.edu 37 3 14105871 14105885 + In_Frame_Del DEL CAGCAGCAGCCCCAG - - rs4684179;rs113575909 by1000genomes SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105871_14105885delCAGCAGCAGCCCCAG uc011avd.1 + 3 650_664 c.195_209delCAGCAGCAGCCCCAG c.(193-210)CCCAGCAGCAGCCCCAGC>CCC p.SSSPS71del TPRXL_uc003byh.1_In_Frame_Del_p.SSSPS71del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSPS71del NR_002223 RecName: Full=Putative protein TPRXL; 0 gcagcagccccagcagcagccccagcagcagcagc 0.033 0.43 8 6 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. "regulation of transcription, DNA-dependent" membrane|nucleus "calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity" skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.36 0.3 31 13 TNFSF10 8743 broad.mit.edu 37 3 172224391 172224391 + Frame_Shift_Del DEL C - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:172224391delC uc003fid.2 - 5 832 c.737delG c.(736-738)GGAfs p.G246fs TNFSF10_uc003fie.2_3'UTR NM_003810 NP_003801 P50591 TNF10_HUMAN "tumor necrosis factor (ligand) superfamily," 246 Extracellular (Potential). activation of caspase activity|activation of pro-apoptotic gene products|cell-cell signaling|immune response|induction of apoptosis by extracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|signal transduction extracellular space|integral to plasma membrane|soluble fraction cytokine activity|metal ion binding|tumor necrosis factor receptor binding skin(4)|lung(1) 5 Ovarian(172;0.00197)|Breast(254;0.158) Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235) CTCAAATATTCCCCCTTGATA 0.358 0.51 227 237 ETV5 2119 broad.mit.edu 37 3 185797673 185797673 + Frame_Shift_Del DEL G - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:185797673delG uc003fpz.2 - 7 830 c.583delC c.(583-585)CGAfs p.R195fs ETV5_uc003fpy.2_Frame_Shift_Del_p.R237fs NM_004454 NP_004445 P41161 ETV5_HUMAN ets variant gene 5 (ets-related molecule) 195 cellular response to oxidative stress nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding ovary(2)|skin(2)|breast(1) 5 all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247) OV - Ovarian serous cystadenocarcinoma(80;1.62e-24) TGTGGTGGTCGGGGGACCGCA 0.587 0.49 36 35 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs "SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA;" GAAGAAGTCGATTAGGAGTTCA 0.545 0.36 25 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.68 59 126 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 49 101 ZNF608 57507 broad.mit.edu 37 5 124079984 124079984 + Frame_Shift_Del DEL C - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:124079984delC uc003ktq.1 - 1 822 c.699delG c.(697-699)GGGfs p.G233fs ZNF608_uc003ktr.1_RNA|ZNF608_uc003kts.1_Frame_Shift_Del_p.G233fs|ZNF608_uc003ktt.1_Frame_Shift_Del_p.G233fs NM_020747 NP_065798 Q9ULD9 ZN608_HUMAN zinc finger protein 608 233 intracellular zinc ion binding skin(3)|ovary(2)|lung(1) 6 all_cancers(142;0.186)|Prostate(80;0.081) KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221) OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783) CATAGAGGTGCCCCCCGGAAG 0.657 0.14 107 17 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 "cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent" cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.63 14 24 DAXX 1616 broad.mit.edu 37 6 33286921 33286921 + Frame_Shift_Del DEL G - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:33286921delG uc003oec.2 - 7 2220 c.2016delC c.(2014-2016)CCCfs p.P672fs ZBTB22_uc003oeb.2_5'Flank|ZBTB22_uc010juu.2_5'Flank|DAXX_uc011drd.1_Frame_Shift_Del_p.P597fs|DAXX_uc011dre.1_Frame_Shift_Del_p.P684fs|DAXX_uc003oed.2_Frame_Shift_Del_p.P672fs NM_001350 NP_001341 Q9UER7 DAXX_HUMAN death-domain associated protein isoform a 672 Interaction with SPOP. activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent chromosome, centromeric region|cytosol|nucleolus|PML body androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding pancreas(18)|ovary(2)|skin(2)|prostate(1) 23 0.000 0.16 1819 339 PKHD1 5314 broad.mit.edu 37 6 51890183 51890184 + Frame_Shift_Ins INS - T T SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:51890183_51890184insT uc003pah.1 - 32 4700_4701 c.4424_4425insA c.(4423-4425)AATfs p.N1475fs PKHD1_uc003pai.2_Frame_Shift_Ins_p.N1475fs NM_138694 NP_619639 P08F94 PKHD1_HUMAN fibrocystin isoform 1 1475 IPT/TIG 9.|Extracellular (Potential). cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body protein binding|receptor activity lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1) 44 Lung NSC(77;0.0605) AAAGAGTGCAATTCCCCTGACA 0.55 0.16 133 26 MAP3K5 4217 broad.mit.edu 37 6 136913578 136913578 + Frame_Shift_Del DEL A - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:136913578delA uc003qhc.2 - 22 3414 c.3053delT c.(3052-3054)TTGfs p.L1018fs MAP3K5_uc011edj.1_Frame_Shift_Del_p.L265fs|MAP3K5_uc011edk.1_Frame_Shift_Del_p.L864fs NM_005923 NP_005914 Q99683 M3K5_HUMAN mitogen-activated protein kinase kinase kinase 1018 activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding ovary(2)|skin(2)|lung(1) 5 Colorectal(23;0.24) GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569) TCTTTACCCCAAAAAGAGTGT 0.433 0.35 172 93 HOXA13 3209 broad.mit.edu 37 7 27239356 27239356 + Frame_Shift_Del DEL G - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:27239356delG uc003szb.1 - 1 370 c.341delC c.(340-342)CCGfs p.P114fs uc003szc.1_5'Flank NM_000522 NP_000513 P31271 HXA13_HUMAN homeobox A13 114 skeletal system development nucleus sequence-specific DNA binding breast(1) 1 0.000 0.16 855 165 EPHB6 2051 broad.mit.edu 37 7 142562397 142562398 + Frame_Shift_Ins INS - C C SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:142562397_142562398insC uc011kst.1 + 7 1626_1627 c.839_840insC c.(838-840)AGCfs p.S280fs EPHB6_uc011ksu.1_Frame_Shift_Ins_p.S280fs|EPHB6_uc003wbs.2_5'UTR|EPHB6_uc003wbt.2_5'UTR|EPHB6_uc003wbu.2_5'UTR|EPHB6_uc003wbv.2_5'Flank NM_004445 NP_004436 O15197 EPHB6_HUMAN ephrin receptor EphB6 precursor 280 Extracellular (Potential).|Cys-rich. extracellular region|integral to plasma membrane ATP binding|ephrin receptor activity lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1) 19 Melanoma(164;0.059) 0.000 0.14 773 125 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.96 1 26 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.40 18 12 WRN 7486 broad.mit.edu 37 8 30924620 30924621 + Frame_Shift_Ins INS - A A SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:30924620_30924621insA uc003xio.3 + 6 1364_1365 c.576_577insA c.(574-579)GACAAGfs p.D192fs NM_000553 NP_000544 Q14191 WRN_HUMAN Werner syndrome protein 192_193 Interaction with WRNIP1 (By similarity).|3'-5' exonuclease. base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance centrosome|nucleolus|nucleoplasm 3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1) 7 Breast(100;0.195) KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192) TCCTGAAAGACAAGTCTATCCG 0.416 0.22 151 43 VPS13B 157680 broad.mit.edu 37 8 100654474 100654474 + Frame_Shift_Del DEL A - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:100654474delA uc003yiv.2 + 34 5842 c.5731delA c.(5731-5733)AAAfs p.K1911fs VPS13B_uc003yiw.2_Frame_Shift_Del_p.K1886fs NM_017890 NP_060360 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13B isoform 5 1911 protein transport ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1) 20 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TCCTTCAGGGAAAAAAATAGG 0.458 0.17 177 36 HSF1 3297 broad.mit.edu 37 8 145535688 145535689 + Frame_Shift_Ins INS - C C SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145535688_145535689insC uc003zbt.3 + 9 1070_1071 c.900_901insC c.(898-903)GAGCCCfs p.E300fs HSF1_uc003zbu.3_RNA NM_005526 NP_005517 Q00613 HSF1_HUMAN heat shock transcription factor 1 300_301 Regulatory domain. cytoplasm protein binding|sequence-specific DNA binding transcription factor activity 0 all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055) 0.000 0.38 314 196 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1 0 41 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.1 119 13 ROR2 4920 broad.mit.edu 37 9 94487005 94487006 + Frame_Shift_Ins INS - G G SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:94487005_94487006insG uc004arj.1 - 9 1969_1970 c.1770_1771insC c.(1768-1773)CCCGACfs p.P590fs ROR2_uc004ari.1_Frame_Shift_Ins_p.P450fs NM_004560 NP_004551 Q01974 ROR2_HUMAN receptor tyrosine kinase-like orphan receptor 2 590_591 Cytoplasmic (Potential).|Protein kinase. negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1) 20 TGCACGAAGTCGGGGGGCTCCA 0.644 0.19 71 17 WNK2 65268 broad.mit.edu 37 9 96015289 96015289 + Frame_Shift_Del DEL C - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:96015289delC uc004ati.1 + 8 1959 c.1959delC c.(1957-1959)AGCfs p.S653fs WNK2_uc011lud.1_Frame_Shift_Del_p.S653fs|WNK2_uc004atj.2_Frame_Shift_Del_p.S653fs|WNK2_uc004atk.2_Frame_Shift_Del_p.S290fs|WNK2_uc010mrc.1_Frame_Shift_Del_p.S653fs NM_006648 NP_006639 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 653 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity p.P641fs*2(1) lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1) 12 GTGTGTGCAGCCCCCCTGTGA 0.692 0.45 48 39 NR4A3 8013 broad.mit.edu 37 9 102590616 102590618 + In_Frame_Del DEL CAC - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:102590616_102590618delCAC uc004baf.1 + 3 1021_1023 c.292_294delCAC c.(292-294)CACdel p.H108del NR4A3_uc004bae.2_In_Frame_Del_p.H108del|NR4A3_uc004bag.1_In_Frame_Del_p.H108del|NR4A3_uc004bai.2_In_Frame_Del_p.H119del NM_006981 NP_008912 Q92570 NR4A3_HUMAN "nuclear receptor subfamily 4, group A, member 3" 108 Poly-His. regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor steroid hormone receptor activity|thyroid hormone receptor activity|zinc ion binding EWSR1/NR4A3(140)|TAF15/NR4A3(33) bone(173) 173 Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189) ccatcaccatcaccaccaccacc 0.483 0.34 23 12 SIRT1 23411 broad.mit.edu 37 10 69669079 69669079 + Frame_Shift_Del DEL T - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:69669079delT uc001jnd.2 + 7 1290 c.1237delT c.(1237-1239)TTTfs p.F413fs SIRT1_uc010qis.1_Frame_Shift_Del_p.F118fs|SIRT1_uc009xpp.2_Frame_Shift_Del_p.F221fs|SIRT1_uc001jne.2_Frame_Shift_Del_p.F110fs NM_012238 NP_036370 Q96EB6 SIRT1_HUMAN sirtuin 1 isoform a 413 Deacetylase sirtuin-type. "apoptosis|cell aging|cellular response to hydrogen peroxide|cellular response to starvation|chromatin silencing at rDNA|DNA repair|DNA replication|establishment of chromatin silencing|histone H3 deacetylation|interspecies interaction between organisms|maintenance of chromatin silencing|muscle organ development|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of fat cell differentiation|negative regulation of helicase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine acetylation|peptidyl-lysine deacetylation|positive regulation of anti-apoptosis|positive regulation of chromatin silencing|positive regulation of DNA repair|regulation of apoptosis|regulation of cell proliferation|regulation of endodeoxyribonuclease activity|regulation of protein import into nucleus, translocation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|rRNA processing|transcription, DNA-dependent|triglyceride mobilization|white fat cell differentiation" chromatin silencing complex|cytoplasm|nuclear euchromatin|nuclear heterochromatin|nuclear inner membrane|nucleolus|PML body|rDNA heterochromatin bHLH transcription factor binding|histone binding|HLH domain binding|identical protein binding|mitogen-activated protein kinase binding|NAD+ binding|NAD-dependent histone deacetylase activity (H3-K9 specific)|p53 binding|protein C-terminus binding|transcription corepressor activity|zinc ion binding 0 AGAGATTGTGTTTTTTGGTGA 0.403 0.46 210 181 MEN1 4221 broad.mit.edu 37 11 64572093 64572093 + Frame_Shift_Del DEL G - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:64572093delG uc001obj.2 - 10 1634 c.1561delC c.(1561-1563)CGGfs p.R521fs MAP4K2_uc001obh.2_5'Flank|MAP4K2_uc001obi.2_5'Flank|MAP4K2_uc010rnp.1_5'Flank|MEN1_uc001obk.2_Frame_Shift_Del_p.R521fs|MEN1_uc001obl.2_Frame_Shift_Del_p.R481fs|MEN1_uc001obm.2_Frame_Shift_Del_p.R516fs|MEN1_uc001obn.2_Frame_Shift_Del_p.R521fs|MEN1_uc001obo.2_Frame_Shift_Del_p.R521fs|MEN1_uc001obp.2_Frame_Shift_Del_p.R516fs|MEN1_uc001obq.2_Frame_Shift_Del_p.R521fs|MEN1_uc001obr.2_Frame_Shift_Del_p.R521fs NM_130800 NP_570712 O00255 MEN1_HUMAN menin isoform 1 521 "DNA repair|histone lysine methylation|MAPKKK cascade|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of JNK cascade|negative regulation of osteoblast differentiation|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of telomerase activity|negative regulation of transcription from RNA polymerase II promoter|osteoblast development|positive regulation of protein binding|positive regulation of transforming growth factor beta receptor signaling pathway|response to gamma radiation|response to UV|transcription, DNA-dependent" chromatin|cleavage furrow|cytosol|histone methyltransferase complex|nuclear matrix|soluble fraction "double-stranded DNA binding|four-way junction DNA binding|protein binding, bridging|protein N-terminus binding|R-SMAD binding|transcription regulatory region DNA binding|Y-form DNA binding" p.R516fs*15(1) parathyroid(105)|pancreas(64)|gastrointestinal_tract_(site_indeterminate)(15)|small_intestine(13)|lung(9)|pituitary(7)|NS(7)|adrenal_gland(5)|soft_tissue(4)|central_nervous_system(4)|thymus(2)|stomach(1)|retroperitoneum(1)|skin(1) 238 GGAGGCTTCCGGGGGGGTCCT 0.716 0.27 24 9 NUMA1 4926 broad.mit.edu 37 11 71746965 71746965 + Frame_Shift_Del DEL C - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:71746965delC uc001orl.1 - 3 197 c.25delG c.(25-27)GCTfs p.A9fs NUMA1_uc001ork.1_Frame_Shift_Del_p.A9fs|NUMA1_uc001orm.1_Frame_Shift_Del_p.A9fs|NUMA1_uc009ysx.1_Frame_Shift_Del_p.A9fs|NUMA1_uc001oro.1_Frame_Shift_Del_p.A9fs|NUMA1_uc009ysy.1_Frame_Shift_Del_p.A9fs|NUMA1_uc001orp.2_Frame_Shift_Del_p.A9fs|NUMA1_uc001orq.2_Frame_Shift_Del_p.A9fs NM_006185 NP_006176 Q14980 NUMA1_HUMAN nuclear mitotic apparatus protein 1 9 G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole protein binding|structural molecule activity ovary(3)|lung(2)|skin(2)|central_nervous_system(1) 8 AGGAGTGCAGCCCCCCGGGTG 0.502 0.37 106 61 PICALM 8301 broad.mit.edu 37 11 85687718 85687718 + Frame_Shift_Del DEL G - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:85687718delG uc001pbm.2 - 18 2073 c.1787delC c.(1786-1788)CCTfs p.P596fs PICALM_uc001pbl.2_Frame_Shift_Del_p.P554fs|PICALM_uc001pbn.2_Frame_Shift_Del_p.P589fs|PICALM_uc010rtl.1_Frame_Shift_Del_p.P495fs|PICALM_uc001pbk.2_Intron|PICALM_uc010rtk.1_Frame_Shift_Del_p.P181fs|PICALM_uc001pbo.1_Frame_Shift_Del_p.P236fs NM_007166 NP_009097 Q13492 PICAL_HUMAN phosphatidylinositol-binding clathrin assembly 596 "clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization" clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane 1-phosphatidylinositol binding|clathrin heavy chain binding urinary_tract(1)|ovary(1) 2 Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092) GGCCATTACAGGGGGTGCCTA 0.363 0.13 189 29 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 "Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent" nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.32 664 311 CASP4 837 broad.mit.edu 37 11 104825504 104825505 + Frame_Shift_Ins INS - A A SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:104825504_104825505insA uc001pid.1 - 2 304_305 c.231_232insT c.(229-234)TTTAACfs p.F77fs CASP4_uc001pib.1_Frame_Shift_Ins_p.F21fs|CASP4_uc009yxg.1_5'UTR|CASP4_uc010rux.1_Frame_Shift_Ins_p.F77fs|CASP4_uc010ruy.1_Frame_Shift_Ins_p.F77fs NM_001225 NP_001216 P49662 CASP4_HUMAN caspase 4 isoform alpha precursor 77_78 CARD. apoptosis|induction of apoptosis|proteolysis intracellular cysteine-type endopeptidase activity|protein binding lung(2)|ovary(1)|skin(1) 4 Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047) BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357) TGGTCTATGTTAAAAAAGGTTT 0.371 0.34 270 142 FLI1 2313 broad.mit.edu 37 11 128680523 128680524 + Frame_Shift_Ins INS - A A SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:128680523_128680524insA uc010sbu.1 + 9 1340_1341 c.999_1000insA c.(997-1002)GACAAGfs p.D333fs FLI1_uc010sbt.1_Frame_Shift_Ins_p.D140fs|FLI1_uc010sbv.1_Frame_Shift_Ins_p.D300fs|FLI1_uc009zci.2_Frame_Shift_Ins_p.D267fs NM_002017 NP_002008 Q01543 FLI1_HUMAN Friend leukemia virus integration 1 333_334 ETS. hemostasis|organ morphogenesis nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity EWSR1/FLI1(2266) bone(2210)|soft_tissue(48)|autonomic_ganglia(4)|central_nervous_system(4)|lung(3)|ovary(2)|pancreas(2) 2273 all_hematologic(175;0.0641) Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182) OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327) TGAATTACGACAAGCTGAGCCG 0.52 0.49 36 35 STAT6 6778 broad.mit.edu 37 12 57496181 57496181 + Frame_Shift_Del DEL C - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:57496181delC uc009zpe.2 - 13 1655 c.1404delG c.(1402-1404)GGGfs p.G468fs STAT6_uc009zpf.2_Frame_Shift_Del_p.G468fs|STAT6_uc001sna.2_Frame_Shift_Del_p.G468fs|STAT6_uc010srb.1_Frame_Shift_Del_p.G358fs|STAT6_uc010src.1_Frame_Shift_Del_p.G358fs|STAT6_uc010srd.1_Frame_Shift_Del_p.G358fs|STAT6_uc009zpg.2_Frame_Shift_Del_p.G517fs NM_003153 NP_003144 P42226 STAT6_HUMAN signal transducer and activator of transcription 468 regulation of transcription from RNA polymerase II promoter cytosol|nucleus calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity ovary(2)|lung(1)|skin(1) 4 CTGGGAGCAGCCCCCGGTTGG 0.587 0.14 114 18 LRP1 4035 broad.mit.edu 37 12 57556222 57556223 + Frame_Shift_Ins INS - CC CC SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:57556222_57556223insCC uc001snd.2 + 14 2791_2792 c.2325_2326insCC c.(2323-2328)GCACCCfs p.A775fs NM_002332 NP_002323 Q07954 LRP1_HUMAN low density lipoprotein-related protein 1 775_776 Extracellular (Potential). aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) TAGGAGGCGCACCCCCCACTGT 0.604 0.13 268 40 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). "histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent" NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.17 199 42 MTUS2 23281 broad.mit.edu 37 13 29600552 29600552 + Frame_Shift_Del DEL C - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:29600552delC uc001usl.3 + 1 1805 c.1747delC c.(1747-1749)CCCfs p.P583fs NM_001033602 NP_001028774 Q5JR59 MTUS2_HUMAN hypothetical protein LOC23281 isoform a 573 cytoplasm|microtubule microtubule binding|protein homodimerization activity 0 GGTAGTTCCACCCCCTACTGA 0.532 0.13 248 38 WBP4 11193 broad.mit.edu 37 13 41645703 41645703 + Frame_Shift_Del DEL A - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:41645703delA uc001uxt.2 + 6 593 c.480delA c.(478-480)TTAfs p.L160fs WBP4_uc010tfd.1_Frame_Shift_Del_p.L139fs NM_007187 NP_009118 O75554 WBP4_HUMAN WW domain-containing binding protein 4 160 "nuclear mRNA cis splicing, via spliceosome" nuclear speck|spliceosomal complex nucleic acid binding|proline-rich region binding|zinc ion binding breast(2)|kidney(1) 3 Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114) all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07) AAGGAGACTTAAAAAAGGTAA 0.274 0.47 61 54 DACH1 1602 broad.mit.edu 37 13 72440538 72440539 + In_Frame_Ins INS - GCCGCC GCCGCC SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:72440538_72440539insGCCGCC uc010thn.1 - 2 786_787 c.363_364insGGCGGC c.(361-366)insGGCGGC p.121_122insGG DACH1_uc010tho.1_In_Frame_Ins_p.121_122insGG|DACH1_uc010thp.1_In_Frame_Ins_p.121_122insGG NM_080759 NP_542937 Q9UI36 DACH1_HUMAN dachshund homolog 1 isoform a 121_122 "multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent" nucleolus DNA binding|nucleotide binding|protein binding breast(1) 1 Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198) GBM - Glioblastoma multiforme(99;0.00032) ccagcgctgatgccgccgccgc 0.079 0.17 48 10 IRS2 8660 broad.mit.edu 37 13 110434973 110434973 + Frame_Shift_Del DEL C - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr13:110434973delC uc001vqv.2 - 1 3942 c.3428delG c.(3427-3429)GGCfs p.G1143fs NM_003749 NP_003740 Q9Y4H2 IRS2_HUMAN insulin receptor substrate 2 1143 fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus cytosol|plasma membrane insulin receptor binding|signal transducer activity large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|skin(1)|ovary(1)|kidney(1) 8 all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155) Breast(118;0.159) all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147) 0.000 0.46 477 399 SPRED1 161742 broad.mit.edu 37 15 38614463 38614463 + Frame_Shift_Del DEL A - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:38614463delA uc001zka.3 + 3 564 c.229delA c.(229-231)AAAfs p.K77fs NM_152594 NP_689807 Q7Z699 SPRE1_HUMAN sprouty-related protein 1 with EVH-1 domain 77 WH1. inactivation of MAPK activity|multicellular organismal development caveola|nucleus stem cell factor receptor binding ovary(2)|lung(2)|skin(1) 5 all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091) GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244) 0.000 0.20 137 35 EIF2AK4 440275 broad.mit.edu 37 15 40324382 40324383 + Frame_Shift_Ins INS - T T SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr15:40324382_40324383insT uc001zkm.1 + 36 4722_4723 c.4672_4673insT c.(4672-4674)CTTfs p.L1558fs EIF2AK4_uc010bbj.1_Frame_Shift_Ins_p.L1259fs|EIF2AK4_uc001zkn.1_Frame_Shift_Ins_p.L658fs|EIF2AK4_uc001zko.1_Frame_Shift_Ins_p.L439fs|EIF2AK4_uc010bbk.1_Intron NM_001013703 NP_001013725 Q9P2K8 E2AK4_HUMAN eukaryotic translation initiation factor 2 alpha 1558 translation cytosolic ribosome aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity lung(2)|stomach(1)|skin(1) 4 all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119) GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616) ACAAACTCGACTTCAGACCTCC 0.386 0.47 140 122 CREBBP 1387 broad.mit.edu 37 16 3779210 3779211 + Frame_Shift_Ins INS - G G SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:3779210_3779211insG uc002cvv.2 - 31 6041_6042 c.5837_5838insC c.(5836-5838)CCAfs p.P1946fs CREBBP_uc002cvw.2_Frame_Shift_Ins_p.P1908fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1946 Poly-Pro. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding p.P1946fs*30(1) haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) GGGCCGGGGGTGGGGGGGCCGG 0.698 0.27 33 12 CDH1 999 broad.mit.edu 37 16 68835781 68835781 + Frame_Shift_Del DEL C - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:68835781delC uc002ewg.1 + 3 496 c.372delC c.(370-372)CGCfs p.R124fs CDH1_uc010vlj.1_RNA|CDH1_uc010cfg.1_Frame_Shift_Del_p.R124fs NM_004360 NP_004351 P12830 CADH1_HUMAN "cadherin 1, type 1 preproprotein" 124 "adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response" actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm cell adhesion molecule binding|gamma-catenin binding p.P126fs*89(1)|p.P127fs*41(1) breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1) 243 all_neural(199;0.0189)|Ovarian(137;0.0563) Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261) ACCACCACCGCCCCCCGCCCC 0.433 0.15 280 50 BCAR1 9564 broad.mit.edu 37 16 75268944 75268944 + Frame_Shift_Del DEL C - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:75268944delC uc002fdv.2 - 5 1976 c.1853delG c.(1852-1854)GGTfs p.G618fs BCAR1_uc002fdt.2_Frame_Shift_Del_p.G71fs|BCAR1_uc002fdu.2_Frame_Shift_Del_p.G408fs|BCAR1_uc010cgu.2_Frame_Shift_Del_p.G607fs|BCAR1_uc010vna.1_Frame_Shift_Del_p.G616fs|BCAR1_uc010vnb.1_Frame_Shift_Del_p.G664fs|BCAR1_uc002fdw.2_Frame_Shift_Del_p.G618fs|BCAR1_uc010vnc.1_Frame_Shift_Del_p.G470fs|BCAR1_uc010vnd.1_Frame_Shift_Del_p.G636fs|BCAR1_uc002fdx.2_Frame_Shift_Del_p.G636fs NM_014567 NP_055382 P56945 BCAR1_HUMAN breast cancer anti-estrogen resistance 1 618 actin filament organization|B cell receptor signaling pathway|blood coagulation|cell adhesion|cell division|cell migration|cell proliferation|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|integrin-mediated signaling pathway|nerve growth factor receptor signaling pathway|platelet-derived growth factor receptor signaling pathway|positive regulation of cell migration|regulation of apoptosis|regulation of cell growth|T cell receptor signaling pathway cytosol|focal adhesion|membrane fraction|ruffle protein kinase binding|protein phosphatase binding|SH3 domain binding|signal transducer activity central_nervous_system(5)|breast(2)|prostate(1) 8 BRCA - Breast invasive adenocarcinoma(221;0.169) 0.000 0.19 1042 239 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 38 442 MYH10 4628 broad.mit.edu 37 17 8383550 8383551 + Frame_Shift_Ins INS - T T SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:8383550_8383551insT uc002gll.2 - 38 5477_5478 c.5381_5382insA c.(5380-5382)AACfs p.N1794fs MYH10_uc002glm.2_Frame_Shift_Ins_p.N1825fs|MYH10_uc010cnx.2_Frame_Shift_Ins_p.N1803fs NM_005964 NP_005955 P35580 MYH10_HUMAN "myosin, heavy polypeptide 10, non-muscle" 1794 Potential. actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape cell cortex|cleavage furrow|midbody|myosin complex|stress fiber actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity ovary(2) 2 TCAGCTCCTTGTTCTGCCGCTC 0.604 0.2 398 101 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.12 71 10 STAC2 342667 broad.mit.edu 37 17 37371472 37371473 + Frame_Shift_Ins INS - C C SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:37371472_37371473insC uc002hrs.2 - 5 816_817 c.597_598insG c.(595-600)GGGAAGfs p.G199fs STAC2_uc010cvt.2_Frame_Shift_Ins_p.G57fs NM_198993 NP_945344 Q6ZMT1 STAC2_HUMAN SH3 and cysteine rich domain 2 199_200 intracellular signal transduction metal ion binding pancreas(1) 1 GGGTCCACCTTCCCACTGTCCC 0.52 0.43 82 62 SOST 50964 broad.mit.edu 37 17 41832944 41832944 + Frame_Shift_Del DEL G - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:41832944delG uc002iec.1 - 2 455 c.408delC c.(406-408)CCCfs p.P136fs NM_025237 NP_079513 Q9BQB4 SOST_HUMAN sclerostin precursor 136 CTCK. negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of ossification|negative regulation of protein complex assembly|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway heparin binding|protein binding 0 Breast(137;0.00725) UCEC - Uterine corpus endometrioid carcinoma (308;0.177)|BRCA - Breast invasive adenocarcinoma(366;0.0741) GGTAGCGGTCGGGGATGCAGC 0.746 0.56 14 18 TRIM37 4591 broad.mit.edu 37 17 57141768 57141769 + Splice_Site INS - A A rs147621691 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:57141768_57141769insA uc002iwy.3 - 10 1254 c.810_splice c.e10-1 p.S270_splice TRIM37_uc002iwz.3_Splice_Site_p.S270_splice|TRIM37_uc002ixa.3_Splice_Site_p.S148_splice|TRIM37_uc010woc.1_Splice_Site_p.S236_splice NM_001005207 NP_001005207 O94972 TRI37_HUMAN tripartite motif-containing 37 protein perinuclear region of cytoplasm|peroxisome ligase activity|protein binding|zinc ion binding lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1) 7 Medulloblastoma(34;0.0922)|all_neural(34;0.101) ACTAATTCACTAAAAAAAAAAA 0.272 0.42 18 13 PPM1D 8493 broad.mit.edu 37 17 58740623 58740624 + Frame_Shift_Ins INS - A A SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:58740623_58740624insA uc002iyt.1 + 6 1750_1751 c.1528_1529insA c.(1528-1530)CAAfs p.Q510fs PPM1D_uc010ddm.1_RNA NM_003620 NP_003611 O15297 PPM1D_HUMAN protein phosphatase 1D 510 negative regulation of cell proliferation|protein dephosphorylation|response to radiation nucleus|protein serine/threonine phosphatase complex metal ion binding|protein binding|protein serine/threonine phosphatase activity upper_aerodigestive_tract(1) 1 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) Epithelial(12;6.75e-12)|all cancers(12;1.96e-10) 0.000 0.14 943 158 ERN1 2081 broad.mit.edu 37 17 62133044 62133045 + Frame_Shift_Ins INS - T T SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:62133044_62133045insT uc002jdz.2 - 13 1775_1776 c.1662_1663insA c.(1660-1665)CAAGACfs p.Q554fs NM_001433 NP_001424 O75460 ERN1_HUMAN endoplasmic reticulum to nucleus signalling 1 554_555 Cytoplasmic (Potential). activation of signaling protein activity involved in unfolded protein response|apoptosis|cell cycle arrest|induction of apoptosis|mRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent integral to endoplasmic reticulum membrane ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(4)|lung(2)|stomach(1)|ovary(1)|kidney(1) 9 0.000 0.13 536 81 FASN 2194 broad.mit.edu 37 17 80043423 80043423 + Frame_Shift_Del DEL G - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:80043423delG uc002kdu.2 - 23 4174 c.4057delC c.(4057-4059)CTCfs p.L1353fs FASN_uc002kdw.1_Frame_Shift_Del_p.L569fs NM_004104 NP_004095 P49327 FAS_HUMAN fatty acid synthase 1353 LGDI -> SGH (in Ref. 2; AAA73576). energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process cytosol|Golgi apparatus|melanosome|plasma membrane "3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding" central_nervous_system(1) 1 all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246) OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237) Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339) ATGTCCCCGAGGGGGTGCCCC 0.706 0.17 40 8 JAK3 3718 broad.mit.edu 37 19 17955111 17955112 + Frame_Shift_Ins INS - G G rs67296869 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:17955111_17955112insG uc002nhn.3 - 2 215_216 c.115_116insC c.(115-117)CAGfs p.Q39fs JAK3_uc010ebh.2_RNA|JAK3_uc002nho.2_Frame_Shift_Ins_p.Q39fs|JAK3_uc010xpx.1_Frame_Shift_Ins_p.Q39fs|JAK3_uc010xpy.1_Frame_Shift_Ins_p.Q39fs NM_000215 NP_000206 P52333 JAK3_HUMAN Janus kinase 3 39 FERM.|Interaction with cytokine/interferon/growth hormone receptors (By similarity). B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis cytoskeleton|cytosol|endomembrane system|membrane ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1) 56 0.000 0.50 786 774 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.83 36 182 CIC 23152 broad.mit.edu 37 19 42791545 42791546 + Frame_Shift_Ins INS - C C SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:42791545_42791546insC uc002otf.1 + 4 566_567 c.526_527insC c.(526-528)GCCfs p.A176fs NM_015125 NP_055940 Q96RK0 CIC_HUMAN capicua homolog 176 "regulation of transcription, DNA-dependent|transcription, DNA-dependent" nucleus DNA binding|protein binding ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1) 11 Prostate(69;0.00682) GTCCCTCAGTGCCCTACCCAAG 0.609 0.4 56 38 LMTK3 114783 broad.mit.edu 37 19 49003133 49003133 + Frame_Shift_Del DEL C - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:49003133delC uc002pjk.2 - 12 1280 c.1280delG c.(1279-1281)CGCfs p.R427fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.37 1389 799 SRC 6714 broad.mit.edu 37 20 36012779 36012780 + Frame_Shift_Ins INS - C C SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:36012779_36012780insC uc002xgx.2 + 4 672_673 c.223_224insC c.(223-225)TCCfs p.S75fs SRC_uc002xgy.2_Frame_Shift_Ins_p.S75fs NM_005417 NP_005408 P12931 SRC_HUMAN proto-oncogene tyrosine-protein kinase SRC 75 axon guidance|bone resorption|cell junction assembly|cellular membrane organization|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular protein kinase cascade|leukocyte migration|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of integrin activation|Ras protein signal transduction|regulation of bone resorption|regulation of vascular permeability|response to interleukin-1|signal complex assembly|T cell costimulation caveola|cytosol|mitochondrial inner membrane ATP binding|heme binding|integrin binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|SH3/SH2 adaptor activity large_intestine(10)|lung(1)|central_nervous_system(1)|endometrium(1) 13 Myeloproliferative disorder(115;0.00878) Dasatinib(DB01254) 0.000 0.25 103 35 SGK2 10110 broad.mit.edu 37 20 42196613 42196613 + Frame_Shift_Del DEL A - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr20:42196613delA uc002xkv.2 + 4 601 c.382delA c.(382-384)AAAfs p.K128fs SGK2_uc002xkt.2_RNA|SGK2_uc002xkr.2_Frame_Shift_Del_p.K68fs|SGK2_uc010ggm.2_Frame_Shift_Del_p.K68fs|SGK2_uc002xks.2_Frame_Shift_Del_p.K68fs|SGK2_uc002xku.2_Frame_Shift_Del_p.K68fs|SGK2_uc002xkq.1_Frame_Shift_Del_p.K68fs NM_016276 NP_057360 Q9HBY8 SGK2_HUMAN serum/glucocorticoid regulated kinase 2 isoform 128 Protein kinase.|Nuclear localization signal (By similarity). intracellular protein kinase cascade|response to oxidative stress ATP binding|potassium channel regulator activity|protein serine/threonine kinase activity|sodium channel regulator activity lung(3)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1) 6 Myeloproliferative disorder(115;0.00452) COAD - Colon adenocarcinoma(18;0.0031) GGTACTACAGAAAAAGTCCAT 0.493 0.21 74 20 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 "B melanoma antigen family, member 2 precursor" 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.12 220 30 COL18A1 80781 broad.mit.edu 37 21 46906788 46906788 + Frame_Shift_Del DEL C - - SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46906788delC uc011afs.1 + 15 2981 c.2960delC c.(2959-2961)GCCfs p.A987fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.A572fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.A752fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 987 Triple-helical region 3 (COL3). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.46 360 310 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 239 775 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN "clathrin, heavy polypeptide-like 1 isoform 1" anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.48 0.96 5 109 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 4 55 ARID1A 8289 broad.mit.edu 37 1 27059284 27059287 + Splice_Site DEL GTGA - - SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr1:27059284_27059287delGTGA uc001bmv.1 + 4 2293 c.1920_splice c.e4+1 p.P640_splice ARID1A_uc001bmt.1_Splice_Site_p.P640_splice|ARID1A_uc001bmu.1_Splice_Site_p.P640_splice|ARID1A_uc001bmw.1_Splice_Site_p.P257_splice NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CAGCTTGCCTGTGAGTATTTCTGC 0.466 0.49 64 62 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.24 34 11 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.11 94 12 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.25 41 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 124 188 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.17 98 20 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.15 739 129 SCRIB 23513 broad.mit.edu 37 8 144890816 144890818 + In_Frame_Del DEL TCC - - SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr8:144890816_144890818delTCC uc003yzp.1 - 15 2083_2085 c.2076_2078delGGA c.(2074-2079)GAGGAC>GAC p.E692del SCRIB_uc003yzo.1_In_Frame_Del_p.E692del NM_015356 NP_056171 Q14160 SCRIB_HUMAN scribble isoform b 692 Potential.|Glu-rich.|Sufficient for targeting to adherens junction and to inhibit cell proliferation. activation of Rac GTPase activity|apoptosis involved in morphogenesis|cell migration|cell proliferation|cell-cell adhesion|establishment of apical/basal cell polarity|interspecies interaction between organisms|mammary gland duct morphogenesis|negative regulation of mitotic cell cycle|positive chemotaxis|positive regulation of apoptosis|positive regulation of receptor recycling|protein localization to adherens junction cell-cell adherens junction|Scrib-APC-beta-catenin complex protein binding urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)|pancreas(1) 5 all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18) CCCCTCCTTGTCCTCCTCCTCAG 0.448 0.27 241 87 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 34 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.16 432 82 FANCF 2188 broad.mit.edu 37 11 22646658 22646659 + Frame_Shift_Del DEL CC - - SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr11:22646658_22646659delCC uc001mql.1 - 1 729_730 c.698_699delGG c.(697-699)GGGfs p.G233fs NM_022725 NP_073562 Q9NPI8 FANCF_HUMAN Fanconi anemia, complementation group F 233 DNA repair nucleoplasm protein binding skin(1) 1 GCACTTGGCTCCCCTCTCCAGG 0.579 0.64 38 67 PAK1 5058 broad.mit.edu 37 11 77069989 77069990 + In_Frame_Ins INS - CAT CAT rs149665907 SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr11:77069989_77069990insCAT uc001oyh.3 - 6 1083_1084 c.550_551insATG c.(550-552)GCT>GATGCT p.183_184insD PAK1_uc010rso.1_In_Frame_Ins_p.85_86insD|PAK1_uc001oyg.3_In_Frame_Ins_p.183_184insD|PAK1_uc001oyi.1_In_Frame_Ins_p.183_184insD|PAK1_uc010rsn.1_Translation_Start_Site NM_002576 NP_002567 Q13153 PAK1_HUMAN p21-activated kinase 1 isoform 2 183_184 Interaction with CRIPAK. apoptosis|axon guidance|cytoskeleton organization|ER-nucleus signaling pathway|positive regulation of JUN kinase activity|positive regulation of peptidyl-serine phosphorylation|protein autophosphorylation|T cell costimulation|T cell receptor signaling pathway cytosol|focal adhesion|Golgi apparatus ATP binding|collagen binding|protein binding|protein serine/threonine kinase activity skin(2)|stomach(1)|lung(1) 4 all_cancers(14;1.75e-18) TGGTGGGGTAGcatcatcatca 0.426 0.17 218 45 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 958 238 CREBBP 1387 broad.mit.edu 37 16 3778448 3778449 + In_Frame_Ins INS - TGT TGT SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr16:3778448_3778449insTGT uc002cvv.2 - 31 6803_6804 c.6599_6600insACA c.(6598-6600)CAG>CAACAG p.2200_2200Q>QQ CREBBP_uc002cvw.2_In_Frame_Ins_p.2162_2162Q>QQ NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 2200 Poly-Gln. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) 0.000 0.19 929 218 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.27 81 30 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.94 33 539 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 123 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 SW1088_CENTRAL_NERVOUS_SYSTEM NA SW1088_CENTRAL_NERVOUS_SYSTEM NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.27 279 101 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 98 26 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 66 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 34 19 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.58 15 21 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.34 148 75 APC 324 broad.mit.edu 37 5 112175576 112175585 + Frame_Shift_Del DEL CAAACCATGC - - rs74535574 SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr5:112175576_112175585delCAAACCATGC uc010jby.2 + 16 4665_4674 c.4285_4294delCAAACCATGC c.(4285-4296)CAAACCATGCCAfs p.Q1429fs APC_uc011cvt.1_Frame_Shift_Del_p.Q1411fs|APC_uc003kpz.3_Frame_Shift_Del_p.Q1429fs|APC_uc003kpy.3_Frame_Shift_Del_p.Q1429fs|APC_uc010jbz.2_Frame_Shift_Del_p.Q1146fs|APC_uc010jca.2_Frame_Shift_Del_p.Q729fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1429_1432 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.Q1429*(33)|p.M1431fs*42(6)|p.Q1429fs*8(4)|p.P1432fs*41(1)|p.Y1376fs*41(1)|p.T1430fs*43(1)|p.?(1)|p.Q1429H(1)|p.P1424fs*19(1)|p.S1411fs*41(1)|p.K1192fs*3(1)|p.Q1429fs*41(1)|p.Q1429R(1)|p.M1431R(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) TAGCCCTGGACAAACCATGCCACCAAGCAG 0.471 0.41 73 50 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039791 + In_Frame_Del DEL CAGCAGCAGCAGCAG - - rs113070757;rs62639301;rs139102413;rs145170448;rs147609454;rs142219087 byFrequency;byFrequency;byFrequency;byFrequency;byFrequency SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr9:2039777_2039791delCAGCAGCAGCAGCAG uc003zhc.2 + 4 766_780 c.667_681delCAGCAGCAGCAGCAG c.(667-681)CAGCAGCAGCAGCAGdel p.QQQQQ233del SMARCA2_uc003zhd.2_In_Frame_Del_p.QQQQQ233del|SMARCA2_uc010mha.2_In_Frame_Del_p.QQQQQ224del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 233_237 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagcagcagcagcagc 0.270 0.40 6 4 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 79 21 NEK3 4752 broad.mit.edu 37 13 52710307 52710308 + Frame_Shift_Del DEL TG - - SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr13:52710307_52710308delTG uc001vgi.2 - 15 1353_1354 c.1118_1119delCA c.(1117-1119)ACAfs p.T373fs NEK3_uc001vgg.2_Frame_Shift_Del_p.T350fs|NEK3_uc001vgh.2_Frame_Shift_Del_p.T377fs|NEK3_uc010tgx.1_RNA|NEK3_uc010tgy.1_Frame_Shift_Del_p.T356fs NM_152720 NP_689933 P51956 NEK3_HUMAN NIMA-related kinase 3 isoform a 373 cell division|mitosis nucleus ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity ovary(1)|stomach(1) 2 Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173) GBM - Glioblastoma multiforme(99;2.81e-08) TTTCCAAAGCTGTAAGAGCTGT 0.371 0.33 60 29 ERCC5 2073 broad.mit.edu 37 13 103506652 103506660 + In_Frame_Del DEL CCAGTCTTA - - SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr13:103506652_103506660delCCAGTCTTA uc001vpw.2 + 4 838_846 c.395_403delCCAGTCTTA c.(394-405)CCCAGTCTTACC>CCC p.SLT133del ERCC5_uc001vpu.1_In_Frame_Del_p.SLT587del|ERCC5_uc010tjb.1_In_Frame_Del_p.SLT133del|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_5'UTR NM_000123 NP_000114 P28715 ERCC5_HUMAN XPG-complementing protein 133_135 negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection nucleoplasm bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding ovary(4)|lung(1)|central_nervous_system(1)|skin(1) 7 all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211) GAAGCACTACCCAGTCTTACCCAAGTTCG 0.411 0.43 44 33 ACIN1 22985 broad.mit.edu 37 14 23549879 23549881 + In_Frame_Del DEL TCC - - rs3841035 SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr14:23549879_23549881delTCC uc001wit.3 - 6 1165_1167 c.837_839delGGA c.(835-840)GAGGAA>GAA p.279_280EE>E ACIN1_uc001wis.3_5'UTR|ACIN1_uc010akg.2_In_Frame_Del_p.279_280EE>E|ACIN1_uc010tnj.1_In_Frame_Del_p.239_240EE>E NM_014977 NP_055792 Q9UKV3 ACINU_HUMAN apoptotic chromatin condensation inducer 1 279_280 Glu-rich. apoptotic chromosome condensation|erythrocyte differentiation|positive regulation of monocyte differentiation cytosol ATPase activity|enzyme binding|nucleic acid binding|nucleotide binding ovary(2)|large_intestine(1)|skin(1) 4 all_cancers(95;1.36e-05) GBM - Glioblastoma multiforme(265;0.00816) atcatcttcttcctcctcctcct 0.325 0.33 8 4 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 1 17 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.12 205 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.84 90 461 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW1116_LARGE_INTESTINE NA SW1116_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 3 25 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW1271_LUNG NA SW1271_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 34 NLRP3 114548 broad.mit.edu 37 1 247588106 247588106 + Frame_Shift_Del DEL G - - SW1271_LUNG NA SW1271_LUNG NA g.chr1:247588106delG uc001icr.2 + 5 1499 c.1361delG c.(1360-1362)CGGfs p.R454fs NLRP3_uc001ics.2_Frame_Shift_Del_p.R454fs|NLRP3_uc001icu.2_Frame_Shift_Del_p.R454fs|NLRP3_uc001icw.2_Frame_Shift_Del_p.R454fs|NLRP3_uc001icv.2_Frame_Shift_Del_p.R454fs|NLRP3_uc010pyw.1_Frame_Shift_Del_p.R452fs|NLRP3_uc001ict.1_Frame_Shift_Del_p.R452fs NM_001079821 NP_001073289 Q96P20 NALP3_HUMAN NLR family, pyrin domain containing 3 isoform a 454 NACHT. detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction cytoplasm ATP binding|peptidoglycan binding|protein binding lung(8)|skin(8)|ovary(7)|upper_aerodigestive_tract(1)|breast(1)|pancreas(1) 26 all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) all_cancers(173;0.0172) OV - Ovarian serous cystadenocarcinoma(106;0.0141) CTGCAGCCCCGGGGAGGGAGC 0.592 0.63 196 331 TTN 7273 broad.mit.edu 37 2 179436503 179436503 + Frame_Shift_Del DEL A - - SW1271_LUNG NA SW1271_LUNG NA g.chr2:179436503delA uc010zfg.1 - 275 66876 c.66652delT c.(66652-66654)TATfs p.Y22218fs uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.Y15913fs|TTN_uc010zfi.1_Frame_Shift_Del_p.Y15846fs|TTN_uc010zfj.1_Frame_Shift_Del_p.Y15721fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 23145 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTAACCACATAATGGCCAACA 0.418 0.18 117 25 HDLBP 3069 broad.mit.edu 37 2 242179467 242179467 + Frame_Shift_Del DEL C - - SW1271_LUNG NA SW1271_LUNG NA g.chr2:242179467delC uc002waz.2 - 18 2468 c.2240delG c.(2239-2241)GGCfs p.G747fs HDLBP_uc002wba.2_Frame_Shift_Del_p.G747fs|HDLBP_uc002wbb.2_Frame_Shift_Del_p.G699fs NM_203346 NP_976221 Q00341 VIGLN_HUMAN high density lipoprotein binding protein 747 KH 9. cholesterol metabolic process|lipid transport cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane lipid binding|protein binding|RNA binding breast(3)|skin(1) 4 all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928) AATTTTGCCGCCCCCCTTGCC 0.542 0.85 4 22 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SW1271_LUNG NA SW1271_LUNG NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.50 15 15 KALRN 8997 broad.mit.edu 37 3 123987907 123987907 + Frame_Shift_Del DEL C - - SW1271_LUNG NA SW1271_LUNG NA g.chr3:123987907delC uc003ehg.2 + 5 895 c.768delC c.(766-768)ATCfs p.I256fs KALRN_uc010hrv.1_Frame_Shift_Del_p.I256fs|KALRN_uc003ehf.1_Frame_Shift_Del_p.I256fs|KALRN_uc011bjy.1_Frame_Shift_Del_p.I256fs NM_001024660 NP_001019831 O60229 KALRN_HUMAN kalirin, RhoGEF kinase isoform 1 256 Spectrin 1. apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport actin cytoskeleton|cytosol ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1) 6 TGCAGTGCATCCGCTGCAGCG 0.622 0.62 31 50 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SW1271_LUNG NA SW1271_LUNG NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.18 130 28 TP63 8626 broad.mit.edu 37 3 189586416 189586417 + Frame_Shift_Ins INS - C C SW1271_LUNG NA SW1271_LUNG NA g.chr3:189586416_189586417insC uc003fry.2 + 8 1129_1130 c.1040_1041insC c.(1039-1041)TGCfs p.C347fs TP63_uc003frx.2_Frame_Shift_Ins_p.C347fs|TP63_uc003frz.2_Frame_Shift_Ins_p.C347fs|TP63_uc010hzc.1_Frame_Shift_Ins_p.C347fs|TP63_uc003fsa.2_Frame_Shift_Ins_p.C253fs|TP63_uc003fsb.2_Frame_Shift_Ins_p.C253fs|TP63_uc003fsc.2_Frame_Shift_Ins_p.C253fs|TP63_uc003fsd.2_Frame_Shift_Ins_p.C253fs|TP63_uc010hzd.1_Frame_Shift_Ins_p.C168fs|TP63_uc003fse.1_Frame_Shift_Ins_p.C228fs NM_003722 NP_003713 Q9H3D4 P63_HUMAN tumor protein p63 isoform 1 347 C -> S (in EEC3). anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1) 12 all_cancers(143;3.35e-10)|Ovarian(172;0.0925) Lung(62;3.33e-05) GBM - Glioblastoma multiforme(93;0.0227) ATCTGTGCTTGCCCAGGAAGAG 0.480 0.26 100 36 TBCK 93627 broad.mit.edu 37 4 107165867 107165868 + Frame_Shift_Ins INS - A A SW1271_LUNG NA SW1271_LUNG NA g.chr4:107165867_107165868insA uc010ilv.2 - 11 1350_1351 c.985_986insT c.(985-987)TGGfs p.W329fs TBCK_uc003hyb.2_Frame_Shift_Ins_p.W72fs|TBCK_uc003hye.2_Frame_Shift_Ins_p.W290fs|TBCK_uc003hyc.2_Frame_Shift_Ins_p.W266fs|TBCK_uc003hyd.2_Frame_Shift_Ins_p.W157fs|TBCK_uc003hyf.2_Frame_Shift_Ins_p.W329fs NM_001163435 NP_001156907 Q8TEA7 TBCK_HUMAN TBC domain-containing protein kinase-like 329 intracellular Rab GTPase activator activity large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1) 5 AGCCAAACACCAAAGGTAATAC 0.347 0.93 6 79 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW1271_LUNG NA SW1271_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 72 88 MAML3 55534 broad.mit.edu 37 4 140811703 140811708 + In_Frame_Del DEL TTCTGA - - SW1271_LUNG NA SW1271_LUNG NA g.chr4:140811703_140811708delTTCTGA uc003ihz.1 - 2 1634_1639 c.882_887delTCAGAA c.(880-888)AATCAGAAC>AAC p.294_296NQN>N MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 294_296 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) GAACAGCTTGTTCTGATTTGAAAGAG 0.432 0.15 296 52 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW1271_LUNG NA SW1271_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.70 35 81 DNAH8 1769 broad.mit.edu 37 6 38791430 38791432 + In_Frame_Del DEL TAT - - SW1271_LUNG NA SW1271_LUNG NA g.chr6:38791430_38791432delTAT uc003ooe.1 + 26 3762_3764 c.3162_3164delTAT c.(3160-3165)CCTATT>CCT p.I1056del NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 AGTTGAAGCCTATTATTGTTGTA 0.330 0.27 193 70 ESR1 2099 broad.mit.edu 37 6 152382234 152382235 + Frame_Shift_Ins INS - A A SW1271_LUNG NA SW1271_LUNG NA g.chr6:152382234_152382235insA uc003qom.3 + 8 1714_1715 c.1344_1345insA c.(1342-1347)CTCAAAfs p.L448fs ESR1_uc010kin.2_Frame_Shift_Ins_p.L448fs|ESR1_uc010kio.2_Frame_Shift_Ins_p.L450fs|ESR1_uc010kip.2_Frame_Shift_Ins_p.L447fs|ESR1_uc003qon.3_Frame_Shift_Ins_p.L448fs|ESR1_uc003qoo.3_Frame_Shift_Ins_p.L448fs|ESR1_uc010kiq.2_Frame_Shift_Ins_p.L46fs|ESR1_uc010kir.2_Frame_Shift_Ins_p.L187fs|ESR1_uc011eet.1_Intron|ESR1_uc011eeu.1_RNA|ESR1_uc011eev.1_Intron|ESR1_uc011eew.1_Intron|ESR1_uc010kis.2_Frame_Shift_Ins_p.L117fs|ESR1_uc011eex.1_Intron|ESR1_uc010kit.1_3'UTR|ESR1_uc011eey.1_Frame_Shift_Ins_p.L185fs NM_001122742 NP_001116214 P03372 ESR1_HUMAN estrogen receptor alpha isoform 4 448_449 Steroid-binding.|Interaction with AKAP13. positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus chromatin remodeling complex|cytoplasm|nucleoplasm beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding central_nervous_system(2)|ovary(1)|lung(1)|breast(1) 5 Ovarian(120;0.0448) BRCA - Breast invasive adenocarcinoma(37;0.0841) OV - Ovarian serous cystadenocarcinoma(155;4.55e-10) Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539) TTGTGTGCCTCAAATCTATTAT 0.416 0.28 116 44 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SW1271_LUNG NA SW1271_LUNG NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.32 13 6 NBN 4683 broad.mit.edu 37 8 90982679 90982680 + Frame_Shift_Del DEL AC - - SW1271_LUNG NA SW1271_LUNG NA g.chr8:90982679_90982680delAC uc003yej.1 - 7 918_919 c.808_809delGT c.(808-810)GTTfs p.V270fs NBN_uc003yei.1_Frame_Shift_Del_p.V188fs|NBN_uc011lgb.1_Frame_Shift_Del_p.V270fs NM_002485 NP_002476 O60934 NBN_HUMAN nibrin 270 cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm protein N-terminus binding|transcription factor binding central_nervous_system(3)|kidney(3)|lung(1) 7 BRCA - Breast invasive adenocarcinoma(11;0.0344) TGTATCAACAACACACGTTCCC 0.386 0.51 159 167 TRPS1 7227 broad.mit.edu 37 8 116599453 116599453 + Frame_Shift_Del DEL C - - SW1271_LUNG NA SW1271_LUNG NA g.chr8:116599453delC uc003ynz.2 - 4 2895 c.2436delG c.(2434-2436)GGGfs p.G812fs TRPS1_uc011lhy.1_Frame_Shift_Del_p.G816fs|TRPS1_uc003yny.2_Frame_Shift_Del_p.G825fs|TRPS1_uc010mcy.2_Frame_Shift_Del_p.G812fs NM_014112 NP_054831 Q9UHF7 TRPS1_HUMAN zinc finger transcription factor TRPS1 812 Mediates interaction with GLI3. negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) GCGTCAGCAGCCCCAGGCTTG 0.572 0.51 76 80 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SW1271_LUNG NA SW1271_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 2 21 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SW1271_LUNG NA SW1271_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.66 119 232 SLK 9748 broad.mit.edu 37 10 105727538 105727539 + Frame_Shift_Ins INS - G G SW1271_LUNG NA SW1271_LUNG NA g.chr10:105727538_105727539insG uc001kxo.1 + 1 69_70 c.35_36insG c.(34-36)TTGfs p.L12fs SLK_uc001kxp.1_Frame_Shift_Ins_p.L12fs NM_014720 NP_055535 Q9H2G2 SLK_HUMAN serine/threonine kinase 2 12 apoptosis|nucleotide-excision repair cytoplasm|plasma membrane ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity ovary(2)|stomach(2)|skin(2)|lung(1)|kidney(1) 8 Colorectal(252;0.178) Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165) ATCTTCAAGTTGGGGAGCGAGA 0.446 0.30 193 81 HBD 3045 broad.mit.edu 37 11 5255285 5255285 + Frame_Shift_Del DEL C - - rs34373781 SW1271_LUNG NA SW1271_LUNG NA g.chr11:5255285delC uc001maf.1 - 2 446 c.251delG c.(250-252)GGCfs p.G84fs NM_000519 NP_000510 P02042 HBD_HUMAN delta globin 84 blood coagulation hemoglobin complex heme binding|oxygen binding|oxygen transporter activity ovary(1) 1 Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212) Epithelial(150;5.69e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135) AGAAAAAGTGCCCTTGAGGTT 0.512 0.10 79 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW1271_LUNG NA SW1271_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 783 236 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SW1271_LUNG NA SW1271_LUNG NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.30 33 14 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SW1271_LUNG NA SW1271_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 14 137 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes SW1271_LUNG NA SW1271_LUNG NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.27 22 8 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SW1271_LUNG NA SW1271_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 15 40 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SW1271_LUNG NA SW1271_LUNG NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.54 38 45 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW1271_LUNG NA SW1271_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 103 444 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW1271_LUNG NA SW1271_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 44 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes SW1271_LUNG NA SW1271_LUNG NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.19 306 72 FAM48B1 100130302 broad.mit.edu 37 X 24382374 24382382 + In_Frame_Del DEL TGCTGCTGC - - rs10560780 SW1353_BONE NA SW1353_BONE NA g.chrX:24382374_24382382delTGCTGCTGC uc011mjx.1 + 1 1497_1505 c.1497_1505delTGCTGCTGC c.(1495-1506)ATTGCTGCTGCT>ATT p.AAA515del NM_001136234 NP_001129706 hypothetical protein LOC100130302 kidney(1) 1 ctgctgctattgctgctgctgctgctgct 0.196 0.10 94 11 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW1353_BONE NA SW1353_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 2 93 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SW1353_BONE NA SW1353_BONE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.24 477 154 DENND4B 9909 broad.mit.edu 37 1 153907278 153907279 + In_Frame_Ins INS - CTG CTG rs141373027 by1000genomes SW1353_BONE NA SW1353_BONE NA g.chr1:153907278_153907279insCTG uc001fdd.1 - 18 3131_3132 c.2730_2731insCAG c.(2728-2733)insCAG p.910_911insQ uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910_911 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) GACACctgctcctgctgctgct 0.455 0.23 96 28 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SW1353_BONE NA SW1353_BONE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.56 28 36 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW1353_BONE NA SW1353_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.68 125 260 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW1353_BONE NA SW1353_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 34 96 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SW1353_BONE NA SW1353_BONE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.67 4 8 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SW1353_BONE NA SW1353_BONE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.54 25 29 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT SW1353_BONE NA SW1353_BONE NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.29 1076 433 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SW1353_BONE NA SW1353_BONE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 6 43 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SW1353_BONE NA SW1353_BONE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.41 19 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SW1353_BONE NA SW1353_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 50 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW1353_BONE NA SW1353_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.45 588 482 DACH1 1602 broad.mit.edu 37 13 72440538 72440539 + In_Frame_Ins INS - GCCGCC GCCGCC SW1353_BONE NA SW1353_BONE NA g.chr13:72440538_72440539insGCCGCC uc010thn.1 - 2 786_787 c.363_364insGGCGGC c.(361-366)insGGCGGC p.121_122insGG DACH1_uc010tho.1_In_Frame_Ins_p.121_122insGG|DACH1_uc010thp.1_In_Frame_Ins_p.121_122insGG NM_080759 NP_542937 Q9UI36 DACH1_HUMAN dachshund homolog 1 isoform a 121_122 multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus DNA binding|nucleotide binding|protein binding breast(1) 1 Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198) GBM - Glioblastoma multiforme(99;0.00032) ccagcgctgatgccgccgccgc 0.079 0.14 63 10 FBN1 2200 broad.mit.edu 37 15 48740975 48740975 + Frame_Shift_Del DEL G - - SW1353_BONE NA SW1353_BONE NA g.chr15:48740975delG uc001zwx.1 - 46 5989 c.5661delC c.(5659-5661)ACCfs p.T1887fs FBN1_uc010beo.1_RNA NM_000138 NP_000129 P35555 FBN1_HUMAN fibrillin 1 precursor 1887 EGF-like 31; calcium-binding. T -> I (in MFS). heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development basement membrane|extracellular space|microfibril calcium ion binding|extracellular matrix structural constituent|protein binding ovary(2)|large_intestine(1) 3 all_lung(180;0.00279) all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05) CCAAGCACATGGTTTGGTCAT 0.323 0.24 148 46 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SW1353_BONE NA SW1353_BONE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 10 180 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SW1353_BONE NA SW1353_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.82 36 165 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW1353_BONE NA SW1353_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 159 455 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW1353_BONE NA SW1353_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 6 155 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 4 89 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.16 656 129 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.39 20 13 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.48 29 27 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 25 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 102 241 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.68 36 77 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.31 9 4 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.46 7 6 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.32 42 20 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 2 36 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.90 3 26 TGFBR1 7046 broad.mit.edu 37 9 101867563 101867564 + Frame_Shift_Ins INS - T T SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr9:101867563_101867564insT uc004azc.2 + 1 152_153 c.76_77insT c.(76-78)GCGfs p.A26fs TGFBR1_uc004azd.2_Frame_Shift_Ins_p.A26fs NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.73 4 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 1152 434 ITPR2 3709 broad.mit.edu 37 12 26784855 26784856 + Frame_Shift_Ins INS - G G SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr12:26784855_26784856insG uc001rhg.2 - 22 3294_3295 c.2877_2878insC c.(2875-2880)ACCGAGfs p.T959fs NM_002223 NP_002214 Q14571 ITPR2_HUMAN inositol 1,4,5-triphosphate receptor, type 2 959_960 Cytoplasmic (Potential). activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 14 Colorectal(261;0.0847) TCCTCGTGCTCGGTGGGGCTCC 0.525 0.35 32 17 SRP14 6727 broad.mit.edu 37 15 40328597 40328605 + In_Frame_Del DEL TGCTGCTGC - - SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr15:40328597_40328605delTGCTGCTGC uc001zkq.2 - 5 412_420 c.340_348delGCAGCAGCA c.(340-348)GCAGCAGCAdel p.AAA114del SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 114_116 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgcggcaggtgctgctgctgctgctgct 0.239 0.51 52 54 TP53 7157 broad.mit.edu 37 17 7577556 7577569 + Frame_Shift_Del DEL CAGGAACTGTTACA - - rs121912655;rs28934573 SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr17:7577556_7577569delCAGGAACTGTTACA uc002gim.2 - 7 906_919 c.712_725delTGTAACAGTTCCTG c.(712-726)TGTAACAGTTCCTGCfs p.C238fs TP53_uc002gig.1_Frame_Shift_Del_p.C238fs|TP53_uc002gih.2_Frame_Shift_Del_p.C238fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.C106fs|TP53_uc010cng.1_Frame_Shift_Del_p.C106fs|TP53_uc002gii.1_Frame_Shift_Del_p.C106fs|TP53_uc010cnh.1_Frame_Shift_Del_p.C238fs|TP53_uc010cni.1_Frame_Shift_Del_p.C238fs|TP53_uc002gij.2_Frame_Shift_Del_p.C238fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.C145fs|TP53_uc002gio.2_Frame_Shift_Del_p.C106fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 238_242 |Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity). Zinc. C -> F (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.S241F(73)|p.C242F(63)|p.C238Y(47)|p.C242Y(37)|p.C238F(34)|p.N239D(29)|p.C242S(25)|p.S241C(24)|p.N239S(19)|p.C238S(18)|p.C242fs*5(16)|p.S240G(14)|p.C238R(14)|p.N239fs*25(12)|p.C242R(11)|p.S240R(8)|p.S241fs*6(8)|p.0?(7)|p.S241Y(7)|p.N239Y(6)|p.N239K(6)|p.S240I(6)|p.S241A(6)|p.S241del(5)|p.S241T(5)|p.N239T(4)|p.C238*(4)|p.N239_C242delNSSC(3)|p.S241S(3)|p.S240C(3)|p.S241P(3)|p.N239_S240insX(2)|p.N239fs*8(2)|p.S240S(2)|p.S240T(2)|p.C242G(2)|p.C238W(2)|p.S240fs*7(2)|p.N239_S240delNS(2)|p.S241fs*22(2)|p.C238fs*2(1)|p.C242fs*20(1)|p.C242fs*23(1)|p.N239fs*26(1)|p.Y236_M243delYMCNSSCM(1)|p.N239fs*1(1)|p.N239_S240insN(1)|p.V225fs*23(1)|p.N239fs*6(1)|p.C242_M246>L(1)|p.N239fs*4(1)|p.S240>CSC(1)|p.C238_M246delCNSSCMGGM(1)|p.C238fs*9(1)|p.S240P(1)|p.S241_C242insX(1)|p.M237_N239delMCN(1)|p.S240fs*23(1)|p.C238del(1)|p.C238G(1)|p.C238fs*21(1)|p.C242fs*98(1)|p.C238C(1)|p.M237fs*1(1)|p.N239N(1)|p.C145F(1)|p.H233fs*6(1)|p.S241fs*7(1)|p.S240fs*26(1)|p.N239*(1)|p.H233_C242del10(1)|p.N239_C242>S(1)|p.S241fs*23(1)|p.S241_G245delSCMGG(1)|p.N239fs*0(1)|p.C238_N239insX(1)|p.N239_C242del(1)|p.M237_C238insX(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GCCGCCCATGCAGGAACTGTTACACATGTAGTTG 0.579 0.75 23 70 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.11 63 8 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.75 5 15 MYH7B 57644 broad.mit.edu 37 20 33585427 33585428 + Frame_Shift_Del DEL CT - - SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr20:33585427_33585428delCT uc002xbi.1 + 30 3949_3950 c.3857_3858delCT c.(3856-3858)ACTfs p.T1286fs NM_020884 NP_065935 A7E2Y1 MYH7B_HUMAN myosin, heavy polypeptide 7B, cardiac muscle, 1244 Potential. membrane|myosin filament actin binding|ATP binding|motor activity ovary(1)|breast(1) 2 BRCA - Breast invasive adenocarcinoma(18;0.00691) AACGTGGAGACTCTGACCCGCG 0.619 0.65 33 60 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 121 298 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW1417_LARGE_INTESTINE NA SW1417_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 12 199 ATRX 546 broad.mit.edu 37 X 76907782 76907784 + In_Frame_Del DEL TCC - - SW1463_LARGE_INTESTINE NA SW1463_LARGE_INTESTINE NA g.chrX:76907782_76907784delTCC uc004ecp.3 - 15 4609_4611 c.4377_4379delGGA c.(4375-4380)GAGGAA>GAA p.1459_1460EE>E ATRX_uc004ecq.3_In_Frame_Del_p.1421_1422EE>E|ATRX_uc004eco.3_In_Frame_Del_p.1244_1245EE>E NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 1459_1460 Poly-Glu. DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) ctcctcctcttcctcctcctcct 0.212 0.33 134 66 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW1463_LARGE_INTESTINE NA SW1463_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 4 46 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW1463_LARGE_INTESTINE NA SW1463_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.63 38 65 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW1463_LARGE_INTESTINE NA SW1463_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 30 55 APC 324 broad.mit.edu 37 5 112157627 112157628 + Frame_Shift_Del DEL TG - - SW1463_LARGE_INTESTINE NA SW1463_LARGE_INTESTINE NA g.chr5:112157627_112157628delTG uc010jby.2 + 11 1727_1728 c.1347_1348delTG c.(1345-1350)GCTGTGfs p.A449fs APC_uc011cvt.1_Frame_Shift_Del_p.A431fs|APC_uc003kpz.3_Frame_Shift_Del_p.A449fs|APC_uc003kpy.3_Frame_Shift_Del_p.A449fs|APC_uc010jbz.2_Frame_Shift_Del_p.A166fs|APC_uc010jca.2_5'UTR NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 449_450 Leu-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) TCTGTCCTGCTGTGTGTGTTCT 0.327 0.89 6 48 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SW1463_LARGE_INTESTINE NA SW1463_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.87 3 20 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SW1463_LARGE_INTESTINE NA SW1463_LARGE_INTESTINE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.43 62 47 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SW1463_LARGE_INTESTINE NA SW1463_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 45 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW1463_LARGE_INTESTINE NA SW1463_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 393 150 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SW1463_LARGE_INTESTINE NA SW1463_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.59 35 50 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW1463_LARGE_INTESTINE NA SW1463_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 173 533 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW1463_LARGE_INTESTINE NA SW1463_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 4 41 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW1783_CENTRAL_NERVOUS_SYSTEM NA SW1783_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 6 95 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SW1783_CENTRAL_NERVOUS_SYSTEM NA SW1783_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.15 292 52 LRP1B 53353 broad.mit.edu 37 2 141625834 141625835 + Splice_Site INS - A A SW1783_CENTRAL_NERVOUS_SYSTEM NA SW1783_CENTRAL_NERVOUS_SYSTEM NA g.chr2:141625834_141625835insA uc002tvj.1 - 26 5142 c.4170_splice c.e26-1 p.G1390_splice LRP1B_uc010fnl.1_Splice_Site_p.G572_splice NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) AAAAGAATTCTaaaaaaaaaaa 0.223 0.18 32 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SW1783_CENTRAL_NERVOUS_SYSTEM NA SW1783_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.36 7 4 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW1783_CENTRAL_NERVOUS_SYSTEM NA SW1783_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 70 69 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW1783_CENTRAL_NERVOUS_SYSTEM NA SW1783_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.77 20 67 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SW1783_CENTRAL_NERVOUS_SYSTEM NA SW1783_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 12 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SW1783_CENTRAL_NERVOUS_SYSTEM NA SW1783_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.80 4 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW1783_CENTRAL_NERVOUS_SYSTEM NA SW1783_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 205 65 Unknown 0 broad.mit.edu 37 17 78286891 78286891 + Frame_Shift_Del DEL G - - SW1783_CENTRAL_NERVOUS_SYSTEM NA SW1783_CENTRAL_NERVOUS_SYSTEM NA g.chr17:78286891delG uc002jyf.2 + 15 2878 c.2735delG c.(2734-2736)AGGfs p.R912fs uc002jyg.1_Frame_Shift_Del_p.R643fs NM_020954 NP_066005 hypothetical protein LOC57714 GCTACGAAAAGGTGGCTCCGA 0.463 0.31 161 74 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SW1783_CENTRAL_NERVOUS_SYSTEM NA SW1783_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.34 122 64 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW1783_CENTRAL_NERVOUS_SYSTEM NA SW1783_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 105 771 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW1783_CENTRAL_NERVOUS_SYSTEM NA SW1783_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 6 76 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SW1990_PANCREAS NA SW1990_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.39 20 13 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 SW1990_PANCREAS NA SW1990_PANCREAS NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.39 137 86 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SW1990_PANCREAS NA SW1990_PANCREAS NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.88 5 37 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SW1990_PANCREAS NA SW1990_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 24 225 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW1990_PANCREAS NA SW1990_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 122 561 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 6 305 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.16 1525 300 AAK1 22848 broad.mit.edu 37 2 69754390 69754390 + Frame_Shift_Del DEL T - - SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr2:69754390delT uc002sfp.2 - 9 1438 c.933delA c.(931-933)TCAfs p.S311fs AAK1_uc010fdk.2_Frame_Shift_Del_p.S311fs|AAK1_uc010yqm.1_Frame_Shift_Del_p.S311fs NM_014911 NP_055726 Q2M2I8 AAK1_HUMAN AP2 associated kinase 1 311 Protein kinase. coated pit|mitochondrion|plasma membrane ATP binding|protein serine/threonine kinase activity 0 GTAGCTTAAATGAGAAGTAGG 0.378 0.33 808 394 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.22 63 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.55 45 54 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 156 175 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 97 60 APC 324 broad.mit.edu 37 5 112174882 112174882 + Frame_Shift_Del DEL C - - SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr5:112174882delC uc010jby.2 + 16 3971 c.3591delC c.(3589-3591)TTCfs p.F1197fs APC_uc011cvt.1_Frame_Shift_Del_p.F1179fs|APC_uc003kpz.3_Frame_Shift_Del_p.F1197fs|APC_uc003kpy.3_Frame_Shift_Del_p.F1197fs|APC_uc010jbz.2_Frame_Shift_Del_p.F914fs|APC_uc010jca.2_Frame_Shift_Del_p.F497fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1197 Ser-rich.|Responsible for down-regulation through a process mediated by direct ubiquitination. F -> S (in gastric cancer). canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.S1198fs*67(1)|p.F1197S(1)|p.K1192fs*3(1)|p.?(1)|p.S1198fs*1(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) CATTTTCATTCTCAAAGAGTT 0.368 0.61 462 729 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 18 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.34 190 100 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 29 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 324 52 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 21 137 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.19 72 17 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 493 101 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 132 461 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW403_LARGE_INTESTINE NA SW403_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 18 240 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW480_LARGE_INTESTINE NA SW480_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 22 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SW480_LARGE_INTESTINE NA SW480_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.27 138 51 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SW480_LARGE_INTESTINE NA SW480_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.31 9 4 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW480_LARGE_INTESTINE NA SW480_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.26 35 12 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW480_LARGE_INTESTINE NA SW480_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.74 9 26 MYST4 23522 broad.mit.edu 37 10 76781905 76781906 + In_Frame_Ins INS - GAA GAA rs138589645;rs111976843 by1000genomes SW480_LARGE_INTESTINE NA SW480_LARGE_INTESTINE NA g.chr10:76781905_76781906insGAA uc001jwn.1 + 16 3781_3782 c.3288_3289insGAA c.(3286-3291)insGAA p.1104_1105insE MYST4_uc001jwm.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwo.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwp.1_In_Frame_Ins_p.921_922insE NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1104_1105 histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) aggaagaagaggaagaagaaga 0.203 0.74 14 39 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW480_LARGE_INTESTINE NA SW480_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 98 22 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SW480_LARGE_INTESTINE NA SW480_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 23 188 RHPN2 85415 broad.mit.edu 37 19 33535248 33535251 + Frame_Shift_Del DEL GTTT - - SW480_LARGE_INTESTINE NA SW480_LARGE_INTESTINE NA g.chr19:33535248_33535251delGTTT uc002nuf.2 - 2 155_158 c.89_92delAAAC c.(88-93)CAAACCfs p.Q30fs RHPN2_uc010xro.1_5'UTR NM_033103 NP_149094 Q8IUC4 RHPN2_HUMAN rhophilin, Rho GTPase binding protein 2 30_31 signal transduction perinuclear region of cytoplasm protein binding central_nervous_system(5)|ovary(1) 6 Esophageal squamous(110;0.137) ACTCCGGCCGGTTTGTGCAAGGGG 0.466 0.65 41 76 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW480_LARGE_INTESTINE NA SW480_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 115 444 FANCB 2187 broad.mit.edu 37 X 14868798 14868799 + Splice_Site INS - A A SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chrX:14868798_14868799insA uc004cwg.1 - 7 1595 c.1327_splice c.e7-1 p.K443_splice FANCB_uc004cwh.1_Splice_Site_p.K443_splice NM_001018113 NP_001018123 Q8NB91 FANCB_HUMAN Fanconi anemia complementation group B DNA repair nucleoplasm lung(1) 1 Hepatocellular(33;0.183) ACATTCCTTCTAAAAAAAAAAG 0.312 0.30 306 132 KDM6A 7403 broad.mit.edu 37 X 44923035 44923036 + Frame_Shift_Ins INS - A A SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chrX:44923035_44923036insA uc004dge.3 + 16 2271_2272 c.1896_1897insA c.(1894-1899)TGGAAAfs p.W632fs KDM6A_uc010nhk.2_Frame_Shift_Ins_p.W598fs|KDM6A_uc011mkz.1_Frame_Shift_Ins_p.W684fs|KDM6A_uc011mla.1_Frame_Shift_Ins_p.W587fs|KDM6A_uc011mlb.1_Frame_Shift_Ins_p.W639fs|KDM6A_uc011mlc.1_Frame_Shift_Ins_p.W336fs|KDM6A_uc011mld.1_Frame_Shift_Ins_p.W271fs NM_021140 NP_066963 O15550 KDM6A_HUMAN ubiquitously transcribed tetratricopeptide 632_633 histone H3-K4 methylation metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2) 84 AGGAGCCGTGGAAAAACCAACT 0.455 0.36 37 21 ARAF 369 broad.mit.edu 37 X 47426415 47426415 + Frame_Shift_Del DEL C - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chrX:47426415delC uc011mlq.1 + 9 891 c.758delC c.(757-759)ACCfs p.T253fs ARAF_uc011mln.1_RNA|ARAF_uc011mlo.1_Frame_Shift_Del_p.T119fs|ARAF_uc011mlp.1_Frame_Shift_Del_p.T253fs|ARAF_uc004dic.1_Frame_Shift_Del_p.T34fs NM_001654 NP_001645 P10398 ARAF_HUMAN v-raf murine sarcoma 3611 viral oncogene 253 intracellular signal transduction|negative regulation of apoptosis|positive regulation of peptidyl-serine phosphorylation ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity large_intestine(3)|lung(2)|ovary(1)|skin(1) 7 Adenosine triphosphate(DB00171) AGTGATGGAACCCCCCGGGGG 0.652 0.30 110 47 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.20 317 80 ATRX 546 broad.mit.edu 37 X 76938089 76938090 + Frame_Shift_Del DEL TC - - rs141180098 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chrX:76938089_76938090delTC uc004ecp.3 - 9 2890_2891 c.2658_2659delGA c.(2656-2661)GAGACTfs p.E886fs ATRX_uc004ecq.3_Frame_Shift_Del_p.E848fs|ATRX_uc004eco.3_Frame_Shift_Del_p.E671fs|ATRX_uc004ecr.2_Frame_Shift_Del_p.E818fs|ATRX_uc010nlx.1_Frame_Shift_Del_p.E857fs|ATRX_uc010nly.1_Frame_Shift_Del_p.E831fs NM_000489 NP_000480 P46100 ATRX_HUMAN transcriptional regulator ATRX isoform 1 886_887 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1) 30 Phosphatidylserine(DB00144) GAAGAGAAAGTCTCTCTCTCTT 0.411 0.40 626 413 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.99 3 237 GPR112 139378 broad.mit.edu 37 X 135404968 135404968 + Frame_Shift_Del DEL T - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chrX:135404968delT uc004ezu.1 + 5 393 c.102delT c.(100-102)GATfs p.D34fs GPR112_uc010nsb.1_Intron NM_153834 NP_722576 Q8IZF6 GP112_HUMAN G-protein coupled receptor 112 34 Extracellular (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1) 12 Acute lymphoblastic leukemia(192;0.000127) AAAAGCTGGATTTTTTTGGAA 0.358 0.51 212 219 CHD5 26038 broad.mit.edu 37 1 6194862 6194863 + Frame_Shift_Ins INS - C C SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr1:6194862_6194863insC uc001amb.1 - 19 3027_3028 c.2927_2928insG c.(2926-2928)GGCfs p.G976fs CHD5_uc001ama.1_RNA|CHD5_uc001amc.1_RNA|CHD5_uc009vlx.1_RNA NM_015557 NP_056372 Q8TDI0 CHD5_HUMAN chromodomain helicase DNA binding protein 5 976 chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1) 12 Ovarian(185;0.0634) all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15) Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193) CTTGGTTCCCGCCCCCCTTGGA 0.579 0.41 328 227 PLEKHG5 57449 broad.mit.edu 37 1 6529182 6529183 + In_Frame_Ins INS - TCC TCC rs141275705;rs113541584 by1000genomes SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr1:6529182_6529183insTCC uc001ano.1 - 20 2437_2438 c.2336_2337insGGA c.(2335-2337)GAA>GAGGAA p.779_779E>EE PLEKHG5_uc001ann.1_In_Frame_Ins_p.760_760E>EE|PLEKHG5_uc001anq.1_In_Frame_Ins_p.800_800E>EE|PLEKHG5_uc001anp.1_In_Frame_Ins_p.800_800E>EE|TNFRSF25_uc001ana.2_5'Flank|TNFRSF25_uc001anb.2_5'Flank|TNFRSF25_uc001anc.2_5'Flank|TNFRSF25_uc001and.2_5'Flank|TNFRSF25_uc009vlz.2_5'Flank|TNFRSF25_uc001ane.2_5'Flank|TNFRSF25_uc001anf.2_5'Flank|TNFRSF25_uc001ang.2_5'Flank|TNFRSF25_uc001anh.2_5'Flank|TNFRSF25_uc001ani.1_5'Flank|PLEKHG5_uc001anj.1_In_Frame_Ins_p.284_284E>EE|PLEKHG5_uc009vma.1_In_Frame_Ins_p.563_563E>EE|PLEKHG5_uc010nzr.1_In_Frame_Ins_p.792_792E>EE|PLEKHG5_uc001ank.1_In_Frame_Ins_p.723_723E>EE|PLEKHG5_uc009vmb.1_In_Frame_Ins_p.723_723E>EE|PLEKHG5_uc001anl.1_In_Frame_Ins_p.723_723E>EE|PLEKHG5_uc001anm.1_In_Frame_Ins_p.723_723E>EE|PLEKHG5_uc001anr.1_5'UTR NM_001042663 NP_001036128 O94827 PKHG5_HUMAN pleckstrin homology domain containing family G 779 Glu-rich. Missing (in Ref. 6; BAC77354). apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|perinuclear region of cytoplasm Rho guanyl-nucleotide exchange factor activity|signal transducer activity liver(1) 1 Ovarian(185;0.02)|all_lung(157;0.154) all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448) Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419) TGtcctcgccttcctcctcctc 0.431 0.31 18 8 EPHA2 1969 broad.mit.edu 37 1 16462199 16462199 + Frame_Shift_Del DEL G - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr1:16462199delG uc001aya.1 - 6 1516 c.1379delC c.(1378-1380)CCGfs p.P460fs EPHA2_uc010oca.1_Frame_Shift_Del_p.P460fs NM_004431 NP_004422 P29317 EPHA2_HUMAN ephrin receptor EphA2 precursor 460 Extracellular (Potential).|Fibronectin type-III 2. activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) 0.000 0.38 315 191 ARID1A 8289 broad.mit.edu 37 1 27101402 27101402 + Frame_Shift_Del DEL C - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr1:27101402delC uc001bmv.1 + 18 5057 c.4684delC c.(4684-4686)CCCfs p.P1562fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.P1561fs|ARID1A_uc001bmu.1_Intron|ARID1A_uc001bmw.1_Frame_Shift_Del_p.P1179fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.P408fs|ARID1A_uc009vsm.1_Intron|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1562 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) TGCCCCTGTGCCCCCCATGAC 0.607 0.43 97 73 MAP3K6 9064 broad.mit.edu 37 1 27685239 27685239 + Frame_Shift_Del DEL G - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr1:27685239delG uc001bny.1 - 19 2793 c.2544delC c.(2542-2544)CCCfs p.P848fs MAP3K6_uc009vsw.1_Frame_Shift_Del_p.P840fs|MAP3K6_uc001bnz.1_Frame_Shift_Del_p.P371fs NM_004672 NP_004663 O95382 M3K6_HUMAN mitogen-activated protein kinase kinase kinase 848 Protein kinase. activation of JUN kinase activity ATP binding|magnesium ion binding|MAP kinase kinase kinase activity p.F709fs*40(1) breast(4)|lung(3)|ovary(1)|central_nervous_system(1) 9 all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419) GCTCGTGGAAGGGGGGGCGAC 0.622 0.49 122 116 NTRK1 4914 broad.mit.edu 37 1 156846308 156846308 + Frame_Shift_Del DEL C - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr1:156846308delC uc001fqh.1 + 14 1805 c.1749delC c.(1747-1749)CGCfs p.R583fs NTRK1_uc001fqf.1_Frame_Shift_Del_p.R547fs|NTRK1_uc009wsi.1_Frame_Shift_Del_p.R282fs|NTRK1_uc001fqi.1_Frame_Shift_Del_p.R577fs|NTRK1_uc009wsk.1_Frame_Shift_Del_p.R580fs NM_002529 NP_002520 P04629 NTRK1_HUMAN neurotrophic tyrosine kinase, receptor, type 1 583 Cytoplasmic (Potential).|Protein kinase. activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction endosome|integral to plasma membrane ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity lung(9)|ovary(6)|stomach(1)|central_nervous_system(1) 17 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) Imatinib(DB00619) CCGAGGGCCGCCCCCTGCTCA 0.667 0.44 224 179 TPR 7175 broad.mit.edu 37 1 186337050 186337053 + Frame_Shift_Del DEL TCAT - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr1:186337050_186337053delTCAT uc001grv.2 - 4 689_692 c.392_395delATGA c.(391-396)AATGAGfs p.N131fs TPR_uc010pop.1_Frame_Shift_Del_p.N207fs NM_003292 NP_003283 P12270 TPR_HUMAN nuclear pore complex-associated protein TPR 131_132 Potential. carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm ATP binding|protein binding|serine-tRNA ligase activity ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1) 7 Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157) Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553) AGATAGTCTCTCATTGGTTCTAAT 0.328 0.14 522 86 SOX11 6664 broad.mit.edu 37 2 5834002 5834002 + Frame_Shift_Del DEL C - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr2:5834002delC uc002qyj.2 + 1 1204 c.1149delC c.(1147-1149)GGCfs p.G383fs NM_003108 NP_003099 P35716 SOX11_HUMAN SRY-box 11 383 cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis cytoplasm|nucleolus enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding central_nervous_system(3) 3 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) OV - Ovarian serous cystadenocarcinoma(76;0.132) 0.000 0.48 246 231 TTN 7273 broad.mit.edu 37 2 179434290 179434291 + In_Frame_Ins INS - CTT CTT SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr2:179434290_179434291insCTT uc010zfg.1 - 275 69088_69089 c.68864_68865insAAG c.(68863-68865)AGG>AGAAGG p.22955_22955R>RR uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Ins_p.16650_16650R>RR|TTN_uc010zfi.1_In_Frame_Ins_p.16583_16583R>RR|TTN_uc010zfj.1_In_Frame_Ins_p.16458_16458R>RR NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 23882 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AGCCACCTGCCCTTATATTTAT 0.406 0.41 260 180 TTN 7273 broad.mit.edu 37 2 179499178 179499180 + In_Frame_Del DEL AAC - - rs34706299 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr2:179499178_179499180delAAC uc010zfg.1 - 179 34848_34850 c.34624_34626delGTT c.(34624-34626)GTTdel p.V11542del TTN_uc010zfh.1_In_Frame_Del_p.V5237del|TTN_uc010zfi.1_In_Frame_Del_p.V5170del|TTN_uc010zfj.1_In_Frame_Del_p.V5045del NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 12469 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AATCATTAATAACAAGAATATGT 0.409 0.45 301 247 ROBO1 6091 broad.mit.edu 37 3 78710235 78710235 + Frame_Shift_Del DEL A - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr3:78710235delA uc003dqe.2 - 16 2473 c.2265delT c.(2263-2265)TTTfs p.F755fs ROBO1_uc003dqb.2_Frame_Shift_Del_p.F716fs|ROBO1_uc003dqc.2_Frame_Shift_Del_p.F719fs|ROBO1_uc003dqd.2_Frame_Shift_Del_p.F719fs|ROBO1_uc010hoh.2_5'UTR|ROBO1_uc011bgl.1_Frame_Shift_Del_p.F327fs|ROBO1_uc003dqf.1_Frame_Shift_Del_p.F434fs NM_002941 NP_002932 Q9Y6N7 ROBO1_HUMAN roundabout 1 isoform a 755 Extracellular (Potential).|Fibronectin type-III 2. activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway cell surface|cytoplasm|integral to plasma membrane axon guidance receptor activity|identical protein binding|LRR domain binding large_intestine(2) 2 Lung SC(41;0.0257)|Lung NSC(201;0.0439) LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274) GAAATTCATTAAAAAAAGGGC 0.398 0.44 322 254 EPHA3 2042 broad.mit.edu 37 3 89391024 89391024 + Frame_Shift_Del DEL A - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr3:89391024delA uc003dqy.2 + 5 1315 c.1090delA c.(1090-1092)AAAfs p.K364fs EPHA3_uc003dqx.1_Frame_Shift_Del_p.K364fs|EPHA3_uc010hon.1_RNA NM_005233 NP_005224 P29320 EPHA3_HUMAN ephrin receptor EphA3 isoform a precursor 364 Extracellular (Potential).|Fibronectin type-III 1. extracellular region|integral to plasma membrane ATP binding lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1) 33 all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612) Lung NSC(201;0.0782) LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942) CATCATATGTAAAAAATGTGG 0.468 0.44 443 353 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.18 62 14 TFDP2 7029 broad.mit.edu 37 3 141692947 141692947 + Frame_Shift_Del DEL T - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr3:141692947delT uc003eun.3 - 8 985 c.606delA c.(604-606)AAAfs p.K202fs TFDP2_uc003euk.3_Frame_Shift_Del_p.K115fs|TFDP2_uc010hur.2_Frame_Shift_Del_p.K142fs|TFDP2_uc003eul.3_Frame_Shift_Del_p.K142fs|TFDP2_uc011bnf.1_Frame_Shift_Del_p.K105fs|TFDP2_uc011bng.1_Frame_Shift_Del_p.K66fs|TFDP2_uc003eum.3_Frame_Shift_Del_p.K142fs NM_006286 NP_006277 Q14188 TFDP2_HUMAN transcription factor Dp-2 (E2F dimerization 202 DEF box.|Potential. cell cycle transcription factor complex DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding kidney(1) 1 ACTTGATTTCTTTTTTTTCCT 0.343 0.41 40 28 FGFR3 2261 broad.mit.edu 37 4 1801138 1801138 + Frame_Shift_Del DEL G - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr4:1801138delG uc003gdr.3 + 3 523 c.267delG c.(265-267)GTGfs p.V89fs FGFR3_uc003gdu.2_Frame_Shift_Del_p.V89fs|FGFR3_uc003gds.3_Frame_Shift_Del_p.V89fs|FGFR3_uc003gdq.3_Frame_Shift_Del_p.V89fs|FGFR3_uc010icb.1_5'Flank|FGFR3_uc003gdt.1_5'Flank NM_000142 NP_000133 P22607 FGFR3_HUMAN fibroblast growth factor receptor 3 isoform 1 89 Ig-like C2-type 1.|Extracellular (Potential). bone maturation|cell growth|insulin receptor signaling pathway|JAK-STAT cascade|MAPKKK cascade|negative regulation of developmental growth|positive regulation of cell proliferation integral to plasma membrane ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|identical protein binding urinary_tract(2177)|skin(314)|upper_aerodigestive_tract(57)|haematopoietic_and_lymphoid_tissue(24)|prostate(9)|cervix(6)|central_nervous_system(4)|large_intestine(3)|lung(3)|testis(2)|pancreas(1) 2600 Breast(71;0.212)|all_epithelial(65;0.241) all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234) Palifermin(DB00039) GTGTCCTGGTGGGGCCCCAGC 0.701 0.31 11 5 PI4K2B 55300 broad.mit.edu 37 4 25278792 25278792 + Frame_Shift_Del DEL T - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr4:25278792delT uc003grk.2 + 10 1562 c.1429delT c.(1429-1431)TTTfs p.F477fs PI4K2B_uc011bxs.1_Frame_Shift_Del_p.F381fs NM_018323 NP_060793 Q8TCG2 P4K2B_HUMAN phosphatidylinositol 4-kinase type 2 beta 477 cytoplasm|membrane 1-phosphatidylinositol 4-kinase activity|ATP binding ovary(2)|skin(2) 4 Breast(46;0.173) CAGGAAGCCATTTTTTTCCTC 0.393 0.45 384 310 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.17 118 24 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.55 192 230 FBXW7 55294 broad.mit.edu 37 4 153244156 153244156 + Frame_Shift_Del DEL C - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr4:153244156delC uc003ims.2 - 12 2150 c.2001delG c.(1999-2001)GGGfs p.G667fs FBXW7_uc011cii.1_Frame_Shift_Del_p.G667fs|FBXW7_uc003imt.2_Frame_Shift_Del_p.G667fs|FBXW7_uc011cih.1_Frame_Shift_Del_p.G491fs|FBXW7_uc003imq.2_Frame_Shift_Del_p.G587fs|FBXW7_uc003imr.2_Frame_Shift_Del_p.G549fs NM_033632 NP_361014 Q969H0 FBXW7_HUMAN F-box and WD repeat domain containing 7 isoform 667 interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex protein binding|protein binding p.S668fs*26(1)|p.S668fs*39(1) haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1) 308 all_hematologic(180;0.093) Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067) CTCCCCCACTCCCCCCACTCT 0.488 0.40 521 344 NKD2 85409 broad.mit.edu 37 5 1038447 1038449 + In_Frame_Del DEL CAC - - rs3840989 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr5:1038447_1038449delCAC uc003jbt.1 + 10 1320_1322 c.1315_1317delCAC c.(1315-1317)CACdel p.H447del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.45 113 92 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 63 127 RASGRF2 5924 broad.mit.edu 37 5 80369088 80369090 + In_Frame_Del DEL CTC - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr5:80369088_80369090delCTC uc003kha.1 + 5 704_706 c.704_706delCTC c.(703-708)TCTCCT>TCT p.P236del RASGRF2_uc011ctn.1_RNA|RASGRF2_uc003khb.1_In_Frame_Del_p.P64del NM_006909 NP_008840 O14827 RGRF2_HUMAN Ras protein-specific guanine 236 apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission cytosol|endoplasmic reticulum membrane|plasma membrane protein binding|Rho guanyl-nucleotide exchange factor activity breast(5)|ovary(3)|large_intestine(2)|central_nervous_system(1)|skin(1) 12 Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357) OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29) TACATTTGTTCTCCTCATGCTGA 0.453 0.46 518 442 STK32A 202374 broad.mit.edu 37 5 146754725 146754725 + Frame_Shift_Del DEL A - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr5:146754725delA uc010jgn.1 + 11 1256 c.976delA c.(976-978)AAAfs p.K326fs STK32A_uc003lom.2_Frame_Shift_Del_p.K326fs|STK32A_uc011dbw.1_Frame_Shift_Del_p.K326fs NM_001112724 NP_001106195 Q8WU08 ST32A_HUMAN serine/threonine kinase 32A isoform 1 326 ATP binding|metal ion binding|protein serine/threonine kinase activity lung(2)|skin(1) 3 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TCTACATAAGAAAAAAAAGCG 0.453 0.42 90 65 EDN1 1906 broad.mit.edu 37 6 12294561 12294561 + Frame_Shift_Del DEL A - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr6:12294561delA uc003nae.3 + 4 791 c.457delA c.(457-459)AAAfs p.K153fs EDN1_uc003nad.2_Frame_Shift_Del_p.K153fs|EDN1_uc003naf.3_Frame_Shift_Del_p.K152fs NM_001955 NP_001946 P05305 EDN1_HUMAN endothelin 1 precursor 153 artery smooth muscle contraction|calcium-mediated signaling|leukocyte activation|negative regulation of blood coagulation|negative regulation of cellular protein metabolic process|negative regulation of nitric-oxide synthase biosynthetic process|negative regulation of transcription from RNA polymerase II promoter|nitric oxide transport|peptide hormone secretion|phosphatidylinositol 3-kinase cascade|positive regulation of cardiac muscle hypertrophy|positive regulation of cell size|positive regulation of endothelial cell migration|positive regulation of heart rate|positive regulation of hormone secretion|positive regulation of JUN kinase activity|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of sarcomere organization|positive regulation of smooth muscle cell proliferation|prostaglandin biosynthetic process|protein kinase C deactivation|regulation of systemic arterial blood pressure by endothelin|regulation of vasoconstriction|vein smooth muscle contraction cytoplasm|extracellular space cytokine activity|endothelin A receptor binding|endothelin B receptor binding|hormone activity skin(1) 1 all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12) all_hematologic(90;0.117) CAAGCTTGGGAAAAAGTGTAT 0.363 0.46 191 165 JARID2 3720 broad.mit.edu 37 6 15497226 15497226 + Frame_Shift_Del DEL C - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr6:15497226delC uc003nbj.2 + 7 2014 c.1770delC c.(1768-1770)ATCfs p.I590fs JARID2_uc011diu.1_Frame_Shift_Del_p.I454fs|JARID2_uc011div.1_Frame_Shift_Del_p.I418fs|JARID2_uc011diw.1_Frame_Shift_Del_p.I552fs NM_004973 NP_004964 Q92833 JARD2_HUMAN jumonji, AT rich interactive domain 2 protein 590 JmjN. central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent chromatin binding ovary(2)|lung(1)|pancreas(1) 4 Breast(50;0.0142)|Ovarian(93;0.103) all_hematologic(90;0.00612) GCAGGGTGATCCCCCCTCCGG 0.642 0.95 5 95 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.16 48 9 HDAC2 3066 broad.mit.edu 37 6 114292039 114292040 + Frame_Shift_Ins INS - T T SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr6:114292039_114292040insT uc003pwd.1 - 1 315_316 c.315_316insA c.(313-318)AAAGTCfs p.K105fs uc003pwf.2_Intron|HDAC2_uc003pwc.1_5'Flank|HDAC2_uc003pwe.1_5'UTR NM_001527 NP_001518 Q92769 HDAC2_HUMAN histone deacetylase 2 11_12 Histone deacetylase. blood coagulation|dendrite development|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|maintenance of chromatin silencing|negative regulation of apoptosis|negative regulation of cell cycle|negative regulation of neuron projection development|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of proteolysis|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter cytoplasm|ESC/E(Z) complex|NuRD complex|Sin3 complex chromatin binding|enzyme binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|sequence-specific DNA binding|transcription factor binding skin(2)|ovary(1)|central_nervous_system(1) 4 all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24) all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832) Vorinostat(DB02546) TAGTAGCAGACTTTTTTTTTGC 0.431 0.43 38 29 AKAP9 10142 broad.mit.edu 37 7 91732039 91732039 + Frame_Shift_Del DEL G - - rs143306820 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr7:91732039delG uc003ulg.2 + 46 11454 c.11229delG c.(11227-11229)ATGfs p.M3743fs AKAP9_uc003ulf.2_Frame_Shift_Del_p.M3735fs|AKAP9_uc003uli.2_Frame_Shift_Del_p.M3366fs|AKAP9_uc003ulj.2_Frame_Shift_Del_p.M1513fs|AKAP9_uc003ull.2_Frame_Shift_Del_p.M639fs NM_005751 NP_005742 Q99996 AKAP9_HUMAN A-kinase anchor protein 9 isoform 2 3747 G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport centrosome|cytosol|Golgi apparatus receptor binding breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1) 26 all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) TTGCCCGGATGGGGGGGCAGC 0.537 0.30 659 285 SMO 6608 broad.mit.edu 37 7 128852004 128852004 + Frame_Shift_Del DEL C - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr7:128852004delC uc003vor.2 + 12 2356 c.2076delC c.(2074-2076)CACfs p.H692fs SMO_uc003vos.2_3'UTR NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 692 Cytoplasmic (Potential). adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 CTGAGCTTCACCCCCCTGCCC 0.592 0.65 8 15 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.89 3 24 KCNH2 3757 broad.mit.edu 37 7 150656679 150656679 + Frame_Shift_Del DEL G - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr7:150656679delG uc003wic.2 - 3 466 c.453delC c.(451-453)CCCfs p.P151fs KCNH2_uc011kux.1_Frame_Shift_Del_p.P55fs|KCNH2_uc003wie.2_Frame_Shift_Del_p.P151fs NM_000238 NP_000229 Q12809 KCNH2_HUMAN voltage-gated potassium channel, subfamily H, 151 Cytoplasmic (Potential). blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent voltage-gated potassium channel complex delayed rectifier potassium channel activity|two-component sensor activity skin(3)|ovary(1) 4 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661) GCCAGCTGGTGGGGGGGCCCC 0.587 0.34 126 65 DLC1 10395 broad.mit.edu 37 8 12957997 12957997 + Frame_Shift_Del DEL G - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr8:12957997delG uc003wwm.2 - 9 2293 c.1849delC c.(1849-1851)CGGfs p.R617fs DLC1_uc003wwk.1_Frame_Shift_Del_p.R180fs|DLC1_uc003wwl.1_Frame_Shift_Del_p.R214fs|DLC1_uc011kxx.1_Frame_Shift_Del_p.R106fs NM_182643 NP_872584 Q96QB1 RHG07_HUMAN deleted in liver cancer 1 isoform 1 617 actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction caveola|cytosol|focal adhesion|nucleus Rho GTPase activator activity|SH2 domain binding ovary(3)|pancreas(2)|lung(1)|kidney(1) 7 GAGTTAGTCCGGGGGGTGGCA 0.652 0.62 6 10 WHSC1L1 54904 broad.mit.edu 37 8 38133981 38133981 + Frame_Shift_Del DEL T - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr8:38133981delT uc003xli.2 - 23 4423 c.3905delA c.(3904-3906)AATfs p.N1302fs WHSC1L1_uc011lbm.1_Frame_Shift_Del_p.N1291fs|WHSC1L1_uc010lwe.2_Frame_Shift_Del_p.N1253fs|WHSC1L1_uc003xlh.2_Frame_Shift_Del_p.N81fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 1302 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TAACTTAGCATTTTTTGCCTT 0.423 0.44 495 383 ADAM18 8749 broad.mit.edu 37 8 39581343 39581344 + Frame_Shift_Ins INS - T T SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr8:39581343_39581344insT uc003xni.2 + 19 2094_2095 c.2094_2095insT c.(2092-2097)CCGTTTfs p.P698fs ADAM18_uc010lww.2_RNA|ADAM18_uc010lwx.2_Frame_Shift_Ins_p.P674fs NM_014237 NP_055052 Q9Y3Q7 ADA18_HUMAN a disintegrin and metalloprotease domain 18 698_699 Helical; (Potential). cell differentiation|multicellular organismal development|proteolysis|spermatogenesis integral to membrane|membrane fraction metalloendopeptidase activity|zinc ion binding central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1) 6 all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112) LUSC - Lung squamous cell carcinoma(45;0.000199) TTTTTCTGCCGTTTTTCATAGT 0.302 0.47 219 195 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 22 DAPK1 1612 broad.mit.edu 37 9 90321802 90321802 + Frame_Shift_Del DEL G - - rs56169226 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr9:90321802delG uc004apc.2 + 26 3954 c.3816delG c.(3814-3816)ATGfs p.M1272fs DAPK1_uc004apd.2_Frame_Shift_Del_p.M1272fs|DAPK1_uc011ltg.1_Frame_Shift_Del_p.M1206fs|DAPK1_uc011lth.1_Frame_Shift_Del_p.M1009fs|DAPK1_uc004apg.2_Frame_Shift_Del_p.M249fs NM_004938 NP_004929 P53355 DAPK1_HUMAN death-associated protein kinase 1 1272 apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade actin cytoskeleton|cytoplasm ATP binding|calmodulin binding|protein serine/threonine kinase activity ovary(1)|breast(1) 2 CCAACACCATGGGGGGGTACA 0.582 0.90 11 101 SMC2 10592 broad.mit.edu 37 9 106896717 106896718 + Frame_Shift_Ins INS - T T SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr9:106896717_106896718insT uc004bbv.2 + 23 3418_3419 c.3130_3131insT c.(3130-3132)ATTfs p.I1044fs SMC2_uc004bbw.2_Frame_Shift_Ins_p.I1044fs|SMC2_uc011lvl.1_Frame_Shift_Ins_p.I1044fs|SMC2_uc004bbx.2_Frame_Shift_Ins_p.I1044fs|SMC2_uc004bby.2_RNA NM_001042551 NP_001036016 O95347 SMC2_HUMAN structural maintenance of chromosomes 2 1044 cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism condensin complex|cytoplasm|nuclear chromosome ATP binding|protein heterodimerization activity ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1) 9 CTTTGGGTCTATTTTTTCTACT 0.381 0.46 271 227 FRMD4A 55691 broad.mit.edu 37 10 13696452 13696452 + Frame_Shift_Del DEL G - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr10:13696452delG uc001ims.2 - 23 3366 c.3014delC c.(3013-3015)CCAfs p.P1005fs PRPF18_uc001imq.2_Intron|FRMD4A_uc009xjf.1_Frame_Shift_Del_p.P1005fs NM_018027 NP_060497 Q9P2Q2 FRM4A_HUMAN FERM domain containing 4A 1005 Ser-rich. cytoplasm|cytoskeleton binding ovary(1)|skin(1)|pancreas(1) 3 GGGGCTGCTTGGGGGGGTGGC 0.537 0.90 1 9 ZNF25 219749 broad.mit.edu 37 10 38241675 38241675 + Frame_Shift_Del DEL T - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr10:38241675delT uc001ize.1 - 6 856 c.751delA c.(751-753)ACAfs p.T251fs ZNF25_uc001izf.1_Frame_Shift_Del_p.T215fs NM_145011 NP_659448 P17030 ZNF25_HUMAN zinc finger protein 25 251 C2H2-type 5. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(2)|ovary(1)|central_nervous_system(1) 4 all_neural(218;0.0218)|Breast(68;0.0389)|Ovarian(717;0.0443)|Renal(717;0.157) CCTGTGTGTGTTTTCTGATGT 0.453 0.53 20 23 ADAMTS14 140766 broad.mit.edu 37 10 72496510 72496510 + Frame_Shift_Del DEL G - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr10:72496510delG uc001jrh.2 + 10 1560 c.1560delG c.(1558-1560)AAGfs p.K520fs ADAMTS14_uc001jrg.2_Frame_Shift_Del_p.K523fs|ADAMTS14_uc001jri.1_Frame_Shift_Del_p.K43fs NM_080722 NP_542453 Q8WXS8 ATS14_HUMAN ADAM metallopeptidase with thrombospondin type 1 520 Disintegrin. collagen catabolic process|proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding ovary(5)|upper_aerodigestive_tract(1) 6 AGACCAAGAAGGGGCCCCCGC 0.617 0.27 72 27 CYP17A1 1586 broad.mit.edu 37 10 104596942 104596942 + Frame_Shift_Del DEL T - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr10:104596942delT uc001kwg.2 - 1 349 c.177delA c.(175-177)AAAfs p.K59fs NM_000102 NP_000093 P05093 CP17A_HUMAN cytochrome P450, family 17 59 androgen biosynthetic process|glucocorticoid biosynthetic process|sex differentiation|xenobiotic metabolic process endoplasmic reticulum membrane electron carrier activity|heme binding|oxygen binding|steroid 17-alpha-monooxygenase activity 0 Colorectal(252;0.122)|all_hematologic(284;0.152) Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215) NADH(DB00157)|Progesterone(DB00396) TGGGGCCATATTTTTTCTGCA 0.542 0.48 310 286 MARK2 2011 broad.mit.edu 37 11 63606994 63606995 + Frame_Shift_Ins INS - C C SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr11:63606994_63606995insC uc001nxw.2 + 1 595_596 c.16_17insC c.(16-18)ACCfs p.T6fs MARK2_uc001nxx.2_Frame_Shift_Ins_p.T6fs|MARK2_uc001nxy.2_Frame_Shift_Ins_p.T6fs|MARK2_uc001nxv.3_Frame_Shift_Ins_p.T6fs NM_001039469 NP_001034558 Q7KZI7 MARK2_HUMAN MAP/microtubule affinity-regulating kinase 2 6 cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress plasma membrane ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity stomach(1)|ovary(1)|lung(1) 3 CAGCGCTCGGACCCCCCTACCC 0.693 0.35 78 42 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 380 55 NPAT 4863 broad.mit.edu 37 11 108040772 108040773 + Splice_Site INS - A A rs35747263 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr11:108040772_108040773insA uc001pjz.3 - 14 2888 c.2786_splice c.e14-1 p.G929_splice NPAT_uc010rvv.1_5'UTR NM_002519 NP_002510 Q14207 NPAT_HUMAN nuclear protein, ataxia-telangiectasia locus positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle Cajal body protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity ovary(2) 2 all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116) TGGCAGATCCTAAAAAAACAAT 0.342 0.38 221 135 NCAPD3 23310 broad.mit.edu 37 11 134078847 134078848 + Splice_Site INS - A A SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr11:134078847_134078848insA uc001qhd.1 - 7 1401 c.795_splice c.e7-1 p.R265_splice NCAPD3_uc010scm.1_Splice_Site|NCAPD3_uc009zda.1_Splice_Site NM_015261 NP_056076 P42695 CNDD3_HUMAN non-SMC condensin II complex, subunit D3 cell division|mitotic chromosome condensation nuclear centromeric heterochromatin|nuclear condensin complex methylated histone residue binding ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1) 5 all_hematologic(175;0.127) all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227) TTAAGAGCTCTAAAAAAAAAAG 0.337 0.27 228 86 PTPN6 5777 broad.mit.edu 37 12 7061149 7061149 + Frame_Shift_Del DEL G - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr12:7061149delG uc001qsb.2 + 3 377 c.135delG c.(133-135)GTGfs p.V45fs PTPN6_uc001qsa.1_Frame_Shift_Del_p.V47fs|PTPN6_uc010sfr.1_Frame_Shift_Del_p.V6fs|PTPN6_uc009zfl.1_Frame_Shift_Del_p.V45fs|PTPN6_uc010sfs.1_Frame_Shift_Del_p.V33fs NM_002831 NP_002822 P29350 PTN6_HUMAN protein tyrosine phosphatase, non-receptor type 45 SH2 1. apoptosis|cell junction assembly|G-protein coupled receptor protein signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|negative regulation of peptidyl-tyrosine phosphorylation|platelet activation|positive regulation of cell proliferation|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of G1/S transition of mitotic cell cycle|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway cytosol|membrane|nucleus protein binding|protein tyrosine phosphatase activity breast(1) 1 CCTGCAGGGTGGGGGATCAGG 0.607 0.42 22 16 PLEKHA5 54477 broad.mit.edu 37 12 19514517 19514518 + Frame_Shift_Ins INS - A A SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr12:19514517_19514518insA uc001reb.2 + 23 3073_3074 c.2987_2988insA c.(2986-2988)TTAfs p.L996fs PLEKHA5_uc010sie.1_Frame_Shift_Ins_p.L1157fs|PLEKHA5_uc001rea.2_Frame_Shift_Ins_p.L1054fs|PLEKHA5_uc009zin.2_Frame_Shift_Ins_p.L754fs|PLEKHA5_uc010sif.1_Frame_Shift_Ins_p.L985fs|PLEKHA5_uc010sig.1_Frame_Shift_Ins_p.L978fs|PLEKHA5_uc010sih.1_Frame_Shift_Ins_p.L951fs|PLEKHA5_uc001rec.1_Frame_Shift_Ins_p.L805fs|PLEKHA5_uc009zio.2_Frame_Shift_Ins_p.L262fs NM_019012 NP_061885 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A 996 1-phosphatidylinositol binding|protein binding ovary(1)|kidney(1)|skin(1) 3 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) ATTCTACAGTTAAAAAAAACTG 0.248 0.42 175 128 ITPR2 3709 broad.mit.edu 37 12 26553091 26553092 + Frame_Shift_Ins INS - A A SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr12:26553091_26553092insA uc001rhg.2 - 53 7916_7917 c.7499_7500insT c.(7498-7500)GTGfs p.V2500fs ITPR2_uc009zjg.1_Frame_Shift_Ins_p.V651fs NM_002223 NP_002214 Q14571 ITPR2_HUMAN inositol 1,4,5-triphosphate receptor, type 2 2500 Extracellular (Potential). activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 14 Colorectal(261;0.0847) GCACATCCCCCACACCACCGCC 0.436 0.50 373 368 PXN 5829 broad.mit.edu 37 12 120662042 120662042 + Frame_Shift_Del DEL G - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr12:120662042delG uc001txt.2 - 2 283 c.152delC c.(151-153)CCAfs p.P51fs PXN_uc001txv.2_5'UTR|PXN_uc001txx.2_5'UTR|PXN_uc001txy.2_Frame_Shift_Del_p.P51fs|PXN_uc001txz.2_RNA NM_001080855 NP_001074324 P49023 PAXI_HUMAN paxillin isoform 1 51 Pro-rich. cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly cytoplasm|focal adhesion|lamellipodium|microtubule associated complex beta-catenin binding|vinculin binding|zinc ion binding ovary(1)|breast(1) 2 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) GGACGGGGGTGGGGGGACGGG 0.617 0.49 21 20 SACS 26278 broad.mit.edu 37 13 23914686 23914687 + Frame_Shift_Ins INS - T T SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr13:23914686_23914687insT uc001uon.2 - 10 3917_3918 c.3328_3329insA c.(3328-3330)ATTfs p.I1110fs SACS_uc001uoo.2_Frame_Shift_Ins_p.I963fs|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 1110 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) TAAGGCTTCAATTTTTTTTGCC 0.381 0.43 518 396 CDX2 1045 broad.mit.edu 37 13 28537278 28537278 + Frame_Shift_Del DEL C - - rs142861632 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr13:28537278delC uc001urv.2 - 3 1090 c.916delG c.(916-918)GTGfs p.V306fs NM_001265 NP_001256 Q99626 CDX2_HUMAN caudal type homeobox 2 306 organ morphogenesis|transcription from RNA polymerase II promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity lung(1) 1 all_cancers(110;0.191)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155) Lung SC(185;0.0156) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199) GGGTTTAGCACCCCCCCAGTT 0.627 0.44 40 31 BRCA2 675 broad.mit.edu 37 13 32913837 32913837 + Frame_Shift_Del DEL A - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr13:32913837delA uc001uub.1 + 11 5572 c.5345delA c.(5344-5346)CAAfs p.Q1782fs NM_000059 NP_000050 P51587 BRCA2_HUMAN breast cancer 2, early onset 1782 cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding p.N1784fs*7(1) ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) GTTGAAGATCAAAAAAACACT 0.318 0.48 368 341 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.56 17 22 BCL11B 64919 broad.mit.edu 37 14 99641169 99641169 + Frame_Shift_Del DEL G - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr14:99641169delG uc001yga.2 - 4 2271 c.2004delC c.(2002-2004)CTCfs p.L668fs BCL11B_uc001ygb.2_Frame_Shift_Del_p.L597fs NM_138576 NP_612808 Q9C0K0 BC11B_HUMAN B-cell CLL/lymphoma 11B isoform 1 668 nucleus zinc ion binding central_nervous_system(8)|large_intestine(1)|lung(1) 10 Melanoma(154;0.0866)|all_epithelial(191;0.241) COAD - Colon adenocarcinoma(157;0.103) 0.000 0.33 85 41 CASC5 57082 broad.mit.edu 37 15 40912892 40912893 + Frame_Shift_Ins INS - T T SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr15:40912892_40912893insT uc010bbs.1 + 11 669_670 c.508_509insT c.(508-510)ATTfs p.I170fs CASC5_uc010ucq.1_5'UTR|CASC5_uc001zme.2_Frame_Shift_Ins_p.I144fs|CASC5_uc010bbt.1_Frame_Shift_Ins_p.I144fs NM_170589 NP_733468 Q8NG31 CASC5_HUMAN cancer susceptibility candidate 5 isoform 1 170 Interaction with BUB1 and BUB1B. acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm protein binding breast(3)|central_nervous_system(1)|skin(1) 5 all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946) GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211) CCAGACAGTCATTTTTTCAGAT 0.342 0.46 354 304 CREBBP 1387 broad.mit.edu 37 16 3779211 3779211 + Frame_Shift_Del DEL G - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr16:3779211delG uc002cvv.2 - 31 6041 c.5837delC c.(5836-5838)CCAfs p.P1946fs CREBBP_uc002cvw.2_Frame_Shift_Del_p.P1908fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1946 Poly-Pro. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding p.P1946fs*30(1) haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) GGCCGGGGGTGGGGGGGCCGG 0.701 0.59 11 16 ZFHX3 463 broad.mit.edu 37 16 72821956 72821956 + Frame_Shift_Del DEL C - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr16:72821956delC uc002fck.2 - 10 10892 c.10219delG c.(10219-10221)GCTfs p.A3407fs ZFHX3_uc002fcl.2_Frame_Shift_Del_p.A2493fs NM_006885 NP_008816 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 isoform A 3407 muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation transcription factor complex enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding ovary(2)|skin(2) 4 Ovarian(137;0.13) GGGGAAGGAGCCCCGGGGGGG 0.413 0.42 30 22 PLCG2 5336 broad.mit.edu 37 16 81819650 81819651 + Frame_Shift_Del DEL AG - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr16:81819650_81819651delAG uc002fgt.2 + 2 208_209 c.56_57delAG c.(55-57)AAGfs p.K19fs PLCG2_uc010chg.1_Frame_Shift_Del_p.K19fs NM_002661 NP_002652 P16885 PLCG2_HUMAN phospholipase C, gamma 2 19 intracellular signal transduction|phospholipid catabolic process|platelet activation plasma membrane phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity large_intestine(4)|lung(2)|ovary(1)|skin(1) 8 AGCCAGATCAAGAGAGCCCTGG 0.579 0.38 399 241 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.77 6 20 ULK2 9706 broad.mit.edu 37 17 19729453 19729453 + Frame_Shift_Del DEL T - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr17:19729453delT uc002gwm.3 - 11 1343 c.834delA c.(832-834)AAAfs p.K278fs ULK2_uc002gwn.2_Frame_Shift_Del_p.K278fs NM_001142610 NP_001136082 Q8IYT8 ULK2_HUMAN unc-51-like kinase 2 278 signal transduction ATP binding|protein binding|protein serine/threonine kinase activity p.K278fs*130(2) skin(2)|large_intestine(1)|stomach(1) 4 all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186) GATACTCACATTTTTTTACTG 0.294 0.42 139 102 VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC - - rs61731354;rs73995411 byFrequency;by1000genomes SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr17:56056605_56056607delTGC uc002ivf.1 - 5 1187_1189 c.1044_1046delGCA c.(1042-1047)CAGCAA>CAA p.348_349QQ>Q VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 348_349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 ttgttgttgttgctgctgctgct 0.305 0.12 69 9 RNF43 54894 broad.mit.edu 37 17 56435161 56435161 + Frame_Shift_Del DEL C - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr17:56435161delC uc002iwf.2 - 8 3932 c.1976delG c.(1975-1977)GGTfs p.G659fs RNF43_uc010wnv.1_Frame_Shift_Del_p.G618fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.G659fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.G659fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.G532fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 659 Pro-rich.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.49 142 135 RNF43 54894 broad.mit.edu 37 17 56437565 56437566 + Frame_Shift_Del DEL CA - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr17:56437565_56437566delCA uc002iwf.2 - 7 2852_2853 c.896_897delTG c.(895-897)GTGfs p.V299fs RNF43_uc010wnv.1_Frame_Shift_Del_p.V258fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.V299fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.V299fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.V172fs NM_017763 NP_060233 Q68DV7 RNF43_HUMAN ring finger protein 43 precursor 299 RING-type; atypical.|Cytoplasmic (Potential). endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding ovary(1) 1 Medulloblastoma(34;0.127)|all_neural(34;0.237) 0.000 0.49 339 322 LAMA1 284217 broad.mit.edu 37 18 7013879 7013879 + Frame_Shift_Del DEL C - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr18:7013879delC uc002knm.2 - 23 3392 c.3298delG c.(3298-3300)GACfs p.D1100fs LAMA1_uc010wzj.1_Frame_Shift_Del_p.D576fs NM_005559 NP_005550 P25391 LAMA1_HUMAN laminin, alpha 1 precursor 1100 Laminin EGF-like 13. axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development extracellular space|laminin-1 complex|laminin-3 complex extracellular matrix structural constituent|receptor binding ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1) 21 Colorectal(10;0.172) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) TTGCAGGCGTCCCCCGACGTC 0.582 0.52 73 78 ATP8B1 5205 broad.mit.edu 37 18 55365040 55365040 + Frame_Shift_Del DEL T - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr18:55365040delT uc002lgw.2 - 6 614 c.614delA c.(613-615)AATfs p.N205fs uc002lgv.1_Intron NM_005603 NP_005594 O43520 AT8B1_HUMAN ATPase, class I, type 8B, member 1 205 Cytoplasmic (Potential). ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent apical plasma membrane|integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity breast(5)|ovary(2)|central_nervous_system(2)|lung(1) 10 Colorectal(73;0.229) AACAAAATCATTTTTTTTCAG 0.388 0.82 16 74 MAP2K7 5609 broad.mit.edu 37 19 7976434 7976434 + Frame_Shift_Del DEL G - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr19:7976434delG uc002mit.2 + 9 1115 c.1050delG c.(1048-1050)TCGfs p.S350fs MAP2K7_uc002miv.2_Frame_Shift_Del_p.S357fs|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_Frame_Shift_Del_p.S357fs|MAP2K7_uc010dvv.2_Frame_Shift_Del_p.S225fs NM_145185 NP_660186 O14733 MP2K7_HUMAN mitogen-activated protein kinase kinase 7 350 Protein kinase. activation of JUN kinase activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleus ATP binding|JUN kinase kinase activity|magnesium ion binding|protein binding|protein kinase binding|protein phosphatase binding|protein serine/threonine kinase activity|protein tyrosine kinase activity large_intestine(7)|central_nervous_system(2)|ovary(1)|lung(1) 11 Etoposide(DB00773) TGGGCTTCTCGGGGGACTTCC 0.597 0.51 53 56 FBN3 84467 broad.mit.edu 37 19 8171075 8171075 + Frame_Shift_Del DEL C - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr19:8171075delC uc002mjf.2 - 37 4751 c.4730delG c.(4729-4731)GGTfs p.G1577fs NM_032447 NP_115823 Q75N90 FBN3_HUMAN fibrillin 3 precursor 1577 EGF-like 24; calcium-binding. proteinaceous extracellular matrix calcium ion binding|extracellular matrix structural constituent ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1) 11 GACGCAGTCACCCCCCTGACA 0.567 0.39 35 22 BRD4 23476 broad.mit.edu 37 19 15366939 15366939 + Frame_Shift_Del DEL T - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr19:15366939delT uc002nar.2 - 9 1909 c.1687delA c.(1687-1689)AGCfs p.S563fs BRD4_uc002nas.2_Frame_Shift_Del_p.S563fs|BRD4_uc002nat.3_Frame_Shift_Del_p.S563fs|BRD4_uc002nau.3_Frame_Shift_Del_p.S563fs NM_058243 NP_490597 O60885 BRD4_HUMAN bromodomain-containing protein 4 isoform long 563 Lys-rich. interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle condensed nuclear chromosome|cytoplasm protein binding ovary(2) 2 OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18) ttggctttgctttttttattc 0.189 0.47 671 601 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.44 74 58 LMTK3 114783 broad.mit.edu 37 19 49002846 49002846 + Frame_Shift_Del DEL C - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr19:49002846delC uc002pjk.2 - 12 1567 c.1567delG c.(1567-1569)GCAfs p.A523fs NM_001080434 NP_001073903 lemur tyrosine kinase 3 lung(5)|central_nervous_system(1) 6 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231) 0.000 0.37 375 217 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.47 8 7 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 334 68 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 63 580 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 18 340 TIMP3 7078 broad.mit.edu 37 22 33255323 33255324 + Frame_Shift_Ins INS - C C SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr22:33255323_33255324insC uc003anb.2 + 5 1781_1782 c.595_596insC c.(595-597)GCCfs p.A199fs SYN3_uc003amx.2_Intron|SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron NM_000362 NP_000353 P35625 TIMP3_HUMAN tissue inhibitor of metalloproteinase 3 199 negative regulation of membrane protein ectodomain proteolysis|visual perception metal ion binding|metalloendopeptidase inhibitor activity|protein binding lung(1) 1 CCGAGGATGGGCCCCCCCGGAT 0.604 0.37 82 49 EP300 2033 broad.mit.edu 37 22 41566525 41566525 + Frame_Shift_Del DEL A - - SW48_LARGE_INTESTINE NA SW48_LARGE_INTESTINE NA g.chr22:41566525delA uc003azl.3 + 27 4797 c.4402delA c.(4402-4404)AAAfs p.K1468fs NM_001429 NP_001420 Q09472 EP300_HUMAN E1A binding protein p300 1468 apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia centrosome|histone acetyltransferase complex androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding p.M1470fs*3(3) haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1) 64 GGAATGGTACAAAAAAATGCT 0.473 0.42 402 290 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW579_THYROID NA SW579_THYROID NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 5 79 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SW579_THYROID NA SW579_THYROID NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.42 230 165 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes SW579_THYROID NA SW579_THYROID NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.35 13 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SW579_THYROID NA SW579_THYROID NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.34 19 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SW579_THYROID NA SW579_THYROID NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 34 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW579_THYROID NA SW579_THYROID NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.56 112 141 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW579_THYROID NA SW579_THYROID NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 24 48 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SW579_THYROID NA SW579_THYROID NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SW579_THYROID NA SW579_THYROID NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 57 SMARCA2 6595 broad.mit.edu 37 9 2039776 2039777 + In_Frame_Ins INS - CAG CAG rs13296987;rs113070757 byFrequency SW579_THYROID NA SW579_THYROID NA g.chr9:2039776_2039777insCAG uc003zhc.2 + 4 765_766 c.666_667insCAG c.(664-669)insCAG p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.27 553 206 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867540 + In_Frame_Del DEL GGC - - SW579_THYROID NA SW579_THYROID NA g.chr9:101867538_101867540delGGC uc004azc.2 + 1 127_129 c.51_53delGGC c.(49-54)CTGGCG>CTG p.A26del TGFBR1_uc004azd.2_In_Frame_Del_p.A26del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 63 7 CDK9 1025 broad.mit.edu 37 9 130550838 130550839 + Frame_Shift_Ins INS - C C SW579_THYROID NA SW579_THYROID NA g.chr9:130550838_130550839insC uc004bse.2 + 6 743_744 c.620_621insC c.(619-621)GGCfs p.G207fs NM_001261 NP_001252 P50750 CDK9_HUMAN cyclin-dependent kinase 9 207 Protein kinase. cell proliferation|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction transcription elongation factor complex ATP binding|cyclin-dependent protein kinase activity|DNA binding|protein binding|RNA polymerase II carboxy-terminal domain kinase activity lung(1) 1 0.000 0.19 853 202 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW579_THYROID NA SW579_THYROID NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 740 293 BMP4 652 broad.mit.edu 37 14 54417128 54417128 + Frame_Shift_Del DEL G - - SW579_THYROID NA SW579_THYROID NA g.chr14:54417128delG uc001xal.3 - 3 1036 c.849delC c.(847-849)GCCfs p.A283fs BMP4_uc010aoh.2_Frame_Shift_Del_p.A283fs|BMP4_uc001xao.3_Frame_Shift_Del_p.A283fs|BMP4_uc001xan.3_Frame_Shift_Del_p.A283fs NM_130851 NP_570912 P12644 BMP4_HUMAN bone morphogenetic protein 4 preproprotein 283 activation of MAPKK activity|blood vessel endothelial cell proliferation involved in sprouting angiogenesis|BMP signaling pathway involved in heart induction|BMP signaling pathway involved in nephric duct formation|branching involved in ureteric bud morphogenesis|bronchus development|bud dilation involved in lung branching|cardiac septum development|cartilage development|endocardial cushion development|epithelial cell proliferation involved in lung morphogenesis|intermediate mesodermal cell differentiation|lung alveolus development|lymphoid progenitor cell differentiation|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway|negative regulation of branching involved in ureteric bud morphogenesis|negative regulation of cell proliferation involved in heart morphogenesis|negative regulation of glomerular mesangial cell proliferation|negative regulation of glomerulus development|negative regulation of immature T cell proliferation in thymus|negative regulation of MAP kinase activity|negative regulation of metanephric comma-shaped body morphogenesis|negative regulation of metanephric S-shaped body morphogenesis|negative regulation of mitosis|negative regulation of myoblast differentiation|negative regulation of phosphorylation|negative regulation of striated muscle tissue development|negative regulation of thymocyte apoptosis|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of apoptosis|positive regulation of bone mineralization|positive regulation of cardiac muscle fiber development|positive regulation of cartilage development|positive regulation of collagen biosynthetic process|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of kidney development|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|protein localization to nucleus|pulmonary artery endothelial tube morphogenesis|secondary heart field specification|SMAD protein signal transduction|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway|steroid hormone mediated signaling pathway extracellular space|proteinaceous extracellular matrix BMP receptor binding|chemoattractant activity|cytokine activity|growth factor activity 0 GTCGGGTCAAGGCATGGCCCC 0.612 0.22 89 25 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes SW579_THYROID NA SW579_THYROID NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.20 132 32 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SW579_THYROID NA SW579_THYROID NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 11 92 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SW579_THYROID NA SW579_THYROID NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.44 110 86 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SW579_THYROID NA SW579_THYROID NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.19 91 21 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW579_THYROID NA SW579_THYROID NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.39 457 289 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW579_THYROID NA SW579_THYROID NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 9 131 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 30 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.29 157 63 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.39 11 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.34 23 12 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.80 10 39 ADAMTS2 9509 broad.mit.edu 37 5 178557071 178557071 + Frame_Shift_Del DEL G - - SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chr5:178557071delG uc003mjw.2 - 16 2319 c.2319delC c.(2317-2319)TTCfs p.F773fs NM_014244 NP_055059 O95450 ATS2_HUMAN ADAM metallopeptidase with thrombospondin type 1 773 Spacer. collagen catabolic process proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding large_intestine(1)|lung(1)|ovary(1)|pancreas(1) 4 all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326) all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GBM - Glioblastoma multiforme(465;0.0473) CATTTAAGATGAACTTGCCTG 0.567 0.47 47 42 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.88 3 21 PRKDC 5591 broad.mit.edu 37 8 48732062 48732097 + Splice_Site DEL TAGAATAATTCTTAAAAAAAAAAAAAAAAAAAAAGG - - rs11311765;rs71762282;rs79167773;rs34345612 SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chr8:48732062_48732097delTAGAATAATTCTTAAAAAAAAAAAAAAAAAAAAAGG uc003xqi.2 - 68 9394 c.9337_splice c.e68-1 p.N3113_splice PRKDC_uc003xqj.2_Splice_Site_p.N3113_splice|PRKDC_uc011ldh.1_Intron NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) 0.000 0.18 54 12 MYST4 23522 broad.mit.edu 37 10 76781905 76781906 + In_Frame_Ins INS - GAA GAA rs138589645;rs111976843 by1000genomes SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chr10:76781905_76781906insGAA uc001jwn.1 + 16 3781_3782 c.3288_3289insGAA c.(3286-3291)insGAA p.1104_1105insE MYST4_uc001jwm.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwo.1_In_Frame_Ins_p.812_813insE|MYST4_uc001jwp.1_In_Frame_Ins_p.921_922insE NM_012330 NP_036462 Q8WYB5 MYST4_HUMAN MYST histone acetyltransferase (monocytic 1104_1105 histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1) 16 all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964) aggaagaagaggaagaagaaga 0.203 0.66 41 78 FADD 8772 broad.mit.edu 37 11 70049816 70049817 + Frame_Shift_Ins INS - G G SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chr11:70049816_70049817insG uc001opm.2 + 1 548_549 c.251_252insG c.(250-252)GCGfs p.A84fs NM_003824 NP_003815 Q13158 FADD_HUMAN Fas-associated via death domain 84 activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction cytosol death receptor binding|identical protein binding ovary(1)|lung(1)|pancreas(1) 3 Esophageal squamous(2;1.19e-45) LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) 0.000 0.10 772 82 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.13 122 18 RHPN2 85415 broad.mit.edu 37 19 33535248 33535251 + Frame_Shift_Del DEL GTTT - - SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chr19:33535248_33535251delGTTT uc002nuf.2 - 2 155_158 c.89_92delAAAC c.(88-93)CAAACCfs p.Q30fs RHPN2_uc010xro.1_5'UTR NM_033103 NP_149094 Q8IUC4 RHPN2_HUMAN rhophilin, Rho GTPase binding protein 2 30_31 signal transduction perinuclear region of cytoplasm protein binding central_nervous_system(5)|ovary(1) 6 Esophageal squamous(110;0.137) ACTCCGGCCGGTTTGTGCAAGGGG 0.466 0.91 8 82 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 104 305 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW620_LARGE_INTESTINE NA SW620_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 47 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 3 96 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.38 24 15 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.41 13 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.69 63 142 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.64 29 51 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.55 5 6 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.88 2 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 52 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 260 28 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.50 13 13 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.35 700 382 NAV3 89795 broad.mit.edu 37 12 78400368 78400372 + Frame_Shift_Del DEL AAAGC - - SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr12:78400368_78400372delAAAGC uc001syp.2 + 8 1223_1227 c.1050_1054delAAAGC c.(1048-1056)GTAAAGCAGfs p.V350fs NAV3_uc001syo.2_Frame_Shift_Del_p.V350fs NM_014903 NP_055718 Q8IVL0 NAV3_HUMAN neuron navigator 3 350_352 nuclear outer membrane ATP binding|nucleoside-triphosphatase activity large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 17 TGTTGACTGTAAAGCAGTCAAGTAC 0.546 0.42 220 161 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.24 97 30 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.65 23 43 CREBBP 1387 broad.mit.edu 37 16 3781324 3781326 + In_Frame_Del DEL AGG - - SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr16:3781324_3781326delAGG uc002cvv.2 - 30 5243_5245 c.5039_5041delCCT c.(5038-5043)TCCTTG>TTG p.S1680del CREBBP_uc002cvw.2_In_Frame_Del_p.S1642del NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1680 Interaction with TRERF1. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) GAGCGGCGCAAGGAGGAGAACTC 0.645 0.86 5 31 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.29 32 13 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.30 145 61 RUNX1 861 broad.mit.edu 37 21 36171636 36171637 + Frame_Shift_Ins INS - TGCC TGCC SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr21:36171636_36171637insTGCC uc002yuh.2 - 5 2425_2426 c.847_848insGGCA c.(847-849)ATGfs p.M283fs RUNX1_uc002yui.2_Frame_Shift_Ins_p.M219fs|RUNX1_uc010gmu.2_Frame_Shift_Ins_p.M310fs|RUNX1_uc010gmv.2_Frame_Shift_Ins_p.M310fs|RUNX1_uc002yuj.3_Frame_Shift_Ins_p.M178fs|RUNX1_uc002yuk.3_Frame_Shift_Ins_p.M310fs|RUNX1_uc002yul.1_Frame_Shift_Ins_p.M75fs|RUNX1_uc002yum.1_Frame_Shift_Ins_p.M114fs NM_001001890 NP_001001890 Q01196 RUNX1_HUMAN runt-related transcription factor 1 isoform 283 Pro/Ser/Thr-rich. Missing: No DNA-binding. myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent nucleus|nucleus ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1) 387 0.000 0.31 615 277 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 50 674 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW780_URINARY_TRACT NA SW780_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 6 64 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW837_LARGE_INTESTINE NA SW837_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 32 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 SW837_LARGE_INTESTINE NA SW837_LARGE_INTESTINE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.45 12 10 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A SW837_LARGE_INTESTINE NA SW837_LARGE_INTESTINE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 38 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 SW837_LARGE_INTESTINE NA SW837_LARGE_INTESTINE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.62 11 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW837_LARGE_INTESTINE NA SW837_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 102 141 FBXW7 55294 broad.mit.edu 37 4 153250851 153250852 + Frame_Shift_Ins INS - A A SW837_LARGE_INTESTINE NA SW837_LARGE_INTESTINE NA g.chr4:153250851_153250852insA uc003ims.2 - 8 1357_1358 c.1208_1209insT c.(1207-1209)TTAfs p.L403fs FBXW7_uc011cii.1_Frame_Shift_Ins_p.L403fs|FBXW7_uc003imt.2_Frame_Shift_Ins_p.L403fs|FBXW7_uc011cih.1_Frame_Shift_Ins_p.L227fs|FBXW7_uc003imq.2_Frame_Shift_Ins_p.L323fs|FBXW7_uc003imr.2_Frame_Shift_Ins_p.L285fs NM_033632 NP_361014 Q969H0 FBXW7_HUMAN F-box and WD repeat domain containing 7 isoform 403 WD 1. interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex protein binding|protein binding p.L403fs*34(2) haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1) 308 all_hematologic(180;0.093) Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067) ACCAAACTTTTAAAGTGTTGTC 0.361 0.98 1 42 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW837_LARGE_INTESTINE NA SW837_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.79 11 41 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes SW837_LARGE_INTESTINE NA SW837_LARGE_INTESTINE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.35 11 6 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SW837_LARGE_INTESTINE NA SW837_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.93 4 55 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SW837_LARGE_INTESTINE NA SW837_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 19 232 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 SW837_LARGE_INTESTINE NA SW837_LARGE_INTESTINE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.35 32 17 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW837_LARGE_INTESTINE NA SW837_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 43 294 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW837_LARGE_INTESTINE NA SW837_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 9 194 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW900_LUNG NA SW900_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 32 KIT 3815 broad.mit.edu 37 4 55594062 55594062 + Frame_Shift_Del DEL G - - rs148853099 by1000genomes SW900_LUNG NA SW900_LUNG NA g.chr4:55594062delG uc010igr.2 + 12 1935 c.1848delG c.(1846-1848)GCGfs p.A616fs KIT_uc010igs.2_Frame_Shift_Del_p.A612fs|KIT_uc010igt.1_Frame_Shift_Del_p.A65fs NM_000222 NP_000213 P10721 KIT_HUMAN v-kit Hardy-Zuckerman 4 feline sarcoma viral 616 Protein kinase.|Cytoplasmic (Potential). male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway extracellular space|integral to membrane ATP binding|protein binding|receptor signaling protein tyrosine kinase activity soft_tissue(3273)|haematopoietic_and_lymphoid_tissue(1572)|skin(99)|testis(49)|bone(21)|genital_tract(18)|kidney(17)|ovary(16)|salivary_gland(15)|large_intestine(11)|thymus(6)|lung(6)|central_nervous_system(4)|NS(3)|eye(2)|endometrium(2)|breast(1)|stomach(1)|autonomic_ganglia(1)|pancreas(1) 5118 all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101) LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209) Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171) Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268) AGTCAGATGCGGCCATGACTG 0.468 0.41 34 24 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW900_LUNG NA SW900_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 76 107 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW900_LUNG NA SW900_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 31 62 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 SW900_LUNG NA SW900_LUNG NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.54 6 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes SW900_LUNG NA SW900_LUNG NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.87 3 20 TRPS1 7227 broad.mit.edu 37 8 116426599 116426600 + Frame_Shift_Ins INS - A A SW900_LUNG NA SW900_LUNG NA g.chr8:116426599_116426600insA uc003ynz.2 - 6 3956_3957 c.3497_3498insT c.(3496-3498)TTGfs p.L1166fs TRPS1_uc011lhy.1_Frame_Shift_Ins_p.L1170fs|TRPS1_uc003yny.2_Frame_Shift_Ins_p.L1179fs|TRPS1_uc010mcy.2_Frame_Shift_Ins_p.L1166fs NM_014112 NP_054831 Q9UHF7 TRPS1_HUMAN zinc finger transcription factor TRPS1 1166 Transcriptional repressor domain (By similarity).|Mediates interaction with RNF4 (By similarity). negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1) 7 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) GCTTGATCGCCAAATCTAGAGG 0.465 0.59 95 139 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SW900_LUNG NA SW900_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 38 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency SW900_LUNG NA SW900_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.19 95 22 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 SW900_LUNG NA SW900_LUNG NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.26 20 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SW900_LUNG NA SW900_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 1.00 0 18 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SW900_LUNG NA SW900_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.75 58 170 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW900_LUNG NA SW900_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 34 277 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW900_LUNG NA SW900_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 80 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 1 21 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.46 7 6 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.54 31 37 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.56 8 10 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.33 27 13 PRKDC 5591 broad.mit.edu 37 8 48815175 48815175 + Frame_Shift_Del DEL T - - SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr8:48815175delT uc003xqi.2 - 27 3280 c.3223delA c.(3223-3225)AGGfs p.R1075fs PRKDC_uc003xqj.2_Frame_Shift_Del_p.R1075fs|PRKDC_uc011ldh.1_Frame_Shift_Del_p.R1075fs NM_006904 NP_008835 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic 1075 cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3) 34 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) GCTCCCAGCCTCTTGAAAGCA 0.428 0.23 50 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 21 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 114 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 211 84 CIT 11113 broad.mit.edu 37 12 120190054 120190055 + Splice_Site INS - GA GA rs141931278 by1000genomes SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr12:120190054_120190055insGA uc001txi.1 - 22 2634 c.2581_splice c.e22-1 p.V861_splice CIT_uc001txh.1_Splice_Site_p.V395_splice|CIT_uc001txj.1_Splice_Site_p.V903_splice NM_007174 NP_009105 O14578 CTRO_HUMAN citron intracellular signal transduction ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1) 10 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) Myeloproliferative disorder(1001;0.0255) BRCA - Breast invasive adenocarcinoma(302;0.211) TAGACTGACCTgagacagagag 0.460 0.19 39 9 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 6 81 TP53 7157 broad.mit.edu 37 17 7579336 7579336 + Frame_Shift_Del DEL C - - SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr17:7579336delC uc002gim.2 - 4 545 c.351delG c.(349-351)GGGfs p.G117fs TP53_uc002gig.1_Frame_Shift_Del_p.G117fs|TP53_uc002gih.2_Frame_Shift_Del_p.G117fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.G117fs|TP53_uc010cni.1_Frame_Shift_Del_p.G117fs|TP53_uc002gij.2_Frame_Shift_Del_p.G117fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Del_p.G78fs|TP53_uc010cnk.1_Frame_Shift_Del_p.G132fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 117 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). G -> E (in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(7)|p.G59fs*23(3)|p.G117E(2)|p.V73fs*9(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.T118fs*27(1)|p.H115fs*27(1)|p.T118fs*6(1)|p.Y107fs*44(1)|p.G117R(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.T118fs*5(1)|p.T118fs*31(1)|p.L114fs*30(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) 0.000 0.98 22 1157 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.38 31 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.81 96 408 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 SW948_LARGE_INTESTINE NA SW948_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 2 31 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 T173_BONE NA T173_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 5 35 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 T173_BONE NA T173_BONE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.25 24 8 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A T173_BONE NA T173_BONE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.11 85 10 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 T173_BONE NA T173_BONE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.16 36 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 T173_BONE NA T173_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.30 73 31 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 T173_BONE NA T173_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.67 17 35 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 T173_BONE NA T173_BONE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.37 204 118 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 T173_BONE NA T173_BONE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.29 45 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 T173_BONE NA T173_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.89 2 16 CDC42BPG 55561 broad.mit.edu 37 11 64591973 64591973 + Frame_Shift_Del DEL A - - T173_BONE NA T173_BONE NA g.chr11:64591973delA uc001obs.3 - 37 4628 c.4628delT c.(4627-4629)CTAfs p.L1543fs NM_017525 NP_059995 Q6DT37 MRCKG_HUMAN CDC42 binding protein kinase gamma (DMPK-like) 1543 actin cytoskeleton reorganization|intracellular signal transduction cell leading edge|centrosome ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity lung(3)|central_nervous_system(1) 4 TTCAGGGGATAGGGGGAGGCT 0.562 0.53 23 26 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 T173_BONE NA T173_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 127 31 IRAK3 11213 broad.mit.edu 37 12 66641621 66641621 + Frame_Shift_Del DEL C - - T173_BONE NA T173_BONE NA g.chr12:66641621delC uc001sth.2 + 12 1563 c.1461delC c.(1459-1461)AACfs p.N487fs IRAK3_uc010ssy.1_Frame_Shift_Del_p.N426fs NM_007199 NP_009130 Q9Y616 IRAK3_HUMAN interleukin-1 receptor-associated kinase 3 487 interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|negative regulation of innate immune response|negative regulation of interleukin-12 production|negative regulation of interleukin-6 production|negative regulation of macrophage cytokine production|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein catabolic process|negative regulation of protein complex disassembly|negative regulation of toll-like receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of macrophage tolerance induction|positive regulation of NF-kappaB transcription factor activity|response to exogenous dsRNA|response to lipopolysaccharide|response to peptidoglycan cytoplasm|nucleus ATP binding|magnesium ion binding|protein heterodimerization activity|protein homodimerization activity|protein serine/threonine kinase activity lung(3)|ovary(2)|breast(2)|central_nervous_system(1) 8 GBM - Glioblastoma multiforme(28;0.0203) GCCAGAATAACAATTTACTAC 0.428 0.42 119 87 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C T173_BONE NA T173_BONE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 12 149 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 T173_BONE NA T173_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.58 22 30 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 T173_BONE NA T173_BONE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.20 99 25 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 T173_BONE NA T173_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 78 492 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 T173_BONE NA T173_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 67 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 T3M10_LUNG NA T3M10_LUNG NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 42 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - T3M10_LUNG NA T3M10_LUNG NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.20 234 59 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 T3M10_LUNG NA T3M10_LUNG NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.18 31 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 T3M10_LUNG NA T3M10_LUNG NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.42 53 38 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 T3M10_LUNG NA T3M10_LUNG NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.43 37 28 ADAMTS2 9509 broad.mit.edu 37 5 178559294 178559295 + Frame_Shift_Ins INS - AA AA T3M10_LUNG NA T3M10_LUNG NA g.chr5:178559294_178559295insAA uc003mjw.2 - 15 2226_2227 c.2226_2227insTT c.(2224-2229)TTTGAGfs p.F742fs NM_014244 NP_055059 O95450 ATS2_HUMAN ADAM metallopeptidase with thrombospondin type 1 742_743 Spacer. collagen catabolic process proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding large_intestine(1)|lung(1)|ovary(1)|pancreas(1) 4 all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326) all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GBM - Glioblastoma multiforme(465;0.0473) GCAGGGATCTCAAACATCTTGA 0.535 0.42 84 60 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 T3M10_LUNG NA T3M10_LUNG NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 12 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency T3M10_LUNG NA T3M10_LUNG NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.38 1025 630 SLC3A2 6520 broad.mit.edu 37 11 62623813 62623813 + Frame_Shift_Del DEL G - - T3M10_LUNG NA T3M10_LUNG NA g.chr11:62623813delG uc001nwd.2 + 1 296 c.72delG c.(70-72)TCGfs p.S24fs SLC3A2_uc001nwb.2_Frame_Shift_Del_p.S24fs|SLC3A2_uc001nwc.2_Frame_Shift_Del_p.S24fs|SLC3A2_uc001nwe.2_Frame_Shift_Del_p.S24fs|SLC3A2_uc001nwf.2_Frame_Shift_Del_p.S24fs|SNHG1_uc001nvp.2_5'Flank|SNHG1_uc001nvo.2_5'Flank|SNHG1_uc001nvq.2_5'Flank|SNHG1_uc001nvs.2_5'Flank|SNHG1_uc001nvr.2_5'Flank|SNHG1_uc001nvt.2_5'Flank|SNHG1_uc001nvu.2_5'Flank|SNORD31_uc009yoj.1_5'Flank|SNORD30_uc001nvw.1_5'Flank|SNORD29_uc001nvx.2_5'Flank|SNORD28_uc001nvy.1_5'Flank|SNORD27_uc001nvz.2_5'Flank|SNORD26_uc009yok.1_5'Flank|SNORD25_uc001nwa.3_5'Flank NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c 24 blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.23 1678 494 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 T3M10_LUNG NA T3M10_LUNG NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 181 49 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 T3M10_LUNG NA T3M10_LUNG NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.59 7 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C T3M10_LUNG NA T3M10_LUNG NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 29 269 STK11 6794 broad.mit.edu 37 19 1207077 1207077 + Frame_Shift_Del DEL G - - T3M10_LUNG NA T3M10_LUNG NA g.chr19:1207077delG uc002lrl.1 + 1 1280 c.165delG c.(163-165)CTGfs p.L55fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 55 ATP (By similarity).|Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.E57fs*7(4)|p.?(3)|p.G56fs*107(1)|p.G52_P179del(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) 0.000 0.99 37 2770 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 T3M10_LUNG NA T3M10_LUNG NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.32 21 10 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 T3M10_LUNG NA T3M10_LUNG NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 246 832 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 T3M10_LUNG NA T3M10_LUNG NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 2 35 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 T3M4_PANCREAS NA T3M4_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 4 49 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - T3M4_PANCREAS NA T3M4_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.30 1294 552 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 T3M4_PANCREAS NA T3M4_PANCREAS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.16 87 16 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A T3M4_PANCREAS NA T3M4_PANCREAS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 339 71 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 T3M4_PANCREAS NA T3M4_PANCREAS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.18 82 18 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 T3M4_PANCREAS NA T3M4_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 263 149 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 T3M4_PANCREAS NA T3M4_PANCREAS NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.19 34 8 PTK7 5754 broad.mit.edu 37 6 43109757 43109758 + Frame_Shift_Ins INS - A A T3M4_PANCREAS NA T3M4_PANCREAS NA g.chr6:43109757_43109758insA uc003oub.1 + 12 2055_2056 c.1857_1858insA c.(1855-1860)CCCAAGfs p.P619fs PTK7_uc003ouc.1_Frame_Shift_Ins_p.P619fs|PTK7_uc003oud.1_Frame_Shift_Ins_p.P579fs|PTK7_uc003oue.1_Frame_Shift_Ins_p.P489fs|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Frame_Shift_Ins_p.P627fs|PTK7_uc010jyj.1_Intron NM_002821 NP_002812 Q13308 PTK7_HUMAN PTK7 protein tyrosine kinase 7 isoform a 619_620 Ig-like C2-type 7.|Extracellular (Potential). actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration cell-cell junction|integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ovary(2)|large_intestine(1) 3 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423) AGGGGGACCCCAAGCCGCTGAT 0.599 0.13 198 29 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency T3M4_PANCREAS NA T3M4_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.58 208 282 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 T3M4_PANCREAS NA T3M4_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 450 75 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 T3M4_PANCREAS NA T3M4_PANCREAS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.64 5 9 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 T3M4_PANCREAS NA T3M4_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 127 328 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 T3M4_PANCREAS NA T3M4_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 10 225 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 T47D_BREAST NA T47D_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.79 6 23 SPEN 23013 broad.mit.edu 37 1 16235913 16235914 + Frame_Shift_Ins INS - A A T47D_BREAST NA T47D_BREAST NA g.chr1:16235913_16235914insA uc001axk.1 + 4 1183_1184 c.979_980insA c.(979-981)GAAfs p.E327fs SPEN_uc010obp.1_Frame_Shift_Ins_p.E286fs NM_015001 NP_055816 Q96T58 MINT_HUMAN spen homolog, transcriptional regulator 327 By similarity. interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway nucleus nucleotide binding|protein binding|RNA binding ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1) 15 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681) TTCATCTCTGGAAAAAGATGAG 0.465 0.93 15 185 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A T47D_BREAST NA T47D_BREAST NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 93 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 T47D_BREAST NA T47D_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.35 64 35 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 T47D_BREAST NA T47D_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.78 24 87 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 T47D_BREAST NA T47D_BREAST NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.13 116 17 MLLT4 4301 broad.mit.edu 37 6 168317783 168317784 + Frame_Shift_Ins INS - A A T47D_BREAST NA T47D_BREAST NA g.chr6:168317783_168317784insA uc003qwd.2 + 19 2698_2699 c.2556_2557insA c.(2554-2559)CTTACCfs p.L852fs MLLT4_uc003qwb.1_Frame_Shift_Ins_p.L837fs|MLLT4_uc003qwc.1_Frame_Shift_Ins_p.L853fs|MLLT4_uc003qwg.1_Frame_Shift_Ins_p.L162fs NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 853_854 Dilute. adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) CGACTTTGCTTACCATGGATAA 0.282 0.97 5 159 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 T47D_BREAST NA T47D_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 T47D_BREAST NA T47D_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.17 211 44 GUCY2C 2984 broad.mit.edu 37 12 14769653 14769653 + Frame_Shift_Del DEL T - - T47D_BREAST NA T47D_BREAST NA g.chr12:14769653delT uc001rcd.2 - 25 3021 c.2884delA c.(2884-2886)ATTfs p.I962fs NM_004963 NP_004954 P25092 GUC2C_HUMAN guanylate cyclase 2C precursor 962 Cytoplasmic (Potential). intracellular signal transduction|receptor guanylyl cyclase signaling pathway integral to membrane ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity ovary(4)|skin(2) 6 CTCACGTGAATTCTCAAAGCT 0.423 0.51 42 44 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 T47D_BREAST NA T47D_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 23 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 T47D_BREAST NA T47D_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.68 135 285 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 T47D_BREAST NA T47D_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 47 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 T84_LARGE_INTESTINE NA T84_LARGE_INTESTINE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.91 5 50 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - T84_LARGE_INTESTINE NA T84_LARGE_INTESTINE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.13 702 105 TTN 7273 broad.mit.edu 37 2 179478842 179478842 + Frame_Shift_Del DEL C - - T84_LARGE_INTESTINE NA T84_LARGE_INTESTINE NA g.chr2:179478842delC uc010zfg.1 - 211 41802 c.41578delG c.(41578-41580)GAAfs p.E13860fs uc002ump.1_RNA|TTN_uc010zfh.1_Frame_Shift_Del_p.E7555fs|TTN_uc010zfi.1_Frame_Shift_Del_p.E7488fs|TTN_uc010zfj.1_Frame_Shift_Del_p.E7363fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 14787 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity p.I13860V(1) ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TACATGTTTTCTGCAGCAACT 0.408 0.12 481 65 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 T84_LARGE_INTESTINE NA T84_LARGE_INTESTINE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.24 28 9 FGF2 2247 broad.mit.edu 37 4 123748258 123748259 + Frame_Shift_Ins INS - G G T84_LARGE_INTESTINE NA T84_LARGE_INTESTINE NA g.chr4:123748258_123748259insG uc003iev.1 + 1 396_397 c.328_329insG c.(328-330)CGGfs p.R110fs NM_002006 NP_001997 P09038 FGF2_HUMAN fibroblast growth factor 2 110 activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing extracellular space fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity ovary(1)|lung(1)|central_nervous_system(1) 3 Pentosan Polysulfate(DB00686) 0.000 0.11 339 41 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 T84_LARGE_INTESTINE NA T84_LARGE_INTESTINE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 90 63 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 T84_LARGE_INTESTINE NA T84_LARGE_INTESTINE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.66 23 45 APC 324 broad.mit.edu 37 5 112175755 112175755 + Frame_Shift_Del DEL A - - T84_LARGE_INTESTINE NA T84_LARGE_INTESTINE NA g.chr5:112175755delA uc010jby.2 + 16 4844 c.4464delA c.(4462-4464)TTAfs p.L1488fs APC_uc011cvt.1_Frame_Shift_Del_p.L1470fs|APC_uc003kpz.3_Frame_Shift_Del_p.L1488fs|APC_uc003kpy.3_Frame_Shift_Del_p.L1488fs|APC_uc010jbz.2_Frame_Shift_Del_p.L1205fs|APC_uc010jca.2_Frame_Shift_Del_p.L788fs NM_001127511 NP_001120983 P25054 APC_HUMAN adenomatous polyposis coli 1488 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.L1488fs*18(18)|p.L1488fs*19(16)|p.T1487fs*17(10)|p.L1488fs*26(5)|p.L1488*(3)|p.L1488fs*20(2)|p.L1488fs*23(2)|p.?(1)|p.K1454fs*3(1)|p.L1488F(1)|p.L1488fs*13(1)|p.K1192fs*3(1)|p.T1487fs*23(1)|p.L1488fs*21(1)|p.L1488fs*22(1)|p.L1488fs*25(1) large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1) 2515 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) CTGATACTTTATTACATTTTG 0.443 0.98 2 83 CDC5L 988 broad.mit.edu 37 6 44374081 44374081 + Frame_Shift_Del DEL A - - T84_LARGE_INTESTINE NA T84_LARGE_INTESTINE NA g.chr6:44374081delA uc003oxl.2 + 7 1039 c.780delA c.(778-780)AGAfs p.R260fs NM_001253 NP_001244 Q99459 CDC5L_HUMAN CDC5-like 260 Interaction with PPP1R8. cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus DNA binding|RNA binding lung(3)|ovary(1)|kidney(1)|skin(1) 6 all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208) Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536) 0.000 0.19 110 26 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - T84_LARGE_INTESTINE NA T84_LARGE_INTESTINE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.71 5 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 T84_LARGE_INTESTINE NA T84_LARGE_INTESTINE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 377 85 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 T84_LARGE_INTESTINE NA T84_LARGE_INTESTINE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.66 217 416 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 T84_LARGE_INTESTINE NA T84_LARGE_INTESTINE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 33 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 65 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.26 109 38 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.19 48 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 144 130 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.25 79 26 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.32 220 103 PKHD1 5314 broad.mit.edu 37 6 51890842 51890842 + Frame_Shift_Del DEL G - - T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr6:51890842delG uc003pah.1 - 32 4042 c.3766delC c.(3766-3768)CAGfs p.Q1256fs PKHD1_uc003pai.2_Frame_Shift_Del_p.Q1256fs NM_138694 NP_619639 P08F94 PKHD1_HUMAN fibrocystin isoform 1 1256 Extracellular (Potential).|IPT/TIG 7. cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body protein binding|receptor activity lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1) 44 Lung NSC(77;0.0605) TCGGGTATCTGGGGGGCTGGC 0.602 0.26 25 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.95 3 58 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.19 59 14 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.89 2 17 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 624 284 ZNF790 388536 broad.mit.edu 37 19 37310183 37310184 + Frame_Shift_Del DEL GA - - T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr19:37310183_37310184delGA uc002oew.2 - 5 1181_1182 c.1062_1063delTC c.(1060-1065)ACTCAGfs p.T354fs uc002oev.1_Intron NM_206894 NP_996777 Q6PG37 ZN790_HUMAN zinc finger protein 790 354_355 C2H2-type 6. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding upper_aerodigestive_tract(1)|skin(1) 2 Esophageal squamous(110;0.183) COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065) CTCTGATGCTGAGTTAGGTGTG 0.386 0.64 4 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.72 38 97 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 46 395 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 T98G_CENTRAL_NERVOUS_SYSTEM NA T98G_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 11 107 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 48 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.48 330 299 ABL2 27 broad.mit.edu 37 1 179077737 179077738 + Frame_Shift_Ins INS - G G TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:179077737_179077738insG uc001gmj.3 - 12 2951_2952 c.2664_2665insC c.(2662-2667)CCCAAGfs p.P888fs ABL2_uc010pnf.1_Frame_Shift_Ins_p.P785fs|ABL2_uc010png.1_Frame_Shift_Ins_p.P764fs|ABL2_uc010pnh.1_Frame_Shift_Ins_p.P867fs|ABL2_uc001gmg.3_Frame_Shift_Ins_p.P770fs|ABL2_uc001gmi.3_Frame_Shift_Ins_p.P873fs|ABL2_uc001gmh.3_Frame_Shift_Ins_p.P852fs|ABL2_uc010pne.1_Frame_Shift_Ins_p.P749fs NM_007314 NP_009298 P42684 ABL2_HUMAN arg tyrosine kinase isoform b 888_889 F-actin-binding (By similarity).|Pro-rich. axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction cytoskeleton|cytosol ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(8)|breast(3)|ovary(2)|central_nervous_system(1) 14 Adenosine triphosphate(DB00171)|Dasatinib(DB01254) TCTTTACCCTTGGGGGCAGCTG 0.619 0.12 257 34 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.41 13 9 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.65 15 28 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.73 140 370 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 26 79 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.77 3 10 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 22 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 37 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.18 107 23 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.93 1 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.52 557 598 DAPK3 1613 broad.mit.edu 37 19 3964934 3964946 + Frame_Shift_Del DEL CGTACTCCTTGCC - - TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:3964934_3964946delCGTACTCCTTGCC uc002lzc.1 - 2 199_211 c.106_118delGGCAAGGAGTACG c.(106-120)GGCAAGGAGTACGCAfs p.G36fs DAPK3_uc002lzd.1_Frame_Shift_Del_p.G36fs NM_001348 NP_001339 O43293 DAPK3_HUMAN death-associated protein kinase 3 36_40 Protein kinase. apoptosis|chromatin modification|induction of apoptosis|intracellular protein kinase cascade cytoplasm|PML body ATP binding|leucine zipper domain binding|protein serine/threonine kinase activity central_nervous_system(3)|lung(2)|ovary(1)|large_intestine(1) 7 Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18) AACTTGGCTGCGTACTCCTTGCCCGTGCCCTTC 0.484 0.95 6 117 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.84 45 228 RUNX1 861 broad.mit.edu 37 21 36252867 36252868 + Frame_Shift_Ins INS - C C TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:36252867_36252868insC uc002yuh.2 - 2 1991_1992 c.413_414insG c.(412-414)GGTfs p.G138fs RUNX1_uc002yui.2_Frame_Shift_Ins_p.G138fs|RUNX1_uc010gmu.2_Frame_Shift_Ins_p.G165fs|RUNX1_uc010gmv.2_Frame_Shift_Ins_p.G165fs|RUNX1_uc002yuj.3_Frame_Shift_Ins_p.G33fs|RUNX1_uc002yuk.3_Frame_Shift_Ins_p.G165fs|RUNX1_uc002yum.1_Frame_Shift_Ins_p.G33fs|RUNX1_uc010gmw.1_Frame_Shift_Ins_p.G165fs|RUNX1_uc002yuo.1_Frame_Shift_Ins_p.G138fs|RUNX1_uc002yur.1_Frame_Shift_Ins_p.G33fs NM_001001890 NP_001001890 Q01196 RUNX1_HUMAN runt-related transcription factor 1 isoform 138 Interaction with DNA.|Runt. myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent nucleus|nucleus ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding p.G165D(2)|p.G165V(2)|p.G165fs*13(1)|p.G165_R166insGG(1)|p.R166fs*47(1) haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1) 387 TTCCACTTCGACCGACAAACCT 0.431 0.19 620 144 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.66 149 293 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 10 139 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TC71_BONE NA TC71_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.44 35 27 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes TC71_BONE NA TC71_BONE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.35 15 8 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 TC71_BONE NA TC71_BONE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.64 32 58 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 TC71_BONE NA TC71_BONE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.45 27 22 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TC71_BONE NA TC71_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.68 146 305 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TC71_BONE NA TC71_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.87 24 163 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC TC71_BONE NA TC71_BONE NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.20 196 50 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 TC71_BONE NA TC71_BONE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.21 103 28 TBP 6908 broad.mit.edu 37 6 170871047 170871052 + In_Frame_Del DEL CAGCAG - - rs56241301;rs112083427 TC71_BONE NA TC71_BONE NA g.chr6:170871047_170871052delCAGCAG uc003qxt.2 + 3 455_460 c.223_228delCAGCAG c.(223-228)CAGCAGdel p.QQ93del TBP_uc003qxu.2_In_Frame_Del_p.QQ93del|TBP_uc011ehf.1_In_Frame_Del_p.QQ73del|TBP_uc011ehg.1_In_Frame_Del_p.QQ93del NM_003194 NP_003185 P20226 TBP_HUMAN TATA box binding protein 93_94 Poly-Gln. Missing. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding ovary(1) 1 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) gcaacagcaacagcagcagcagcagc 0.170 0.21 543 141 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes TC71_BONE NA TC71_BONE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 5 32 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - TC71_BONE NA TC71_BONE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.85 5 28 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 TC71_BONE NA TC71_BONE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.36 95 54 CSPP1 79848 broad.mit.edu 37 8 67986498 67986499 + Frame_Shift_Ins INS - T T TC71_BONE NA TC71_BONE NA g.chr8:67986498_67986499insT uc003xxi.2 + 2 150_151 c.119_120insT c.(118-120)AATfs p.N40fs CSPP1_uc003xxg.1_Frame_Shift_Ins_p.N40fs|CSPP1_uc003xxh.1_RNA|CSPP1_uc003xxj.2_Frame_Shift_Ins_p.N40fs NM_001077204 NP_001070672 Q1MSJ5 CSPP1_HUMAN centrosome spindle pole associated protein 1 40 Potential. centrosome|microtubule|spindle ovary(3)|breast(2) 5 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153) ATGGCTGATAATTTGGATGAAT 0.332 0.36 178 98 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TC71_BONE NA TC71_BONE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 1 31 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - TC71_BONE NA TC71_BONE NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.42 227 162 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TC71_BONE NA TC71_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.52 759 820 ZMYM2 7750 broad.mit.edu 37 13 20567995 20568006 + In_Frame_Del DEL TGGTAGAATGAA - - TC71_BONE NA TC71_BONE NA g.chr13:20567995_20568006delTGGTAGAATGAA uc001umr.2 + 4 1081_1092 c.783_794delTGGTAGAATGAA c.(781-795)CCTGGTAGAATGAAT>CCT p.GRMN262del ZMYM2_uc001umq.2_In_Frame_Del_p.GRMN175del|ZMYM2_uc001ums.2_In_Frame_Del_p.GRMN262del|ZMYM2_uc001umt.2_In_Frame_Del_p.GRMN262del|ZMYM2_uc009zzn.1_In_Frame_Del_p.GRMN197del NM_003453 NP_003444 Q9UBW7 ZMYM2_HUMAN zinc finger protein 198 262_265 regulation of transcription, DNA-dependent|transcription, DNA-dependent PML body ubiquitin conjugating enzyme binding|zinc ion binding lung(3)|ovary(2)|prostate(1) 6 all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856) CTTTTAATCCTGGTAGAATGAATGTGGCAGGA 0.373 0.33 485 243 VEZF1 7716 broad.mit.edu 37 17 56056604 56056605 + In_Frame_Ins INS - TGCTGC TGCTGC rs138088904;rs61731354 byFrequency TC71_BONE NA TC71_BONE NA g.chr17:56056604_56056605insTGCTGC uc002ivf.1 - 5 1189_1190 c.1046_1047insGCAGCA c.(1045-1047)CAA>CAGCAGCAA p.349_349Q>QQQ VEZF1_uc010dcn.1_In_Frame_Ins_p.199_199Q>QQQ NM_007146 NP_009077 Q14119 VEZF1_HUMAN zinc finger protein 161 349 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding ovary(1)|breast(1) 2 gttgttgttgttgctgctgctg 0.307 0.29 166 67 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TC71_BONE NA TC71_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.39 179 115 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TC71_BONE NA TC71_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 122 292 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TC71_BONE NA TC71_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 7 136 MN1 4330 broad.mit.edu 37 22 28195158 28195171 + Frame_Shift_Del DEL GCGCGGCCTCTTGG - - TC71_BONE NA TC71_BONE NA g.chr22:28195158_28195171delGCGCGGCCTCTTGG uc003adj.2 - 1 2316_2329 c.1361_1374delCCAAGAGGCCGCGC c.(1360-1374)GCCAAGAGGCCGCGCfs p.A454fs NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 454_458 binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 GAAAGTCGAAGCGCGGCCTCTTGGCCACGTTCAT 0.640 0.47 8 7 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 18 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.21 297 77 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 57 76 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 48 78 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.75 56 171 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.70 3 7 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 25 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.33 36 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 3 51 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.21 31 8 MAMDC4 158056 broad.mit.edu 37 9 139752643 139752644 + Frame_Shift_Ins INS - TT TT TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr9:139752643_139752644insTT uc004cjs.2 + 21 2639_2640 c.2589_2590insTT c.(2587-2592)GTGTTTfs p.V863fs MAMDC4_uc011mej.1_Frame_Shift_Ins_p.V200fs NM_206920 NP_996803 Q6UXC1 AEGP_HUMAN apical early endosomal glycoprotein precursor 942_943 MAM 5.|Extracellular (Potential). protein transport integral to membrane breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1) 7 all_cancers(76;0.0763)|all_epithelial(76;0.198) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171) 0.000 0.41 317 223 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.60 6 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 281 95 KTN1 3895 broad.mit.edu 37 14 56084768 56084770 + In_Frame_Del DEL GAG - - TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr14:56084768_56084770delGAG uc001xcb.2 + 5 1050_1052 c.748_750delGAG c.(748-750)GAGdel p.E250del KTN1_uc001xce.2_In_Frame_Del_p.E250del|KTN1_uc001xcc.2_In_Frame_Del_p.E250del|KTN1_uc001xcd.2_In_Frame_Del_p.E250del|KTN1_uc010trb.1_In_Frame_Del_p.E250del|KTN1_uc001xcf.1_In_Frame_Del_p.E250del NM_182926 NP_891556 Q86UP2 KTN1_HUMAN kinectin 1 isoform a 250 Lumenal (Potential). microtubule-based movement endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction breast(3)|ovary(2)|lung(1)|central_nervous_system(1) 7 AGATAAGAGAGAGGTTATTGATT 0.369 0.35 110 60 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 6 61 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.11 653 78 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 27 292 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TCCPAN2_PANCREAS NA TCCPAN2_PANCREAS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 6 73 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.99 2 149 FGR 2268 broad.mit.edu 37 1 27943394 27943408 + In_Frame_Del DEL ACCGAGTTGAACTGA - - rs2231877 byFrequency;by1000genomes TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr1:27943394_27943408delACCGAGTTGAACTGA uc001boj.2 - 5 788_802 c.642_656delTCAGTTCAACTCGGT c.(640-657)GTTCAGTTCAACTCGGTG>GTG p.214_219VQFNSV>V FGR_uc001boi.2_5'Flank|FGR_uc001bok.2_In_Frame_Del_p.214_219VQFNSV>V|FGR_uc001bol.2_In_Frame_Del_p.214_219VQFNSV>V|FGR_uc001bom.2_In_Frame_Del_p.214_219VQFNSV>V NM_005248 NP_005239 P09769 FGR_HUMAN proto-oncogene tyrosine-protein kinase FGR 214_219 SH2. platelet activation|response to virus cytosol ATP binding|non-membrane spanning protein tyrosine kinase activity skin(2) 2 all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419) CAGCTCCTGCACCGAGTTGAACTGAACCCGTGTGG 0.381 0.15 1075 195 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.31 1269 569 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.22 83 24 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 379 80 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 71 51 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.48 166 154 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.37 29 17 GRM3 2913 broad.mit.edu 37 7 86394589 86394590 + Frame_Shift_Del DEL GC - - TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr7:86394589_86394590delGC uc003uid.2 + 2 1227_1228 c.128_129delGC c.(127-129)GGCfs p.G43fs GRM3_uc010lef.2_Frame_Shift_Del_p.G41fs|GRM3_uc010leg.2_Intron|GRM3_uc010leh.2_Intron NM_000840 NP_000831 Q14832 GRM3_HUMAN glutamate receptor, metabotropic 3 precursor 43 Extracellular (Potential). synaptic transmission integral to plasma membrane lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1) 13 Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142) Acamprosate(DB00659)|Nicotine(DB00184) 0.000 0.11 1051 129 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.83 2 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 174 33 CHD8 57680 broad.mit.edu 37 14 21897160 21897171 + In_Frame_Del DEL CTTTGTCCTGGG - - TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr14:21897160_21897171delCTTTGTCCTGGG uc001was.1 - 3 424_435 c.330_341delCCCAGGACAAAG c.(328-342)AGCCCAGGACAAAGA>AGA p.SPGQ110del CHD8_uc001war.1_In_Frame_Del_p.SPGQ6del NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 389_392 Gln-rich. ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) TACTGAAAGTCTTTGTCCTGGGCTTTGTCCTG 0.505 0.17 575 119 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.44 35 28 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.50 8 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 232 543 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 34 320 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 TE11_OESOPHAGUS NA TE11_OESOPHAGUS NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 gctgttgctgttgctgctgctg 0.396 0.25 43 14 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.88 7 50 BRDT 676 broad.mit.edu 37 1 92428315 92428316 + Frame_Shift_Del DEL TC - - rs55806733 TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr1:92428315_92428316delTC uc001dok.3 + 2 353_354 c.4_5delTC c.(4-6)TCTfs p.S2fs BRDT_uc001dol.3_Frame_Shift_Del_p.S2fs|BRDT_uc010osz.1_Frame_Shift_Del_p.S2fs|BRDT_uc009wdf.2_Intron|BRDT_uc010ota.1_Frame_Shift_Del_p.S2fs|BRDT_uc010otb.1_Frame_Shift_Del_p.S2fs|BRDT_uc001dom.3_Frame_Shift_Del_p.S2fs NM_207189 NP_997072 Q58F21 BRDT_HUMAN testis-specific bromodomain protein 2 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein serine/threonine kinase activity|transcription coactivator activity stomach(2)|ovary(1)|lung(1) 4 all_lung(203;0.00531)|Lung NSC(277;0.0194) all cancers(265;0.0228)|Epithelial(280;0.133) GTTAAGAATGTCTCTGCCAAGT 0.376 0.36 50 28 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 64 12 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.21 33 9 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.35 79 42 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 13 36 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 16 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.71 14 34 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 16 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.11 56 7 Unknown 0 broad.mit.edu 37 9 138899253 138899254 + Frame_Shift_Ins INS - CA CA rs148058561;rs145884511 by1000genomes TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr9:138899253_138899254insCA uc011mds.1 - 1 128_129 c.95_96insTG c.(94-96)TGCfs p.C32fs Homo sapiens cDNA FLJ30516 fis, clone BRAWH2000697. ACACGCACGTGcacacagacgc 0.193 0.70 3 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 180 59 TRIM29 23650 broad.mit.edu 37 11 120008680 120008681 + Frame_Shift_Ins INS - T T TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr11:120008680_120008681insT uc001pwz.2 - 1 183_184 c.59_60insA c.(58-60)CGGfs p.R20fs TRIM29_uc001pxa.2_RNA NM_012101 NP_036233 Q14134 TRI29_HUMAN tripartite motif protein TRIM29 20 transcription from RNA polymerase II promoter cytoplasm protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1)|breast(1)|kidney(1)|skin(1) 4 Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;5.37e-06) 0.000 1.00 0 11 SRP14 6727 broad.mit.edu 37 15 40328596 40328597 + In_Frame_Ins INS - TGC TGC TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr15:40328596_40328597insTGC uc001zkq.2 - 5 420_421 c.348_349insGCA c.(346-351)insGCA p.116_117insA SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank NM_003134 NP_003125 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous 116_117 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding 0 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) gctgcggcaggtgctgctgctg 0.228 0.16 43 8 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 4 79 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.36 48 27 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 74 542 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TE125T_SOFT_TISSUE NA TE125T_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 56 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TE14_OESOPHAGUS NA TE14_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.86 3 19 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TE14_OESOPHAGUS NA TE14_OESOPHAGUS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.40 243 161 TTN 7273 broad.mit.edu 37 2 179412467 179412472 + In_Frame_Del DEL CACCAG - - TE14_OESOPHAGUS NA TE14_OESOPHAGUS NA g.chr2:179412467_179412472delCACCAG uc010zfg.1 - 288 86401_86406 c.86177_86182delCTGGTG c.(86176-86184)GCTGGTGTT>GTT p.AG28726del uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_In_Frame_Del_p.AG22421del|TTN_uc010zfi.1_In_Frame_Del_p.AG22354del|TTN_uc010zfj.1_In_Frame_Del_p.AG22229del NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 29653_29654 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AATGTTTTAACACCAGCTGTATTTTC 0.476 0.56 78 98 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 TE14_OESOPHAGUS NA TE14_OESOPHAGUS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.28 21 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TE14_OESOPHAGUS NA TE14_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.35 50 27 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TE14_OESOPHAGUS NA TE14_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.65 14 26 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 TE14_OESOPHAGUS NA TE14_OESOPHAGUS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.19 77 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TE14_OESOPHAGUS NA TE14_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 183 43 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TE14_OESOPHAGUS NA TE14_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 109 301 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TE14_OESOPHAGUS NA TE14_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.82 7 33 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.27 193 71 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.35 55 29 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 9 27 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.44 113 90 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.30 40 17 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.40 404 274 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.21 122 33 MAPK6 5597 broad.mit.edu 37 15 52338753 52338754 + Frame_Shift_Ins INS - T T TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr15:52338753_52338754insT uc002abp.2 + 2 890_891 c.96_97insT c.(94-99)GGCTTGfs p.G32fs NM_002748 NP_002739 Q16659 MK06_HUMAN mitogen-activated protein kinase 6 32_33 ATP (By similarity).|Protein kinase. cell cycle ATP binding|MAP kinase activity lung(3)|ovary(1) 4 all cancers(107;0.0028) GAGGCAATGGCTTGGTTTTTTC 0.396 0.15 39 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 11 184 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 0.94 1 16 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.57 17 23 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.19 96 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 65 715 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TE159T_SOFT_TISSUE NA TE159T_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 71 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.26 119 42 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 63 DENND4B 9909 broad.mit.edu 37 1 153907278 153907279 + In_Frame_Ins INS - CTG CTG rs141373027 by1000genomes TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr1:153907278_153907279insCTG uc001fdd.1 - 18 3131_3132 c.2730_2731insCAG c.(2728-2733)insCAG p.910_911insQ uc001fdc.1_RNA NM_014856 NP_055671 O75064 DEN4B_HUMAN DENN/MADD domain containing 4B 910_911 Gln-rich. ovary(1) 1 all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) GACACctgctcctgctgctgct 0.455 0.15 53 9 TPRXL 348825 broad.mit.edu 37 3 14106182 14106202 + In_Frame_Del DEL GCAGCAGCCCCAGTAGCAGCG - - rs72439874;rs141923761;rs114832501 by1000genomes;by1000genomes TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr3:14106182_14106202delGCAGCAGCCCCAGTAGCAGCG uc011avd.1 + 3 961_981 c.506_526delGCAGCAGCCCCAGTAGCAGCG c.(505-528)AGCAGCAGCCCCAGTAGCAGCGGC>AGC p.SSPSSSG170del TPRXL_uc003byh.1_In_Frame_Del_p.SSPSSSG170del|TPRXL_uc003byg.2_In_Frame_Del_p.SSPSSSG170del NR_002223 RecName: Full=Putative protein TPRXL; 0 agtcccagcagcagcagccccagtagcagcggcagcagccc 0.050 0.36 7 4 BMP2K 55589 broad.mit.edu 37 4 79792083 79792085 + In_Frame_Del DEL CAG - - rs35071794 TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr4:79792083_79792085delCAG uc003hlk.2 + 11 1544_1546 c.1378_1380delCAG c.(1378-1380)CAGdel p.Q486del BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.Q486del|BMP2K_uc003hll.2_5'Flank NM_198892 NP_942595 Q9NSY1 BMP2K_HUMAN BMP-2 inducible kinase isoform a 486 Gln/His-rich. Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity lung(1) 1 TCATCCTCACcagcagcagcagc 0.256 0.19 172 40 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 102 152 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 22 35 CCNB1 891 broad.mit.edu 37 5 68464105 68464116 + In_Frame_Del DEL GAGCCAGAACCT - - rs147065029 TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr5:68464105_68464116delGAGCCAGAACCT uc003jvm.2 + 3 475_486 c.298_309delGAGCCAGAACCT c.(298-309)GAGCCAGAACCTdel p.EPEP104del CCNB1_uc011crd.1_In_Frame_Del_p.EPEP104del|CCNB1_uc010ixb.2_In_Frame_Del_p.EPEP104del NM_031966 NP_114172 P14635 CCNB1_HUMAN cyclin B1 104_107 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitotic cell cycle spindle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|mitotic spindle stabilization|positive regulation of attachment of spindle microtubules to kinetochore|positive regulation of mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of cyclin-dependent protein kinase activity condensed nuclear chromosome outer kinetochore|cytosol|microtubule organizing center|nucleoplasm|spindle pole 0 Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198) OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177) gccagtgccagagccagaacctgagccagaac 0.292 0.19 88 20 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.42 7 5 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.51 18 19 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.95 1 18 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.10 317 36 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.90 6 56 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.11 86 11 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.13 97 15 PIPSL 266971 broad.mit.edu 37 10 95720202 95720202 + Frame_Shift_Del DEL C - - TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr10:95720202delC uc009xuj.2 - 1 1471 c.952delG c.(952-954)GCTfs p.A318fs NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CCCCGTCGAGCCTCTCCCTGG 0.522 0.36 97 55 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 918 195 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.55 50 62 CASC5 57082 broad.mit.edu 37 15 40939273 40939277 + Splice_Site DEL GTAAA - - TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr15:40939273_40939277delGTAAA uc010bbs.1 + 18 6333 c.6172_splice c.e18+1 p.E2058_splice CASC5_uc010bbt.1_Splice_Site_p.E2032_splice NM_170589 NP_733468 Q8NG31 CASC5_HUMAN cancer susceptibility candidate 5 isoform 1 acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm protein binding breast(3)|central_nervous_system(1)|skin(1) 5 all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946) GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211) 0.000 0.59 14 20 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.88 17 127 ERN1 2081 broad.mit.edu 37 17 62133220 62133221 + In_Frame_Ins INS - GCT GCT TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr17:62133220_62133221insGCT uc002jdz.2 - 13 1599_1600 c.1486_1487insAGC c.(1486-1488)CTG>CAGCTG p.495_496insQ NM_001433 NP_001424 O75460 ERN1_HUMAN endoplasmic reticulum to nucleus signalling 1 495_496 Cytoplasmic (Potential). activation of signaling protein activity involved in unfolded protein response|apoptosis|cell cycle arrest|induction of apoptosis|mRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent integral to endoplasmic reticulum membrane ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(4)|lung(2)|stomach(1)|ovary(1)|kidney(1) 9 GTGGAAGGGCAgctgctgctgc 0.559 0.35 28 15 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.72 53 134 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.21 108 29 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 56 308 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TE441T_SOFT_TISSUE NA TE441T_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 3 128 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 13 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.18 318 68 TTN 7273 broad.mit.edu 37 2 179575918 179575918 + Frame_Shift_Del DEL T - - TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr2:179575918delT uc010zfg.1 - 94 24537 c.24313delA c.(24313-24315)ACAfs p.T8105fs TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.T4766fs NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 9032 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AAAAATGATGTTTGTACATTT 0.433 0.17 414 82 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.32 61 29 ADAM29 11086 broad.mit.edu 37 4 175897645 175897645 + Frame_Shift_Del DEL G - - TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr4:175897645delG uc003iuc.2 + 5 1639 c.969delG c.(967-969)TTGfs p.L323fs ADAM29_uc003iud.2_Frame_Shift_Del_p.L323fs|ADAM29_uc010irr.2_Frame_Shift_Del_p.L323fs|ADAM29_uc011cki.1_Frame_Shift_Del_p.L323fs NM_014269 NP_055084 Q9UKF5 ADA29_HUMAN ADAM metallopeptidase domain 29 preproprotein 323 Peptidase M12B.|Extracellular (Potential). proteolysis|spermatogenesis integral to plasma membrane metalloendopeptidase activity|zinc ion binding skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1) 16 Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164) all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286) ACAAAACTTTGGGCACTTTTT 0.408 0.47 61 54 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.81 10 43 CAMK4 814 broad.mit.edu 37 5 110710603 110710604 + Frame_Shift_Ins INS - A A TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr5:110710603_110710604insA uc011cvj.1 + 4 395_396 c.296_297insA c.(295-297)CCAfs p.P99fs CAMK4_uc003kpf.2_Frame_Shift_Ins_p.P99fs|CAMK4_uc010jbv.2_Intron NM_001744 NP_001735 Q16566 KCC4_HUMAN calcium/calmodulin-dependent protein kinase IV 99 Protein kinase. activation of phospholipase C activity|nerve growth factor receptor signaling pathway|synaptic transmission cytosol|nucleoplasm ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity ovary(3)|lung(2) 5 all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244) OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109) CTCTCACATCCAAACATTGTAA 0.391 0.89 14 108 HMMR 3161 broad.mit.edu 37 5 162917425 162917426 + Frame_Shift_Ins INS - A A TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr5:162917425_162917426insA uc003lzf.2 + 17 2171_2172 c.1989_1990insA c.(1987-1992)GCTAAAfs p.A663fs HMMR_uc003lzh.2_Frame_Shift_Ins_p.A664fs|HMMR_uc003lzg.2_Frame_Shift_Ins_p.A648fs|HMMR_uc011dem.1_Frame_Shift_Ins_p.A577fs|uc003lzi.2_Intron NM_012484 NP_036616 O75330 HMMR_HUMAN hyaluronan-mediated motility receptor isoform b 663_664 Hyaluronic acid-binding (Potential). cell surface|cytoplasm hyaluronic acid binding 0 Renal(175;0.000281) Medulloblastoma(196;0.00853)|all_neural(177;0.0408) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848) GTCAGCTTGCTAAAAAAAAACA 0.307 0.40 32 21 TBX18 9096 broad.mit.edu 37 6 85473694 85473694 + Frame_Shift_Del DEL C - - TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr6:85473694delC uc003pkl.1 - 1 206 c.206delG c.(205-207)GGAfs p.G69fs TBX18_uc010kbq.1_5'Flank NM_001080508 NP_001073977 O95935 TBX18_HUMAN T-box 18 69 multicellular organismal development nucleus DNA binding|sequence-specific DNA binding transcription factor activity ovary(2)|pancreas(2)|lung(1) 5 all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858) BRCA - Breast invasive adenocarcinoma(108;0.0267) GCCTTCGTCTCCCTCAGAAGA 0.517 0.92 1 12 MLLT4 4301 broad.mit.edu 37 6 168297596 168297597 + Frame_Shift_Ins INS - T T TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr6:168297596_168297597insT uc003qwd.2 + 10 1400_1401 c.1258_1259insT c.(1258-1260)CTTfs p.L420fs MLLT4_uc003qwb.1_Frame_Shift_Ins_p.L405fs|MLLT4_uc003qwc.1_Frame_Shift_Ins_p.L421fs|MLLT4_uc003qwf.2_Frame_Shift_Ins_p.L106fs NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 421 adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) GCTTTACCGCCTTCAGTTAAGT 0.426 0.95 6 106 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.82 2 9 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.49 95 92 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 61 12 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.64 4 7 HSP90AB4P 664618 broad.mit.edu 37 15 58984805 58984806 + Frame_Shift_Ins INS - G G TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr15:58984805_58984806insG uc002afh.1 - 1 519_520 c.519_520insC c.(517-522)GTCAAAfs p.V173fs ADAM10_uc002afd.1_Intron|ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron|ADAM10_uc002afg.2_Intron NR_002927 RecName: Full=Putative heat shock protein HSP 90-beta 4; 0 ACTACTTCTTTGACCCACCTCT 0.401 0.47 74 65 STK11 6794 broad.mit.edu 37 19 1221314 1221314 + Frame_Shift_Del DEL C - - rs67873004 TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr19:1221314delC uc002lrl.1 + 6 1952 c.837delC c.(835-837)GGCfs p.G279fs NM_000455 NP_000446 Q15831 STK11_HUMAN serine/threonine protein kinase 11 279 Protein kinase. anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleus ATP binding|magnesium ion binding|protein serine/threonine kinase activity p.0?(19)|p.P281fs*6(2)|p.?(2)|p.Y246fs*3(1)|p.G279F(1) lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1) 266 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) GCGACTGTGGCCCCCCGCTCT 0.607 0.85 2 11 ZNF331 55422 broad.mit.edu 37 19 54080640 54080641 + Frame_Shift_Del DEL TG - - TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr19:54080640_54080641delTG uc002qbx.1 + 7 2260_2261 c.826_827delTG c.(826-828)TGTfs p.C276fs ZNF331_uc002qby.1_Frame_Shift_Del_p.C276fs|ZNF331_uc002qbz.1_Frame_Shift_Del_p.C276fs|ZNF331_uc002qca.1_Frame_Shift_Del_p.C276fs|ZNF331_uc010eqr.1_Frame_Shift_Del_p.C276fs|ZNF331_uc002qcb.1_Frame_Shift_Del_p.C276fs|ZNF331_uc002qcc.1_Frame_Shift_Del_p.C276fs|ZNF331_uc002qcd.1_Frame_Shift_Del_p.C276fs NM_018555 NP_061025 Q9NQX6 ZN331_HUMAN zinc finger protein 331 276 C2H2-type 6. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding skin(3)|upper_aerodigestive_tract(1)|ovary(1)|lung(1) 6 GBM - Glioblastoma multiforme(134;0.00555) GTGTAAAGACTGTGGGAAGGCT 0.421 0.34 19 10 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 34 186 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TE4_OESOPHAGUS NA TE4_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 72 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 2 63 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.40 284 187 ASTN1 460 broad.mit.edu 37 1 176926916 176926917 + Frame_Shift_Ins INS - A A TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr1:176926916_176926917insA uc001glc.2 - 11 1996_1997 c.1784_1785insT c.(1783-1785)TTAfs p.L595fs ASTN1_uc001glb.1_Frame_Shift_Ins_p.L595fs|ASTN1_uc001gld.1_Frame_Shift_Ins_p.L595fs|ASTN1_uc009wwx.1_Frame_Shift_Ins_p.L595fs NM_004319 NP_004310 O14525 ASTN1_HUMAN astrotactin isoform 1 603 cell migration|neuron cell-cell adhesion integral to membrane ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1) 15 CAAAGGAATCTAAGAGAACCTC 0.540 0.29 136 56 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.64 4 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.18 47 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.60 50 75 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.63 170 284 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.33 60 29 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.10 193 22 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 199 89 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 59 966 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.13 244 38 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 34 26 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 43 205 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TE5_OESOPHAGUS NA TE5_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.86 10 60 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TE617T_SOFT_TISSUE NA TE617T_SOFT_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 5 67 LRP1B 53353 broad.mit.edu 37 2 141625834 141625835 + Splice_Site INS - A A TE617T_SOFT_TISSUE NA TE617T_SOFT_TISSUE NA g.chr2:141625834_141625835insA uc002tvj.1 - 26 5142 c.4170_splice c.e26-1 p.G1390_splice LRP1B_uc010fnl.1_Splice_Site_p.G572_splice NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) AAAAGAATTCTaaaaaaaaaaa 0.223 0.23 27 8 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 TE617T_SOFT_TISSUE NA TE617T_SOFT_TISSUE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.80 2 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TE617T_SOFT_TISSUE NA TE617T_SOFT_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.50 78 79 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TE617T_SOFT_TISSUE NA TE617T_SOFT_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 15 26 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TE617T_SOFT_TISSUE NA TE617T_SOFT_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.24 297 92 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TE617T_SOFT_TISSUE NA TE617T_SOFT_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.50 267 264 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TE617T_SOFT_TISSUE NA TE617T_SOFT_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 1 50 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.86 2 12 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 419 88 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.53 14 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 50 28 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.35 31 17 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.86 2 12 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.43 8 6 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.34 59 31 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.94 1 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 136 15 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.51 26 27 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.44 98 77 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 265 1057 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TE6_OESOPHAGUS NA TE6_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 4 76 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TE8_OESOPHAGUS NA TE8_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.82 4 18 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TE8_OESOPHAGUS NA TE8_OESOPHAGUS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.19 153 37 DHFRL1 200895 broad.mit.edu 37 3 93780059 93780059 + Frame_Shift_Del DEL T - - TE8_OESOPHAGUS NA TE8_OESOPHAGUS NA g.chr3:93780059delT uc003dri.2 - 2 463 c.297delA c.(295-297)AAAfs p.K99fs DHFRL1_uc003drj.2_Frame_Shift_Del_p.K99fs|NSUN3_uc003drk.2_5'Flank|NSUN3_uc003drl.1_5'Flank NM_176815 NP_789785 Q86XF0 DYRL1_HUMAN dihydrofolate reductase-like 1 99 DHFR. glycine biosynthetic process|nucleotide biosynthetic process|one-carbon metabolic process dihydrofolate reductase activity|NADP binding 0 GTTCAGTAAGTTTTAAGGCAT 0.388 0.60 67 102 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TE8_OESOPHAGUS NA TE8_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.31 44 20 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TE8_OESOPHAGUS NA TE8_OESOPHAGUS NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.15 46 8 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency TE8_OESOPHAGUS NA TE8_OESOPHAGUS NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.65 333 609 CREBBP 1387 broad.mit.edu 37 16 3779755 3779755 + Frame_Shift_Del DEL G - - TE8_OESOPHAGUS NA TE8_OESOPHAGUS NA g.chr16:3779755delG uc002cvv.2 - 31 5497 c.5293delC c.(5293-5295)CAGfs p.Q1765fs CREBBP_uc002cvw.2_Frame_Shift_Del_p.Q1727fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1765 TAZ-type 2.|Interaction with TRERF1. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) CGTGACTCCTGGGGGCTCTTT 0.632 0.85 6 34 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C TE8_OESOPHAGUS NA TE8_OESOPHAGUS NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 48 428 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT TE8_OESOPHAGUS NA TE8_OESOPHAGUS NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.11 1010 127 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TE8_OESOPHAGUS NA TE8_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.75 118 355 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TE8_OESOPHAGUS NA TE8_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 3 53 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.65 13 24 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.36 178 101 PDE4DIP 9659 broad.mit.edu 37 1 144994676 144994677 + Frame_Shift_Ins INS - TC TC TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr1:144994676_144994677insTC uc001elw.3 - 1 346_347 c.55_56insGA c.(55-57)AACfs p.N19fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Frame_Shift_Ins_p.N19fs|PDE4DIP_uc001ell.1_Frame_Shift_Ins_p.N22fs|PDE4DIP_uc001elm.3_5'UTR|PDE4DIP_uc001eln.3_Frame_Shift_Ins_p.N85fs|PDE4DIP_uc001elo.2_Frame_Shift_Ins_p.N156fs|PDE4DIP_uc001elx.3_Frame_Shift_Ins_p.N85fs|PDE4DIP_uc001emc.1_Frame_Shift_Ins_p.N19fs|PDE4DIP_uc001emd.1_Frame_Shift_Ins_p.N19fs|PDE4DIP_uc001emg.1_Frame_Shift_Ins_p.N19fs|PDE4DIP_uc001emh.2_Frame_Shift_Ins_p.N156fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 19 cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) GAGGCTGAAGTTCTCCTTCTTC 0.579 0.14 704 117 DDR2 4921 broad.mit.edu 37 1 162745619 162745627 + In_Frame_Del DEL TGTACGCAC - - TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr1:162745619_162745627delTGTACGCAC uc001gcf.2 + 16 2499_2507 c.2034_2042delTGTACGCAC c.(2032-2043)GATGTACGCACT>GAT p.VRT679del DDR2_uc001gcg.2_In_Frame_Del_p.VRT679del NM_001014796 NP_001014796 Q16832 DDR2_HUMAN discoidin domain receptor family, member 2 679_681 Cytoplasmic (Potential).|Protein kinase. cell adhesion integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(2)|central_nervous_system(2)|ovary(1)|kidney(1) 6 all_hematologic(112;0.115) BRCA - Breast invasive adenocarcinoma(70;0.113) CCTCCAGCGATGTACGCACTGTCAGGTAA 0.478 0.23 404 119 CAMK1G 57172 broad.mit.edu 37 1 209786212 209786214 + In_Frame_Del DEL ATT - - TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr1:209786212_209786214delATT uc001hhd.2 + 12 1525_1527 c.1423_1425delATT c.(1423-1425)ATTdel p.I475del CAMK1G_uc001hhe.2_In_Frame_Del_p.I475del NM_020439 NP_065172 Q96NX5 KCC1G_HUMAN calcium/calmodulin-dependent protein kinase IG 475 Golgi membrane|plasma membrane ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity breast(1) 1 OV - Ovarian serous cystadenocarcinoma(81;0.0475) AGTCTGTCTCATTATGTGATTCC 0.537 0.84 30 153 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.28 29 11 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.31 165 75 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.58 8 11 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 144 128 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.98 13 548 SMARCA2 6595 broad.mit.edu 37 9 2039806 2039807 + In_Frame_Ins INS - CAA CAA TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr9:2039806_2039807insCAA uc003zhc.2 + 4 795_796 c.696_697insCAA c.(694-699)insCAA p.238_239insQ SMARCA2_uc003zhd.2_In_Frame_Ins_p.238_239insQ|SMARCA2_uc010mha.2_In_Frame_Ins_p.229_230insQ NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238_239 Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.23 224 66 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.82 2 9 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.25 230 78 HERC2P2 400322 broad.mit.edu 37 15 23318603 23318614 + In_Frame_Del DEL ACAGGGAGCTGC - - TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr15:23318603_23318614delACAGGGAGCTGC uc001yvr.2 - 15 2210_2221 c.2010_2021delGCAGCTCCCTGT c.(2008-2022)GTGCAGCTCCCTGTT>GTT p.670_674VQLPV>V HERC2P2_uc010ayf.1_RNA|HERC2P2_uc001yvp.3_RNA RecName: Full=Putative HERC2-like protein 3; 0 TGGCCCTGAAACAGGGAGCTGCACAGGAGCCG 0.514 0.43 30 23 FMNL1 752 broad.mit.edu 37 17 43319229 43319229 + Frame_Shift_Del DEL C - - TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr17:43319229delC uc002iin.2 + 15 1801 c.1601delC c.(1600-1602)GCAfs p.A534fs FMNL1_uc002iiq.2_Frame_Shift_Del_p.A112fs|FMNL1_uc010dag.2_RNA NM_005892 NP_005883 O95466 FMNL_HUMAN formin-like 1 534 Pro-rich. actin cytoskeleton organization actin binding|Rho GTPase binding pancreas(1) 1 0.000 0.79 3 11 MALT1 10892 broad.mit.edu 37 18 56363646 56363647 + Frame_Shift_Ins INS - G G TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr18:56363646_56363647insG uc002lhm.1 + 3 683_684 c.425_426insG c.(424-426)CAGfs p.Q142fs MALT1_uc002lhn.1_Frame_Shift_Ins_p.Q142fs NM_006785 NP_006776 Q9UDY8 MALT1_HUMAN mucosa associated lymphoid tissue lymphoma 142 Ig-like C2-type 1. activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway CBM complex|cytosol|nucleus|perinuclear region of cytoplasm cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity ovary(2)|lung(1)|central_nervous_system(1) 4 TTGGCTGGACAGTTTGTGAAAC 0.312 0.92 19 229 TRIB3 57761 broad.mit.edu 37 20 368784 368784 + Frame_Shift_Del DEL C - - TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr20:368784delC uc002wdm.2 + 2 636 c.130delC c.(130-132)CCCfs p.P44fs TRIB3_uc002wdn.2_Frame_Shift_Del_p.P71fs NM_021158 NP_066981 Q96RU7 TRIB3_HUMAN tribbles 3 44 apoptosis|cellular lipid metabolic process|insulin receptor signaling pathway|negative regulation of fat cell differentiation|negative regulation of fatty acid biosynthetic process|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein binding|positive regulation of ubiquitin-protein ligase activity|regulation of glucose transport|regulation of MAP kinase activity|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent cytosol|nucleus|plasma membrane ATP binding|protein kinase activity|protein kinase binding|protein kinase inhibitor activity|transcription corepressor activity|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity central_nervous_system(2) 2 all_epithelial(17;0.165)|Lung NSC(37;0.191)|Breast(17;0.231) Colorectal(46;0.101)|COAD - Colon adenocarcinoma(99;0.112) GCCCAGACTGCCCCCCTGCCT 0.627 0.23 30 9 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.31 42 19 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.74 53 154 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TE9_OESOPHAGUS NA TE9_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 4 47 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.93 5 71 MCF2 4168 broad.mit.edu 37 X 138711899 138711899 + Frame_Shift_Del DEL T - - TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chrX:138711899delT uc004fau.2 - 4 687 c.393delA c.(391-393)ATAfs p.I131fs MCF2_uc004fav.2_Frame_Shift_Del_p.I131fs|MCF2_uc011mwl.1_Frame_Shift_Del_p.I92fs|MCF2_uc010nsh.1_Frame_Shift_Del_p.I131fs|MCF2_uc011mwm.1_Frame_Shift_Del_p.I92fs|MCF2_uc011mwn.1_Frame_Shift_Del_p.I276fs|MCF2_uc004faw.2_Frame_Shift_Del_p.I191fs|MCF2_uc011mwo.1_Frame_Shift_Del_p.I191fs NM_005369 NP_005360 P10911 MCF2_HUMAN MCF.2 cell line derived transforming sequence 131 apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytoskeleton|cytosol|membrane|membrane fraction protein binding|Rho guanyl-nucleotide exchange factor activity lung(1)|pleura(1) 2 Acute lymphoblastic leukemia(192;0.000127) GAATTTCTTCTATTGAGGGAA 0.393 1.00 1 275 LCK 3932 broad.mit.edu 37 1 32741225 32741225 + Frame_Shift_Del DEL G - - TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr1:32741225delG uc001bux.2 + 6 571 c.433delG c.(433-435)GGGfs p.G145fs LCK_uc001buy.2_Frame_Shift_Del_p.G145fs|LCK_uc001buz.2_Frame_Shift_Del_p.G145fs|LCK_uc010ohc.1_Frame_Shift_Del_p.G189fs|LCK_uc001bva.2_Frame_Shift_Del_p.G203fs NM_005356 NP_005347 P06239 LCK_HUMAN lymphocyte-specific protein tyrosine kinase 145 SH2. activation of caspase activity|cellular zinc ion homeostasis|induction of apoptosis|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of T cell receptor signaling pathway|regulation of defense response to virus by virus|release of sequestered calcium ion into cytosol|response to drug|T cell costimulation|T cell differentiation|T cell receptor signaling pathway|viral reproduction cytosol|Golgi apparatus|membrane raft|pericentriolar material|plasma membrane ATP binding|ATPase binding|CD4 receptor binding|CD8 receptor binding|glycoprotein binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol 3-kinase binding|protein C-terminus binding|protein kinase binding|protein serine/threonine phosphatase activity|SH2 domain binding lung(3)|central_nervous_system(2)|ovary(1) 6 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212) Dasatinib(DB01254) CCTGGCGCCCGGGAACACTCA 0.716 0.68 8 17 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 1.00 0 10 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.54 11 13 HTT 3064 broad.mit.edu 37 4 3076604 3076606 + In_Frame_Del DEL CAG - - rs10618869 TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr4:3076604_3076606delCAG uc011bvq.1 + 2 203_205 c.58_60delCAG c.(58-60)CAGdel p.Q40del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagc 0.335 0.24 65 20 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.72 106 271 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.73 19 51 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.75 8 24 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.12 119 17 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.80 6 24 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.32 19 9 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.97 2 62 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCAGCAGCA GCAGCAGCA rs3832799;rs72405287 TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr12:103352171_103352172insGCAGCAGCA uc001tjr.3 + 1 720_721 c.149_150insGCAGCAGCA c.(148-150)GCG>GCGCAGCAGCAG p.62_63insQQQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.22 28 8 Unknown 0 broad.mit.edu 37 14 23574096 23574098 + In_Frame_Del DEL GCA - - TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr14:23574096_23574098delGCA uc010aki.1 - 1 80_82 c.32_34delTGC c.(31-36)CTGCCG>CCG p.L11del Homo sapiens cDNA clone IMAGE:40134016. ACTAGTGgcggcagcagcagcag 0.448 0.55 13 16 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.86 28 176 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.24 127 40 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 157 493 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TEN_ENDOMETRIUM NA TEN_ENDOMETRIUM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 11 164 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 37 PDE4DIP 9659 broad.mit.edu 37 1 144864303 144864306 + Frame_Shift_Del DEL CTTT - - TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144864303_144864306delCTTT uc001elw.3 - 36 6080_6083 c.5789_5792delAAAG c.(5788-5793)GAAAGCfs p.E1930fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E1824fs|PDE4DIP_uc001elv.3_Frame_Shift_Del_p.E937fs|PDE4DIP_uc001ema.2_Frame_Shift_Del_p.E117fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 1930_1931 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) CTCCCTCAGGCTTTCTGTTTCCTG 0.534 0.16 377 70 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.40 180 120 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.19 29 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.39 83 54 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.80 40 158 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.35 11 6 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.23 43 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.90 2 19 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.30 471 200 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.60 12 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 271 66 NAV3 89795 broad.mit.edu 37 12 78444673 78444673 + Frame_Shift_Del DEL A - - TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:78444673delA uc001syp.2 + 11 2435 c.2262delA c.(2260-2262)GGAfs p.G754fs NAV3_uc001syo.2_Frame_Shift_Del_p.G754fs|NAV3_uc010sub.1_Frame_Shift_Del_p.G254fs NM_014903 NP_055718 Q8IVL0 NAV3_HUMAN neuron navigator 3 754 nuclear outer membrane ATP binding|nucleoside-triphosphatase activity large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1) 17 TTCAGGCGGGAGATGCTCCCT 0.577 0.47 38 34 CDH3 1001 broad.mit.edu 37 16 68679613 68679614 + Frame_Shift_Ins INS - A A TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:68679613_68679614insA uc002ewf.2 + 2 1252_1253 c.120_121insA c.(118-123)GCGGGAfs p.A40fs CDH3_uc010vli.1_Intron NM_001793 NP_001784 P22223 CADH3_HUMAN cadherin 3, type 1 preproprotein 40_41 adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception integral to membrane calcium ion binding p.?(1) ovary(3)|breast(1)|skin(1) 5 Ovarian(137;0.0564) OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384) 0.000 1.00 0 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.95 2 41 TP53 7157 broad.mit.edu 37 17 7577529 7577529 + Frame_Shift_Del DEL A - - TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:7577529delA uc002gim.2 - 7 946 c.752delT c.(751-753)ATCfs p.I251fs TP53_uc002gig.1_Frame_Shift_Del_p.I251fs|TP53_uc002gih.2_Frame_Shift_Del_p.I251fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.I119fs|TP53_uc010cng.1_Frame_Shift_Del_p.I119fs|TP53_uc002gii.1_Frame_Shift_Del_p.I119fs|TP53_uc010cnh.1_Frame_Shift_Del_p.I251fs|TP53_uc010cni.1_Frame_Shift_Del_p.I251fs|TP53_uc002gij.2_Frame_Shift_Del_p.I251fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.I158fs|TP53_uc002gio.2_Frame_Shift_Del_p.I119fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 251 |Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). I -> S (in sporadic cancers; somatic mutation).|I -> V (in sporadic cancers; somatic mutation).|I -> M (in LFS; germline mutation).|I -> F (in sporadic cancers; somatic mutation).|I -> T (in sporadic cancers; somatic mutation).|I -> L (in sporadic cancers; somatic mutation).|I -> N (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.I251fs*94(12)|p.I251S(11)|p.I251N(7)|p.0?(7)|p.I251F(6)|p.I251T(4)|p.I251_T253delILT(4)|p.I251I(3)|p.I251del(2)|p.I251L(2)|p.I251V(2)|p.P250_L252delPIL(2)|p.I251fs*13(2)|p.P250_I251insXXXXXX(1)|p.R249_I251delRPI(1)|p.P250_T253delPILT(1)|p.I251fs*12(1)|p.P250_I251insXXXXXXX(1)|p.I251fs*96(1)|p.R249_T256delRPILTIIT(1)|p.P250_I251insX(1)|p.I251_L252insX(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GATGGTGAGGATGGGCCTCCG 0.582 0.37 59 35 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.27 121 44 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 174 1572 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 50 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 42 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.29 362 150 CDKL4 344387 broad.mit.edu 37 2 39414801 39414802 + Frame_Shift_Ins INS - AA AA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:39414801_39414802insAA uc002rrm.2 - 6 701_702 c.701_702insTT c.(700-702)TTCfs p.F234fs CDKL4_uc010fal.1_Frame_Shift_Ins_p.F234fs NM_001009565 NP_001009565 Q5MAI5 CDKL4_HUMAN cyclin-dependent kinase-like 4 234 Protein kinase. cytoplasm ATP binding|cyclin-dependent protein kinase activity ovary(1) 1 all_hematologic(82;0.248) TGATGCCATGGAAAAACCCGTT 0.327 0.38 66 40 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.67 7 14 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.38 8 5 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.57 90 118 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.38 55 33 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 32 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.61 31 49 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 54 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagc 0.271 0.18 68 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 496 217 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.26 55 19 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.33 31 15 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 31 208 TP53 7157 broad.mit.edu 37 17 7578385 7578410 + Frame_Shift_Del DEL CAGCGCTCATGGTGGGGGCAGCGCCT - - rs138525931;rs68130327;rs147002414;rs28934578;rs138729528 by1000genomes THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:7578385_7578410delCAGCGCTCATGGTGGGGGCAGCGCCT uc002gim.2 - 5 714_739 c.520_545delAGGCGCTGCCCCCACCATGAGCGCTG c.(520-546)AGGCGCTGCCCCCACCATGAGCGCTGCfs p.R174fs TP53_uc002gig.1_Frame_Shift_Del_p.R174fs|TP53_uc002gih.2_Frame_Shift_Del_p.R174fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.R42fs|TP53_uc010cng.1_Frame_Shift_Del_p.R42fs|TP53_uc002gii.1_Frame_Shift_Del_p.R42fs|TP53_uc010cnh.1_Frame_Shift_Del_p.R174fs|TP53_uc010cni.1_Frame_Shift_Del_p.R174fs|TP53_uc002gij.2_Frame_Shift_Del_p.R174fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.R81fs|TP53_uc002gio.2_Frame_Shift_Del_p.R42fs|TP53_uc010vug.1_Frame_Shift_Del_p.R135fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 174_182 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> Y (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.R175H(729)|p.C176F(102)|p.H179R(98)|p.H179Y(74)|p.C176Y(55)|p.H179L(31)|p.R181H(20)|p.R175L(19)|p.C176S(18)|p.H179Q(17)|p.P177L(17)|p.P177R(15)|p.R181P(14)|p.H178fs*69(13)|p.H179N(13)|p.E180*(13)|p.R181C(13)|p.R175C(12)|p.C176W(11)|p.R175G(11)|p.H179D(10)|p.P177P(10)|p.C176R(8)|p.H178Y(8)|p.P177_C182delPHHERC(8)|p.P177S(8)|p.C182S(8)|p.R174W(8)|p.C176fs*71(7)|p.0?(7)|p.H178P(6)|p.C176*(6)|p.E180K(5)|p.H178fs*3(5)|p.H178Q(5)|p.R175S(5)|p.R43H(5)|p.R175P(5)|p.R82H(5)|p.R174fs*73(4)|p.H178D(4)|p.R175R(4)|p.R174K(4)|p.C176_R181delCPHHER(3)|p.C176G(3)|p.H179P(3)|p.E180D(3)|p.H178N(3)|p.P177H(3)|p.R175_E180delRCPHHE(3)|p.R181L(3)|p.R174fs*24(3)|p.C176fs*5(3)|p.H179fs*68(2)|p.H179H(2)|p.R174fs*1(2)|p.H178H(2)|p.R175fs*5(2)|p.P177fs*3(2)|p.C182Y(2)|p.C182R(2)|p.R181R(2)|p.R174S(2)|p.V173fs*59(2)|p.R174R(2)|p.R174M(2)|p.V173fs*69(1)|p.R175_H178>X(1)|p.V172_R174delVVR(1)|p.E180G(1)|p.E180fs*67(1)|p.E180Q(1)|p.C83Y(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.H178fs*6(1)|p.H178L(1)|p.R174fs*3(1)|p.R174fs*7(1)|p.V157_C176del20(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175fs*6(1)|p.P177fs*4(1)|p.H168fs*69(1)|p.C176del(1)|p.E180>DGRCPHQ(1)|p.H178del(1)|p.P177I(1)|p.E180_S183del(1)|p.P177T(1)|p.K164_P219del(1)|p.R49P(1)|p.S149fs*72(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.H179del(1)|p.C176_P177delCP(1)|p.P177fs*69(1)|p.R42fs*24(1)|p.R88P(1)|p.R175fs*72(1)|p.C182fs*4(1)|p.R174_E180>K(1)|p.P177_E180delPHHE(1)|p.C182fs*65(1)|p.C176fs*65(1)|p.R181G(1)|p.C176fs*68(1)|p.R174_H178>S(1)|p.C44Y(1)|p.R181>XXXXXXX(1)|p.H178_H179>QY(1)|p.C176fs*72(1)|p.R174_C176delRRC(1)|p.?(1)|p.R174G(1)|p.R81fs*24(1)|p.C176fs*6(1)|p.P177_H179delPHH(1)|p.E180fs*6(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCC 0.637 0.56 19 24 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.51 65 67 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.78 123 448 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 6 103 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TM31_CENTRAL_NERVOUS_SYSTEM NA TM31_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.87 2 13 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TM31_CENTRAL_NERVOUS_SYSTEM NA TM31_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.51 115 118 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TM31_CENTRAL_NERVOUS_SYSTEM NA TM31_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 27 15 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 TM31_CENTRAL_NERVOUS_SYSTEM NA TM31_CENTRAL_NERVOUS_SYSTEM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.65 67 123 PIP5K1P1 206426 broad.mit.edu 37 6 7988241 7988242 + Frame_Shift_Ins INS - T T rs150856424 by1000genomes TM31_CENTRAL_NERVOUS_SYSTEM NA TM31_CENTRAL_NERVOUS_SYSTEM NA g.chr6:7988241_7988242insT uc003mxx.3 + 1 1907_1908 c.1472_1473insT c.(1471-1473)GGTfs p.G491fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 GTGGAGCCAGGTGTTCACCTTG 0.490 0.69 17 37 HOXA13 3209 broad.mit.edu 37 7 27239320 27239337 + In_Frame_Del DEL GCAGCGGCAGCCGCGGCA - - rs35861510 TM31_CENTRAL_NERVOUS_SYSTEM NA TM31_CENTRAL_NERVOUS_SYSTEM NA g.chr7:27239320_27239337delGCAGCGGCAGCCGCGGCA uc003szb.1 - 1 389_406 c.360_377delTGCCGCGGCTGCCGCTGC c.(358-378)GCTGCCGCGGCTGCCGCTGCA>GCA p.120_126AAAAAAA>A uc003szc.1_5'Flank NM_000522 NP_000513 P31271 HXA13_HUMAN homeobox A13 120_126 Poly-Ala. skeletal system development nucleus sequence-specific DNA binding breast(1) 1 0.000 0.24 275 89 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 TM31_CENTRAL_NERVOUS_SYSTEM NA TM31_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.67 6 12 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TM31_CENTRAL_NERVOUS_SYSTEM NA TM31_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 75 8 NF1 4763 broad.mit.edu 37 17 29562657 29562660 + Frame_Shift_Del DEL TGTT - - TM31_CENTRAL_NERVOUS_SYSTEM NA TM31_CENTRAL_NERVOUS_SYSTEM NA g.chr17:29562657_29562660delTGTT uc002hgg.2 + 28 4070_4073 c.3737_3740delTGTT c.(3736-3741)CTGTTTfs p.L1246fs NF1_uc002hgh.2_Frame_Shift_Del_p.L1246fs|NF1_uc010csn.1_Frame_Shift_Del_p.L1106fs|NF1_uc002hgi.1_Frame_Shift_Del_p.L279fs NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 1246_1247 Ras-GAP. actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) CTGGTTACTCTGTTTGATTCTCGG 0.412 0.99 1 77 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TM31_CENTRAL_NERVOUS_SYSTEM NA TM31_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.42 15 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TM31_CENTRAL_NERVOUS_SYSTEM NA TM31_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.83 67 332 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 38 IRS1 3667 broad.mit.edu 37 2 227661396 227661398 + In_Frame_Del DEL TGC - - TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:227661396_227661398delTGC uc002voh.3 - 1 2109_2111 c.2057_2059delGCA c.(2056-2061)AGCAAC>AAC p.S686del NM_005544 NP_005535 P35568 IRS1_HUMAN insulin receptor substrate 1 686 Poly-Ser. fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1) 12 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) GGGACGGCGTtgctgctgctgct 0.547 0.68 26 54 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.38 8 5 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.17 40 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 88 99 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.24 143 45 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.30 324 141 CREBBP 1387 broad.mit.edu 37 16 3781324 3781326 + In_Frame_Del DEL AGG - - TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:3781324_3781326delAGG uc002cvv.2 - 30 5243_5245 c.5039_5041delCCT c.(5038-5043)TCCTTG>TTG p.S1680del CREBBP_uc002cvw.2_In_Frame_Del_p.S1642del NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 1680 Interaction with TRERF1. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) GAGCGGCGCAAGGAGGAGAACTC 0.645 0.58 5 7 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 28 302 TP53 7157 broad.mit.edu 37 17 7578253 7578257 + Frame_Shift_Del DEL CCTTC - - TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:7578253_7578257delCCTTC uc002gim.2 - 6 786_790 c.592_596delGAAGG c.(592-597)GAAGGAfs p.E198fs TP53_uc002gig.1_Frame_Shift_Del_p.E198fs|TP53_uc002gih.2_Frame_Shift_Del_p.E198fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.E66fs|TP53_uc010cng.1_Frame_Shift_Del_p.E66fs|TP53_uc002gii.1_Frame_Shift_Del_p.E66fs|TP53_uc010cnh.1_Frame_Shift_Del_p.E198fs|TP53_uc010cni.1_Frame_Shift_Del_p.E198fs|TP53_uc002gij.2_Frame_Shift_Del_p.E198fs|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Frame_Shift_Del_p.E105fs|TP53_uc002gio.2_Frame_Shift_Del_p.E66fs|TP53_uc010vug.1_Frame_Shift_Del_p.E159fs NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 198_199 Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity). G -> V (in sporadic cancers; somatic mutation).|G -> E (in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation).|G -> A (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.E198*(17)|p.G199E(11)|p.G199R(9)|p.0?(7)|p.G199fs*48(5)|p.G199V(5)|p.E198K(4)|p.G199*(3)|p.E198fs*11(2)|p.E198Q(2)|p.K164_P219del(1)|p.G67fs*>24(1)|p.P191fs*6(1)|p.G106fs*48(1)|p.G199fs*42(1)|p.N200fs*4(1)|p.E198fs*7(1)|p.E198G(1)|p.I195_G199delIRVEG(1)|p.E198_L201>V(1)|p.E198_G199ins21(1)|p.G199A(1)|p.E198fs*49(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) ACGCAAATTTCCTTCCACTCGGATA 0.546 0.94 3 47 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.50 24 24 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.79 104 387 COL18A1 80781 broad.mit.edu 37 21 46932173 46932182 + Frame_Shift_Del DEL GGCGGACGGA - - TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46932173_46932182delGGCGGACGGA uc011afs.1 + 42 5138_5147 c.5117_5126delGGCGGACGGA c.(5116-5127)TGGCGGACGGAGfs p.W1706fs COL18A1_uc002zhg.2_Frame_Shift_Del_p.W1291fs|COL18A1_uc002zhi.2_Frame_Shift_Del_p.W1471fs|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_Frame_Shift_Del_p.W272fs|COL18A1_uc002zhk.2_Frame_Shift_Del_p.W116fs NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor 1709_1712 Nonhelical region 11 (NC11). cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.41 454 318 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 3 41 ADRBK2 157 broad.mit.edu 37 22 26059613 26059614 + Frame_Shift_Ins INS - T T TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:26059613_26059614insT uc003abx.3 + 5 530_531 c.383_384insT c.(382-384)GCTfs p.A128fs ADRBK2_uc010gux.2_Frame_Shift_Ins_p.A128fs|ADRBK2_uc003abw.2_Frame_Shift_Ins_p.A15fs|ADRBK2_uc003aby.3_RNA NM_005160 NP_005151 P35626 ARBK2_HUMAN beta-adrenergic receptor kinase 2 128 N-terminal.|RGS. ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity lung(3)|ovary(2)|stomach(1)|central_nervous_system(1) 7 Adenosine triphosphate(DB00171) TCAAAGCAAGCTGTAGAACACG 0.248 0.45 41 34 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TT2609C02_THYROID NA TT2609C02_THYROID NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 2 45 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TT2609C02_THYROID NA TT2609C02_THYROID NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.32 253 118 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 TT2609C02_THYROID NA TT2609C02_THYROID NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.20 28 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TT2609C02_THYROID NA TT2609C02_THYROID NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 71 128 HAVCR1 26762 broad.mit.edu 37 5 156479444 156479446 + In_Frame_Del DEL TTG - - rs45439103;rs74944471 TT2609C02_THYROID NA TT2609C02_THYROID NA g.chr5:156479444_156479446delTTG uc010jij.1 - 4 784_786 c.599_601delCAA c.(598-603)ACAAGT>AGT p.T200del HAVCR1_uc011ddl.1_In_Frame_Del_p.T31del|HAVCR1_uc003lwi.2_In_Frame_Del_p.T200del|HAVCR1_uc011ddm.1_In_Frame_Del_p.T200del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 195 10.|Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich. Missing. interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACTGGAACACTTGTTGTTGTTGG 0.463 0.50 5 5 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes TT2609C02_THYROID NA TT2609C02_THYROID NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.97 1 29 PCM1 5108 broad.mit.edu 37 8 17883149 17883150 + Frame_Shift_Del DEL GA - - TT2609C02_THYROID NA TT2609C02_THYROID NA g.chr8:17883149_17883150delGA uc003wyi.3 + 38 6453_6454 c.6031_6032delGA c.(6031-6033)GAGfs p.E2011fs PCM1_uc011kyh.1_Frame_Shift_Del_p.E2003fs|PCM1_uc003wyj.3_Frame_Shift_Del_p.E1847fs|PCM1_uc011kyi.1_Frame_Shift_Del_p.E810fs|PCM1_uc011kyj.1_Frame_Shift_Del_p.E767fs|PCM1_uc003wyk.3_Frame_Shift_Del_p.E693fs|PCM1_uc011kyk.1_Frame_Shift_Del_p.E627fs NM_006197 NP_006188 Q15154 PCM1_HUMAN pericentriolar material 1 2011 Interaction with BBS4. centrosome organization|cilium assembly|G2/M transition of mitotic cell cycle|interkinetic nuclear migration|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome centriolar satellite|cytosol|nuclear membrane|pericentriolar material identical protein binding PCM1/JAK2(30) haematopoietic_and_lymphoid_tissue(30)|breast(4)|ovary(2) 36 Colorectal(111;0.0789) TGGAAATTCTGAGACACTAAAA 0.297 0.41 16 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TT2609C02_THYROID NA TT2609C02_THYROID NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.18 954 210 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 TT2609C02_THYROID NA TT2609C02_THYROID NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.35 52 28 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TT2609C02_THYROID NA TT2609C02_THYROID NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.70 128 304 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TT2609C02_THYROID NA TT2609C02_THYROID NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 1.00 0 138 CLTCL1 8218 broad.mit.edu 37 22 19230342 19230343 + Frame_Shift_Ins INS - A A TT2609C02_THYROID NA TT2609C02_THYROID NA g.chr22:19230342_19230343insA uc002zpb.2 - 4 711_712 c.636_637insT c.(634-639)CCTGCCfs p.P212fs CLTCL1_uc011agv.1_Frame_Shift_Ins_p.P212fs|CLTCL1_uc011agw.1_Frame_Shift_Ins_p.P212fs NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 212_213 Globular terminal domain. anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) AAAAGGGTGGCAGGCTTGGCAT 0.505 0.48 126 117 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 41 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.70 267 610 EPAS1 2034 broad.mit.edu 37 2 46603681 46603682 + Frame_Shift_Ins INS - A A TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr2:46603681_46603682insA uc002ruv.2 + 9 1526_1527 c.1038_1039insA c.(1036-1041)GAGATTfs p.E346fs NM_001430 NP_001421 Q99814 EPAS1_HUMAN endothelial PAS domain protein 1 346_347 PAC. angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia transcription factor complex histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding ovary(1)|skin(1) 2 all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18) LUSC - Lung squamous cell carcinoma(58;0.151) 0.000 0.18 600 129 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 97 79 MAML3 55534 broad.mit.edu 37 4 140810659 140810664 + In_Frame_Del DEL TGCTGT - - TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr4:140810659_140810664delTGCTGT uc003ihz.1 - 3 2666_2671 c.1914_1919delACAGCA c.(1912-1920)CAACAGCAG>CAG p.638_640QQQ>Q MAML3_uc011chd.1_Intron NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 638_640 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) ctgctgctgctgctgttgctgttgct 0.417 0.71 46 112 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.85 2 11 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.14 54 9 DNAH8 1769 broad.mit.edu 37 6 38821119 38821120 + Frame_Shift_Del DEL CA - - TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr6:38821119_38821120delCA uc003ooe.1 + 39 5678_5679 c.5078_5079delCA c.(5077-5079)GCAfs p.A1693fs NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 CACTTTCCAGCACAGGTGAGAA 0.386 0.14 72 12 FRK 2444 broad.mit.edu 37 6 116289819 116289820 + Frame_Shift_Del DEL AA - - rs142511122 TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr6:116289819_116289820delAA uc003pwi.1 - 3 996_997 c.549_550delTT c.(547-552)TTTTCAfs p.F183fs NM_002031 NP_002022 P42685 FRK_HUMAN fyn-related kinase 183_184 SH2. negative regulation of cell proliferation cytoplasm|nucleus ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding ovary(3)|lung(3) 6 all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465) all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625) TTCAGTGTTGAAAAGATTCTTC 0.411 0.85 7 40 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 10 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.79 4 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 47 STK33 65975 broad.mit.edu 37 11 8414196 8414196 + Frame_Shift_Del DEL G - - TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr11:8414196delG uc001mgi.1 - 12 2325 c.1406delC c.(1405-1407)TCAfs p.S469fs STK33_uc001mgj.1_Frame_Shift_Del_p.S469fs|STK33_uc001mgk.1_Frame_Shift_Del_p.S469fs|STK33_uc010rbn.1_Frame_Shift_Del_p.S428fs|STK33_uc001mgl.3_Frame_Shift_Del_p.S282fs NM_030906 NP_112168 Q9BYT3 STK33_HUMAN serine/threonine kinase 33 469 Golgi apparatus|nucleus|perinuclear region of cytoplasm ATP binding|protein serine/threonine kinase activity ovary(2)|lung(2)|pancreas(1)|central_nervous_system(1)|skin(1) 7 Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239) TGTGAAACTTGAACTGCACAT 0.413 0.14 166 27 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 800 279 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.67 31 62 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.29 110 45 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.17 54 11 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.66 179 348 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TT_OESOPHAGUS NA TT_OESOPHAGUS NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 2 51 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TT_THYROID NA TT_THYROID NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.85 7 40 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TT_THYROID NA TT_THYROID NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.23 274 83 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes TT_THYROID NA TT_THYROID NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.35 11 6 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 TT_THYROID NA TT_THYROID NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.13 62 9 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 TT_THYROID NA TT_THYROID NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.34 29 15 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TT_THYROID NA TT_THYROID NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 127 175 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TT_THYROID NA TT_THYROID NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.79 15 56 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 TT_THYROID NA TT_THYROID NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.22 189 54 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes TT_THYROID NA TT_THYROID NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.73 4 11 DNAH8 1769 broad.mit.edu 37 6 38841024 38841024 + Frame_Shift_Del DEL A - - TT_THYROID NA TT_THYROID NA g.chr6:38841024delA uc003ooe.1 + 50 7441 c.6841delA c.(6841-6843)AAAfs p.K2281fs NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 ATGGTTGAAGAAACGCACTGC 0.423 0.44 66 51 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes TT_THYROID NA TT_THYROID NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TT_THYROID NA TT_THYROID NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.92 6 66 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TT_THYROID NA TT_THYROID NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.36 490 273 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes TT_THYROID NA TT_THYROID NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.12 78 11 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 TT_THYROID NA TT_THYROID NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.55 20 24 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TT_THYROID NA TT_THYROID NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.34 135 70 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 TT_THYROID NA TT_THYROID NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.28 91 35 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TT_THYROID NA TT_THYROID NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 90 404 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TT_THYROID NA TT_THYROID NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 7 85 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 16 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 209 81 PIK3C2B 5287 broad.mit.edu 37 1 204394164 204394166 + In_Frame_Del DEL ACC - - TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr1:204394164_204394166delACC uc001haw.2 - 34 5198_5200 c.4719_4721delGGT c.(4717-4722)TTGGTA>TTA p.V1574del PIK3C2B_uc010pqv.1_In_Frame_Del_p.V1546del NM_002646 NP_002637 O00750 P3C2B_HUMAN phosphoinositide-3-kinase, class 2 beta 1574 C2. cell communication|phosphatidylinositol-mediated signaling endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1) 7 all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227) GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193) CCCATCATATACCAACTGCAAAC 0.562 0.31 38 17 VHL 7428 broad.mit.edu 37 3 10191564 10191564 + Frame_Shift_Del DEL A - - TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr3:10191564delA uc003bvc.2 + 3 770 c.557delA c.(556-558)GAAfs p.E186fs VHL_uc003bvd.2_Frame_Shift_Del_p.E145fs NM_000551 NP_000542 P40337 VHL_HUMAN von Hippel-Lindau tumor suppressor isoform 1 186 E -> K (in VHLD; type I).|Missing (in VHLD). anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus protein binding|transcription factor binding p.E186*(2)|p.E186fs*28(1)|p.E186fs*14(1)|p.E186fs*27(1)|p.Y185fs*11(1) kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1) 1346 Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569) TCGCTCTACGAAGATCTGGAA 0.507 0.94 3 46 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.30 19 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.30 69 29 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.29 50 20 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.81 5 21 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 16 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.23 174 51 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.26 26 9 FANCI 55215 broad.mit.edu 37 15 89805094 89805094 + Frame_Shift_Del DEL C - - TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr15:89805094delC uc010bnp.1 + 6 578 c.488delC c.(487-489)ACCfs p.T163fs FANCI_uc002bnm.1_Frame_Shift_Del_p.T163fs|FANCI_uc002bnn.1_RNA|FANCI_uc002bno.2_Frame_Shift_Del_p.T163fs|FANCI_uc002bnp.1_5'Flank NM_001113378 NP_001106849 Q9NVI1 FANCI_HUMAN Fanconi anemia, complementation group I isoform 163 cell cycle|DNA repair nucleoplasm protein binding ovary(2) 2 Lung NSC(78;0.0472)|all_lung(78;0.089) TTGATTAACACCCTGTGTTCT 0.358 0.26 111 38 MYLK3 91807 broad.mit.edu 37 16 46744687 46744688 + Frame_Shift_Ins INS - A A rs150139689 by1000genomes TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr16:46744687_46744688insA uc002eei.3 - 11 2244_2245 c.2128_2129insT c.(2128-2130)TCCfs p.S710fs MYLK3_uc010vge.1_Frame_Shift_Ins_p.S369fs NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 710 Protein kinase. cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TAGAAATGGGGACAAGCCACTG 0.470 0.26 40 14 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 30 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 220 554 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 1 34 SMARCB1 6598 broad.mit.edu 37 22 24175837 24175838 + Frame_Shift_Ins INS - C C TUHR10TKB_KIDNEY NA TUHR10TKB_KIDNEY NA g.chr22:24175837_24175838insC uc002zyb.2 + 8 1272_1273 c.1065_1066insC c.(1063-1068)ACTCTGfs p.T355fs SMARCB1_uc002zya.2_Intron|SMARCB1_uc002zyc.2_Frame_Shift_Ins_p.T346fs|SMARCB1_uc002zyd.2_Frame_Shift_Ins_p.T364fs NM_003073 NP_003064 Q12824 SNF5_HUMAN SWI/SNF related, matrix associated, actin 355_356 cell cycle|chromatin remodeling|DNA integration|interspecies interaction between organisms|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|retroviral genome replication|transcription, DNA-dependent nBAF complex|npBAF complex|nucleolus|nucleoplasm|SWI/SNF complex p53 binding p.?(2)|p.L266_*386del(1) soft_tissue(193)|central_nervous_system(172)|haematopoietic_and_lymphoid_tissue(23)|meninges(5)|skin(5)|bone(4)|ovary(2)|endometrium(1)|lung(1)|pancreas(1) 407 Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05) 0.000 0.88 46 324 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 1 16 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.50 225 221 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.48 11 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.31 68 30 FBXW7 55294 broad.mit.edu 37 4 153253862 153253864 + In_Frame_Del DEL AGA - - TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chr4:153253862_153253864delAGA uc003ims.2 - 6 1018_1020 c.869_871delTCT c.(868-873)CTCTAT>CAT p.290_291LY>H FBXW7_uc011cii.1_In_Frame_Del_p.290_291LY>H|FBXW7_uc003imt.2_In_Frame_Del_p.290_291LY>H|FBXW7_uc011cih.1_In_Frame_Del_p.114_115LY>H|FBXW7_uc003imq.2_In_Frame_Del_p.210_211LY>H|FBXW7_uc003imr.2_In_Frame_Del_p.172_173LY>H NM_033632 NP_361014 Q969H0 FBXW7_HUMAN F-box and WD repeat domain containing 7 isoform 290_291 F-box. interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex protein binding|protein binding haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1) 308 all_hematologic(180;0.093) Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067) GAAAGCACATAGAGTGCCAACTA 0.345 0.24 60 19 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.67 4 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 1 9 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.30 43 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 1 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.16 87 16 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.23 31 9 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.30 88 37 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 57 356 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TUHR14TKB_KIDNEY NA TUHR14TKB_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 6 65 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 37 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.52 201 215 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.21 92 24 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.50 13 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.44 45 35 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.25 76 26 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.59 7 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.11 108 14 MYH8 4626 broad.mit.edu 37 17 10314206 10314206 + Frame_Shift_Del DEL A - - TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chr17:10314206delA uc002gmm.2 - 15 1570 c.1475delT c.(1474-1476)TTCfs p.F492fs uc002gml.1_Intron NM_002472 NP_002463 P13535 MYH8_HUMAN myosin, heavy chain 8, skeletal muscle, 492 Myosin head-like. muscle filament sliding cytosol|muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle skin(6)|ovary(3)|breast(2) 11 GTGGTGGTTGAAAAACTGTTG 0.443 0.68 40 85 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.32 17 8 NCOA3 8202 broad.mit.edu 37 20 46281232 46281235 + Frame_Shift_Del DEL CCAG - - TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chr20:46281232_46281235delCCAG uc002xtk.2 + 21 4234_4237 c.4029_4032delCCAG c.(4027-4032)TCCCAGfs p.S1343fs NCOA3_uc002xtl.2_Frame_Shift_Del_p.S1339fs|NCOA3_uc002xtm.2_Frame_Shift_Del_p.S1338fs|NCOA3_uc002xtn.2_Frame_Shift_Del_p.S1342fs|NCOA3_uc010zyc.1_Frame_Shift_Del_p.S1138fs NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 1343_1344 androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 TGGGTCCCTCCCAGAATCCCATGA 0.485 0.26 99 35 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.14 100 16 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 117 522 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TUHR4TKB_KIDNEY NA TUHR4TKB_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 51 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 TYKNU_OVARY NA TYKNU_OVARY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.89 6 48 ARID1A 8289 broad.mit.edu 37 1 27023164 27023174 + Frame_Shift_Del DEL CGGCGGCGGGC - - TYKNU_OVARY NA TYKNU_OVARY NA g.chr1:27023164_27023174delCGGCGGCGGGC uc001bmv.1 + 1 643_653 c.270_280delCGGCGGCGGGC c.(268-282)AGCGGCGGCGGGCCCfs p.S90fs ARID1A_uc001bmt.1_Frame_Shift_Del_p.S90fs|ARID1A_uc001bmu.1_Frame_Shift_Del_p.S90fs NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 90_94 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 0.000 0.95 49 954 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - TYKNU_OVARY NA TYKNU_OVARY NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.46 193 163 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 TYKNU_OVARY NA TYKNU_OVARY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 20 9 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A TYKNU_OVARY NA TYKNU_OVARY NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 92 21 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 TYKNU_OVARY NA TYKNU_OVARY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 110 75 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 TYKNU_OVARY NA TYKNU_OVARY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.19 95 23 MLL3 58508 broad.mit.edu 37 7 151875096 151875097 + Splice_Site INS - T T TYKNU_OVARY NA TYKNU_OVARY NA g.chr7:151875096_151875097insT uc003wla.2 - 38 7662 c.7443_splice c.e38-1 p.R2481_splice MLL3_uc003wkz.2_Splice_Site_p.R1542_splice|MLL3_uc003wky.2_Splice_Site NM_170606 NP_733751 Q8NEZ4 MLL3_HUMAN myeloid/lymphoid or mixed-lineage leukemia 3 intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent DNA binding|protein binding|zinc ion binding large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1) 63 all_neural(206;0.187) all_hematologic(28;0.0592)|Prostate(32;0.0906) OV - Ovarian serous cystadenocarcinoma(82;0.00715) UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462) AAATCCAAATCTTTTaaaaaaa 0.332 0.46 104 87 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 TYKNU_OVARY NA TYKNU_OVARY NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.44 10 8 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency TYKNU_OVARY NA TYKNU_OVARY NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.62 212 347 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 TYKNU_OVARY NA TYKNU_OVARY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 640 161 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency TYKNU_OVARY NA TYKNU_OVARY NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.33 47 23 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 TYKNU_OVARY NA TYKNU_OVARY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 32 376 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 TYKNU_OVARY NA TYKNU_OVARY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 3 90 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 4 72 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.10 1887 215 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.67 11 22 TPRXL 348825 broad.mit.edu 37 3 14106317 14106318 + In_Frame_Ins INS - CAGCAGTCCCAGCAC CAGCAGTCCCAGCAC U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr3:14106317_14106318insCAGCAGTCCCAGCAC uc011avd.1 + 3 1096_1097 c.641_642insCAGCAGTCCCAGCAC c.(640-642)ACC>ACCAGCAGTCCCAGCACC p.214_214T>TSSPST TPRXL_uc003byh.1_In_Frame_Ins_p.214_214T>TSSPST|TPRXL_uc003byg.2_In_Frame_Ins_p.214_214T>TSSPST NR_002223 RecName: Full=Putative protein TPRXL; 0 agctccagcaccagcagtccca 0.233 0.57 6 8 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.43 13 10 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.13 203 31 HTT 3064 broad.mit.edu 37 4 3076604 3076606 + In_Frame_Del DEL CAG - - rs10618869 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr4:3076604_3076606delCAG uc011bvq.1 + 2 203_205 c.58_60delCAG c.(58-60)CAGdel p.Q40del NM_002111 NP_002102 P42858 HD_HUMAN huntingtin Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) CAAGTCCTTCcagcagcagcagc 0.335 0.18 121 26 HTT 3064 broad.mit.edu 37 4 3076672 3076673 + In_Frame_Ins INS - CCGCCG CCGCCG rs76533208 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr4:3076672_3076673insCCGCCG uc011bvq.1 + 2 271_272 c.126_127insCCGCCG c.(124-129)insCCGCCG p.50_51insPP NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 48_49 Poly-Pro. establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) aacagccgccaccgccgccgcc 0.084 0.30 77 33 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.47 23 20 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 82 189 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.41 84 58 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.91 1 10 ATXN1 6310 broad.mit.edu 37 6 16327864 16327865 + In_Frame_Ins INS - TGC TGC U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr6:16327864_16327865insTGC uc003nbt.2 - 8 1648_1649 c.677_678insGCA c.(676-678)CAC>CAGCAC p.225_226insQ ATXN1_uc010jpi.2_In_Frame_Ins_p.225_226insQ|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 225_226 cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) CCCTGCTGAGGtgctgctgctg 0.366 0.39 126 81 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.35 76 41 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 1 23 PTEN 5728 broad.mit.edu 37 10 89717695 89717696 + Frame_Shift_Ins INS - TT TT U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr10:89717695_89717696insTT uc001kfb.2 + 8 1751_1752 c.720_721insTT c.(718-723)TACTTTfs p.Y240fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 240_241 C2 tensin-type. F -> S (in MCEPHAS). activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R55fs*1(4)|p.N212fs*1(2)|p.Y27fs*1(2)|p.F241L(1)|p.G165_*404del(1)|p.?(1)|p.G165_K342del(1)|p.F241fs*1(1)|p.R234fs*9(1)|p.K237_Y240>N(1)|p.F241fs*17(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) AGTTCATGTACTTTGAGTTCCC 0.411 0.93 35 432 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.49 576 560 ASCL1 429 broad.mit.edu 37 12 103352171 103352172 + In_Frame_Ins INS - GCA GCA rs3832799;rs72405287 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr12:103352171_103352172insGCA uc001tjr.3 + 1 720_721 c.149_150insGCA c.(148-150)GCG>GCGCAG p.62_63insQ NM_004316 NP_004307 P50553 ASCL1_HUMAN achaete-scute complex homolog 1 62_63 cerebral cortex GABAergic interneuron differentiation|negative regulation of apoptosis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|noradrenergic neuron fate commitment|Notch signaling pathway|positive regulation of neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|response to retinoic acid|sympathetic nervous system development nucleus bHLH transcription factor binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity 0 gcgcagagcgcgcagcagcagc 0.446 0.39 11 7 FES 2242 broad.mit.edu 37 15 91436886 91436886 + Frame_Shift_Del DEL A - - U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr15:91436886delA uc002bpv.2 + 17 2144 c.2048delA c.(2047-2049)GACfs p.D683fs FES_uc010uqj.1_Frame_Shift_Del_p.D555fs|FES_uc010uqk.1_Frame_Shift_Del_p.D665fs|FES_uc002bpw.2_RNA|FES_uc010bny.2_Frame_Shift_Del_p.D542fs|FES_uc002bpx.2_Frame_Shift_Del_p.D613fs|FES_uc002bpy.2_Frame_Shift_Del_p.D625fs NM_002005 NP_001996 P07332 FES_HUMAN feline sarcoma oncogene isoform 1 683 Protein kinase. Proton acceptor (By similarity). axon guidance|cell proliferation|peptidyl-tyrosine phosphorylation cytosol ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(2) 2 Lung NSC(78;0.0771)|all_lung(78;0.137) Lung(145;0.229) TCACCCAGGGACCTGGCTGCT 0.592 0.22 80 23 MEF2A 4205 broad.mit.edu 37 15 100252710 100252712 + In_Frame_Del DEL CAG - - U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr15:100252710_100252712delCAG uc010urw.1 + 11 1617_1619 c.1258_1260delCAG c.(1258-1260)CAGdel p.Q430del MEF2A_uc010urv.1_In_Frame_Del_p.Q360del|MEF2A_uc010bos.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvf.2_In_Frame_Del_p.Q422del|MEF2A_uc002bve.2_In_Frame_Del_p.Q428del|MEF2A_uc002bvg.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvi.2_In_Frame_Del_p.Q420del|MEF2A_uc010bot.2_In_Frame_Del_p.Q352del NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 430 Gln/Pro-rich. Missing (in Ref. 4; AAB17195/AAB17196). apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) ATCGGGCTTCcagcagcagcagc 0.493 0.44 29 23 SALL1 6299 broad.mit.edu 37 16 51175655 51175656 + In_Frame_Ins INS - GCT GCT rs113614842 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr16:51175655_51175656insGCT uc010vgs.1 - 2 508_509 c.477_478insAGC c.(475-480)insAGC p.159_160insS SALL1_uc010vgr.1_In_Frame_Ins_p.62_63insS|SALL1_uc010cbv.2_Intron NM_002968 NP_002959 Q9NSC2 SALL1_HUMAN sal-like 1 isoform a 159_160 Poly-Gly. adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development chromocenter|cytoplasm|heterochromatin|nucleus beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding skin(5)|ovary(3) 8 all_cancers(37;0.0322) COAD - Colon adenocarcinoma(2;0.24) ccgccgccgccgctgctgctgc 0.460 0.64 14 25 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.87 32 219 RAI1 10743 broad.mit.edu 37 17 17697094 17697096 + In_Frame_Del DEL CAG - - rs113303801 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr17:17697094_17697096delCAG uc002grm.2 + 3 1301_1303 c.832_834delCAG c.(832-834)CAGdel p.Q291del RAI1_uc002grn.1_In_Frame_Del_p.Q291del NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 291 Gln-rich.|Poly-Gln. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) CAGCTATGACcagcagcagcagc 0.507 0.10 106 12 ACACA 31 broad.mit.edu 37 17 35557393 35557398 + In_Frame_Del DEL GGCGCC - - U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr17:35557393_35557398delGGCGCC uc002hnm.2 - 34 4165_4170 c.3974_3979delGGCGCC c.(3973-3981)CGGCGCCTT>CTT p.RR1325del ACACA_uc002hnk.2_In_Frame_Del_p.RR1247del|ACACA_uc002hnl.2_In_Frame_Del_p.RR1267del|ACACA_uc002hnn.2_In_Frame_Del_p.RR1325del|ACACA_uc002hno.2_In_Frame_Del_p.RR1362del|ACACA_uc010cuy.2_In_Frame_Del_p.RR19del NM_198836 NP_942133 Q13085 ACACA_HUMAN acetyl-Coenzyme A carboxylase alpha isoform 2 1325_1326 acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process cytosol acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding large_intestine(1)|ovary(1) 2 Breast(25;0.00157)|Ovarian(249;0.15) Biotin(DB00121) AGGAAAGTAAGGCGCCGGATCCCATG 0.383 0.10 185 21 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.84 34 173 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 91 370 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 U251MG_CENTRAL_NERVOUS_SYSTEM NA U251MG_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 8 97 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 40 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.17 123 26 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.43 118 88 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.60 27 40 PHF3 23469 broad.mit.edu 37 6 64421859 64421859 + Frame_Shift_Del DEL T - - U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:64421859delT uc003pep.1 + 15 4401 c.4375delT c.(4375-4377)TTAfs p.L1459fs PHF3_uc003pen.2_Frame_Shift_Del_p.L1371fs|PHF3_uc011dxs.1_Frame_Shift_Del_p.L728fs NM_015153 NP_055968 Q92576 PHF3_HUMAN PHD finger protein 3 1459 multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding ovary(3)|lung(1)|skin(1) 5 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) TACTCTGGAATTAGCAAATAA 0.438 0.46 74 62 MLLT4 4301 broad.mit.edu 37 6 168369796 168369797 + In_Frame_Ins INS - CAAACT CAAACT U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:168369796_168369797insCAAACT uc003qwd.2 + 33 5411_5412 c.5269_5270insCAAACT c.(5269-5271)CCA>CCAAACTCA p.1759_1760insNS NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 1749_1750 adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) TGGAAAAGGACCAAACTCTTAC 0.426 0.30 189 80 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.31 44 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.20 177 44 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.82 4 18 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.91 39 402 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 77 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 U2OS_BONE NA U2OS_BONE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 3 56 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - U2OS_BONE NA U2OS_BONE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.12 1764 249 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 U2OS_BONE NA U2OS_BONE NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.24 65 21 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 U2OS_BONE NA U2OS_BONE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.25 135 44 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 U2OS_BONE NA U2OS_BONE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.48 182 168 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 U2OS_BONE NA U2OS_BONE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 67 113 PAXIP1 22976 broad.mit.edu 37 7 154753272 154753282 + Frame_Shift_Del DEL ATAACCCGTAT - - U2OS_BONE NA U2OS_BONE NA g.chr7:154753272_154753282delATAACCCGTAT uc003wlp.2 - 11 2247_2257 c.2204_2214delATACGGGTTAT c.(2203-2214)TATACGGGTTATfs p.Y735fs PAXIP1_uc003wlq.1_Frame_Shift_Del_p.Y701fs|PAXIP1_uc011kvs.1_Frame_Shift_Del_p.Y699fs NM_007349 NP_031375 Q6ZW49 PAXI1_HUMAN PAX interacting protein 1 735_738 Interaction with TP53BP1.|BRCT 4. DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent histone methyltransferase complex|nuclear matrix lung(2)|ovary(1)|breast(1)|pancreas(1) 5 all_neural(206;0.119) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.0296) UCEC - Uterine corpus endometrioid carcinoma (81;0.178) TGCGGCATAGATAACCCGTATATTTGGCACC 0.332 0.68 38 81 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 U2OS_BONE NA U2OS_BONE NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.26 198 70 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency U2OS_BONE NA U2OS_BONE NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.11 261 33 TGFBR1 7046 broad.mit.edu 37 9 101867538 101867546 + In_Frame_Del DEL GGCGGCGGC - - U2OS_BONE NA U2OS_BONE NA g.chr9:101867538_101867546delGGCGGCGGC uc004azc.2 + 1 127_135 c.51_59delGGCGGCGGC c.(49-60)CTGGCGGCGGCG>CTG p.AAA24del TGFBR1_uc004azd.2_In_Frame_Del_p.AAA24del NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 24_26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.10 137 15 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 U2OS_BONE NA U2OS_BONE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.10 276 29 RAB15 376267 broad.mit.edu 37 14 65417684 65417685 + Frame_Shift_Ins INS - G G U2OS_BONE NA U2OS_BONE NA g.chr14:65417684_65417685insG uc001xhz.2 - 4 512_513 c.431_432insC c.(430-432)CCAfs p.P144fs FNTB_uc010tsl.1_Intron|FNTB_uc010tsm.1_Intron|RAB15_uc010aqk.2_RNA NM_198686 NP_941959 P59190 RAB15_HUMAN RAB15, member RAS onocogene family Error:Variant_position_missing_in_P59190_after_alignment protein transport|small GTPase mediated signal transduction plasma membrane GTP binding ovary(1) 1 all cancers(60;0.00136)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.0102) TCCAGGGCTGTGGAAGGCAAAG 0.604 0.10 347 40 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C U2OS_BONE NA U2OS_BONE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.94 36 538 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 U2OS_BONE NA U2OS_BONE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 26 71 NCOA3 8202 broad.mit.edu 37 20 46279815 46279817 + In_Frame_Del DEL GCA - - rs3830810 U2OS_BONE NA U2OS_BONE NA g.chr20:46279815_46279817delGCA uc002xtk.2 + 20 3946_3948 c.3741_3743delGCA c.(3739-3744)ATGCAG>ATG p.Q1276del NCOA3_uc010ght.1_In_Frame_Del_p.Q1267del|NCOA3_uc002xtl.2_In_Frame_Del_p.Q1272del|NCOA3_uc002xtm.2_In_Frame_Del_p.Q1271del|NCOA3_uc002xtn.2_In_Frame_Del_p.Q1275del|NCOA3_uc010zyc.1_In_Frame_Del_p.Q1071del NM_181659 NP_858045 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 isoform a 1276 Poly-Gln.|Acetyltransferase. androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding ovary(3)|lung(1)|skin(1) 5 CTATGATGATgcagcagcagcag 0.286 0.10 131 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 U2OS_BONE NA U2OS_BONE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.82 58 264 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 U2OS_BONE NA U2OS_BONE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 22 210 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 6 122 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.27 67 25 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.13 339 50 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 210 349 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.48 113 103 NUP153 9972 broad.mit.edu 37 6 17633077 17633078 + Splice_Site INS - AA AA rs36027788;rs147103527 U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chr6:17633077_17633078insAA uc003ncd.1 - 17 2665 c.2465_splice c.e17-1 p.G822_splice NUP153_uc011dje.1_Splice_Site_p.G853_splice|NUP153_uc010jpl.1_Splice_Site_p.G780_splice NM_005124 NP_005115 P49790 NU153_HUMAN nucleoporin 153kDa carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm DNA binding|protein binding|transporter activity|zinc ion binding lung(4)|ovary(2)|breast(2)|skin(1) 9 Breast(50;0.0259)|Ovarian(93;0.0584) all_hematologic(90;0.125) all cancers(50;0.0981)|Epithelial(50;0.112) CTGAACTTCCTAAAAAAAAAAA 0.406 0.17 86 18 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 42 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.96 1 25 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 284 147 Unknown 0 broad.mit.edu 37 12 63359550 63359555 + In_Frame_Del DEL CTGCTG - - U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chr12:63359550_63359555delCTGCTG uc001srn.1 + 1 451_456 c.446_451delCTGCTG c.(445-453)ACTGCTGCT>ACT p.AA158del SubName: Full=Putative uncharacterized protein RPL14P1; ACTAAGGGTActgctgctgctgctgc 0.379 0.50 6 6 NF1 4763 broad.mit.edu 37 17 29562657 29562660 + Frame_Shift_Del DEL TGTT - - U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chr17:29562657_29562660delTGTT uc002hgg.2 + 28 4070_4073 c.3737_3740delTGTT c.(3736-3741)CTGTTTfs p.L1246fs NF1_uc002hgh.2_Frame_Shift_Del_p.L1246fs|NF1_uc010csn.1_Frame_Shift_Del_p.L1106fs|NF1_uc002hgi.1_Frame_Shift_Del_p.L279fs NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 1246_1247 Ras-GAP. actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.?(2) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) CTGGTTACTCTGTTTGATTCTCGG 0.412 0.38 668 414 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.80 42 169 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.88 43 314 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 U87MG_CENTRAL_NERVOUS_SYSTEM NA U87MG_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 44 387 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.94 2 30 TTN 7273 broad.mit.edu 37 2 179544685 179544686 + In_Frame_Ins INS - TCT TCT U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr2:179544685_179544686insTCT uc010zfg.1 - 137 30007_30008 c.29783_29784insAGA c.(29782-29784)GAG>GAAGAG p.9928_9928E>EE TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_In_Frame_Ins_p.6589_6589E>EE|TTN_uc010fre.1_Intron|TTN_uc002una.1_5'Flank|TTN_uc010frf.1_5'Flank NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 10855 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CATGAATGTACTCTTCTTCTTC 0.436 0.15 127 23 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.33 10 5 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 38 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 60 49 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 23 37 CCND3 896 broad.mit.edu 37 6 41903745 41903746 + Frame_Shift_Ins INS - G G rs143180698 by1000genomes U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:41903745_41903746insG uc003orn.2 - 5 976_977 c.811_812insC c.(811-813)CGGfs p.R271fs CCND3_uc003orp.2_Frame_Shift_Ins_p.R190fs|CCND3_uc011duk.1_Frame_Shift_Ins_p.R75fs|CCND3_uc003orm.2_Frame_Shift_Ins_p.R221fs|CCND3_uc003oro.2_Frame_Shift_Ins_p.R199fs NM_001760 NP_001751 P30281 CCND3_HUMAN cyclin D3 isoform 2 271 cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus protein kinase binding 0 Colorectal(47;0.121) Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152) GCTGGAGCCCCGGGGGGCTTTG 0.653 0.16 160 30 AKAP9 10142 broad.mit.edu 37 7 91624069 91624070 + Frame_Shift_Del DEL AT - - U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr7:91624069_91624070delAT uc003ulg.2 + 6 936_937 c.711_712delAT c.(709-714)AAATTAfs p.K237fs AKAP9_uc003uld.3_Frame_Shift_Del_p.K237fs|AKAP9_uc003ule.2_Frame_Shift_Del_p.K249fs|AKAP9_uc003ulf.2_Frame_Shift_Del_p.K237fs NM_005751 NP_005742 Q99996 AKAP9_HUMAN A-kinase anchor protein 9 isoform 2 249_250 Potential.|Gln-rich. G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport centrosome|cytosol|Golgi apparatus receptor binding breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1) 26 all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) 0.000 0.12 90 12 PTEN 5728 broad.mit.edu 37 10 89692903 89692904 + Frame_Shift_Ins INS - CGCC CGCC rs121909224 U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr10:89692903_89692904insCGCC uc001kfb.2 + 6 1418_1419 c.387_388insCGCC c.(385-390)GGACGAfs p.G129fs NM_000314 NP_000305 P60484 PTEN_HUMAN phosphatase and tensin homolog 129_130 Phosphatase tensin-type. R -> L (in CD and endometrial hyperplasia; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes).|R -> Q (in CD; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes).|R -> G (loss of phosphatase activity towards Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3). R->M: Does not affect the ability to inhibit AKT/PKB activation. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.R130G(62)|p.R130*(54)|p.G129R(6)|p.R55fs*1(4)|p.G129*(3)|p.K128_R130del(3)|p.?(2)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.G129V(1)|p.R130R(1)|p.K128fs*47(1)|p.A121_F145del(1)|p.G129E(1)|p.G129fs*5(1)|p.F56fs*2(1)|p.G129fs*50(1)|p.G129fs*51(1) endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1) 2334 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) CTGGAAAGGGACGAACTGGTGT 0.406 0.72 10 26 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 211 77 NPAT 4863 broad.mit.edu 37 11 108043691 108043692 + Frame_Shift_Ins INS - AA AA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:108043691_108043692insAA uc001pjz.3 - 13 2121_2122 c.2019_2020insTT c.(2017-2022)TTTCTCfs p.F673fs NPAT_uc010rvv.1_5'Flank|NPAT_uc001pka.2_Frame_Shift_Ins_p.F468fs NM_002519 NP_002510 Q14207 NPAT_HUMAN nuclear protein, ataxia-telangiectasia locus 673_674 positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle Cajal body protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity ovary(2) 2 all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116) CCTAAAGAGAGAAAAATAGTAT 0.416 0.47 54 47 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.97 3 88 ACACA 31 broad.mit.edu 37 17 35454852 35454853 + In_Frame_Ins INS - GTTCTT GTTCTT U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr17:35454852_35454853insGTTCTT uc002hnm.2 - 53 6712_6713 c.6521_6522insAAGAAC c.(6520-6522)TTC>TTAAGAACC p.2174_2174F>LRT ACACA_uc002hnk.2_In_Frame_Ins_p.2096_2096F>LRT|ACACA_uc002hnl.2_In_Frame_Ins_p.2116_2116F>LRT|ACACA_uc002hnn.2_In_Frame_Ins_p.2174_2174F>LRT|ACACA_uc002hno.2_In_Frame_Ins_p.2211_2211F>LRT|ACACA_uc010cuy.2_In_Frame_Ins_p.819_819F>LRT|ACACA_uc010wdb.1_In_Frame_Ins_p.212_212F>LRT|ACACA_uc010wdc.1_In_Frame_Ins_p.300_300F>LRT NM_198836 NP_942133 Q13085 ACACA_HUMAN acetyl-Coenzyme A carboxylase alpha isoform 2 2174 Carboxyltransferase. acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process cytosol acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding large_intestine(1)|ovary(1) 2 Breast(25;0.00157)|Ovarian(249;0.15) Biotin(DB00121) TGGGAATTAGGAATTCCTCCCG 0.510 0.34 80 41 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.60 24 36 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.90 81 744 SHROOM4 57477 broad.mit.edu 37 X 50350728 50350729 + In_Frame_Ins INS - TCC TCC rs143151534 UACC257_SKIN NA UACC257_SKIN NA g.chrX:50350728_50350729insTCC uc004dpe.2 - 6 3439_3440 c.3413_3414insGGA c.(3412-3414)GAA>GAGGAA p.1138_1138E>EE SHROOM4_uc004dpd.3_RNA NM_020717 NP_065768 Q9ULL8 SHRM4_HUMAN shroom family member 4 1138 Glu-rich. actin filament organization|brain development|cell morphogenesis|cognition apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus actin filament binding upper_aerodigestive_tract(1) 1 Ovarian(276;0.236) cttcttcttcttcctcctcctc 0.223 0.75 3 9 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 UACC257_SKIN NA UACC257_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 5 108 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - UACC257_SKIN NA UACC257_SKIN NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.22 1377 399 SCYL3 57147 broad.mit.edu 37 1 169823869 169823870 + Frame_Shift_Del DEL CC - - UACC257_SKIN NA UACC257_SKIN NA g.chr1:169823869_169823870delCC uc001ggs.2 - 13 1908_1909 c.1710_1711delGG c.(1708-1713)TGGGATfs p.W570fs SCYL3_uc010plw.1_Frame_Shift_Del_p.W162fs|SCYL3_uc001ggt.2_Frame_Shift_Del_p.W516fs|SCYL3_uc001ggu.2_RNA NM_181093 NP_851607 Q8IZE3 PACE1_HUMAN SCY1-like 3 isoform 2 570_571 Interaction with EZR. cell migration Golgi apparatus|lamellipodium ATP binding|protein binding|protein kinase activity ovary(1)|skin(1) 2 all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181) TCGCAGTCATCCCAAGATGACT 0.475 0.43 806 610 ALS2 57679 broad.mit.edu 37 2 202606468 202606468 + Frame_Shift_Del DEL A - - UACC257_SKIN NA UACC257_SKIN NA g.chr2:202606468delA uc002uyo.2 - 11 2636 c.2280delT c.(2278-2280)CTTfs p.L760fs ALS2_uc002uyp.3_Frame_Shift_Del_p.L760fs|ALS2_uc002uyq.2_Frame_Shift_Del_p.L760fs|ALS2_uc010ftl.2_RNA NM_020919 NP_065970 Q96Q42 ALS2_HUMAN alsin isoform 1 760 DH. cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity skin(5)|lung(1)|breast(1) 7 TTACCCCATGAAGGAAGCTGC 0.488 0.45 602 486 SCLY 51540 broad.mit.edu 37 2 239006899 239006900 + Frame_Shift_Ins INS - A A UACC257_SKIN NA UACC257_SKIN NA g.chr2:239006899_239006900insA uc010fyv.2 + 12 1305_1306 c.1241_1242insA c.(1240-1242)CTCfs p.L414fs SCLY_uc002vxm.3_Frame_Shift_Ins_p.L381fs|SCLY_uc010znq.1_Frame_Shift_Ins_p.L208fs|SCLY_uc010znr.1_Frame_Shift_Ins_p.L320fs|SCLY_uc002vxp.3_RNA|ESPNL_uc002vxq.3_5'Flank NM_016510 NP_057594 Q96I15 SCLY_HUMAN selenocysteine lyase 414 cellular amino acid metabolic process cytosol pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity ovary(2) 2 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285) 0.000 0.92 1 11 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 UACC257_SKIN NA UACC257_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.21 54 14 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A UACC257_SKIN NA UACC257_SKIN NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.20 227 58 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 UACC257_SKIN NA UACC257_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.68 25 53 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 UACC257_SKIN NA UACC257_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.53 114 129 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 UACC257_SKIN NA UACC257_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.44 68 53 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes UACC257_SKIN NA UACC257_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 UACC257_SKIN NA UACC257_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.30 184 79 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 UACC257_SKIN NA UACC257_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 30 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 UACC257_SKIN NA UACC257_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.14 466 79 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C UACC257_SKIN NA UACC257_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.82 12 53 HRC 3270 broad.mit.edu 37 19 49657889 49657890 + In_Frame_Ins INS - TCC TCC rs147238387 by1000genomes UACC257_SKIN NA UACC257_SKIN NA g.chr19:49657889_49657890insTCC uc002pmv.2 - 1 792_793 c.605_606insGGA c.(604-606)GAA>GAGGAA p.202_202E>EE NM_002152 NP_002143 P23327 SRCH_HUMAN histidine rich calcium binding protein 202 4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats. muscle contraction sarcoplasmic reticulum lumen calcium ion binding ovary(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622) AGGcctcctcttcctcctcctc 0.455 0.77 3 10 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 UACC257_SKIN NA UACC257_SKIN NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.34 294 152 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 UACC257_SKIN NA UACC257_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.89 59 481 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 UACC257_SKIN NA UACC257_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 22 309 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 UACC812_BREAST NA UACC812_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 11 100 PLK3 1263 broad.mit.edu 37 1 45267606 45267612 + Splice_Site DEL TGAGTTT - - rs17880195 UACC812_BREAST NA UACC812_BREAST NA g.chr1:45267606_45267612delTGAGTTT uc001cmn.2 + 5 753 c.653_splice c.e5+2 p.K218_splice PLK3_uc001cmo.2_Splice_Site NM_004073 NP_004064 Q9H4B4 PLK3_HUMAN polo-like kinase 3 membrane ATP binding|protein binding|protein serine/threonine kinase activity 0 Acute lymphoblastic leukemia(166;0.155) GAGGAAGAAGTGAGTTTTGAGGAAAGG 0.507 0.68 25 52 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - UACC812_BREAST NA UACC812_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.53 481 541 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376119 + In_Frame_Del DEL TGCTGCTGC - - rs143860374;rs62265537;rs62265538 UACC812_BREAST NA UACC812_BREAST NA g.chr3:113376111_113376119delTGCTGCTGC uc003eam.2 - 7 4821_4829 c.4410_4418delGCAGCAGCA c.(4408-4419)CAGCAGCAGCAA>CAA p.1470_1473QQQQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1414_1417QQQQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1470_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgctgctgct 0.359 0.41 10 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 UACC812_BREAST NA UACC812_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.33 20 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 UACC812_BREAST NA UACC812_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.51 83 85 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 UACC812_BREAST NA UACC812_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.62 33 54 RASA1 5921 broad.mit.edu 37 5 86564664 86564665 + Frame_Shift_Ins INS - G G UACC812_BREAST NA UACC812_BREAST NA g.chr5:86564664_86564665insG uc003kiw.2 + 1 514_515 c.396_397insG c.(394-399)GGCGGTfs p.G132fs RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_5'Flank|RASA1_uc011ctv.1_5'Flank|RASA1_uc011ctw.1_5'Flank|RASA1_uc010jaw.2_5'Flank|RASA1_uc011ctu.1_Frame_Shift_Ins_p.G132fs NM_002890 NP_002881 P20936 RASA1_HUMAN RAS p21 protein activator 1 isoform 1 132_133 cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis cytosol|intrinsic to internal side of plasma membrane glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding upper_aerodigestive_tract(3)|ovary(1)|lung(1) 5 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) GGCCAGGCGGCGGTTTTCCCCC 0.535 0.30 31 13 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes UACC812_BREAST NA UACC812_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 15 WHSC1L1 54904 broad.mit.edu 37 8 38187218 38187219 + Frame_Shift_Ins INS - G G UACC812_BREAST NA UACC812_BREAST NA g.chr8:38187218_38187219insG uc003xli.2 - 6 1776_1777 c.1258_1259insC c.(1258-1260)CGAfs p.R420fs WHSC1L1_uc011lbm.1_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc010lwe.2_Frame_Shift_Ins_p.R420fs|WHSC1L1_uc003xlj.2_Frame_Shift_Ins_p.R420fs NM_023034 NP_075447 Q9BZ95 NSD3_HUMAN WHSC1L1 protein isoform long 420 cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome histone-lysine N-methyltransferase activity|zinc ion binding breast(1) 1 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TCTTGGTCGTCGGGTTTTTTTA 0.436 0.12 515 71 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039791 + In_Frame_Del DEL CAGCAGCAGCAGCAG - - rs113070757;rs62639301;rs139102413;rs145170448;rs147609454;rs142219087 byFrequency;byFrequency;byFrequency;byFrequency;byFrequency UACC812_BREAST NA UACC812_BREAST NA g.chr9:2039777_2039791delCAGCAGCAGCAGCAG uc003zhc.2 + 4 766_780 c.667_681delCAGCAGCAGCAGCAG c.(667-681)CAGCAGCAGCAGCAGdel p.QQQQQ233del SMARCA2_uc003zhd.2_In_Frame_Del_p.QQQQQ233del|SMARCA2_uc010mha.2_In_Frame_Del_p.QQQQQ224del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 233_237 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) gcagcagcaacagcagcagcagcagcagcagcagc 0.270 0.19 35 8 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 UACC812_BREAST NA UACC812_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 734 134 ATN1 1822 broad.mit.edu 37 12 7045880 7045885 + In_Frame_Del DEL CAGCAA - - UACC812_BREAST NA UACC812_BREAST NA g.chr12:7045880_7045885delCAGCAA uc001qrw.1 + 5 1687_1692 c.1450_1455delCAGCAA c.(1450-1455)CAGCAAdel p.QQ500del ATN1_uc001qrx.1_In_Frame_Del_p.QQ500del|ATN1_uc001qry.1_In_Frame_Del_p.QQ485del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 500_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 CCATCACCACcagcaacagcaacagc 0.447 0.39 30 19 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency UACC812_BREAST NA UACC812_BREAST NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.41 42 29 MEF2A 4205 broad.mit.edu 37 15 100252710 100252712 + In_Frame_Del DEL CAG - - UACC812_BREAST NA UACC812_BREAST NA g.chr15:100252710_100252712delCAG uc010urw.1 + 11 1617_1619 c.1258_1260delCAG c.(1258-1260)CAGdel p.Q430del MEF2A_uc010urv.1_In_Frame_Del_p.Q360del|MEF2A_uc010bos.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvf.2_In_Frame_Del_p.Q422del|MEF2A_uc002bve.2_In_Frame_Del_p.Q428del|MEF2A_uc002bvg.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvi.2_In_Frame_Del_p.Q420del|MEF2A_uc010bot.2_In_Frame_Del_p.Q352del NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 430 Gln/Pro-rich. Missing (in Ref. 4; AAB17195/AAB17196). apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) ATCGGGCTTCcagcagcagcagc 0.493 0.33 12 6 MYH1 4619 broad.mit.edu 37 17 10411917 10411918 + Frame_Shift_Del DEL TG - - UACC812_BREAST NA UACC812_BREAST NA g.chr17:10411917_10411918delTG uc002gmo.2 - 16 1753_1754 c.1659_1660delCA c.(1657-1662)AACAAGfs p.N553fs uc002gml.1_Intron NM_005963 NP_005954 P12882 MYH1_HUMAN myosin, heavy chain 1, skeletal muscle, adult 553_554 Myosin head-like. muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1) 21 TCATACAGCTTGTTCTTGAAGG 0.475 0.96 8 192 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 UACC812_BREAST NA UACC812_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.92 47 517 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 UACC812_BREAST NA UACC812_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.92 7 78 MN1 4330 broad.mit.edu 37 22 28194912 28194913 + In_Frame_Ins INS - TGC TGC rs45520238 UACC812_BREAST NA UACC812_BREAST NA g.chr22:28194912_28194913insTGC uc003adj.2 - 1 2574_2575 c.1619_1620insGCA c.(1618-1620)CAA>CAGCAA p.540_540Q>QQ NM_002430 NP_002421 Q10571 MN1_HUMAN meningioma 1 540 Poly-Gln. binding central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1) 10 0.000 0.14 376 61 CARD10 29775 broad.mit.edu 37 22 37906308 37906309 + In_Frame_Ins INS - CTCCTT CTCCTT rs140363084;rs113275238 by1000genomes UACC812_BREAST NA UACC812_BREAST NA g.chr22:37906308_37906309insCTCCTT uc003asx.1 - 4 822_823 c.819_820insAAGGAG c.(817-822)insAAGGAG p.273_274insKE CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_In_Frame_Ins_p.273_274insKE NM_014550 NP_055365 Q9BWT7 CAR10_HUMAN caspase recruitment domain protein 10 273_274 Potential. activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis CBM complex receptor signaling complex scaffold activity upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1) 6 Melanoma(58;0.0574) ACATTGTCTGGctccttctcct 0.545 0.13 131 20 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 UACC893_BREAST NA UACC893_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.58 52 71 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 UACC893_BREAST NA UACC893_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.14 42 7 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 UACC893_BREAST NA UACC893_BREAST NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.42 14 10 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 UACC893_BREAST NA UACC893_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.62 112 182 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 UACC893_BREAST NA UACC893_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.89 5 42 BRD2 6046 broad.mit.edu 37 6 32945740 32945741 + Frame_Shift_Del DEL AG - - UACC893_BREAST NA UACC893_BREAST NA g.chr6:32945740_32945741delAG uc003ocn.3 + 9 3237_3238 c.1536_1537delAG c.(1534-1539)TCAGAGfs p.S512fs BRD2_uc003oco.2_RNA|BRD2_uc003ocq.3_Frame_Shift_Del_p.S512fs|BRD2_uc003ocp.3_Frame_Shift_Del_p.S392fs|BRD2_uc010juh.2_Frame_Shift_Del_p.S512fs NM_005104 NP_005095 P25440 BRD2_HUMAN bromodomain containing 2 512_513 Glu/Ser-rich. spermatogenesis nucleus protein serine/threonine kinase activity central_nervous_system(3)|stomach(2) 5 GCTCAGACTCAGAGGAAGAAAG 0.351 0.41 16 11 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes UACC893_BREAST NA UACC893_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.67 4 8 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency UACC893_BREAST NA UACC893_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.75 135 398 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 UACC893_BREAST NA UACC893_BREAST NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.45 12 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C UACC893_BREAST NA UACC893_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.90 41 379 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 UACC893_BREAST NA UACC893_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.60 62 92 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 UACC893_BREAST NA UACC893_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 111 245 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 UACC893_BREAST NA UACC893_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.89 3 25 HNRNPH2 3188 broad.mit.edu 37 X 100667239 100667240 + Frame_Shift_Ins INS - T T UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chrX:100667239_100667240insT uc004ehm.2 + 2 433_434 c.263_264insT c.(262-264)TCTfs p.S88fs HNRNPH2_uc004ehn.2_Frame_Shift_Ins_p.S88fs NM_019597 NP_062543 P55795 HNRH2_HUMAN heterogeneous nuclear ribonucleoprotein H2 88 RRM 1. nuclear mRNA splicing, via spliceosome actin cytoskeleton|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm nucleotide binding|protein binding|RNA binding 0 GTATTCAAGTCTAACAGTGTTG 0.450 0.75 22 66 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.43 28 21 NRD1 4898 broad.mit.edu 37 1 52306064 52306066 + In_Frame_Del DEL TCT - - rs145326984;rs72496486 UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr1:52306064_52306066delTCT uc001ctc.3 - 2 784_786 c.462_464delAGA c.(460-465)GAAGAT>GAT p.E154del NRD1_uc009vzb.2_Translation_Start_Site|NRD1_uc001ctd.3_In_Frame_Del_p.E154del|NRD1_uc001cte.2_In_Frame_Del_p.E22del|NRD1_uc001ctf.2_In_Frame_Del_p.E154del|NRD1_uc010ong.1_RNA|NRD1_uc009vzc.1_In_Frame_Del_p.E22del|NRD1_uc001ctg.1_5'Flank NM_002525 NP_002516 O43847 NRDC_HUMAN nardilysin isoform a Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity cell surface|cytosol epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding 0 ttcatcatcatcttcttcttctt 0.158 0.60 4 6 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.28 71 28 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.30 33 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.32 38 18 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.79 6 23 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.91 1 10 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.20 32 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.86 2 12 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.50 5 5 ABCC3 8714 broad.mit.edu 37 17 48745322 48745322 + Frame_Shift_Del DEL A - - UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr17:48745322delA uc002isl.2 + 13 1814 c.1734delA c.(1732-1734)TTAfs p.L578fs NM_003786 NP_003777 O15438 MRP3_HUMAN ATP-binding cassette, sub-family C, member 3 578 Helical; Name=11; (By similarity).|ABC transmembrane type-1 1. bile acid metabolic process integral to plasma membrane|membrane fraction ATP binding|bile acid-exporting ATPase activity|organic anion transmembrane transporter activity skin(3)|central_nervous_system(1) 4 BRCA - Breast invasive adenocarcinoma(22;3.05e-09) Glibenclamide(DB01016) TTAATATCTTAAGACTTCCCC 0.532 0.38 113 69 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.55 13 16 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.39 43 27 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.71 50 124 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 UBLC1_URINARY_TRACT NA UBLC1_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 1 24 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 UMUC1_URINARY_TRACT NA UMUC1_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.98 1 57 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 UMUC1_URINARY_TRACT NA UMUC1_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.41 83 57 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 UMUC1_URINARY_TRACT NA UMUC1_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 29 49 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 UMUC1_URINARY_TRACT NA UMUC1_URINARY_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 18 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 UMUC1_URINARY_TRACT NA UMUC1_URINARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 200 46 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 UMUC1_URINARY_TRACT NA UMUC1_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.60 10 15 TOP1 7150 broad.mit.edu 37 20 39690048 39690049 + Frame_Shift_Del DEL AA - - UMUC1_URINARY_TRACT NA UMUC1_URINARY_TRACT NA g.chr20:39690048_39690049delAA uc002xjl.2 + 3 319_320 c.73_74delAA c.(73-75)AAAfs p.K25fs TOP1_uc010gge.1_Intron NM_003286 NP_003277 P11387 TOP1_HUMAN DNA topoisomerase I 25 Lys-rich. DNA topological change|interspecies interaction between organisms|phosphorylation|programmed cell death|response to drug chromosome|nucleolus|nucleoplasm ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity|protein binding breast(3)|ovary(2)|central_nervous_system(1)|kidney(1) 7 Myeloproliferative disorder(115;0.00878) Irinotecan(DB00762)|Lucanthone(DB04967)|Topotecan(DB01030) TCataaacacaaagataaacac 0.401 0.10 60 7 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 UMUC1_URINARY_TRACT NA UMUC1_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.93 36 447 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 UMUC1_URINARY_TRACT NA UMUC1_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 102 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 UMUC3_URINARY_TRACT NA UMUC3_URINARY_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.92 5 56 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - UMUC3_URINARY_TRACT NA UMUC3_URINARY_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.36 177 98 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 UMUC3_URINARY_TRACT NA UMUC3_URINARY_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.51 90 95 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 UMUC3_URINARY_TRACT NA UMUC3_URINARY_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.60 14 21 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 UMUC3_URINARY_TRACT NA UMUC3_URINARY_TRACT NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.15 230 42 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 UMUC3_URINARY_TRACT NA UMUC3_URINARY_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 514 187 ATM 472 broad.mit.edu 37 11 108214080 108214080 + Frame_Shift_Del DEL G - - UMUC3_URINARY_TRACT NA UMUC3_URINARY_TRACT NA g.chr11:108214080delG uc001pkb.1 + 57 8785 c.8400delG c.(8398-8400)CAGfs p.Q2800fs ATM_uc009yxr.1_Frame_Shift_Del_p.Q2800fs|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron|ATM_uc001pke.1_Frame_Shift_Del_p.Q1452fs NM_000051 NP_000042 Q13315 ATM_HUMAN ataxia telangiectasia mutated isoform 1 2800 PI3K/PI4K. cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence cytoplasmic membrane-bounded vesicle|nucleoplasm 1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding p.F2799fs*4(1) haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1) 240 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147) GTGCCTTTCAGTGCCAAAAGA 0.358 0.10 104 12 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 UMUC3_URINARY_TRACT NA UMUC3_URINARY_TRACT NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.56 8 10 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 UMUC3_URINARY_TRACT NA UMUC3_URINARY_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.46 28 24 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 UMUC3_URINARY_TRACT NA UMUC3_URINARY_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.23 48 14 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 UMUC3_URINARY_TRACT NA UMUC3_URINARY_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.86 57 341 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 UMUC3_URINARY_TRACT NA UMUC3_URINARY_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.99 1 88 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 VCAP_PROSTATE NA VCAP_PROSTATE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.96 1 25 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes VCAP_PROSTATE NA VCAP_PROSTATE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.36 9 5 ULK4 54986 broad.mit.edu 37 3 41860984 41860985 + Frame_Shift_Ins INS - T T VCAP_PROSTATE NA VCAP_PROSTATE NA g.chr3:41860984_41860985insT uc003ckv.3 - 19 1979_1980 c.1778_1779insA c.(1777-1779)AAGfs p.K593fs ULK4_uc003ckw.2_Frame_Shift_Ins_p.K593fs NM_017886 NP_060356 Q96C45 ULK4_HUMAN unc-51-like kinase 4 593 ATP binding|protein serine/threonine kinase activity 0 KIRC - Kidney renal clear cell carcinoma(284;0.214) CTCTAGGGTTCTTTTTTTTTTC 0.450 0.17 58 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 VCAP_PROSTATE NA VCAP_PROSTATE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.58 102 139 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 VCAP_PROSTATE NA VCAP_PROSTATE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.45 32 26 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes VCAP_PROSTATE NA VCAP_PROSTATE NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.50 7 7 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 VCAP_PROSTATE NA VCAP_PROSTATE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.21 30 8 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes VCAP_PROSTATE NA VCAP_PROSTATE NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.87 2 13 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - VCAP_PROSTATE NA VCAP_PROSTATE NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.88 2 14 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 VCAP_PROSTATE NA VCAP_PROSTATE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 1153 164 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 VCAP_PROSTATE NA VCAP_PROSTATE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.58 22 31 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 VCAP_PROSTATE NA VCAP_PROSTATE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.28 112 43 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 VCAP_PROSTATE NA VCAP_PROSTATE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 106 434 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 VCAP_PROSTATE NA VCAP_PROSTATE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 5 135 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 34 VHL 7428 broad.mit.edu 37 3 10191487 10191488 + Frame_Shift_Del DEL GC - - rs5030818 VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chr3:10191487_10191488delGC uc003bvc.2 + 3 693_694 c.480_481delGC c.(478-483)GAGCGAfs p.E160fs VHL_uc003bvd.2_Frame_Shift_Del_p.E119fs NM_000551 NP_000542 P40337 VHL_HUMAN von Hippel-Lindau tumor suppressor isoform 1 160_161 Interaction with Elongin BC complex. R -> P (in pheochromocytoma and VHLD; type I).|R -> Q (in pheochromocytoma and VHLD; type II). anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus protein binding|transcription factor binding p.R161*(10)|p.E160K(5)|p.E160fs*10(3)|p.E160fs*14(2)|p.E160*(2)|p.R161del(1)|p.R161fs*13(1)|p.K159fs*13(1)|p.E160fs*9(1)|p.?fs(1)|p.E160del(1)|p.L158fs*6(1)|p.E160fs*13(1) kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1) 1346 Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569) CTCTGAAAGAGCGATGCCTCCA 0.500 1.00 0 31 TGFBR2 7048 broad.mit.edu 37 3 30713211 30713211 + Frame_Shift_Del DEL C - - VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chr3:30713211delC uc003ceo.2 + 4 918 c.536delC c.(535-537)GCCfs p.A179fs TGFBR2_uc003cen.2_Frame_Shift_Del_p.A204fs NM_003242 NP_003233 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II 179 Helical; (Potential). activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis caveola|external side of plasma membrane ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1) 26 CTGGGAGTTGCCATATCTGTC 0.493 0.96 5 132 BAP1 8314 broad.mit.edu 37 3 52437305 52437305 + Frame_Shift_Del DEL T - - VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chr3:52437305delT uc003ddx.2 - 14 1854 c.1739delA c.(1738-1740)AAGfs p.K580fs BAP1_uc003ddw.2_RNA|BAP1_uc010hmg.2_RNA|BAP1_uc010hmh.2_Intron NM_004656 NP_004647 Q92560 BAP1_HUMAN BRCA1 associated protein-1 580 monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process cytoplasm|nucleolus|PR-DUB complex chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1) 65 BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277) CGAGGAACCCTTCCCACCCTC 0.587 0.99 2 134 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.44 79 61 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.52 29 31 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.98 1 57 TGFBR1 7046 broad.mit.edu 37 9 101867563 101867564 + Frame_Shift_Ins INS - T T VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chr9:101867563_101867564insT uc004azc.2 + 1 152_153 c.76_77insT c.(76-78)GCGfs p.A26fs TGFBR1_uc004azd.2_Frame_Shift_Ins_p.A26fs NM_004612 NP_004603 P36897 TGFR1_HUMAN transforming growth factor, beta receptor I 26 Missing (in allele TGFBR1*6A; could be a tumor susceptibility allele).|A -> AA (in allele TGFBR1*10A; rare polymorphism). activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding lung(2)|ovary(1) 3 Acute lymphoblastic leukemia(62;0.0559) 0.000 0.77 3 10 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.26 238 83 LCP1 3936 broad.mit.edu 37 13 46730655 46730656 + In_Frame_Ins INS - ATT ATT VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chr13:46730655_46730656insATT uc001vaz.3 - 5 534_535 c.408_409insAAT c.(406-411)insAAT p.136_137insN LCP1_uc001vba.3_In_Frame_Ins_p.136_137insN NM_002298 NP_002289 P13796 PLSL_HUMAN L-plastin 136_137 Actin-binding 1.|CH 1. regulation of intracellular protein transport|T cell activation involved in immune response cell junction|cytosol|ruffle membrane calcium ion binding lung(4)|ovary(3) 7 Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262) KIRC - Kidney renal clear cell carcinoma(16;0.234) GBM - Glioblastoma multiforme(144;5.39e-05) CAATCAGGATCATTTTCCAGGG 0.371 0.87 10 69 CES3 23491 broad.mit.edu 37 16 66997260 66997260 + Frame_Shift_Del DEL G - - VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chr16:66997260delG uc002eqt.2 + 2 334 c.261delG c.(259-261)GTGfs p.V87fs CES3_uc010cdz.2_Frame_Shift_Del_p.V87fs|CES3_uc010cea.2_RNA NM_024922 NP_079198 Q6UWW8 EST3_HUMAN carboxylesterase 3 precursor 87 endoplasmic reticulum lumen carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity ovary(3)|central_nervous_system(2) 5 Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127) 0.000 0.94 1 16 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.22 32 9 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.72 170 436 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 VMRCRCW_KIDNEY NA VMRCRCW_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.93 4 52 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.99 1 66 MKNK1 8569 broad.mit.edu 37 1 47024296 47024297 + Frame_Shift_Ins INS - G G VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chr1:47024296_47024297insG uc001cqb.2 - 14 1592_1593 c.1348_1349insC c.(1348-1350)CTGfs p.L450fs MKNK1_uc010omd.1_Frame_Shift_Ins_p.L314fs|MKNK1_uc001cqc.2_Frame_Shift_Ins_p.L409fs|MKNK1_uc009vyi.2_3'UTR|MKNK1_uc010ome.1_3'UTR NM_003684 NP_003675 Q9BUB5 MKNK1_HUMAN MAP kinase-interacting serine/threonine kinase 1 450 intracellular protein kinase cascade|peptidyl-serine phosphorylation|regulation of translation cytoplasm|nucleus ATP binding|protein binding|protein serine/threonine kinase activity lung(2) 2 Acute lymphoblastic leukemia(166;0.155) TGCCTGGGCCAGGGCCCGTCTC 0.629 0.11 138 17 CCR3 1232 broad.mit.edu 37 3 46307351 46307351 + Frame_Shift_Del DEL G - - rs145010080 VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chr3:46307351delG uc003cpg.1 + 4 1245 c.702delG c.(700-702)AAGfs p.K234fs CCR3_uc003cpi.1_Frame_Shift_Del_p.K234fs|CCR3_uc003cpj.1_Frame_Shift_Del_p.K234fs|CCR3_uc003cpk.1_Frame_Shift_Del_p.K255fs|CCR3_uc010hjb.1_Frame_Shift_Del_p.K252fs|CCR3_uc003cpl.1_Frame_Shift_Del_p.K267fs NM_178329 NP_847899 P51677 CCR3_HUMAN CC chemokine receptor 3 isoform 1 234 Cytoplasmic (Potential). cell adhesion|cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cAMP nucleotide second messenger|inflammatory response|interspecies interaction between organisms|positive regulation of angiogenesis integral to plasma membrane ovary(3)|lung(3)|breast(1)|kidney(1) 8 BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216) 0.000 0.11 407 48 BAP1 8314 broad.mit.edu 37 3 52442616 52442632 + Splice_Site DEL TACAGGGCTGGGGGAAG - - VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chr3:52442616_52442632delTACAGGGCTGGGGGAAG uc003ddx.2 - 4 238 c.123_splice c.e4-1 p.G41_splice PHF7_uc003ddy.2_5'Flank|PHF7_uc003ddz.2_5'Flank NM_004656 NP_004647 Q92560 BAP1_HUMAN BRCA1 associated protein-1 monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process cytoplasm|nucleolus|PR-DUB complex chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1) 65 BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277) 0.000 0.57 23 30 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.46 14 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 78 138 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.61 16 25 PIP5K1P1 206426 broad.mit.edu 37 6 7986805 7986806 + Frame_Shift_Ins INS - G G VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chr6:7986805_7986806insG uc003mxx.3 + 1 471_472 c.36_37insG c.(34-39)GTCGGTfs p.V12fs TXNDC5_uc003mxw.2_Intron NR_027712 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 CGTTGGCGGTCGGTTTTTCATC 0.619 0.24 35 11 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.37 771 448 ZNF469 84627 broad.mit.edu 37 16 88498057 88498057 + Frame_Shift_Del DEL T - - VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chr16:88498057delT uc002fku.2 + 2 4095 c.4095delT c.(4093-4095)TGTfs p.C1365fs NM_001127464 NP_001120936 Q96JG9 ZN469_HUMAN zinc finger protein 469 1365 Pro-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding 0 0.000 1.00 0 10 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.93 4 54 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.78 40 142 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.94 44 686 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 VMRCRCZ_KIDNEY NA VMRCRCZ_KIDNEY NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 111 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 WM115_SKIN NA WM115_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 18 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 WM115_SKIN NA WM115_SKIN NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.75 4 12 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 WM115_SKIN NA WM115_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.36 58 32 PDGFA 5154 broad.mit.edu 37 7 540842 540842 + Frame_Shift_Del DEL A - - WM115_SKIN NA WM115_SKIN NA g.chr7:540842delA uc003sir.2 - 5 1334 c.491delT c.(490-492)TTAfs p.L164fs PDGFA_uc003sis.2_Frame_Shift_Del_p.L164fs|PDGFA_uc003sit.1_Frame_Shift_Del_p.L178fs NM_002607 NP_002598 P04085 PDGFA_HUMAN platelet-derived growth factor alpha isoform 1 164 actin cytoskeleton organization|angiogenesis|cell projection assembly|embryo development|hair follicle development|lung alveolus development|negative chemotaxis|negative regulation of phosphatidylinositol biosynthetic process|negative regulation of platelet activation|organ morphogenesis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of DNA replication|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|positive regulation of MAP kinase activity|positive regulation of mesenchymal cell proliferation|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein autophosphorylation|positive regulation of protein kinase B signaling cascade|regulation of actin cytoskeleton organization|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling|regulation of peptidyl-tyrosine phosphorylation|regulation of smooth muscle cell migration|skin development cell surface|endoplasmic reticulum lumen|extracellular space|Golgi membrane|microvillus|platelet alpha granule lumen collagen binding|eukaryotic cell surface binding|growth factor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein heterodimerization activity|protein homodimerization activity 0 Ovarian(82;0.0112) UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15) GACTTCTTTTAATTTTGGCTT 0.557 0.21 325 89 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes WM115_SKIN NA WM115_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.77 3 10 PCDH15 65217 broad.mit.edu 37 10 55581909 55581910 + Frame_Shift_Ins INS - TTAA TTAA WM115_SKIN NA WM115_SKIN NA g.chr10:55581909_55581910insTTAA uc001jju.1 - 33 5971_5972 c.5576_5577insTTAA c.(5575-5577)AAGfs p.K1859fs PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Frame_Shift_Ins_p.K1856fs|PCDH15_uc010qhw.1_Frame_Shift_Ins_p.K1819fs|PCDH15_uc010qhx.1_Frame_Shift_Ins_p.K1790fs|PCDH15_uc010qhy.1_Frame_Shift_Ins_p.K1866fs|PCDH15_uc010qhz.1_Frame_Shift_Ins_p.K1861fs|PCDH15_uc010qia.1_Frame_Shift_Ins_p.K1839fs|PCDH15_uc010qib.1_Frame_Shift_Ins_p.K1836fs NM_033056 NP_149045 Q96QU1 PCD15_HUMAN protocadherin 15 isoform CD1-4 precursor 1859 Cytoplasmic (Potential). equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse calcium ion binding pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2) 13 Melanoma(3;0.117)|Lung SC(717;0.238) TCATAGAGGACTTAATTTTCTC 0.386 0.73 35 96 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 WM115_SKIN NA WM115_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.15 111 20 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C WM115_SKIN NA WM115_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.92 4 48 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 WM115_SKIN NA WM115_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 72 404 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 WM115_SKIN NA WM115_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 5 49 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 WM1799_SKIN NA WM1799_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.38 18 11 PRDM2 7799 broad.mit.edu 37 1 14105104 14105105 + Frame_Shift_Ins INS - A A WM1799_SKIN NA WM1799_SKIN NA g.chr1:14105104_14105105insA uc001avi.2 + 8 1670_1671 c.814_815insA c.(814-816)GAGfs p.E272fs PRDM2_uc001avg.2_Intron|PRDM2_uc001avh.2_Frame_Shift_Ins_p.E272fs|PRDM2_uc001avj.2_Intron|PRDM2_uc009vod.1_Intron|PRDM2_uc001avk.2_Frame_Shift_Ins_p.E71fs|PRDM2_uc009voe.2_Intron|PRDM2_uc009vof.2_Intron NM_012231 NP_036363 Q13029 PRDM2_HUMAN retinoblastoma protein-binding zinc finger 272 Asp/Glu-rich (acidic). Golgi apparatus|nucleus DNA binding|histone-lysine N-methyltransferase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1) 1 Ovarian(185;0.249) all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255) GBM - Glioblastoma multiforme(2;0.00182) UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145) 0.000 1.00 0 18 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes WM1799_SKIN NA WM1799_SKIN NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.53 7 8 TPRXL 348825 broad.mit.edu 37 3 14106310 14106311 + In_Frame_Ins INS - CCAGCACCAGCAGTC CCAGCACCAGCAGTC WM1799_SKIN NA WM1799_SKIN NA g.chr3:14106310_14106311insCCAGCACCAGCAGTC uc011avd.1 + 3 1089_1090 c.634_635insCCAGCACCAGCAGTC c.(634-636)TCC>TCCAGCACCAGCAGTCCC p.217_218insSTSSP TPRXL_uc003byh.1_In_Frame_Ins_p.217_218insSTSSP|TPRXL_uc003byg.2_In_Frame_Ins_p.217_218insSTSSP NR_002223 RecName: Full=Putative protein TPRXL; 0 cagcagcagctccagcaccagc 0.213 0.64 4 7 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 WM1799_SKIN NA WM1799_SKIN NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.31 18 8 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 WM1799_SKIN NA WM1799_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.70 49 114 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 WM1799_SKIN NA WM1799_SKIN NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.62 39 65 ATXN1 6310 broad.mit.edu 37 6 16327916 16327918 + In_Frame_Del DEL TGC - - rs28555263 WM1799_SKIN NA WM1799_SKIN NA g.chr6:16327916_16327918delTGC uc003nbt.2 - 8 1595_1597 c.624_626delGCA c.(622-627)CAGCAT>CAT p.Q208del ATXN1_uc010jpi.2_In_Frame_Del_p.Q208del|ATXN1_uc010jpj.1_Intron NM_000332 NP_000323 P54253 ATX1_HUMAN ataxin 1 208 Poly-Gln. cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association skin(3)|central_nervous_system(1) 4 Breast(50;0.063)|Ovarian(93;0.0733) all_hematologic(90;0.000682)|Ovarian(999;0.00973) ctgatgctgatgctgctgctgct 0.379 0.11 66 8 SMO 6608 broad.mit.edu 37 7 128829039 128829040 + In_Frame_Ins INS - GCT GCT WM1799_SKIN NA WM1799_SKIN NA g.chr7:128829039_128829040insGCT uc003vor.2 + 1 327_328 c.47_48insGCT c.(46-48)GGG>GGGCTG p.23_24insL NM_005631 NP_005622 Q99835 SMO_HUMAN smoothened precursor 23_24 adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding p.G16_L17insLL(1) skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1) 37 0.000 0.44 331 259 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes WM1799_SKIN NA WM1799_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.87 3 20 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - WM1799_SKIN NA WM1799_SKIN NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.94 1 15 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 WM1799_SKIN NA WM1799_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 62 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 WM1799_SKIN NA WM1799_SKIN NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 1.00 0 20 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 WM1799_SKIN NA WM1799_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.34 576 292 MEF2A 4205 broad.mit.edu 37 15 100252710 100252712 + In_Frame_Del DEL CAG - - WM1799_SKIN NA WM1799_SKIN NA g.chr15:100252710_100252712delCAG uc010urw.1 + 11 1617_1619 c.1258_1260delCAG c.(1258-1260)CAGdel p.Q430del MEF2A_uc010urv.1_In_Frame_Del_p.Q360del|MEF2A_uc010bos.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvf.2_In_Frame_Del_p.Q422del|MEF2A_uc002bve.2_In_Frame_Del_p.Q428del|MEF2A_uc002bvg.2_In_Frame_Del_p.Q420del|MEF2A_uc002bvi.2_In_Frame_Del_p.Q420del|MEF2A_uc010bot.2_In_Frame_Del_p.Q352del NM_005587 NP_005578 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A isoform 1 430 Gln/Pro-rich. Missing (in Ref. 4; AAB17195/AAB17196). apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development nuclear chromatin|nucleoplasm activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding ovary(1) 1 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) ATCGGGCTTCcagcagcagcagc 0.493 0.21 26 7 E2F4 1874 broad.mit.edu 37 16 67229794 67229802 + In_Frame_Del DEL CAGCAGCAG - - rs112970553;rs72133338 WM1799_SKIN NA WM1799_SKIN NA g.chr16:67229794_67229802delCAGCAGCAG uc002erz.2 + 7 981_989 c.918_926delCAGCAGCAG c.(916-927)GACAGCAGCAGC>GAC p.SSS316del NM_001950 NP_001941 Q16254 E2F4_HUMAN E2F transcription factor 4 316_318 Poly-Ser. G1 phase of mitotic cell cycle transcription factor complex DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription factor binding central_nervous_system(1) 1 Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325) CCCTGCTGGAcagcagcagcagcagcagc 0.440 0.33 10 5 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 WM1799_SKIN NA WM1799_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.27 96 36 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 WM1799_SKIN NA WM1799_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.69 112 251 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 WM1799_SKIN NA WM1799_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.85 9 50 SHROOM4 57477 broad.mit.edu 37 X 50350758 50350759 + In_Frame_Ins INS - TGCTGCTGCTGT TGCTGCTGCTGT WM88_SKIN NA WM88_SKIN NA g.chrX:50350758_50350759insTGCTGCTGCTGT uc004dpe.2 - 6 3409_3410 c.3383_3384insACAGCAGCAGCA c.(3382-3384)CAG>CAACAGCAGCAGCAG p.1128_1128Q>QQQQQ SHROOM4_uc004dpd.3_RNA NM_020717 NP_065768 Q9ULL8 SHRM4_HUMAN shroom family member 4 1128 Gln-rich. actin filament organization|brain development|cell morphogenesis|cognition apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus actin filament binding upper_aerodigestive_tract(1) 1 Ovarian(276;0.236) cctgttgcttctgctgctgctg 0.252 0.70 3 7 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 WM88_SKIN NA WM88_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.68 18 39 MPL 4352 broad.mit.edu 37 1 43804365 43804378 + Frame_Shift_Del DEL AGCGAGTCCTCTTT - - WM88_SKIN NA WM88_SKIN NA g.chr1:43804365_43804378delAGCGAGTCCTCTTT uc001ciw.2 + 3 410_423 c.365_378delAGCGAGTCCTCTTT c.(364-378)CAGCGAGTCCTCTTTfs p.Q122fs MPL_uc001civ.2_Frame_Shift_Del_p.Q122fs|MPL_uc009vwr.2_Frame_Shift_Del_p.Q115fs NM_005373 NP_005364 P40238 TPOR_HUMAN myeloproliferative leukemia virus oncogene 122_126 Extracellular (Potential). cell proliferation|platelet activation integral to plasma membrane cytokine receptor activity haematopoietic_and_lymphoid_tissue(361)|upper_aerodigestive_tract(1)|pancreas(1) 363 all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0505) ACTCGGACTCAGCGAGTCCTCTTTGTGGACAGTG 0.575 0.37 47 28 TPRXL 348825 broad.mit.edu 37 3 14106026 14106037 + In_Frame_Del DEL CCAGCAGTAGCT - - rs139011213 by1000genomes WM88_SKIN NA WM88_SKIN NA g.chr3:14106026_14106037delCCAGCAGTAGCT uc011avd.1 + 3 805_816 c.350_361delCCAGCAGTAGCT c.(349-363)CCCAGCAGTAGCTCC>CCC p.SSSS122del TPRXL_uc003byh.1_In_Frame_Del_p.SSSS122del|TPRXL_uc003byg.2_In_Frame_Del_p.SSSS122del NR_002223 RecName: Full=Putative protein TPRXL; 0 agcagcagccccagcagtagctccagcagcag 0.000 0.62 10 16 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 WM88_SKIN NA WM88_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.59 97 142 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 WM88_SKIN NA WM88_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.79 15 55 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes WM88_SKIN NA WM88_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.94 1 16 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - WM88_SKIN NA WM88_SKIN NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.94 1 15 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 WM88_SKIN NA WM88_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.45 6 5 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 WM88_SKIN NA WM88_SKIN NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.96 2 52 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 WM88_SKIN NA WM88_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.29 363 149 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 WM88_SKIN NA WM88_SKIN NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.61 18 28 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 WM88_SKIN NA WM88_SKIN NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.32 64 30 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 WM88_SKIN NA WM88_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.76 96 305 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 WM88_SKIN NA WM88_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 8 71 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 WM983B_SKIN NA WM983B_SKIN NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.74 11 31 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - WM983B_SKIN NA WM983B_SKIN NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.14 274 45 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes WM983B_SKIN NA WM983B_SKIN NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.44 14 11 KIAA2018 205717 broad.mit.edu 37 3 113376110 113376111 + In_Frame_Ins INS - TGC TGC rs138829151;rs147651764;rs143860374 by1000genomes WM983B_SKIN NA WM983B_SKIN NA g.chr3:113376110_113376111insTGC uc003eam.2 - 7 4829_4830 c.4418_4419insGCA c.(4417-4419)CAA>CAGCAA p.1473_1473Q>QQ KIAA2018_uc003eal.2_In_Frame_Ins_p.1417_1417Q>QQ NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 gttgttgctgttgctgctgctg 0.361 0.14 85 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 WM983B_SKIN NA WM983B_SKIN NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.45 138 112 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 WM983B_SKIN NA WM983B_SKIN NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.72 20 52 HAVCR1 26762 broad.mit.edu 37 5 156479558 156479572 + In_Frame_Del DEL TTGGAACAGTCGTCA - - rs45623443;rs139041445;rs74384617;rs75340804;rs2862716 by1000genomes WM983B_SKIN NA WM983B_SKIN NA g.chr5:156479558_156479572delTTGGAACAGTCGTCA uc010jij.1 - 4 658_672 c.473_487delTGACGACTGTTCCAA c.(472-489)ATGACGACTGTTCCAACG>ACG p.MTTVP158del HAVCR1_uc011ddl.1_5'UTR|HAVCR1_uc003lwi.2_In_Frame_Del_p.MTTVP158del|HAVCR1_uc011ddm.1_In_Frame_Del_p.MTTVP158del NM_001099414 NP_001092884 Q96D42 HAVR1_HUMAN hepatitis A virus cellular receptor 1 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment interspecies interaction between organisms integral to membrane receptor activity ovary(1)|skin(1) 2 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT 0.488 0.64 8 14 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 WM983B_SKIN NA WM983B_SKIN NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.22 64 18 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes WM983B_SKIN NA WM983B_SKIN NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.65 11 20 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - WM983B_SKIN NA WM983B_SKIN NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.42 7 5 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 WM983B_SKIN NA WM983B_SKIN NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.62 5 8 CACNB2 783 broad.mit.edu 37 10 18823156 18823157 + Splice_Site INS - GTAA GTAA WM983B_SKIN NA WM983B_SKIN NA g.chr10:18823156_18823157insGTAA uc001ipr.2 + 11 1266 c.1206_splice c.e11+1 p.K402_splice CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Splice_Site_p.K378_splice|CACNB2_uc001ipt.2_Splice_Site_p.K364_splice|CACNB2_uc001ipu.2_Splice_Site_p.K374_splice|CACNB2_uc001ipv.2_Splice_Site_p.K350_splice|CACNB2_uc009xka.1_Splice_Site_p.K336_splice|CACNB2_uc001ipw.2_Splice_Site_p.K309_splice|CACNB2_uc001ipx.2_Splice_Site_p.K347_splice|CACNB2_uc001ipz.2_Splice_Site_p.K324_splice|CACNB2_uc001ipy.2_Splice_Site_p.K348_splice|CACNB2_uc010qco.1_Splice_Site_p.K316_splice|CACNB2_uc001iqa.2_Splice_Site_p.K354_splice|NSUN6_uc001iqb.2_Intron NM_201596 NP_963890 Q08289 CACB2_HUMAN calcium channel, voltage-dependent, beta 2 axon guidance|neuromuscular junction development integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity large_intestine(1)|central_nervous_system(1)|skin(1) 3 Magnesium Sulfate(DB00653)|Verapamil(DB00661) CTTCTCCTAAGGTAAGTAGGAC 0.356 0.63 14 24 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 WM983B_SKIN NA WM983B_SKIN NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.40 6 4 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 WM983B_SKIN NA WM983B_SKIN NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.28 415 162 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes WM983B_SKIN NA WM983B_SKIN NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.32 15 7 THAP11 57215 broad.mit.edu 37 16 67876806 67876826 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAACAG - - rs143101373;rs143185886;rs34138555;rs28647874;rs34213159;rs3982383;rs63117363 by1000genomes;byFrequency;byFrequency;byFrequency WM983B_SKIN NA WM983B_SKIN NA g.chr16:67876806_67876826delCAGCAGCAGCAGCAGCAACAG uc002euo.2 + 1 594_614 c.349_369delCAGCAGCAGCAGCAGCAACAG c.(349-369)CAGCAGCAGCAGCAGCAACAGdel p.QQQQQQQ124del CENPT_uc002eun.3_Intron NM_020457 NP_065190 Q96EK4 THA11_HUMAN THAP domain containing 11 124_130 Gln-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|identical protein binding|metal ion binding 0 Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118) acagcagcaacagcagcagcagcagcaacagcagcagcagc 0.335 0.27 186 70 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C WM983B_SKIN NA WM983B_SKIN NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 31 258 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 WM983B_SKIN NA WM983B_SKIN NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.34 126 65 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 WM983B_SKIN NA WM983B_SKIN NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 56 325 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 WM983B_SKIN NA WM983B_SKIN NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.90 17 146 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.97 1 30 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 224 47 TPRXL 348825 broad.mit.edu 37 3 14105964 14105965 + In_Frame_Ins INS - AGC AGC rs142895893;rs138518200 by1000genomes WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr3:14105964_14105965insAGC uc011avd.1 + 3 743_744 c.288_289insAGC c.(286-291)insAGC p.102_103insS TPRXL_uc003byh.1_In_Frame_Ins_p.102_103insS|TPRXL_uc003byg.2_In_Frame_Ins_p.102_103insS NR_002223 RecName: Full=Putative protein TPRXL; 0 gtagcagctctagcagcagcag 0.000 0.52 11 12 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.45 16 13 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.64 107 188 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.63 17 29 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.23 163 49 NOTCH4 4855 broad.mit.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC - - rs144295198;rs9281675;rs66501724 WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr6:32191659_32191661delAGC uc003obb.2 - 1 184_186 c.45_47delGCT c.(43-48)CTGCTA>CTA p.15_16LL>L NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA|NOTCH4_uc003obc.2_In_Frame_Del_p.15_16LL>L NM_004557 NP_004548 Q99466 NOTC4_HUMAN notch4 preproprotein 15_16 cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|protein heterodimerization activity|receptor activity lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1) 22 TGAGACACATagcagcagcagca 0.532 0.31 29 13 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.91 4 43 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.27 744 282 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.37 53 31 MAPK3 5595 broad.mit.edu 37 16 30134513 30134514 + In_Frame_Ins INS - GCC GCC WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr16:30134513_30134514insGCC uc002dws.2 - 1 117_118 c.17_18insGGC c.(16-18)GCT>GCGGCT p.6_6A>AA uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MAPK3_uc002dwr.2_5'Flank|MAPK3_uc002dwv.3_In_Frame_Ins_p.6_6A>AA|MAPK3_uc002dwt.2_In_Frame_Ins_p.6_6A>AA|MAPK3_uc002dwu.2_RNA|MAPK3_uc010bzp.2_RNA NM_002746 NP_002737 P27361 MK03_HUMAN mitogen-activated protein kinase 3 isoform 1 6 activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle|cellular response to mechanical stimulus|epidermal growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway|interleukin-1-mediated signaling pathway|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of transcription from RNA polymerase II promoter|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription initiation from RNA polymerase I promoter cytosol|nucleoplasm ATP binding|MAP kinase activity|phosphatase binding 0 Arsenic trioxide(DB01169)|Isoproterenol(DB01064)|Simvastatin(DB00641)|Sulindac(DB00605) 0.000 0.37 102 59 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.43 115 87 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.22 45 13 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 44 300 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 4 105 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 YD15_SALIVARY_GLAND NA YD15_SALIVARY_GLAND NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 26 SLC2A1 6513 broad.mit.edu 37 1 43395631 43395631 + Frame_Shift_Del DEL G - - YD15_SALIVARY_GLAND NA YD15_SALIVARY_GLAND NA g.chr1:43395631delG uc001cik.2 - 5 1117 c.592delC c.(592-594)CTGfs p.L198fs NM_006516 NP_006507 P11166 GTR1_HUMAN solute carrier family 2 (facilitated glucose 198 Helical; Name=6; (Potential). carbohydrate metabolic process|energy reserve metabolic process|regulation of insulin secretion|water-soluble vitamin metabolic process integral to membrane|melanosome|membrane fraction|midbody D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity central_nervous_system(2)|pancreas(2)|ovary(1) 5 Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0122) Etomidate(DB00292) 0.000 0.35 587 318 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - YD15_SALIVARY_GLAND NA YD15_SALIVARY_GLAND NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 222 46 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 YD15_SALIVARY_GLAND NA YD15_SALIVARY_GLAND NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.25 46 15 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 YD15_SALIVARY_GLAND NA YD15_SALIVARY_GLAND NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.18 53 12 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 YD15_SALIVARY_GLAND NA YD15_SALIVARY_GLAND NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.27 52 19 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 YD15_SALIVARY_GLAND NA YD15_SALIVARY_GLAND NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 13 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency YD15_SALIVARY_GLAND NA YD15_SALIVARY_GLAND NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.52 199 212 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 YD15_SALIVARY_GLAND NA YD15_SALIVARY_GLAND NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.12 186 26 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 YD15_SALIVARY_GLAND NA YD15_SALIVARY_GLAND NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.55 5 6 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 YD15_SALIVARY_GLAND NA YD15_SALIVARY_GLAND NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.77 78 261 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 YD15_SALIVARY_GLAND NA YD15_SALIVARY_GLAND NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.96 3 80 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 42 PTPN22 26191 broad.mit.edu 37 1 114362264 114362265 + Frame_Shift_Ins INS - A A YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr1:114362264_114362265insA uc001eds.2 - 20 2423_2424 c.2293_2294insT c.(2293-2295)TCTfs p.S765fs PTPN22_uc009wgq.2_Frame_Shift_Ins_p.S710fs|PTPN22_uc010owo.1_Frame_Shift_Ins_p.S521fs|PTPN22_uc001edt.2_Frame_Shift_Ins_p.I160fs|PTPN22_uc009wgr.2_Frame_Shift_Ins_p.S765fs|PTPN22_uc009wgs.2_Frame_Shift_Ins_p.S638fs NM_015967 NP_057051 Q9Y2R2 PTN22_HUMAN protein tyrosine phosphatase, non-receptor type 765 negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation internal side of plasma membrane|nucleus|perinuclear region of cytoplasm kinase binding|protein tyrosine phosphatase activity|SH3 domain binding kidney(2)|lung(1)|skin(1) 4 Lung SC(450;0.184) all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06) Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133) TGGTGGGCAAGAATTACAGATA 0.322 0.30 99 43 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.11 370 44 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.19 111 26 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.37 12 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.44 45 36 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.75 19 57 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.62 85 137 FYN 2534 broad.mit.edu 37 6 112024233 112024233 + Frame_Shift_Del DEL G - - rs146187358 YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr6:112024233delG uc003pvj.2 - 7 892 c.552delC c.(550-552)GCCfs p.A184fs FYN_uc003pvi.2_Frame_Shift_Del_p.A184fs|FYN_uc003pvk.2_Frame_Shift_Del_p.A184fs|FYN_uc003pvh.2_Frame_Shift_Del_p.A184fs|FYN_uc010kdy.1_5'UTR NM_002037 NP_002028 P06241 FYN_HUMAN protein-tyrosine kinase fyn isoform a 184 SH2. A -> S (in Ref. 1; AAA36615). axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction cytosol|endosome|plasma membrane ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity lung(5)|central_nervous_system(1)|skin(1) 7 all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211) all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102) Dasatinib(DB01254) AAAGTGAATAGGCACCTGGTA 0.383 0.19 108 26 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.73 3 8 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 0.88 2 15 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.53 220 253 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.40 6 4 CHD8 57680 broad.mit.edu 37 14 21860016 21860018 + In_Frame_Del DEL CTT - - YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr14:21860016_21860018delCTT uc001was.1 - 35 6116_6118 c.6022_6024delAAG c.(6022-6024)AAGdel p.K2008del CHD8_uc001war.1_In_Frame_Del_p.K1904del NM_020920 NP_065971 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 2287 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1) 10 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) TTCTGTTCCCCTTCTTCTTATGA 0.414 0.31 184 81 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.85 52 304 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 YD38_UPPER_AERODIGESTIVE_TRACT NA YD38_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.94 4 68 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 61 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.49 122 119 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 73 14 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.27 66 25 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.28 88 35 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.66 64 125 PTK7 5754 broad.mit.edu 37 6 43109757 43109758 + Frame_Shift_Ins INS - A A YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chr6:43109757_43109758insA uc003oub.1 + 12 2055_2056 c.1857_1858insA c.(1855-1860)CCCAAGfs p.P619fs PTK7_uc003ouc.1_Frame_Shift_Ins_p.P619fs|PTK7_uc003oud.1_Frame_Shift_Ins_p.P579fs|PTK7_uc003oue.1_Frame_Shift_Ins_p.P489fs|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Frame_Shift_Ins_p.P627fs|PTK7_uc010jyj.1_Intron NM_002821 NP_002812 Q13308 PTK7_HUMAN PTK7 protein tyrosine kinase 7 isoform a 619_620 Ig-like C2-type 7.|Extracellular (Potential). actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration cell-cell junction|integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ovary(2)|large_intestine(1) 3 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423) AGGGGGACCCCAAGCCGCTGAT 0.599 0.18 40 9 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.33 405 201 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.33 85 42 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.19 30 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.62 11 18 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.10 111 12 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 80 327 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 YD8_UPPER_AERODIGESTIVE_TRACT NA YD8_UPPER_AERODIGESTIVE_TRACT NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.95 2 39 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 1.00 0 19 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.27 108 39 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.37 24 14 Unknown 0 broad.mit.edu 37 4 88815163 88815164 + Frame_Shift_Ins INS - TTAGG TTAGG rs139378826;rs143229674 YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr4:88815163_88815164insTTAGG uc010iko.1 + 4 1790_1791 c.1790_1791insTTAGG c.(1789-1791)GATfs p.D597fs SubName: Full=Heat shock protein 90kDa alpha (Cytosolic), class B member 1, isoform CRA_a; SubName: Full=cDNA, FLJ92550, Homo sapiens heat shock 90kDa protein 1, beta (HSPCB), mRNA; GAAGAAGTCGATTAGGAGTTCA 0.545 0.47 9 8 CCNA2 890 broad.mit.edu 37 4 122743803 122743804 + Splice_Site INS - A A YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr4:122743803_122743804insA uc003iec.3 - 2 519 c.214_splice c.e2-1 p.V72_splice NM_001237 NP_001228 P20248 CCNA2_HUMAN cyclin A cell division|mitosis|mitotic cell cycle G2/M transition DNA damage checkpoint|Ras protein signal transduction|regulation of cyclin-dependent protein kinase activity cytoplasm|nucleoplasm protein kinase binding ovary(1) 1 GGGTGCAACCTAAAAAAAAATT 0.406 0.29 60 25 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.47 112 98 NKD2 85409 broad.mit.edu 37 5 1038447 1038455 + In_Frame_Del DEL CACCACCAC - - rs3840989;rs143388141 by1000genomes YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr5:1038447_1038455delCACCACCAC uc003jbt.1 + 10 1320_1328 c.1315_1323delCACCACCAC c.(1315-1323)CACCACCACdel p.HHH445del NKD2_uc010itf.1_3'UTR NM_033120 NP_149111 Q969F2 NKD2_HUMAN naked cuticle homolog 2 445_447 His-rich. exocytosis|Wnt receptor signaling pathway cytoplasmic membrane-bounded vesicle|plasma membrane calcium ion binding|ubiquitin protein ligase binding 0 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09) Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165) 0.000 0.59 277 401 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.31 247 112 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 1.00 0 19 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.40 6 4 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638316 + Splice_Site DEL TAATAA - - rs7106895 YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr11:62638311_62638316delTAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.30 16 7 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.31 549 251 C14orf4 64207 broad.mit.edu 37 14 77493794 77493795 + In_Frame_Ins INS - TGC TGC rs28718623 YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr14:77493794_77493795insTGC uc001xsy.2 - 1 1240_1241 c.341_342insGCA c.(340-342)CAA>CAGCAA p.114_114Q>QQ NM_024496 NP_078772 Q9H1B7 I2BPL_HUMAN chromosome 14 open reading frame 4 114 Poly-Gln.|Potential. nucleus 0 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878) gctgctgctgttgctgctgctg 0.262 0.68 12 26 CREBBP 1387 broad.mit.edu 37 16 3778455 3778456 + Frame_Shift_Ins INS - C C YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr16:3778455_3778456insC uc002cvv.2 - 31 6796_6797 c.6592_6593insG c.(6592-6594)CTGfs p.L2198fs CREBBP_uc002cvw.2_Frame_Shift_Ins_p.L2160fs NM_004380 NP_004371 Q92793 CBP_HUMAN CREB binding protein isoform a 2198 cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1) 127 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) ctgctgctgcagcagctgcCTC 0.416 0.28 181 70 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.91 25 244 CEBPA 1050 broad.mit.edu 37 19 33792731 33792732 + In_Frame_Ins INS - GCGGGT GCGGGT YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr19:33792731_33792732insGCGGGT uc002nun.2 - 1 699_700 c.589_590insACCCGC c.(589-591)CCG>CACCCGCCG p.196_197insHP LOC80054_uc002nuo.2_5'Flank NM_004364 NP_004355 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein alpha 196_197 cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.H195_P196insPH(6)|p.H195_P196>insHPHPH(1)|p.P185_P197del(1)|p.S190_P198del(1) haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1) 734 Esophageal squamous(110;0.137) 0.000 0.15 1132 203 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.73 35 96 BAGE2 85319 broad.mit.edu 37 21 11029597 11029597 + Splice_Site DEL C - - rs138714104 YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr21:11029597delC uc002yit.1 - 7 1596 c.1388_splice c.e7+1 TPTE_uc002yis.1_Splice_Site NM_182482 NP_872288 B melanoma antigen family, member 2 precursor 0 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATTTTATGTACCACTTTGATG 0.413 0.16 43 8 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.73 89 236 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 YH13_CENTRAL_NERVOUS_SYSTEM NA YH13_CENTRAL_NERVOUS_SYSTEM NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.97 2 70 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ZR751_BREAST NA ZR751_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.95 2 38 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 ZR751_BREAST NA ZR751_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.26 20 7 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ZR751_BREAST NA ZR751_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.26 73 26 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 ZR751_BREAST NA ZR751_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.69 15 34 MSH3 4437 broad.mit.edu 37 5 79950727 79950728 + In_Frame_Ins INS - CAGCGCCCG CAGCGCCCG rs1574197 ZR751_BREAST NA ZR751_BREAST NA g.chr5:79950727_79950728insCAGCGCCCG uc003kgz.2 + 1 434_435 c.181_182insCAGCGCCCG c.(181-183)GCA>GCAGCGCCCGCA p.61_61A>AAPA DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR NM_002439 NP_002430 P20585 MSH3_HUMAN mutS homolog 3 61 Poly-Ala. Missing. maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) 0.000 0.42 84 60 MLLT4 4301 broad.mit.edu 37 6 168363223 168363227 + Frame_Shift_Del DEL AACAA - - ZR751_BREAST NA ZR751_BREAST NA g.chr6:168363223_168363227delAACAA uc003qwd.2 + 31 5095_5099 c.4953_4957delAACAA c.(4951-4959)CGAACAAAAfs p.R1651fs MLLT4_uc003qwc.1_Frame_Shift_Del_p.R1639fs|MLLT4_uc003qwg.1_Frame_Shift_Del_p.R950fs NM_001040001 NP_001035090 P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia 1641_1643 Potential. adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction adherens junction|cell-cell junction|cytosol|nucleus protein C-terminus binding ovary(2)|lung(1)|kidney(1)|central_nervous_system(1) 5 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) 0.000 0.86 23 140 ASPH 444 broad.mit.edu 37 8 62550924 62550925 + Splice_Site INS - A A rs34108497;rs146125714 ZR751_BREAST NA ZR751_BREAST NA g.chr8:62550924_62550925insA uc003xuj.2 - 11 1060 c.791_splice c.e11-1 p.A264_splice ASPH_uc011leg.1_Splice_Site_p.A235_splice|ASPH_uc003xuo.2_Splice_Site_p.A245_splice|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Splice_Site_p.A250_splice|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Splice_Site_p.A207_splice|ASPH_uc003xun.2_Splice_Site_p.A221_splice|ASPH_uc011lek.1_Splice_Site_p.A245_splice|ASPH_uc003xum.2_Splice_Site_p.A264_splice NM_004318 NP_004309 Q12797 ASPH_HUMAN aspartate beta-hydroxylase isoform a muscle contraction integral to endoplasmic reticulum membrane calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle ovary(3) 3 Lung SC(2;0.153) Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101) L-Aspartic Acid(DB00128)|Succinic acid(DB00139) CATATACTGCTAAAAAAAAAAA 0.257 0.35 49 26 MEN1 4221 broad.mit.edu 37 11 64572271 64572271 + Frame_Shift_Del DEL G - - ZR751_BREAST NA ZR751_BREAST NA g.chr11:64572271delG uc001obj.2 - 10 1456 c.1383delC c.(1381-1383)CGCfs p.R461fs MAP4K2_uc001obh.2_5'Flank|MAP4K2_uc001obi.2_5'Flank|MAP4K2_uc010rnp.1_5'Flank|MEN1_uc001obk.2_Frame_Shift_Del_p.R461fs|MEN1_uc001obl.2_Frame_Shift_Del_p.R421fs|MEN1_uc001obm.2_Frame_Shift_Del_p.R456fs|MEN1_uc001obn.2_Frame_Shift_Del_p.R461fs|MEN1_uc001obo.2_Frame_Shift_Del_p.R461fs|MEN1_uc001obp.2_Frame_Shift_Del_p.R456fs|MEN1_uc001obq.2_Frame_Shift_Del_p.R461fs|MEN1_uc001obr.2_Frame_Shift_Del_p.R461fs NM_130800 NP_570712 O00255 MEN1_HUMAN menin isoform 1 461 DNA repair|histone lysine methylation|MAPKKK cascade|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of JNK cascade|negative regulation of osteoblast differentiation|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of telomerase activity|negative regulation of transcription from RNA polymerase II promoter|osteoblast development|positive regulation of protein binding|positive regulation of transforming growth factor beta receptor signaling pathway|response to gamma radiation|response to UV|transcription, DNA-dependent chromatin|cleavage furrow|cytosol|histone methyltransferase complex|nuclear matrix|soluble fraction double-stranded DNA binding|four-way junction DNA binding|protein binding, bridging|protein N-terminus binding|R-SMAD binding|transcription regulatory region DNA binding|Y-form DNA binding parathyroid(105)|pancreas(64)|gastrointestinal_tract_(site_indeterminate)(15)|small_intestine(13)|lung(9)|pituitary(7)|NS(7)|adrenal_gland(5)|soft_tissue(4)|central_nervous_system(4)|thymus(2)|stomach(1)|retroperitoneum(1)|skin(1) 238 0.000 0.93 36 460 MAML2 84441 broad.mit.edu 37 11 95825375 95825383 + In_Frame_Del DEL TGCTGCTGC - - rs11277537;rs113349418 ZR751_BREAST NA ZR751_BREAST NA g.chr11:95825375_95825383delTGCTGCTGC uc001pfw.1 - 2 3097_3105 c.1812_1820delGCAGCAGCA c.(1810-1821)CAGCAGCAGCAA>CAA p.604_607QQQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 604_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgctgct 0.124 0.19 110 26 ATN1 1822 broad.mit.edu 37 12 7045892 7045912 + In_Frame_Del DEL CAGCAGCAGCAGCAGCAGCAG - - rs66756893;rs67074116;rs145352906;rs142238167;rs140703448;rs146235850;rs139352180;rs144280633 byFrequency;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes;byFrequency;by1000genomes ZR751_BREAST NA ZR751_BREAST NA g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG uc001qrw.1 + 5 1699_1719 c.1462_1482delCAGCAGCAGCAGCAGCAGCAG c.(1462-1482)CAGCAGCAGCAGCAGCAGCAGdel p.QQQQQQQ495del ATN1_uc001qrx.1_In_Frame_Del_p.QQQQQQQ495del NM_001007026 NP_001007027 P54259 ATN1_HUMAN atrophin-1 495_501 Poly-Gln. cell death|central nervous system development cytoplasm|nucleus protein domain specific binding ovary(2)|breast(2)|pancreas(1)|skin(1) 6 gcaacagcaacagcagcagcagcagcagcagcagcagcagc 0.475 0.21 26 7 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 ZR751_BREAST NA ZR751_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.27 40 15 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ZR751_BREAST NA ZR751_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.80 68 266 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ZR751_BREAST NA ZR751_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.98 2 91 CACNA1F 778 broad.mit.edu 37 X 49076224 49076225 + In_Frame_Ins INS - TCC TCC rs112450928 ZR7530_BREAST NA ZR7530_BREAST NA g.chrX:49076224_49076225insTCC uc004dnb.2 - 20 2506_2507 c.2444_2445insGGA c.(2443-2445)GAA>GAGGAA p.815_815E>EE CACNA1F_uc010nip.2_In_Frame_Ins_p.804_804E>EE NM_005183 NP_005174 O60840 CAC1F_HUMAN calcium channel, voltage-dependent, L type, 815 Poly-Glu.|Cytoplasmic (Potential). axon guidance|detection of light stimulus involved in visual perception voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity breast(3)|ovary(1)|kidney(1)|skin(1) 6 Verapamil(DB00661) cttcctcttcttcctcctcctc 0.257 0.45 47 38 GRIA3 2892 broad.mit.edu 37 X 122318386 122318387 + Splice_Site INS - G G rs150805613;rs149356970 ZR7530_BREAST NA ZR7530_BREAST NA g.chrX:122318386_122318387insG uc004etq.3 + 1 291 c.-2_splice c.e1+1 GRIA3_uc004etr.3_Splice_Site|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR NM_007325 NP_015564 P42263 GRIA3_HUMAN glutamate receptor, ionotrophic, AMPA 3 isoform glutamate signaling pathway|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity ovary(3)|central_nervous_system(1)|pancreas(1) 5 L-Glutamic Acid(DB00142) TTTTAGGCGTACATGGCCAGGC 0.500 0.90 7 60 PDE4DIP 9659 broad.mit.edu 37 1 144923729 144923729 + Frame_Shift_Del DEL T - - ZR7530_BREAST NA ZR7530_BREAST NA g.chr1:144923729delT uc001elw.3 - 6 1020 c.729delA c.(727-729)GAAfs p.E243fs NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Frame_Shift_Del_p.E309fs|PDE4DIP_uc001emc.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emd.1_Frame_Shift_Del_p.E243fs|PDE4DIP_uc001emb.1_Frame_Shift_Del_p.E406fs|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Frame_Shift_Del_p.E30fs NM_014644 NP_055459 Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein isoform 243 Potential. cellular protein complex assembly centrosome|Golgi apparatus|myofibril|nucleus enzyme binding ovary(4)|haematopoietic_and_lymphoid_tissue(1) 5 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TTTCCTGGAGTTCTGCCAAGT 0.448 0.17 572 119 KIAA2018 205717 broad.mit.edu 37 3 113376111 113376113 + In_Frame_Del DEL TGC - - rs143860374;rs62265537 ZR7530_BREAST NA ZR7530_BREAST NA g.chr3:113376111_113376113delTGC uc003eam.2 - 7 4827_4829 c.4416_4418delGCA c.(4414-4419)CAGCAA>CAA p.1472_1473QQ>Q KIAA2018_uc003eal.2_In_Frame_Del_p.1416_1417QQ>Q NM_001009899 NP_001009899 Q68DE3 K2018_HUMAN hypothetical protein LOC205717 1472_1473 Gln-rich. regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 ttgttgctgttgctgctgctgct 0.360 0.34 31 16 PIK3R4 30849 broad.mit.edu 37 3 130447530 130447531 + Splice_Site INS - A A ZR7530_BREAST NA ZR7530_BREAST NA g.chr3:130447530_130447531insA uc003enj.2 - 6 2167 c.1586_splice c.e6-1 p.E529_splice NM_014602 NP_055417 Q99570 PI3R4_HUMAN phosphoinositide-3-kinase, regulatory subunit 4 fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway cytosol ATP binding|protein binding|protein serine/threonine kinase activity ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1) 12 CTTGGAGCTCTAaaaaaaaaaa 0.282 0.16 187 35 MAML3 55534 broad.mit.edu 37 4 140651585 140651587 + Splice_Site DEL CTG - - rs144812697 ZR7530_BREAST NA ZR7530_BREAST NA g.chr4:140651585_140651587delCTG uc003ihz.1 - 4 3053 c.2301_splice c.e4+1 p.Q767_splice MGST2_uc010ioi.1_Intron|MAML3_uc011chd.1_In_Frame_Del_p.Q235del NM_018717 NP_061187 Q96JK9 MAML3_HUMAN mastermind-like 3 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity ovary(1) 1 all_hematologic(180;0.162) CCGCCAAAATctgctgctgctgc 0.276 0.48 98 92 MAP3K1 4214 broad.mit.edu 37 5 56177849 56177851 + In_Frame_Del DEL CAA - - rs34869245 ZR7530_BREAST NA ZR7530_BREAST NA g.chr5:56177849_56177851delCAA uc003jqw.3 + 14 3323_3325 c.2822_2824delCAA c.(2821-2826)TCAACA>TCA p.T949del NM_005921 NP_005912 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 949 Poly-Thr. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding ovary(1)|skin(1) 2 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) CCTTCTAGTTcaacaacaacaac 0.374 0.77 26 89 SSPO 23145 broad.mit.edu 37 7 149506211 149506212 + Frame_Shift_Ins INS - C C rs149666960;rs71194663 by1000genomes ZR7530_BREAST NA ZR7530_BREAST NA g.chr7:149506211_149506212insC uc010lpk.2 + 64 9203_9204 c.9203_9204insC c.(9202-9204)AGCfs p.S3068fs NM_198455 NP_940857 A2VEC9 SSPO_HUMAN SCO-spondin precursor 3068 TSP type-1 10. cell adhesion extracellular space peptidase inhibitor activity 0 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CGAGGCAGCAGCTGCGCAGCCT 0.668 0.90 1 9 MNX1 3110 broad.mit.edu 37 7 156802752 156802752 + Frame_Shift_Del DEL C - - ZR7530_BREAST NA ZR7530_BREAST NA g.chr7:156802752delC uc003wnd.1 - 1 596 c.293delG c.(292-294)GGCfs p.G98fs MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_Frame_Shift_Del_p.G98fs|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank NM_005515 NP_005506 P50219 MNX1_HUMAN motor neuron and pancreas homeobox 1 isoform 1 98 Poly-Gly. humoral immune response|regulation of transcription from RNA polymerase II promoter nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00301) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) 0.000 0.64 4 7 RECQL4 9401 broad.mit.edu 37 8 145738768 145738768 + Frame_Shift_Del DEL G - - rs11362176 ZR7530_BREAST NA ZR7530_BREAST NA g.chr8:145738768delG uc003zdj.2 - 15 2328 c.2296delC c.(2296-2298)CGGfs p.R766fs NM_004260 NP_004251 O94761 RECQ4_HUMAN RecQ protein-like 4 766 Helicase C-terminal. DNA duplex unwinding|DNA recombination|DNA repair cytoplasm|nucleus ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding breast(2)|lung(1)|skin(1) 4 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) ACCACCACCCGGCAACTGGCC 0.677 1.00 0 10 SMARCA2 6595 broad.mit.edu 37 9 2039777 2039779 + In_Frame_Del DEL CAG - - rs113070757;rs62639301 byFrequency ZR7530_BREAST NA ZR7530_BREAST NA g.chr9:2039777_2039779delCAG uc003zhc.2 + 4 766_768 c.667_669delCAG c.(667-669)CAGdel p.Q238del SMARCA2_uc003zhd.2_In_Frame_Del_p.Q238del|SMARCA2_uc010mha.2_In_Frame_Del_p.Q229del NM_003070 NP_003061 P51531 SMCA2_HUMAN SWI/SNF-related matrix-associated 238 Poly-Gln. Missing (in Ref. 1; CAA51407). chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding ovary(2)|central_nervous_system(1) 3 all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) GBM - Glioblastoma multiforme(50;0.0475) 0.000 0.50 302 299 SLC3A2 6520 broad.mit.edu 37 11 62638311 62638322 + Splice_Site DEL TAATAATAATAA - - rs7106895;rs12272749 ZR7530_BREAST NA ZR7530_BREAST NA g.chr11:62638311_62638322delTAATAATAATAA uc001nwd.2 + 2 429 c.205_splice c.e2+2 p.E69_splice SLC3A2_uc001nwb.2_Splice_Site_p.E69_splice|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron NM_002394 NP_002385 P08195 4F2_HUMAN solute carrier family 3, member 2 isoform c blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding 0 0.000 0.62 5 8 NUMA1 4926 broad.mit.edu 37 11 71727573 71727573 + Frame_Shift_Del DEL A - - ZR7530_BREAST NA ZR7530_BREAST NA g.chr11:71727573delA uc001orl.1 - 14 1295 c.1123delT c.(1123-1125)TGCfs p.C375fs NUMA1_uc009ysw.1_5'Flank|NUMA1_uc001ork.1_Frame_Shift_Del_p.C375fs|NUMA1_uc001orm.1_Frame_Shift_Del_p.C375fs|NUMA1_uc001orn.2_5'Flank|NUMA1_uc009ysx.1_Frame_Shift_Del_p.C375fs|NUMA1_uc001oro.1_Frame_Shift_Del_p.C375fs NM_006185 NP_006176 Q14980 NUMA1_HUMAN nuclear mitotic apparatus protein 1 375 Potential. G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole protein binding|structural molecule activity ovary(3)|lung(2)|skin(2)|central_nervous_system(1) 8 TCTTCAAGGCATTTCTGGGAG 0.502 0.41 84 59 MAML2 84441 broad.mit.edu 37 11 95825375 95825380 + In_Frame_Del DEL TGCTGC - - rs11277537 ZR7530_BREAST NA ZR7530_BREAST NA g.chr11:95825375_95825380delTGCTGC uc001pfw.1 - 2 3100_3105 c.1815_1820delGCAGCA c.(1813-1821)CAGCAGCAA>CAA p.605_607QQQ>Q NM_032427 NP_115803 Q8IZL2 MAML2_HUMAN mastermind-like 2 605_607 Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity CRTC1/MAML2(516)|CRTC3/MAML2(26) salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1) 546 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) ctgctgctgttgctgctgctgctgct 0.117 0.17 153 31 EP400 57634 broad.mit.edu 37 12 132547068 132547069 + In_Frame_Ins INS - GCA GCA rs140417193;rs68030464 byFrequency ZR7530_BREAST NA ZR7530_BREAST NA g.chr12:132547068_132547069insGCA uc001ujn.2 + 46 8191_8192 c.8156_8157insGCA c.(8155-8157)AGG>AGGCAG p.2748_2749insQ EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR NM_015409 NP_056224 Q96L91 EP400_HUMAN E1A binding protein p400 2784_2785 Interaction with ZNF42 (By similarity). histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) CAGCTTCTCAGgcagcagcagc 0.292 0.19 42 10 CSNK1A1L 122011 broad.mit.edu 37 13 37678404 37678405 + Frame_Shift_Ins INS - T T ZR7530_BREAST NA ZR7530_BREAST NA g.chr13:37678404_37678405insT uc001uwm.1 - 1 1397_1398 c.989_990insA c.(988-990)AACfs p.N330fs NM_145203 NP_660204 Q8N752 KC1AL_HUMAN casein kinase 1, alpha 1-like 330 Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity large_intestine(1) 1 Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109) all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407) CATTATTCTTGTTTTTTTCAGT 0.460 0.24 162 51 DICER1 23405 broad.mit.edu 37 14 95590947 95590963 + Frame_Shift_Del DEL ACTTTATCTGCACACCA - - ZR7530_BREAST NA ZR7530_BREAST NA g.chr14:95590947_95590963delACTTTATCTGCACACCA uc001ydw.2 - 9 1128_1144 c.946_962delTGGTGTGCAGATAAAGT c.(946-963)TGGTGTGCAGATAAAGTAfs p.W316fs DICER1_uc001ydv.2_Frame_Shift_Del_p.W306fs|DICER1_uc001ydx.2_Frame_Shift_Del_p.W316fs NM_030621 NP_085124 Q9UPY3 DICER_HUMAN dicer1 316_321 Required for interaction with PRKRA and TARBP2. negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference cytosol|RNA-induced silencing complex ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity skin(2)|ovary(1)|pancreas(1)|lung(1) 5 all_cancers(154;0.0621)|all_epithelial(191;0.223) Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215) CATTCCAGCTACTTTATCTGCACACCAGGGTCCCAGA 0.359 0.38 283 171 MVD 4597 broad.mit.edu 37 16 88722072 88722073 + Frame_Shift_Ins INS - C C ZR7530_BREAST NA ZR7530_BREAST NA g.chr16:88722072_88722073insC uc002flg.1 - 6 676_677 c.669_670insG c.(667-672)CCCCTGfs p.P223fs MVD_uc002flf.1_Frame_Shift_Ins_p.P92fs NM_002461 NP_002452 P53602 MVD1_HUMAN diphosphomevalonate decarboxylase 223_224 cholesterol biosynthetic process|positive regulation of cell proliferation cytosol ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity 0 BRCA - Breast invasive adenocarcinoma(80;0.0478) 0.000 0.89 6 51 NUMBL 9253 broad.mit.edu 37 19 41173893 41173898 + In_Frame_Del DEL TGCTGT - - rs59088184 ZR7530_BREAST NA ZR7530_BREAST NA g.chr19:41173893_41173898delTGCTGT uc002oon.2 - 10 1473_1478 c.1305_1310delACAGCA c.(1303-1311)CAACAGCAG>CAG p.435_437QQQ>Q NUMBL_uc010xvq.1_In_Frame_Del_p.394_396QQQ>Q|NUMBL_uc002ooo.2_In_Frame_Del_p.434_436QQQ>Q|NUMBL_uc010xvr.1_In_Frame_Del_p.394_396QQQ>Q NM_004756 NP_004747 Q9Y6R0 NUMBL_HUMAN numb homolog (Drosophila)-like 435_437 Poly-Gln. cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process cytoplasm protein binding lung(3)|ovary(1)|breast(1) 5 Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105) ctgctgctgctgctgttgctgttgct 0.466 0.74 24 69 COL18A1 80781 broad.mit.edu 37 21 46924426 46924434 + Splice_Site DEL GGCCCCCCA - - rs28696990 ZR7530_BREAST NA ZR7530_BREAST NA g.chr21:46924426_46924434delGGCCCCCCA uc011afs.1 + 33 4090 c.4069_splice c.e33+1 p.G1357_splice COL18A1_uc002zhg.2_Splice_Site_p.G942_splice|COL18A1_uc002zhi.2_Splice_Site_p.G1122_splice|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'UTR|COL18A1_uc002zhk.2_5'Flank NM_130444 NP_569711 P39060 COIA1_HUMAN alpha 1 type XVIII collagen isoform 3 precursor cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception collagen|extracellular space extracellular matrix structural constituent|metal ion binding|protein binding central_nervous_system(1) 1 Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929) 0.000 0.87 58 373 CLTCL1 8218 broad.mit.edu 37 22 19189003 19189004 + Splice_Site INS - C C rs72564418;rs11386977 ZR7530_BREAST NA ZR7530_BREAST NA g.chr22:19189003_19189004insC uc002zpb.2 - 24 3677 c.3602_splice c.e24-1 p.V1201_splice CLTCL1_uc011agv.1_Splice_Site_p.V1201_splice|CLTCL1_uc011agw.1_Splice_Site_p.L1201_splice|CLTCL1_uc011agt.1_Splice_Site|CLTCL1_uc011agu.1_Splice_Site|CLTCL1_uc010grm.1_Splice_Site|CLTCL1_uc002zpe.2_Splice_Site_p.L161_splice|CLTCL1_uc002zpd.1_Splice_Site_p.I108_splice NM_007098 NP_009029 P53675 CLH2_HUMAN clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) GCGGTCTCCAACTACGGATAAT 0.480 0.91 7 72